├── .gitignore ├── BuildWithMake ├── CygwinHelpers │ ├── clean-env.sh │ ├── intel_fortran_12_x64 │ ├── intel_fortran_14_x64 │ ├── msvc_2010_x64 │ ├── msvc_2013_x64 │ ├── parse_reg_dir.sh │ └── parse_reg_dir_with_extra_space.sh ├── Docs │ ├── Doxygen │ │ └── mainpage.cxx │ ├── Makefile │ ├── flowsolver.Doxyfile │ ├── index.html │ ├── simvascular.Doxyfile │ └── styles.css ├── MakeHelpers │ ├── compiler.clang.x64_macosx.mk │ ├── compiler.gcc.x64_linux.mk │ ├── compiler.gcc.x64_macosx.mk │ ├── compiler.gfortran.x64_linux.mk │ ├── compiler.gfortran.x64_macosx.mk │ ├── compiler.icpc.x64_linux.mk │ ├── compiler.ifort.x64_cygwin.mk │ ├── compiler.ifort.x64_linux.mk │ ├── compiler.ifort.x64_macosx.mk │ ├── compiler.mingw-gcc.x64_cygwin.mk │ ├── compiler.mingw-gfortran.x64_cygwin.mk │ ├── compiler.vs10.1.x64_cygwin.mk │ ├── compiler.vs12.5.x64_cygwin.mk │ ├── leslib-1.5.x64_cygwin.mk │ ├── leslib-1.5.x64_linux.mk │ ├── mpich.x64_linux.mk │ ├── mpich.x64_macosx.mk │ ├── mpich2-1.4p1.x64_cygwin.mk │ ├── msmpi.x64_cygwin.mk │ ├── openmpi.x64_linux.mk │ ├── openmpi.x64_macosx.mk │ ├── rules.x64_cygwin.mk │ ├── rules.x64_linux.mk │ ├── rules.x64_macosx.mk │ ├── tcltk-8.6.4.x64_cygwin.mk │ ├── tcltk-8.6.4.x64_linux.mk │ ├── tcltk-8.6.4.x64_macosx.mk │ ├── vtk-6.2.0.x64_cygwin.mk │ ├── vtk-6.2.0.x64_linux.mk │ └── vtk-6.2.0.x64_macosx.mk ├── Makefile ├── README-build-linux.txt ├── README-build-macosx.txt ├── README-build-windows.txt ├── Release │ ├── License.rtf │ ├── Makefile │ ├── developer_wrapper_scripts │ │ ├── developer-core-script │ │ ├── developer-svpost-script │ │ ├── developer-svpre-script │ │ ├── developer-svsolver-mpi-linux-script │ │ ├── developer-svsolver-mpi-macosx-script │ │ ├── developer-svsolver-mpi-windows-script │ │ ├── developer-svsolver-nompi-linux-script │ │ ├── developer-svsolver-nompi-macosx-script │ │ └── developer-svsolver-nompi-windows-script │ ├── linux_wrapper_scripts │ │ ├── linux-dist-core-script │ │ ├── linux-dist-svpost-script │ │ ├── linux-dist-svpre-script │ │ ├── linux-dist-svsolver-mpi-script │ │ └── linux-dist-svsolver-nompi-script │ ├── platform_independent_scripts │ │ ├── generic-launch-script │ │ ├── post-install.sh │ │ ├── post-solver-install.sh │ │ └── post-svsolver-install.sh │ ├── tcl_helper_scripts │ │ ├── create_tclIndex.tcl │ │ └── d2u_files.tcl │ ├── windows_installer_packages │ │ ├── msi-logo.png │ │ ├── w_fcompxe_redist_intel64_2013_sp1.5.239.msi │ │ └── wix-simvascular-svsolver-bundle.wxs │ ├── windows_msi_helpers │ │ ├── makewxs-svsolver.tcl │ │ ├── msi-banner.bmp │ │ ├── msi-banner.jpg │ │ ├── msi-dialog.bmp │ │ ├── msi-dialog.jpg │ │ ├── simvascular.ico │ │ └── uuidgen.c │ └── windows_wrapper_scripts │ │ ├── windows-dist-core-script │ │ ├── windows-dist-svpost-script │ │ ├── windows-dist-svpre-script │ │ ├── windows-dist-svsolver-mpi-script │ │ └── windows-dist-svsolver-nompi-script ├── SampleOverrides │ ├── centos_6 │ │ └── global_overrides.mk │ ├── macosx_11 │ │ └── global_overrides.mk │ ├── ubuntu_14 │ │ └── global_overrides.mk │ └── windows │ │ └── global_overrides.mk ├── get-vtk-binaries.sh ├── include.mk └── targetlib.mk ├── CMakeLists.txt ├── Code ├── CMake │ ├── FindINTELRUNTIME.cmake │ ├── SVFSILSConfig.cmake │ ├── SimVascularDependentOptions.cmake │ ├── SimVascularExternals.cmake │ ├── SimVascularFunctionCheckCompilerFlags.cmake │ ├── SimVascularFunctions.cmake │ ├── SimVascularInstallLibs.cmake │ ├── SimVascularInstallSetup.cmake │ ├── SimVascularInternals.cmake │ ├── SimVascularMacros.cmake │ ├── SimVascularOptions.cmake │ ├── SimVascularSystemSetup.cmake │ ├── SimVascularThirdParty.cmake │ └── Superbuild.cmake ├── CMakeLists.txt ├── Scripts │ ├── CMakeLists.txt │ ├── README-install │ ├── README-postinstall │ ├── SimVascularScriptMacros.cmake │ ├── executable │ │ ├── developer │ │ │ ├── locate-linux-script.in │ │ │ ├── svFSI-linux.in │ │ │ ├── svpost-linux.in │ │ │ ├── svpost-windows.in │ │ │ ├── svpre-linux.in │ │ │ ├── svpre-windows.in │ │ │ ├── svsolver-linux.in │ │ │ ├── svsolver-nompi-linux.in │ │ │ ├── svsolver-nompi-windows.in │ │ │ └── svsolver-windows.in │ │ └── install │ │ │ ├── svFSI-linux.in │ │ │ ├── svpost-linux.in │ │ │ ├── svpost-windows.in │ │ │ ├── svpre-linux.in │ │ │ ├── svpre-windows.in │ │ │ ├── svsolver-linux.in │ │ │ ├── svsolver-nompi-linux.in │ │ │ ├── svsolver-nompi-windows.in │ │ │ └── svsolver-windows.in │ └── home-locate-linux.sh ├── Source │ ├── CMakeLists.txt │ ├── Include │ │ ├── CMakeLists.txt │ │ ├── SimVascular.h │ │ ├── cvFlowsolverOptions.h.in │ │ ├── simvascular_options.h.in │ │ └── simvascular_version.h.in │ ├── Makefile │ ├── svFSI │ │ ├── ALLFUN.f │ │ ├── BAFINI.f │ │ ├── BF.f │ │ ├── CEP.f │ │ ├── CEPION.f │ │ ├── CEPMOD.f │ │ ├── CEPMOD_AP.f │ │ ├── CEPMOD_BO.f │ │ ├── CEPMOD_FN.f │ │ ├── CEPMOD_TTP.f │ │ ├── CHNL.f │ │ ├── CMM.f │ │ ├── CMakeLists.txt │ │ ├── COMU.f │ │ ├── CONSTS.f │ │ ├── CONTACT.f │ │ ├── DEBUG.f │ │ ├── DISTRIBUTE.f │ │ ├── ECMOD_DCPLD.f │ │ ├── EC_DCPLD.f │ │ ├── EQASSEM.f │ │ ├── FFT.f │ │ ├── FLUID.f │ │ ├── FS.f │ │ ├── FSI.f │ │ ├── HEATF.f │ │ ├── HEATS.f │ │ ├── IB.f │ │ ├── INITIALIZE.f │ │ ├── LELAS.f │ │ ├── LHSA.f │ │ ├── LIST.f │ │ ├── LOADMSH.f │ │ ├── LOADNRB.f │ │ ├── LS.f │ │ ├── MAIN.f │ │ ├── MATFUN.f │ │ ├── MATMODELS.f │ │ ├── MESH.f │ │ ├── MOD.f │ │ ├── NN.f │ │ ├── NURBS.f │ │ ├── OUTPUT.f │ │ ├── PARAMS_AP.f │ │ ├── PARAMS_BO.f │ │ ├── PARAMS_EC_DCPLD.f │ │ ├── PARAMS_FN.f │ │ ├── PARAMS_TTP.f │ │ ├── PIC.f │ │ ├── POST.f │ │ ├── READFILES.f │ │ ├── READMSH.f │ │ ├── REMESH.f │ │ ├── SETBC.f │ │ ├── SHELLS.f │ │ ├── SPLIT.c │ │ ├── STOKES.f │ │ ├── STRUCT.f │ │ ├── TXT.f │ │ ├── TYPEMOD.f │ │ ├── USTRUCT.f │ │ ├── UTIL.f │ │ ├── VTKXML.f │ │ ├── remeshTet.cpp │ │ ├── trilinos_linear_solver.cpp │ │ ├── trilinos_linear_solver.h │ │ ├── vtkComMod.f90 │ │ ├── vtkLegacyParser.f90 │ │ ├── vtkTypeParams.f90 │ │ ├── vtkXMLParser.f90 │ │ └── vtkZpipe.c │ └── svFSILS │ │ ├── ADDBCMUL.f │ │ ├── BC.f │ │ ├── BCAST.f │ │ ├── BICGS.f │ │ ├── CGRAD.f │ │ ├── CMakeLists.txt │ │ ├── COMMU.f │ │ ├── CPUT.f │ │ ├── DOT.f │ │ ├── FSILS.h │ │ ├── FSILS_API.h │ │ ├── FSILS_STD.h │ │ ├── FSILS_STRUCT.h │ │ ├── FSILS_TYPEDEF.h │ │ ├── FSILS_api_c.h │ │ ├── FSILS_c.h │ │ ├── FSILS_struct_c.h │ │ ├── FSISOLVER.f │ │ ├── GE.f │ │ ├── GMRES.f │ │ ├── HRCPUT.c │ │ ├── INCOMMU.f │ │ ├── LHS.f │ │ ├── LS.f │ │ ├── NORM.f │ │ ├── NSSOLVER.f │ │ ├── OMPLA.f │ │ ├── PCGMRES.f │ │ ├── PRECOND.f │ │ ├── SOLVE.f │ │ └── SPARMUL.f └── ThirdParty │ ├── README │ ├── metis_svfsi │ ├── CMakeLists.txt │ ├── simvascular_metis_svfsi.h.in │ └── simvascular_metis_svfsi │ │ ├── CHANGES │ │ ├── CMakeLists.txt │ │ ├── INSTALL │ │ ├── LICENSE.txt │ │ ├── METISLib │ │ ├── CMakeLists.txt │ │ ├── Makefile │ │ ├── balance.c │ │ ├── bucketsort.c │ │ ├── ccgraph.c │ │ ├── checkgraph.c │ │ ├── coarsen.c │ │ ├── compress.c │ │ ├── debug.c │ │ ├── defs.h │ │ ├── estmem.c │ │ ├── fm.c │ │ ├── fortran.c │ │ ├── frename.c │ │ ├── graph.c │ │ ├── initpart.c │ │ ├── kmetis.c │ │ ├── kvmetis.c │ │ ├── kwayfm.c │ │ ├── kwayrefine.c │ │ ├── kwayvolfm.c │ │ ├── kwayvolrefine.c │ │ ├── macros.h │ │ ├── match.c │ │ ├── mbalance.c │ │ ├── mbalance2.c │ │ ├── mcoarsen.c │ │ ├── memory.c │ │ ├── mesh.c │ │ ├── meshpart.c │ │ ├── metis.h │ │ ├── mfm.c │ │ ├── mfm2.c │ │ ├── mincover.c │ │ ├── minitpart.c │ │ ├── minitpart2.c │ │ ├── mkmetis.c │ │ ├── mkwayfmh.c │ │ ├── mkwayrefine.c │ │ ├── mmatch.c │ │ ├── mmd.c │ │ ├── mpmetis.c │ │ ├── mrefine.c │ │ ├── mrefine2.c │ │ ├── mutil.c │ │ ├── myqsort.c │ │ ├── ometis.c │ │ ├── out │ │ ├── parmetis.c │ │ ├── parmetis.h │ │ ├── pmetis.c │ │ ├── pqueue.c │ │ ├── proto.h │ │ ├── refine.c │ │ ├── rename.h │ │ ├── separator.c │ │ ├── sfm.c │ │ ├── srefine.c │ │ ├── stat.c │ │ ├── stats.c │ │ ├── stdheaders.h │ │ ├── struct.h │ │ ├── subdomains.c │ │ ├── temp │ │ │ ├── metis.h │ │ │ └── metis_defs.h │ │ ├── timing.c │ │ └── util.c │ │ ├── Makefile │ │ ├── Makefile.in │ │ ├── README │ │ └── VERSION │ ├── msmpi │ ├── Include │ │ ├── mpi.f90 │ │ ├── mpi.h │ │ ├── mpi.h.org │ │ ├── mpif.h │ │ ├── mpif.h.org │ │ ├── mpio.h │ │ ├── mspms.h │ │ ├── pmidbg.h │ │ ├── x64 │ │ │ └── mpifptr.h │ │ └── x86 │ │ │ └── mpifptr.h │ ├── Installers │ │ └── msmpisdk.msi │ └── License │ │ └── license_sdk.rtf │ ├── parmetis_svfsi │ ├── CMakeLists.txt │ ├── simvascular_parmetis_svfsi.h.in │ └── simvascular_parmetis_svfsi │ │ ├── CHANGES │ │ ├── CMakeLists.txt │ │ ├── INSTALL │ │ ├── LICENSE.txt │ │ ├── Makefile │ │ ├── Makefile.in │ │ ├── ParMETISLib │ │ ├── CMakeLists.txt │ │ ├── Makefile │ │ ├── adrivers.c │ │ ├── akwayfm.c │ │ ├── ametis.c │ │ ├── backcompat.c │ │ ├── balancemylink.c │ │ ├── comm.c │ │ ├── csrmatch.c │ │ ├── debug.c │ │ ├── defs.h │ │ ├── diffutil.c │ │ ├── fpqueue.c │ │ ├── frename.c │ │ ├── gkmetis.c │ │ ├── grsetup.c │ │ ├── iidxsort.c │ │ ├── iintsort.c │ │ ├── ikeysort.c │ │ ├── ikeyvalsort.c │ │ ├── initbalance.c │ │ ├── initmsection.c │ │ ├── initpart.c │ │ ├── kmetis.c │ │ ├── kwaybalance.c │ │ ├── kwayfm.c │ │ ├── kwayrefine.c │ │ ├── macros.h │ │ ├── match.c │ │ ├── mdiffusion.c │ │ ├── memory.c │ │ ├── mesh.c │ │ ├── mmetis.c │ │ ├── move.c │ │ ├── msetup.c │ │ ├── node_refine.c │ │ ├── ometis.c │ │ ├── parmetis.h │ │ ├── parmetislib.h │ │ ├── proto.h │ │ ├── pspases.c │ │ ├── redomylink.c │ │ ├── remap.c │ │ ├── rename.h │ │ ├── rmetis.c │ │ ├── selectq.c │ │ ├── serial.c │ │ ├── setup.c │ │ ├── stat.c │ │ ├── stdheaders.h │ │ ├── struct.h │ │ ├── temp │ │ │ ├── metis.h │ │ │ ├── metis_defs.h │ │ │ ├── parmetis.h │ │ │ └── parmetislib.h │ │ ├── timer.c │ │ ├── util.c │ │ ├── wave.c │ │ ├── weird.c │ │ └── xyzpart.c │ │ ├── README │ │ └── VERSION │ ├── tetgen │ ├── CMakeLists.txt │ ├── Makefile │ ├── simvascular_tetgen.h.in │ └── simvascular_tetgen │ │ ├── CMakeLists.txt │ │ ├── LICENSE │ │ ├── Makefile │ │ ├── README │ │ ├── README.simvascular │ │ ├── example.poly │ │ ├── makefile.tetgen.org │ │ ├── predicates.cxx │ │ ├── tetgen.cxx │ │ └── tetgen.h │ └── zlib │ ├── CMakeLists.txt │ ├── Makefile │ ├── simvascular_zlib.h.in │ └── simvascular_zlib │ ├── CMakeLists.txt │ ├── Makefile │ ├── READ.simvascular │ ├── adler32.c │ ├── compress.c │ ├── crc32.c │ ├── crc32.h │ ├── deflate.c │ ├── deflate.h │ ├── example.c │ ├── gzio.c │ ├── infback.c │ ├── inffast.c │ ├── inffast.h │ ├── inffixed.h │ ├── inflate.c │ ├── inflate.h │ ├── inftrees.c │ ├── inftrees.h │ ├── minigzip.c │ ├── simvascular_zlib_mangle.h │ ├── trees.c │ ├── trees.h │ ├── uncompr.c │ ├── zconf.h │ ├── zconf.in.h │ ├── zlib.def │ ├── zlib.h │ ├── ztest2978.c │ ├── zutil.c │ └── zutil.h ├── Distribution ├── CMakeLists.txt ├── OSX │ ├── Info.plist.in │ ├── cpmview.icns │ ├── simvascular.icns │ ├── simvascular.sh │ └── simvascular.sh.in ├── license.txt └── windows │ ├── msi-banner.bmp │ ├── msi-banner.jpg │ ├── msi-dialog.bmp │ ├── msi-dialog.jpg │ ├── mywix.template-notargets.in │ ├── mywix.template.in │ ├── registry-patch-notargets.xml.in │ ├── registry-patch.xml.in │ └── simvascular.ico ├── Docker ├── Dockerfile └── README.md ├── Documentation └── simvascular.Doxyfile.in ├── Externals ├── BuildHelpers │ ├── CompileScripts │ │ ├── compile-cmake-vtk-generic.sh │ │ ├── compile-make-tcl-generic.sh │ │ ├── sed-script-x64_cygwin-options-cl.sh │ │ ├── sed-script-x64_linux-options-gcc.sh │ │ ├── sed-script-x64_mac_osx-options-clang.sh │ │ ├── tcl-linux-generic.sh │ │ ├── tcl-mac_osx-generic.sh │ │ ├── tcl-mingw64-generic.sh │ │ ├── tcl-osx-generic.sh │ │ └── tcl-windows-generic.sh │ ├── CygwinHelpers │ │ ├── clean-env.sh │ │ ├── msvc_2010_x64 │ │ └── msvc_2013_x64 │ ├── Patches │ │ ├── patch-source-tcltk-8.5.sh │ │ ├── patch-source-vtk-6.2.sh │ │ ├── patch-source-vtk-6.3.sh │ │ ├── tk-8.5.18-win-ttkWinXPTheme.c │ │ ├── vtk-6.2.0-IO-Video-vtkWin32VideoSource.cxx.from-master-2015-07-20 │ │ ├── vtk-6.2.0-ThirdParty-TclTk-internals-tk8.5-tkWinPort.h │ │ ├── vtk-6.2.0-ThirdParty-hdf5-vtkhdf5-src-H5system.c │ │ ├── vtk-6.2.0-ThirdParty-hdf5-vtkhdf5-src-H5win32defs.h │ │ ├── vtk-6.3.0-ThirdParty-TclTk-internals-tk8.5-tkWinPort.h │ │ ├── vtk-6.3.0-ThirdParty-hdf5-vtkhdf5-src-H5system.c │ │ └── vtk-6.3.0-ThirdParty-hdf5-vtkhdf5-src-H5win32defs.h │ └── Scripts │ │ ├── create-archives-generic.sh │ │ ├── superbuild-linux-gcc.sh │ │ ├── superbuild-mac_osx-clang.sh │ │ ├── superbuild-windows-cl.sh │ │ ├── tar-to-zip-all.sh │ │ └── untar-unzip-source-all.sh ├── CMakeExternals │ └── SvExtOptions.cmake ├── CMakeLists.txt ├── build-sv-externals-helper-wget-generic.sh ├── build-sv-externals-linux.sh ├── build-sv-externals-mac_osx.sh └── build-sv-externals-windows.sh ├── INSTALL-DEPS.md ├── INSTALL.md ├── License.txt ├── Licenses ├── ExternalOpenSourcePackages │ ├── README-external-licenses-academic-use-only.txt │ ├── README-external-licenses-gpl.txt │ ├── README-external-licenses-lgpl.txt │ └── README-external-licenses-unrestrictive.txt └── LesLib │ └── README-LESLIB.txt ├── README.md ├── svFSI_master.inp └── travis ├── travis_build.sh └── travis_cmake_config.sh /.gitignore: -------------------------------------------------------------------------------- 1 | # Prerequisites 2 | *.d 3 | 4 | # Compiled Object files 5 | *.slo 6 | *.lo 7 | *.o 8 | *.obj 9 | 10 | # Precompiled Headers 11 | *.gch 12 | *.pch 13 | 14 | # Compiled Dynamic libraries 15 | *.so 16 | *.dylib 17 | *.dll 18 | 19 | # Fortran module files 20 | *.mod 21 | *.smod 22 | 23 | # Compiled Static libraries 24 | *.lai 25 | *.la 26 | *.a 27 | *.lib 28 | 29 | # Executables 30 | *.exe 31 | *.out 32 | *.app 33 | 34 | # System files osx 35 | **/.DS_Store 36 | -------------------------------------------------------------------------------- /BuildWithMake/CygwinHelpers/clean-env.sh: -------------------------------------------------------------------------------- 1 | # visual studio 2010 defines 2 | export VS100COMNTOOLS= 3 | export VSINSTALLDIR= 4 | export VCINSTALLDIR= 5 | export FrameworkDir= 6 | export FrameworkVersion= 7 | export WindowsSdkDir= 8 | export Platform= 9 | export CommandPromptType= 10 | export INCLUDE= 11 | export LIB= 12 | export PATH=/usr/bin:/bin:/cygdrive/c/Windows/system32/reg:/cygdrive/c/Windows/system32:/cygdrive/c/Windows/SysWOW64 13 | export LIBPATH= 14 | # visual studio 2013 defines 15 | export VisualStudioVersion= 16 | export Framework40Version= 17 | export WindowsSdkDir= 18 | export ExtensionSdkDir= 19 | export WindowsSDK_ExecutablePath_x64= 20 | export VS120COMNTOOLS= 21 | export VSINSTALLDIR= 22 | export VCINSTALLDIR= 23 | export FrameworkDir= 24 | export FrameworkVersion= 25 | export Platform= 26 | export CommandPromptType= 27 | export INCLUDE= 28 | export LIB= 29 | export PATH=/usr/bin:/bin:/cygdrive/c/Windows/system32/reg:/cygdrive/c/Windows/system32:/cygdrive/c/Windows/SysWOW64 30 | export LIBPATH= 31 | -------------------------------------------------------------------------------- /BuildWithMake/CygwinHelpers/intel_fortran_12_x64: -------------------------------------------------------------------------------- 1 | 2 | export ROOT=/cygdrive/c/Program\ Files\ \(x86\)/Intel/Composer\ XE\ 2011\ SP1 3 | export TARGET_ARCH=intel64 4 | export ARCH_PATH=intel64 5 | 6 | export PATH=$ROOT/bin/$TARGET_ARCH:$ROOT/redist/$ARCH_PATH/compiler:$PATH 7 | export PATH=$PATH:$ROOT/redist/$ARCH_PATH/mpirt 8 | 9 | export LIB=`cygpath -w "$ROOT/compiler/lib"`\;`cygpath -w "$ROOT/compiler/lib/$ARCH_PATH"`\;$LIB 10 | 11 | export INCLUDE=`cygpath -w "$ROOT/compiler/include"`\;`cygpath -w "$ROOT/compiler/include/$ARCH_PATH"`\;$INCLUDE 12 | 13 | INTEL_LICENSE_FILE=/cygdrive/c/Program\ Files\ \(x86\)/Common\ Files/Intel/Licenses 14 | export INTEL_LICENSE_FILE=`cygpath -m "$INTEL_LICENSE_FILE"` 15 | -------------------------------------------------------------------------------- /BuildWithMake/CygwinHelpers/intel_fortran_14_x64: -------------------------------------------------------------------------------- 1 | export INTEL_COMPILER_ROOT=/cygdrive/c/Program\ Files\ \(x86\)/Intel/Composer\ XE\ 2013\ SP1 2 | 3 | export TARGET_ARCH=intel64 4 | export TARGET_VS_ARCH=amd64 5 | export ARCH_PATH=intel64 6 | #export ARCH_PATH_MPI=em64t 7 | 8 | #export BUNDLE_NAME="Intel(R) Parallel Studio XE 2013 SP1" 9 | #export PRODUCT_NAME="Intel Composer XE 2013 SP1" 10 | #export PRODUCT_NAME_FULL="Intel(R) Composer XE 2013 SP1 Update 2 (package 176)" 11 | #export WIN_TITLE=$PRODUCT_NAME 12 | #export WIN_TITLE_ARCH="Intel(R) 64" 13 | #export WIN_TITLE_VS="Visual Studio 2010" 14 | #export WIN_TITLE="$WIN_TITLE $WIN_TITLE_ARCH $WIN_TITLE_VS" 15 | 16 | export PATH=$INTEL_COMPILER_ROOT/bin/$TARGET_ARCH:$INTEL_COMPILER_ROOT/redist/$ARCH_PATH/compiler:$PATH 17 | export PATH=$PATH:$INTEL_COMPILER_ROOT/redist/$ARCH_PATH/mpirt 18 | 19 | export LIB=`cygpath -w "$INTEL_COMPILER_ROOT/compiler/lib"`\;`cygpath -w "$INTEL_COMPILER_ROOT/compiler/lib/$ARCH_PATH"`\;$LIB 20 | 21 | #set MIC_LD_LIBRARY_PATH=%INTEL_COMPILER_ROOT%\compiler\lib\mic;%MIC_LD_LIBRARY_PATH% 22 | 23 | export INCLUDE=`cygpath -w "$INTEL_COMPILER_ROOT/compiler/include"`\;`cygpath -w "$INTEL_COMPILER_ROOT/compiler/include/$ARCH_PATH"`\;$INCLUDE 24 | 25 | INTEL_LICENSE_FILE=/cygdrive/c/Program\ Files\ \(x86\)/Common\ Files/Intel/Licenses 26 | export INTEL_LICENSE_FILE=`cygpath -m "$INTEL_LICENSE_FILE"` 27 | -------------------------------------------------------------------------------- /BuildWithMake/CygwinHelpers/parse_reg_dir.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh -f 2 | # HKLM\\SOFTWARE\\Wow6432Node\\Microsoft\\VisualStudio\\SxS\\VS7 3 | 4 | reg query "$1" /v $2 | sed ':a;N;$!ba;s/\n//g;s/\r//g;s+\\+/+g' | awk '{gsub(/^[ \t]+/,"",$0);gsub(/^[ \t]+$/,"",$0);print}' | awk '{$1="";$2="";$3="";print}' | awk '{gsub(/^[ \t]+/,"",$0);gsub(/^[ \t]+$/,"",$0);print}' 5 | 6 | -------------------------------------------------------------------------------- /BuildWithMake/CygwinHelpers/parse_reg_dir_with_extra_space.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh -f 2 | 3 | reg query "$1" /v $2 | sed ':a;N;$!ba;s/\n//g;s/\r//g;s+\\+/+g' | awk '{gsub(/^[ \t]+/,"",$0);gsub(/^[ \t]+$/,"",$0);print}' | awk '{$1="";$2="";$3="";$4="";print}' | awk '{gsub(/^[ \t]+/,"",$0);gsub(/^[ \t]+$/,"",$0);print}' 4 | 5 | -------------------------------------------------------------------------------- /BuildWithMake/Docs/Doxygen/mainpage.cxx: -------------------------------------------------------------------------------- 1 | /* Copyright (c) 2009-2011 Open Source Medical Software Corporation, 2 | * University of California, San Diego. 3 | * 4 | * Portions of the code Copyright (c) 1998-2007 Stanford University, 5 | * Charles Taylor, Nathan Wilson, Ken Wang. 6 | * 7 | * Permission is hereby granted, free of charge, to any person obtaining 8 | * a copy of this software and associated documentation files (the 9 | * "Software"), to deal in the Software without restriction, including 10 | * without limitation the rights to use, copy, modify, merge, publish, 11 | * distribute, sublicense, and/or sell copies of the Software, and to 12 | * permit persons to whom the Software is furnished to do so, subject 13 | * to the following conditions: 14 | * 15 | * The above copyright notice and this permission notice shall be included 16 | * in all copies or substantial portions of the Software. 17 | * 18 | * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS 19 | * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED 20 | * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 21 | * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER 22 | * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 23 | * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 24 | * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 25 | * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 26 | * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 27 | * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 28 | * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 29 | */ 30 | 31 | /*! \mainpage SimVascular Documentation 32 | * 33 | * 34 | * \section cvsim_main_sec 35 | * 36 | * Software for modeling and simulating blood flow. 37 | * 38 | * \section useful_sec Useful Links 39 | * 40 | * VTK 41 | *
42 | * ITK 43 | *
44 | * Tcl/Tk 45 | *
46 | * 47 | *
48 | * 49 | */ 50 | 51 | -------------------------------------------------------------------------------- /BuildWithMake/Docs/Makefile: -------------------------------------------------------------------------------- 1 | # Hey emacs, this is a -*- makefile -*- 2 | 3 | TOP = .. 4 | 5 | include $(TOP)/include.mk 6 | 7 | DATEVAR = `date +%F` 8 | 9 | all: cxxdocs tcldocs flowsolverdocs post-build 10 | 11 | cxxdocs: 12 | -rm -f sedscript 13 | -rm -f useme.Doxyfile 14 | -rm -Rf htmldocs/cxx_html 15 | -mkdir -p htmldocs 16 | -echo "puts \"s+REPLACEME_SV_DOX_OUTPUT_DIR+[file rootname `pwd`]/htmldocs+g\"" | tclsh > sedscript 17 | -echo "puts \"s+REPLACEME_SV_DOX_INPUT_DIR+[file rootname `pwd`]/../../Code+g\"" | tclsh >> sedscript 18 | -echo "puts \"s+REPLACEME_SV_PROJECT_NUMBER+${DATEVAR}+g\"" | tclsh >> sedscript 19 | -sed -f sedscript simvascular.Doxyfile > useme.Doxyfile 20 | -doxygen useme.Doxyfile 21 | -rm useme.Doxyfile 22 | -rm sedscript 23 | 24 | tcldocs: 25 | -rm -f htmldocs/tcl_all_html 26 | -mkdir -p htmldocs/tcl_all_html 27 | -tclsh /SV15/src/autodoc/autodoc -srcdir `pwd`/../../Tcl/SimVascular_2.0 -outputdir `pwd`/htmldocs/tcl_all_html 28 | -cp styles.css `pwd`/htmldocs/tcl_all_html 29 | -rm -f htmldocs/tcl_common_and_core_html 30 | -rm -f -R TclCode 31 | -mkdir -p htmldocs/tcl_common_and_core_html 32 | -mkdir -p TclCode 33 | -svn export --force $(TOP)/../Tcl/Common TclCode/Common 34 | -svn export --force $(TOP)/../Tcl/SimVascular_2.0/Core TclCode/Core 35 | -tclsh /SV15/src/autodoc/autodoc -srcdir `pwd`/TclCode -outputdir `pwd`/htmldocs/tcl_common_and_core_html 36 | -cp styles.css `pwd`/htmldocs/tcl_common_and_core_html 37 | -rm -f -R TclCode 38 | 39 | flowsolverdocs: 40 | -rm -f sedscript 41 | -rm -f useme.Doxyfile 42 | -rm -f htmldocs/flowsolver_html 43 | -mkdir -p htmldocs 44 | -echo "puts \"s+REPLACEME_SV_DOX_OUTPUT_DIR+[file rootname `pwd`]/htmldocs+g\"" | tclsh > sedscript 45 | -echo "s+REPLACEME_SV_PROJECT_NUMBER+${DATEVAR}+g" >> sedscript 46 | -sed -f sedscript flowsolver.Doxyfile > useme.Doxyfile 47 | -doxygen useme.Doxyfile 48 | -rm useme.Doxyfile 49 | -rm sedscript 50 | 51 | post-build: 52 | -cp index.html htmldocs/ 53 | -rm -f htmldocs-${DATEVAR}.tar.gz 54 | -tar cvzf htmldocs-${DATEVAR}.tar.gz htmldocs/ 55 | 56 | clean: veryclean 57 | 58 | veryclean: 59 | if [ -e sedscript ];then /bin/rm -f sedscript;fi 60 | if [ -e useme.Doxyfile ];then /bin/rm -f useme.Doxyfile;fi 61 | if [ -e htmldocs ];then /bin/rm -Rf htmldocs;fi 62 | if [ -e TclCode ];then /bin/rm -Rf TclCode;fi 63 | 64 | # 65 | -------------------------------------------------------------------------------- /BuildWithMake/Docs/index.html: -------------------------------------------------------------------------------- 1 | 2 |

3 | SimVascular C++ Docs 4 |
5 | svSolver Fortran Docs 6 |
7 | SV Tcl Docs (common&core) 8 |
9 | SV Tcl (all) 10 |
11 |

12 | 13 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.clang.x64_macosx.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_macosx) 2 | SHELL =/bin/sh 3 | CXX = clang++ -pthread -w 4 | CC = clang -pthread -w 5 | CXXDEP = $(CXX) -MM 6 | CCDEP = $(CC) -MM 7 | AR = ar -cru 8 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 9 | OPT_FLAGS = -O3 -fPIC 10 | DEBUG_FLAGS = 11 | LINK_EXE = $(CXX) -o 12 | else 13 | ifeq ($(MAKE_OPTIMIZED),1) 14 | DEBUG_FLAGS = 15 | OPT_FLAGS = -O2 -fPIC 16 | LINK_EXE = $(CXX) -o 17 | else 18 | DEBUG_FLAGS = -O0 -g -fstack-protector-all 19 | OPT_FLAGS = 20 | LINK_EXE = $(CXX) -g -fstack-protector-all -o 21 | endif 22 | endif 23 | # SHAR = $(CXX) -dynamiclib -current_version 1.0 -compatibility_version 1.0 -fvisibility=hidden -o 24 | SHAR = $(CXX) -dynamiclib -current_version 1.0 -compatibility_version 1.0 -o 25 | SOEXT = dylib 26 | STATICEXT = a 27 | OBJECTEXT = o 28 | EXEEXT = 29 | BUILDFLAGS = $(GLOBAL_DEFINES) 30 | GLOBAL_CXXFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 31 | GLOBAL_CXXFLAGS += -fpermissive 32 | ifeq ($(SV_USE_CXX11),1) 33 | GLOBAL_CXXFLAGS += -std=c++11 34 | endif 35 | GLOBAL_CCFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 36 | GLOBAL_LFLAGS = -lz -framework GLUT -framework OpenGL -framework Cocoa 37 | ifeq ($(USE_SYSTEM_TCLTK),1) 38 | GLOBAL_LFLAGS += -framework Tcl -framework Tk 39 | endif 40 | ifeq ($(LINK_WITH_DEBUG),1) 41 | GLOBAL_LFLAGS += -g 42 | endif 43 | GLOBAL_LFLAGS += -lm 44 | SHARED_LFLAGS = 45 | STATIC_FLAG = 46 | DYNAMIC_FLAG = 47 | TEMPLATE_AR = $(AR) 48 | CC_LIBS = 49 | CXX_LIBS = 50 | # LINK_EXE = $(CXX) -L$(TOP)/Lib -o 51 | LIBPATH_COMPILER_FLAG = -L 52 | LIBFLAG = -l 53 | SVLIBFLAG = -l 54 | endif 55 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.gcc.x64_linux.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_linux) 2 | SHELL =/bin/sh 3 | CXX = g++ -pthread -w 4 | CC = gcc -pthread -w 5 | CXXDEP = $(CXX) -MM 6 | CCDEP = $(CC) -MM 7 | AR = ar -cru 8 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 9 | OPT_FLAGS = -O3 -fPIC 10 | DEBUG_FLAGS = 11 | LINK_EXE = $(CXX) -o 12 | else 13 | ifeq ($(MAKE_OPTIMIZED),1) 14 | DEBUG_FLAGS = 15 | OPT_FLAGS = -O2 -fPIC 16 | LINK_EXE = $(CXX) -o 17 | else 18 | DEBUG_FLAGS = -O0 -g -fstack-protector-all 19 | OPT_FLAGS = 20 | LINK_EXE = $(CXX) -g -fstack-protector-all -o 21 | endif 22 | endif 23 | ifeq ($(SV_USE_OPENCASCADE),1) 24 | OPT_FLAGS = -std=gnu++11 -fPIC 25 | endif 26 | SHAR = $(CXX) -shared -o 27 | SOEXT = so 28 | STATICEXT = a 29 | OBJECTEXT = o 30 | EXEEXT = 31 | BUILDFLAGS = $(GLOBAL_DEFINES) 32 | GLOBAL_CXXFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 33 | GLOBAL_CXXFLAGS += -fpermissive 34 | GLOBAL_CCFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 35 | GLOBAL_LFLAGS = 36 | ifeq ($(LINK_WITH_DEBUG),1) 37 | GLOBAL_LFLAGS += -g 38 | endif 39 | GLOBAL_LFLAGS += -lm 40 | SHARED_LFLAGS = 41 | STATIC_FLAG = 42 | DYNAMIC_FLAG = 43 | TEMPLATE_AR = $(AR) 44 | CC_LIBS = 45 | CXX_LIBS = 46 | # LINK_EXE = $(CXX) -L$(TOP)/Lib -o 47 | LIBPATH_COMPILER_FLAG = -L 48 | LIBFLAG = -l 49 | SVLIBFLAG = -l 50 | LIBLINKEXT = 51 | endif 52 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.gcc.x64_macosx.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_macosx) 2 | SHELL =/bin/sh 3 | CXX = g++-mp-5 -pthread -w 4 | CC = gcc-mp-5 -pthread -w 5 | CXXDEP = $(CXX) -MM 6 | CCDEP = $(CC) -MM 7 | AR = ar -cru 8 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 9 | OPT_FLAGS = -O3 -fPIC 10 | DEBUG_FLAGS = 11 | LINK_EXE = $(CXX) -o 12 | else 13 | ifeq ($(MAKE_OPTIMIZED),1) 14 | DEBUG_FLAGS = 15 | OPT_FLAGS = -O2 -fPIC 16 | LINK_EXE = $(CXX) -o 17 | else 18 | DEBUG_FLAGS = -O0 -g -fstack-protector-all 19 | OPT_FLAGS = 20 | LINK_EXE = $(CXX) -g -fstack-protector-all -o 21 | endif 22 | endif 23 | SHAR = $(CXX) -shared -o 24 | SOEXT = so 25 | STATICEXT = a 26 | OBJECTEXT = o 27 | EXEEXT = 28 | BUILDFLAGS = $(GLOBAL_DEFINES) 29 | GLOBAL_CXXFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 30 | GLOBAL_CXXFLAGS += -fpermissive 31 | GLOBAL_CCFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 32 | GLOBAL_LFLAGS = 33 | ifeq ($(LINK_WITH_DEBUG),1) 34 | GLOBAL_LFLAGS += -g 35 | endif 36 | GLOBAL_LFLAGS += -lm 37 | SHARED_LFLAGS = 38 | STATIC_FLAG = 39 | DYNAMIC_FLAG = 40 | TEMPLATE_AR = $(AR) 41 | CC_LIBS = 42 | CXX_LIBS = 43 | # LINK_EXE = $(CXX) -L$(TOP)/Lib -o 44 | LIBPATH_COMPILER_FLAG = -L 45 | LIBFLAG = -l 46 | SVLIBFLAG = -l 47 | endif 48 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.gfortran.x64_linux.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_linux) 2 | F90 = gfortran -pthread -cpp 3 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 4 | OPT_FFLAGS = -O3 -fPIC 5 | DEBUG_FFLAGS = 6 | else 7 | ifeq ($(MAKE_OPTIMIZED),1) 8 | OPT_FFLAGS = -O2 -fPIC 9 | DEBUG_FFLAGS = 10 | else 11 | OPT_FFLAGS = 12 | DEBUG_FFLAGS = -O0 -g 13 | endif 14 | endif 15 | GLOBAL_FFLAGS = $(BUILDFLAGS) $(DEBUG_FFLAGS) $(OPT_FFLAGS) -ffixed-line-length-132 -fmax-stack-var-size=256 16 | F90_LIBS = -lgfortran -lm 17 | ifeq ($(LINK_WITH_DEBUG),1) 18 | GLOBAL_LFLAGS += -g 19 | endif 20 | endif 21 | 22 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.gfortran.x64_macosx.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_macosx) 2 | F90 = gfortran -pthread -cpp 3 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 4 | OPT_FFLAGS = -O3 -fPIC 5 | DEBUG_FFLAGS = 6 | else 7 | ifeq ($(MAKE_OPTIMIZED),1) 8 | OPT_FFLAGS = -O2 -fPIC 9 | DEBUG_FFLAGS = 10 | else 11 | OPT_FFLAGS = 12 | DEBUG_FFLAGS = -O0 -g 13 | endif 14 | endif 15 | GLOBAL_FFLAGS = $(BUILDFLAGS) $(DEBUG_FFLAGS) $(OPT_FFLAGS) -ffixed-line-length-132 -fmax-stack-var-size=256 16 | F90_LIBS = $(wordlist 2,99,$(shell mpif90 -link_info)) -lm 17 | ifeq ($(LINK_WITH_DEBUG),1) 18 | GLOBAL_LFLAGS += -g 19 | endif 20 | endif 21 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.icpc.x64_linux.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_linux) 2 | SHELL =/bin/sh 3 | CXX = icpc -pthread 4 | CC = icc -pthread 5 | CXXDEP = icpc -MM 6 | CCDEP = icc -MM 7 | AR = ar -cru 8 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 9 | OPT_FLAGS = -O3 -fPIC 10 | DEBUG_FLAGS = 11 | LINK_EXE = $(CXX) -o 12 | else 13 | ifeq ($(MAKE_OPTIMIZED),1) 14 | DEBUG_FLAGS = 15 | OPT_FLAGS = -O2 -fPIC 16 | LINK_EXE = $(CXX) -o 17 | else 18 | DEBUG_FLAGS = -O0 -debug -g -fp-stack-check -fstack-protector-all 19 | OPT_FLAGS = 20 | LINK_EXE = $(CXX) -debug -g -fp-stack-check -fstack-protector-all -traceback -o 21 | endif 22 | endif 23 | SHAR = $(CXX) -shared -o 24 | SOEXT = so 25 | STATICEXT = a 26 | OBJECTEXT = o 27 | EXEEXT = 28 | BUILDFLAGS = $(GLOBAL_DEFINES) 29 | GLOBAL_CXXFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 30 | GLOBAL_CCFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 31 | GLOBAL_LFLAGS = 32 | GLOBAL_LFLAGS += -lm 33 | SHARED_LFLAGS = 34 | STATIC_FLAG = 35 | DYNAMIC_FLAG = 36 | TEMPLATE_AR = $(AR) 37 | CC_LIBS = 38 | CXX_LIBS = 39 | ifeq ($(LINK_WITH_DEBUG),1) 40 | GLOBAL_LFLAGS += -debug -g 41 | endif 42 | # LINK_EXE = $(CXX) -L$(TOP)/Lib -o 43 | LIBPATH_COMPILER_FLAG = -L 44 | LIBFLAG = -l 45 | SVLIBFLAG = -l 46 | endif 47 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.ifort.x64_cygwin.mk: -------------------------------------------------------------------------------- 1 | # ---------------------------------- 2 | # Platform-specific compiler options 3 | # ---------------------------------- 4 | 5 | ifeq ($(CLUSTER), x64_cygwin) 6 | F90 = ifort -fpp 7 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 8 | DEBUG_FFLAGS = 9 | OPT_FFLAGS = /MD /Ox 10 | else 11 | ifeq ($(MAKE_OPTIMIZED),1) 12 | DEBUG_FFLAGS = 13 | OPT_FFLAGS = /MD /Zi /O2 14 | else 15 | DEBUG_FFLAGS = /MD /Zi /Od /debug:all /debug:all /check:all -traceback 16 | endif 17 | endif 18 | GLOBAL_FFLAGS = $(BUILDFLAGS) $(DEBUG_FFLAGS) $(OPT_FFLAGS) /W0 /4L132 /heap-arrays:256 19 | ifeq ($(LINK_WITH_DEBUG),1) 20 | GLOBAL_LFLAGS += /DEBUG 21 | endif 22 | F90_LIBS = libifcore.lib libifport.lib libmmds.lib svml_disp.lib 23 | endif 24 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.ifort.x64_linux.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_linux) 2 | F90 = ifort -threads -fpp 3 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 4 | OPT_FFLAGS = -O3 -fPIC 5 | DEBUG_FFLAGS = 6 | else 7 | ifeq ($(MAKE_OPTIMIZED),1) 8 | OPT_FFLAGS = -O2 -fPIC 9 | DEBUG_FFLAGS = 10 | else 11 | OPT_FFLAGS = 12 | DEBUG_FFLAGS = -O0 -fPIC -debug -g -check -traceback 13 | endif 14 | endif 15 | GLOBAL_FFLAGS = $(BUILDFLAGS) $(DEBUG_FFLAGS) $(OPT_FFLAGS) \ 16 | -W0 -132 -heap-arrays 256 17 | ifeq ($(LINK_WITH_DEBUG),1) 18 | GLOBAL_LFLAGS += -g 19 | endif 20 | # F90_LIBS = -lifcoremt -lifport -limf -lintlc -ldl 21 | F90_LIBS = -lifcoremt -lifport -limf 22 | endif 23 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.ifort.x64_macosx.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_macosx) 2 | F90 = ifort -threads -fpp 3 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 4 | OPT_FFLAGS = -O3 -fPIC 5 | DEBUG_FFLAGS = 6 | else 7 | ifeq ($(MAKE_OPTIMIZED),1) 8 | OPT_FFLAGS = -O2 -fPIC 9 | DEBUG_FFLAGS = 10 | else 11 | OPT_FFLAGS = 12 | DEBUG_FFLAGS = -O0 -fPIC -debug -g -check -traceback 13 | endif 14 | endif 15 | GLOBAL_FFLAGS = $(BUILDFLAGS) $(DEBUG_FFLAGS) $(OPT_FFLAGS) \ 16 | -W0 -132 -heap-arrays 256 17 | ifeq ($(LINK_WITH_DEBUG),1) 18 | GLOBAL_LFLAGS += -g 19 | endif 20 | # F90_LIBS = -lifcoremt -lifport -limf -lintlc -ldl 21 | # F90_LIBS = -lifcoremt -lifport -limf 22 | F90_LIBS = /opt/intel/compilers_and_libraries_2016/mac/lib/libifcoremt.a \ 23 | /opt/intel/compilers_and_libraries_2016/mac/lib/libifport.a \ 24 | /opt/intel/compilers_and_libraries_2016/mac/lib/libimf.a \ 25 | /opt/intel/compilers_and_libraries_2016/mac/lib/libintlc.dylib \ 26 | /opt/intel/compilers_and_libraries_2016/mac/lib/libsvml.a 27 | endif 28 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.mingw-gcc.x64_cygwin.mk: -------------------------------------------------------------------------------- 1 | # ---------------------------------- 2 | # Platform-specific compiler options 3 | # ---------------------------------- 4 | 5 | ifeq ($(CLUSTER), x64_cygwin) 6 | SHELL =/bin/sh 7 | CXX = x86_64-w64-mingw32-g++ -w -fpermissive 8 | CC = x86_64-w64-mingw32-gcc -w 9 | CXXDEP = x86_64-w64-mingw32-g++ -MM 10 | CCDEP = x86_64-w64-mingw32-gcc -MM 11 | AR = x86_64-w64-mingw32-ar -cru 12 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 13 | DEBUG_FLAGS = 14 | OPT_FLAGS = -O3 15 | else 16 | ifeq ($(MAKE_OPTIMIZED),1) 17 | DEBUG_FLAGS = 18 | OPT_FLAGS = -O2 -g 19 | else 20 | OPT_FLAGS = 21 | DEBUG_FLAGS = -g 22 | endif 23 | endif 24 | SHAR = 25 | SOEXT = dll 26 | STATICEXT = lib 27 | OBJECTEXT = obj 28 | BUILDFLAGS = $(GLOBAL_DEFINES) 29 | GLOBAL_CXXFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 30 | GLOBAL_CCFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 31 | # GLOBAL_LFLAGS = /STACK:64000000,64000000 32 | # SOLVER_STCKSZ = /STACK:512000000,512000000 33 | ifeq ($(LINK_WITH_DEBUG),1) 34 | GLOBAL_LFLAGS += -g 35 | endif 36 | 37 | 38 | GLOBAL_LFLAGS = 39 | SHARED_LFLAGS = /DLL $(GLOBAL_LFLAGS) $(CXX_LIBS) 40 | STATIC_FLAG = 41 | DYNAMIC_FLAG = 42 | TEMPLATE_AR = $(AR) 43 | CC_LIBS = 44 | LINK_EXE = $(CXX) -L$(TOP)/Lib -o 45 | LIBPATH_COMPILER_FLAG = -L 46 | LIBFLAG = -l 47 | LIBCMD = lib 48 | SVLIBFLAG = -llib 49 | endif 50 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.mingw-gfortran.x64_cygwin.mk: -------------------------------------------------------------------------------- 1 | # ---------------------------------- 2 | # Platform-specific compiler options 3 | # ---------------------------------- 4 | 5 | ifeq ($(CLUSTER), x64_cygwin) 6 | F90 = x86_64-w64-mingw32-gfortran.exe -cpp 7 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 8 | DEBUG_FFLAGS = 9 | OPT_FFLAGS = -O2 10 | else 11 | ifeq ($(MAKE_OPTIMIZED),1) 12 | DEBUG_FFLAGS = 13 | OPT_FFLAGS = -g -O2 14 | else 15 | DEBUG_FFLAGS = -g -fcheck=all 16 | endif 17 | endif 18 | GLOBAL_FFLAGS = $(BUILDFLAGS) $(DEBUG_FFLAGS) $(OPT_FFLAGS) -ffixed-line-length-132 -fmax-stack-var-size=256 19 | ifeq ($(LINK_WITH_DEBUG),1) 20 | GLOBAL_LFLAGS += -g 21 | endif 22 | endif 23 | 24 | # required by msmpi headers 25 | GLOBAL_FFLAGS += -fno-range-check 26 | 27 | F90_LIBS = -lgfortran 28 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.vs10.1.x64_cygwin.mk: -------------------------------------------------------------------------------- 1 | # ---------------------------------- 2 | # Platform-specific compiler options 3 | # ---------------------------------- 4 | 5 | ifeq ($(CLUSTER), x64_cygwin) 6 | SHELL =/bin/sh 7 | CXX = CL 8 | CC = CL 9 | CXXDEP = g++ -MM 10 | CCDEP = gcc -MM 11 | AR = lib -out: 12 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 13 | DEBUG_FLAGS = 14 | OPT_FLAGS = /MD /Ox /EHsc 15 | else 16 | ifeq ($(MAKE_OPTIMIZED),1) 17 | DEBUG_FLAGS = 18 | OPT_FLAGS = /MD /Zi /O2 /EHsc /GS 19 | else 20 | OPT_FLAGS = 21 | DEBUG_FLAGS = /MD /Zi /Od /EHsc -D_CRT_SECURE_NO_DEPRECATE /GS /GR 22 | endif 23 | endif 24 | SHAR = link 25 | SOEXT = dll 26 | STATICEXT = lib 27 | OBJECTEXT = obj 28 | BUILDFLAGS = $(GLOBAL_DEFINES) 29 | GLOBAL_CXXFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 30 | GLOBAL_CCFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 31 | GLOBAL_LFLAGS = /STACK:64000000,64000000 32 | SOLVER_STCKSZ = /STACK:512000000,512000000 33 | ifeq ($(LINK_WITH_DEBUG),1) 34 | GLOBAL_LFLAGS += /DEBUG 35 | endif 36 | GLOBAL_LFLAGS += /LARGEADDRESSAWARE /INCREMENTAL:NO /FIXED:NO /RELEASE /NOLOGO \ 37 | /VERBOSE:LIB \ 38 | /NODEFAULTLIB:libc.lib /NODEFAULTLIB:libcd.lib \ 39 | /NODEFAULTLIB:libcmt.lib /NODEFAULTLIB:libcpmt.lib \ 40 | /NODEFAULTLIB:libcmtd.lib /NODEFAULTLIB:libcpmtd.lib \ 41 | /NODEFAULTLIB:msvcrtd.lib \ 42 | /MACHINE:X64 -subsystem:console 43 | 44 | SHARED_LFLAGS = /DLL $(GLOBAL_LFLAGS) $(CXX_LIBS) 45 | STATIC_FLAG = 46 | DYNAMIC_FLAG = 47 | TEMPLATE_AR = $(AR) 48 | CC_LIBS = 49 | CXX_LIBS = Advapi32.lib Ws2_32.lib Shlwapi.lib 50 | LINK_EXE = link /out: 51 | LIBPATH_COMPILER_FLAG = /LIBPATH: 52 | LIBFLAG = 53 | LIBCMD = lib 54 | SVLIBFLAG =lib 55 | LIBLINKEXT =.lib 56 | endif 57 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/compiler.vs12.5.x64_cygwin.mk: -------------------------------------------------------------------------------- 1 | # ---------------------------------- 2 | # Platform-specific compiler options 3 | # ---------------------------------- 4 | 5 | ifeq ($(CLUSTER), x64_cygwin) 6 | SHELL =/bin/sh 7 | CXX = CL 8 | CC = CL 9 | CXXDEP = g++ -MM 10 | CCDEP = gcc -MM 11 | AR = lib -out: 12 | ifeq ($(MAKE_FULLY_OPTIMIZED),1) 13 | DEBUG_FLAGS = 14 | OPT_FLAGS = /MD /Ox /EHsc /MP /FS 15 | else 16 | ifeq ($(MAKE_OPTIMIZED),1) 17 | DEBUG_FLAGS = 18 | OPT_FLAGS = /MD /Zi /O2 /EHsc /GS /MP /FS 19 | else 20 | OPT_FLAGS = 21 | DEBUG_FLAGS = /MD /Zi /Od /EHsc -D_CRT_SECURE_NO_DEPRECATE /GS /GR /MP /FS 22 | endif 23 | endif 24 | SHAR = "/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 12.0/VC/BIN/amd64/link.exe" 25 | SOEXT = dll 26 | STATICEXT = lib 27 | OBJECTEXT = obj 28 | BUILDFLAGS = $(GLOBAL_DEFINES) 29 | GLOBAL_CXXFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 30 | GLOBAL_CCFLAGS = $(BUILDFLAGS) $(DEBUG_FLAGS) $(OPT_FLAGS) 31 | GLOBAL_LFLAGS = /STACK:64000000,64000000 32 | SOLVER_STCKSZ = /STACK:512000000,512000000 33 | ifeq ($(LINK_WITH_DEBUG),1) 34 | GLOBAL_LFLAGS += /DEBUG 35 | endif 36 | GLOBAL_LFLAGS += /LARGEADDRESSAWARE /INCREMENTAL:NO /FIXED:NO /RELEASE /NOLOGO \ 37 | /VERBOSE:LIB \ 38 | /NODEFAULTLIB:libc.lib /NODEFAULTLIB:libcd.lib \ 39 | /NODEFAULTLIB:libcmt.lib /NODEFAULTLIB:libcpmt.lib \ 40 | /NODEFAULTLIB:libcmtd.lib /NODEFAULTLIB:libcpmtd.lib \ 41 | /NODEFAULTLIB:msvcrtd.lib \ 42 | /MACHINE:X64 -subsystem:console 43 | 44 | SHARED_LFLAGS = /DLL $(GLOBAL_LFLAGS) $(CXX_LIBS) 45 | STATIC_FLAG = 46 | DYNAMIC_FLAG = 47 | TEMPLATE_AR = $(AR) 48 | CC_LIBS = 49 | CXX_LIBS = Advapi32.lib Ws2_32.lib Shlwapi.lib 50 | LINK_EXE = "/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 12.0/VC/BIN/amd64/link.exe" /out: 51 | LIBPATH_COMPILER_FLAG = /LIBPATH: 52 | LIBFLAG = 53 | LIBCMD = lib 54 | SVLIBFLAG =lib 55 | LIBLINKEXT =.lib 56 | endif 57 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/leslib-1.5.x64_cygwin.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_cygwin) 2 | LESLIB_DEFS = -DACUSIM_NT -DACUSIM_WIN -DACUSIM_WIN64 3 | LESLIB_INCDIR = -I $(LESLIB_TOP) 4 | LESLIB_TOP = $(LICENSED_SOFTWARE_TOPLEVEL)/leslib-1.5/win/x64 5 | LESLIB_LIBS = $(LIBPATH_COMPILER_FLAG)$(LESLIB_TOP) $(LIBFLAG)libles.lib 6 | LESLIB_LIBS += $(LIBFLAG)Advapi32.lib $(LIBFLAG)Ws2_32.lib 7 | endif 8 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/leslib-1.5.x64_linux.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_linux) 2 | LESLIB_DEFS = -DACUSIM_LINUX 3 | LESLIB_TOP = $(LICENSED_SOFTWARE_TOPLEVEL)/leslib-1.5/x64_linux 4 | LESLIB_INCDIR = -I $(LESLIB_TOP) 5 | LESLIB_LIBS = -L$(LESLIB_TOP) -lles 6 | #LESLIB_LIBS = -L$(LESLIB_TOP)/shared -lles -llapack 7 | endif 8 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/mpich.x64_linux.mk: -------------------------------------------------------------------------------- 1 | MPI_NAME = mpich 2 | MPI_INCDIR = $(wordlist 2,99,$(shell mpif90 -link_info)) 3 | MPI_LIBS = $(wordlist 2,99,$(shell mpicxx -link_info)) $(wordlist 2,99,$(shell mpif90 -link_info)) 4 | MPI_SO_PATH = 5 | MPIEXEC_PATH = 6 | MPIEXEC = mpiexec 7 | 8 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/mpich.x64_macosx.mk: -------------------------------------------------------------------------------- 1 | MPI_NAME = mpich 2 | MPI_INCDIR = $(wordlist 2,99,$(shell /opt/local/bin/mpif90-mpich-devel-clang -link_info)) 3 | MPI_LIBS = $(wordlist 2,99,$(shell /opt/local/bin/mpicxx-mpich-devel-clang -link_info)) $(wordlist 2,99,$(shell /opt/local/bin/mpif90-mpich-devel-clang -link_info)) 4 | MPI_SO_PATH = 5 | MPIEXEC_PATH = 6 | MPIEXEC = /opt/local/bin/mpiexec-mpich-devel-clang 7 | 8 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/mpich2-1.4p1.x64_cygwin.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_cygwin) 2 | MPI_NAME = mpich 3 | MPI_TOP = $(OPEN_SOFTWARE_BINARIES_TOPLEVEL)/../../unknown/x64/mpich2-1.4p1 4 | MPI_INCDIR = -I $(MPI_TOP)/include 5 | MPI_LIBS = $(LIBPATH_COMPILER_FLAG)$(MPI_TOP)/lib $(LIBFLAG)mpi.lib $(LIBFLAG)fmpich2.lib 6 | MPI_SO_PATH = $(MPI_TOP)/lib 7 | MPIEXEC_PATH = $(MPI_TOP)/bin 8 | MPIEXEC = mpiexec.exe 9 | endif 10 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/msmpi.x64_cygwin.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_cygwin) 2 | MPI_NAME = msmpi 3 | #MPI_TOP = C:/Program\ Files\ \(x86\)/Microsoft\ SDKs/MPI 4 | #MPI_INCDIR = -I$(MPI_TOP)/Include -I$(MPI_TOP)/Include/x64 5 | 6 | MPI_TOP = $(TOP)/../Code/ThirdParty/msmpi 7 | MPI_INCDIR = -I$(MPI_TOP)/Include -I$(MPI_TOP)/Include/x64 8 | MPI_LIBS = $(LIBPATH_COMPILER_FLAG)$(MPI_TOP)/Lib/x64 $(LIBFLAG)msmpifmc$(LIBLINKEXT) $(LIBFLAG)msmpi$(LIBLINKEXT) 9 | 10 | MPI_SO_PATH = 11 | MPIEXEC_PATH = 12 | MPIEXEC = 13 | endif 14 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/openmpi.x64_linux.mk: -------------------------------------------------------------------------------- 1 | MPI_NAME = openmpi 2 | MPI_INCDIR = $(shell mpif90 --showme:compile) 3 | MPI_LIBS = $(shell mpicxx --showme:link) $(shell mpif90 --showme:link) 4 | MPI_SO_PATH = $(shell which mpiexec)/../.. 5 | MPIEXEC_PATH = $(dir $(shell which mpiexec)) 6 | MPIEXEC = mpiexec 7 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/openmpi.x64_macosx.mk: -------------------------------------------------------------------------------- 1 | MPI_NAME = openmpi 2 | MPI_INCDIR = $(shell mpif90 --showme:compile) 3 | MPI_LIBS = $(shell mpicxx --showme:link) $(shell mpif90 --showme:link) 4 | MPI_SO_PATH = $(shell which mpiexec)/../.. 5 | MPIEXEC_PATH = $(dir $(shell which mpiexec)) 6 | MPIEXEC = mpiexec 7 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/rules.x64_cygwin.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_cygwin) 2 | 3 | $(BUILD_DIR)/%.d: %.cxx 4 | $(SHELL) -ec '$(CXXDEP) $(CXXFLAGS) $< \ 5 | | sed '\''s/\($*\)\.o[ :]*/\1.obj $@ : /g'\'' > $@; \ 6 | [ -s $@ ] || rm -f $@' 7 | 8 | $(BUILD_DIR)/%.d: %.c 9 | $(SHELL) -ec '$(CCDEP) $(CCFLAGS) $< \ 10 | | sed '\''s/\($*\)\.o[ :]*/\1.obj $@ : /g'\'' > $@; \ 11 | [ -s $@ ] || rm -f $@' 12 | 13 | $(BUILD_MPI_DIR)/%.d: %.cxx 14 | $(SHELL) -ec '$(CXXDEP) $(CXXFLAGS) $< \ 15 | | sed '\''s/\($*\)\.o[ :]*/\1.obj $@ : /g'\'' > $@; \ 16 | [ -s $@ ] || rm -f $@' 17 | 18 | $(BUILD_MPI_DIR)/%.d: %.c 19 | $(SHELL) -ec '$(CCDEP) $(CCFLAGS) $< \ 20 | | sed '\''s/\($*\)\.o[ :]*/\1.obj $@ : /g'\'' > $@; \ 21 | [ -s $@ ] || rm -f $@' 22 | 23 | ifeq ($(CXX_COMPILER_VERSION),mingw-gcc) 24 | $(BUILD_DIR)/%.obj: %.cxx 25 | $(CXX) $(DEBUG_FLAGS) $(OPT_FLAGS) $(CXXFLAGS) -c $< -o $@ 26 | $(BUILD_DIR)/%.obj: %.c 27 | $(CC) $(DEBUG_FLAGS) $(OPT_FLAGS) $(CCFLAGS) -c $< -o $@ 28 | $(BUILD_MPI_DIR)/%.obj: %.cxx 29 | mkdir -p $(dir $@) 30 | $(CXX) $(DEBUG_FLAGS) $(OPT_FLAGS) $(CXXFLAGS) -c $< -o $@ 31 | $(BUILD_MPI_DIR)/%.obj: %.c 32 | mkdir -p $(dir $@) 33 | $(CC) $(DEBUG_FLAGS) $(OPT_FLAGS) $(CCFLAGS) -c $< -o $@ 34 | else 35 | $(BUILD_DIR)/%.obj: %.cxx 36 | $(CXX) $(DEBUG_FLAGS) $(OPT_FLAGS) $(CXXFLAGS) /Fd:$(BUILD_DIR)/vc.pdb -c $< /Fo: $@ 37 | $(BUILD_DIR)/%.obj: %.c 38 | $(CC) $(DEBUG_FLAGS) $(OPT_FLAGS) $(CCFLAGS) /Fd:$(BUILD_DIR)/vc.pdb -c $< /Fo: $@ 39 | $(BUILD_MPI_DIR)/%.obj: %.cxx 40 | mkdir -p $(dir $@) 41 | $(CXX) $(DEBUG_FLAGS) $(OPT_FLAGS) $(CXXFLAGS) /Fd:$(BUILD_MPI_DIR)/vc.pdb -c $< /Fo: $@ 42 | $(BUILD_MPI_DIR)/%.obj: %.c 43 | mkdir -p $(dir $@) 44 | $(CC) $(DEBUG_FLAGS) $(OPT_FLAGS) $(CCFLAGS) /Fd:$(BUILD_MPI_DIR)/vc.pdb -c $< /Fo: $@ 45 | endif 46 | 47 | ifeq ($(FORTRAN_COMPILER_VERSION),mingw-gfortran) 48 | $(BUILD_DIR)/%.obj: %.f 49 | $(F90) $(FFLAGS) -c $< -o $@ 50 | $(BUILD_MPI_DIR)/%.obj: %.f 51 | mkdir -p $(dir $@) 52 | $(F90) $(FFLAGS) -c $< -o $@ 53 | else 54 | $(BUILD_DIR)/%.obj: %.f 55 | $(F90) $(FFLAGS) -c $< /Fd:$(BUILD_DIR)/vc.pdb /module:$(BUILD_DIR) /Fo$@ 56 | $(BUILD_DIR)/%.obj: %.f90 57 | $(F90) $(FFLAGS) -c $< /Fd:$(BUILD_DIR)/vc.pdb /module:$(BUILD_DIR) /Fo$@ 58 | $(BUILD_MPI_DIR)/%.obj: %.f 59 | mkdir -p $(dir $@) 60 | $(F90) $(FFLAGS) -c $< /Fd:$(BUILD_MPI_DIR)/vc.pdb /module:$(BUILD_MPI_DIR) /Fo$@ 61 | $(BUILD_MPI_DIR)/%.obj: %.f90 62 | mkdir -p $(dir $@) 63 | $(F90) $(F90FLAGS) -c $< /Fd:$(BUILD_MPI_DIR)/vc.pdb /module:$(BUILD_MPI_DIR) /Fo$@ 64 | endif 65 | 66 | endif 67 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/rules.x64_linux.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_linux) 2 | $(BUILD_DIR)/%.d: %.cxx 3 | $(SHELL) -ec '$(CXXDEP) $(CXXFLAGS) $< \ 4 | | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@; \ 5 | [ -s $@ ] || rm -f $@' 6 | 7 | $(BUILD_DIR)/%.d: %.c 8 | $(SHELL) -ec '$(CCDEP) $(CCFLAGS) $< \ 9 | | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@; \ 10 | [ -s $@ ] || rm -f $@' 11 | 12 | $(BUILD_MPI_DIR)/%.d: %.cxx 13 | $(SHELL) -ec '$(CXXDEP) $(CXXFLAGS) $< \ 14 | | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@; \ 15 | [ -s $@ ] || rm -f $@' 16 | 17 | $(BUILD_MPI_DIR)/%.d: %.c 18 | $(SHELL) -ec '$(CCDEP) $(CCFLAGS) $< \ 19 | | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@; \ 20 | [ -s $@ ] || rm -f $@' 21 | 22 | $(BUILD_DIR)/%.o: %.cxx 23 | $(CXX) $(CXXFLAGS) -c $< -o $@ 24 | 25 | $(BUILD_DIR)/%.o: %.c 26 | $(CC) $(CCFLAGS) -c $< -o $@ 27 | 28 | $(BUILD_DIR)/%.o: %.f 29 | $(F90) $(FFLAGS) -c $< -o $@ 30 | 31 | $(BUILD_DIR)/%.o: %.f90 32 | $(F90) $(F90FLAGS) -c $< -o $@ 33 | 34 | $(BUILD_MPI_DIR)/%.o: %.cxx 35 | mkdir -p $(dir $@) 36 | $(CXX) $(CXXFLAGS) -c $< -o $@ 37 | 38 | $(BUILD_MPI_DIR)/%.o: %.c 39 | mkdir -p $(dir $@) 40 | $(CC) $(CCFLAGS) -c $< -o $@ 41 | 42 | $(BUILD_MPI_DIR)/%.o: %.f 43 | mkdir -p $(dir $@) 44 | $(F90) $(FFLAGS) -c $< -o $@ 45 | 46 | $(BUILD_MPI_DIR)/%.o: %.f90 47 | mkdir -p $(dir $@) 48 | $(F90) $(FFLAGS) -c $< -o $@ 49 | 50 | endif 51 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/rules.x64_macosx.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_macosx) 2 | $(BUILD_DIR)/%.d: %.cxx 3 | $(SHELL) -ec '$(CXXDEP) $(CXXFLAGS) $< \ 4 | | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@; \ 5 | [ -s $@ ] || rm -f $@' 6 | 7 | $(BUILD_DIR)/%.d: %.c 8 | $(SHELL) -ec '$(CCDEP) $(CCFLAGS) $< \ 9 | | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@; \ 10 | [ -s $@ ] || rm -f $@' 11 | 12 | $(BUILD_MPI_DIR)/%.d: %.cxx 13 | $(SHELL) -ec '$(CXXDEP) $(CXXFLAGS) $< \ 14 | | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@; \ 15 | [ -s $@ ] || rm -f $@' 16 | 17 | $(BUILD_MPI_DIR)/%.d: %.c 18 | $(SHELL) -ec '$(CCDEP) $(CCFLAGS) $< \ 19 | | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@; \ 20 | [ -s $@ ] || rm -f $@' 21 | 22 | $(BUILD_DIR)/%.o: %.cxx 23 | $(CXX) $(CXXFLAGS) -c $< -o $@ 24 | 25 | $(BUILD_DIR)/%.o: %.c 26 | $(CC) $(CCFLAGS) -c $< -o $@ 27 | 28 | $(BUILD_DIR)/%.o: %.f 29 | $(F90) $(FFLAGS) -c $< -o $@ 30 | 31 | $(BUILD_DIR)/%.o: %.f90 32 | $(F90) $(FFLAGS) -c $< -o $@ 33 | 34 | $(BUILD_MPI_DIR)/%.o: %.cxx 35 | mkdir -p $(dir $@) 36 | $(CXX) $(CXXFLAGS) -c $< -o $@ 37 | 38 | $(BUILD_MPI_DIR)/%.o: %.c 39 | mkdir -p $(dir $@) 40 | $(CC) $(CCFLAGS) -c $< -o $@ 41 | 42 | $(BUILD_MPI_DIR)/%.o: %.f 43 | mkdir -p $(dir $@) 44 | $(F90) $(FFLAGS) -c $< -o $@ 45 | 46 | $(BUILD_MPI_DIR)/%.o: %.f90 47 | mkdir -p $(dir $@) 48 | $(F90) $(F90FLAGS) -c $< -o $@ 49 | 50 | endif 51 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/tcltk-8.6.4.x64_cygwin.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_cygwin) 2 | BUILDFLAGS += -D__NON_STD_TCL_INSTALL 3 | TCL_BASE = $(OPEN_SOFTWARE_BINARIES_TOPLEVEL)/tcltk-8.6.4 4 | TK_BASE = $(OPEN_SOFTWARE_BINARIES_TOPLEVEL)/tcltk-8.6.4 5 | TCLTK_INCDIR = -I$(TCL_BASE)/include -I$(TK_BASE)/include 6 | TCLTK_LIBDIR = $(LIBPATH_COMPILER_FLAG)$(TCL_BASE)/lib $(LIBPATH_COMPILER_FLAG)$(TK_BASE)/lib 7 | TCLTK_DLLS = $(TCL_BASE)/bin/tcl86.$(SOEXT) $(TCL_BASE)/bin/tk86.$(SOEXT) 8 | TCLTK_LIBS = $(TCLTK_LIBDIR) \ 9 | $(LIBFLAG)tcl86$(LIBLINKEXT) $(LIBFLAG)tk86$(LIBLINKEXT) \ 10 | $(LIBFLAG)user32$(LIBLINKEXT) $(LIBFLAG)advapi32$(LIBLINKEXT) \ 11 | $(LIBFLAG)gdi32$(LIBLINKEXT) $(LIBFLAG)comdlg32$(LIBLINKEXT) \ 12 | $(LIBFLAG)imm32$(LIBLINKEXT) $(LIBFLAG)comctl32$(LIBLINKEXT) \ 13 | $(LIBFLAG)shell32$(LIBLINKEXT) $(LIBFLAG)Shlwapi$(LIBLINKEXT) 14 | # Shlwapi was added to make mingw32 compile happy 15 | TCLTK_LIBS +=$(LIBFLAG)Shlwapi$(LIBLINKEXT) 16 | TKCXIMAGE_BASE = $(OPEN_SOFTWARE_BINARIES_TOPLEVEL)/tkcximage-0.98.9/tcltk-8.6.4 17 | TKCXIMAGE_DLL = $(TKCXIMAGE_BASE)/bin/Tkcximage.$(SOEXT) 18 | TCLTK_SO_PATH = $(TCL_BASE)/bin 19 | TCL_LIBRARY = $(TCL_BASE)/lib/tcl8.6 20 | TK_LIBRARY = $(TCL_BASE)/lib/tk8.6 21 | TCLSH = $(TCL_BASE)/bin/tclsh86.exe 22 | endif 23 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/tcltk-8.6.4.x64_linux.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_linux) 2 | BUILDFLAGS += -D__NON_STD_TCL_INSTALL 3 | TCL_BASE = $(OPEN_SOFTWARE_BINARIES_TOPLEVEL)/tcltk-8.6.4 4 | TK_BASE = $(OPEN_SOFTWARE_BINARIES_TOPLEVEL)/tcltk-8.6.4 5 | TCLTK_INCDIR = -I$(TCL_BASE)/include -I$(TK_BASE)/include 6 | TCLTK_LIBDIR = -L$(TCL_BASE)/lib -L$(TK_BASE)/lib 7 | TCLTK_DLLS = $(TCL_BASE)/bin/tcl8.6.$(SOEXT) $(TCL_BASE)/bin/tk8.6.$(SOEXT) 8 | TCLTK_LIBS = $(TCLTK_LIBDIR) -ltcl8.6 -ltk8.6 9 | TKCXIMAGE_BASE = $(OPEN_SOFTWARE_BINARIES_TOPLEVEL)/tkcximage-0.98.9/tcltk-8.6.4 10 | TKCXIMAGE_DLL = $(TKCXIMAGE_BASE)/bin/Tkcximage.$(SOEXT) 11 | TCLTK_SO_PATH = $(TCL_BASE)/lib 12 | TCL_LIBRARY = $(TCL_BASE)/lib/tcl8.6 13 | TK_LIBRARY = $(TCL_BASE)/lib/tk8.6 14 | TCLSH = $(TCL_BASE)/bin/tclsh8.6 15 | endif 16 | -------------------------------------------------------------------------------- /BuildWithMake/MakeHelpers/tcltk-8.6.4.x64_macosx.mk: -------------------------------------------------------------------------------- 1 | ifeq ($(CLUSTER), x64_macosx) 2 | BUILDFLAGS += -D__NON_STD_TCL_INSTALL 3 | TCL_BASE = $(OPEN_SOFTWARE_BINARIES_TOPLEVEL)/tcltk-8.6.4 4 | TK_BASE = $(OPEN_SOFTWARE_BINARIES_TOPLEVEL)/tcltk-8.6.4 5 | TCLTK_INCDIR = -I$(TCL_BASE)/include -I$(TK_BASE)/include 6 | TCLTK_LIBDIR = -L$(TCL_BASE)/lib -L$(TK_BASE)/lib 7 | TCLTK_DLLS = $(TCL_BASE)/bin/tcl8.6.$(SOEXT) $(TCL_BASE)/bin/tk8.6.$(SOEXT) 8 | TCLTK_LIBS = $(TCLTK_LIBDIR) -ltcl8.6 -ltk8.6 9 | TKCXIMAGE_BASE = $(OPEN_SOFTWARE_BINARIES_TOPLEVEL)/tkcximage-0.98.9/tcltk-8.6.4 10 | TKCXIMAGE_DLL = $(TKCXIMAGE_BASE)/bin/Tkcximage.$(SOEXT) 11 | TCLTK_SO_PATH = $(TCL_BASE)/lib 12 | TCL_LIBRARY = $(TCL_BASE)/lib/tcl8.6 13 | TK_LIBRARY = $(TCL_BASE)/lib/tk8.6 14 | TCLSH = $(TCL_BASE)/bin/tclsh8.6 15 | endif 16 | -------------------------------------------------------------------------------- /BuildWithMake/README-build-macosx.txt: -------------------------------------------------------------------------------- 1 | ------------------------------------------------------------------------ 2 | Compiling Instructions for svSolver on Mac OSX 3 | Revised 2016-09-18 4 | ------------------------------------------------------------------------ 5 | 6 | -------- 7 | Overview 8 | -------- 9 | 10 | By default, svSolver is configured to build on osx using 11 | makefiles. Our base test configuration for OSX is: 12 | 13 | Apple OSX 10.11 64-bit 14 | Intel 7 processor 15 | 16 | clang/clang++ version 7.3 17 | macports mpich/gfortran5 18 | 19 | and/or 20 | 21 | ifort/icpc/icc intel compilers 22 | 23 | NOTE: The CMake system is currently broken for svSolver and 24 | is under revision. 25 | 26 | ----------- 27 | Major Steps 28 | ----------- 29 | 30 | 1. System Prerequisities 31 | ------------------------ 32 | The following packages are required to build svsolver 33 | 34 | XCode command line tools are required 35 | % xcode-select --install 36 | % sudo xcodebuild -license 37 | 38 | MacPorts is required which can be downloaded at https://www.macports.org 39 | The following packages are required to build simvascular 40 | 41 | ### compilers 42 | % sudo port install gcc5 43 | % sudo port install gfortran5 44 | % sudo port install mpich-devel-clang 45 | 46 | 2. Checkout svSolver source code 47 | -------------------------------- 48 | % git clone https://github.com/SimVascular/svSolver.git svsolver 49 | 50 | 3. vtk libraries 51 | ---------------- 52 | svSolver requires vtk libraries. They can be build using the 53 | the scripts in "../Externals", or pre-built binaries can be 54 | downloaded using the script 55 | 56 | % cd svsolver/BuildWithMake 57 | % ./get-vtk-binaries.sh macosx_11 58 | 59 | 4. Override options 60 | ------------------- 61 | Override defaults with: 62 | 63 | * cluster_overrides.mk 64 | * global_overrides.mk 65 | * site_overrides.mk 66 | * pkg_overrides.mk 67 | 68 | See include.mk for all options. Sample override files 69 | can be found in: 70 | 71 | SampleOverrides 72 | 73 | to use one of these files, copy into local BuildWithMake 74 | directory and modify as needed, e.g.: 75 | 76 | % cd svsolver/BuildWithMake 77 | % cp SampleOverrides/macosx_11/global_overrides.mk 78 | 79 | 6. Build 80 | -------- 81 | % cd svsolver/BuildWithMake 82 | % make 83 | 84 | 7. Running developer version 85 | ---------------------------- 86 | Binaries are in "BuildWithMake/Bin" directory. 87 | 88 | You may need to set the path for the intel shared libraries before running svsolver, e.g.: 89 | 90 | % export DYLD_LIBRARY_PATH=/opt/intel/compilers_and_libraries_2016.1.111/mac/compiler/lib/ 91 | 92 | 8. Build release (NOTE: out-of-date!) 93 | ----------------- 94 | To be updated. 95 | 96 | 9. Installing a distribution (NOTE: out-of-date!) 97 | ---------------------------- 98 | To be updated. 99 | -------------------------------------------------------------------------------- /BuildWithMake/README-build-windows.txt: -------------------------------------------------------------------------------- 1 | ------------------------------------------------------------------------ 2 | Compiling Instructions for svSolver on Windows 3 | Revised 2016-09-18 4 | ------------------------------------------------------------------------ 5 | 6 | -------- 7 | Overview 8 | -------- 9 | 10 | By default, svSolver is configured to build on linux using 11 | makefiles. You must override this to build on Windows. 12 | 13 | Our base test configuration for linux is: 14 | 15 | Windows 10 16 | Intel 7 processor 17 | 18 | Microsoft Visual Studio 2013 C++ compiler 19 | 20 | and/or 21 | 22 | ifort/icpc/icc intel 14 compilers 23 | 24 | NOTE: The CMake system is currently broken for svSolver and 25 | is under revision. 26 | 27 | ----------- 28 | Major Steps 29 | ----------- 30 | 31 | 1. Windows Prerequisities 32 | ------------------------- 33 | The following packages are required to build svsolver 34 | 35 | Cygwin 64-bit version (install in C:/cygwin64) 36 | with required build tools (e.g. make, tclsh, zip) 37 | 38 | Microsoft Visual Studio 2013 compiler 39 | 40 | Intel Fortran Compiler 41 | 42 | 3. Checkout svSolver source code 43 | -------------------------------- 44 | % git clone https://github.com/SimVascular/svSolver.git svsolver 45 | 46 | 2. vtk libraries 47 | ---------------- 48 | svSolver requires vtk libraries. They can be build using the 49 | the scripts in "../Externals", or pre-built binaries can be 50 | downloaded using the script 51 | 52 | % cd svsolver/BuildWithMake 53 | % ./get-vtk-binaries.sh msvc-12.5 54 | 55 | 4. Override options 56 | ------------------- 57 | Override defaults with: 58 | 59 | * cluster_overrides.mk 60 | * global_overrides.mk 61 | * site_overrides.mk 62 | * pkg_overrides.mk 63 | 64 | See include.mk for all options. Sample override files 65 | can be found in: 66 | 67 | SampleOverrides 68 | 69 | to use one of these files, copy into local BuildWithMake 70 | directory and modify as needed, e.g.: 71 | 72 | cygwin64% cd svsolver/BuildWithMake 73 | cygwin64% cp SampleOverrides/windows/global_overrides.mk . 74 | 75 | 6. Build 76 | -------- 77 | cygwin64% cd svsolver/BuildWithMake 78 | cygwin64% source CygwinHelpers/msvc_2013_x64 79 | cygwin64% source CygwinHelpers/intel_fortan_14_x64 80 | cygwin64% make 81 | 82 | 7. Running developer version 83 | ---------------------------- 84 | Binaries are in "BuildWithMake/Bin" directory. 85 | 86 | 8. Build release (NOTE: out-of-date!) 87 | ----------------- 88 | cygwin64% cd svsolver/BuildWithMake/Release 89 | cygwin64% make 90 | 91 | 9. Installing a distribution (NOTE: out-of-date!) 92 | ---------------------------- 93 | To be updated. 94 | -------------------------------------------------------------------------------- /BuildWithMake/Release/developer_wrapper_scripts/developer-core-script: -------------------------------------------------------------------------------- 1 | #!/bin/bash -f 2 | 3 | # simvascular specific additions 4 | 5 | export SV_OS=REPLACEME_SV_OS 6 | export SOFTWARE_PLATFORM=REPLACEME_SOFTWARE_PLATFORM 7 | export CXX_COMPILER_VERSION=REPLACEME_CXX_COMPILER_VERSION 8 | export FORTRAN_COMPILER_VERSION=REPLACEME_FORTRAN_COMPILER_VERSION 9 | export LIB_BUILD_DIR=REPLACEME_LIB_BUILD_DIR 10 | export SV_VERSION=REPLACEME_SV_VERSION 11 | 12 | # must specify paths in unix style 13 | export OPEN_SOFTWARE_BINARIES_TOPLEVEL=REPLACEME_OPEN_SOFTWARE_BINARIES_TOPLEVEL 14 | export LICENSED_SOFTWARE_TOPLEVEL=REPLACEME_LICENSED_SOFTWARE_TOPLEVEL 15 | export SV_HOME=REPLACEME_SV_HOME 16 | 17 | #export SV_STATIC_BUILD=REPLACEME_SV_STATIC_BUILD 18 | 19 | ################################################################ 20 | # YOU PROBABLY DON'T NEED TO CHANGE ANYTHING BELOW THIS LINE. # 21 | ################################################################ 22 | 23 | # simvascular addition 24 | export LD_LIBRARY_PATH=$SV_HOME/BuildWithMake/Lib/$LIB_BUILD_DIR:$LD_LIBRARY_PATH 25 | 26 | # Tcl/Tk additions 27 | export TCL_LIBRARY=REPLACEME_TCL_LIBRARY 28 | export TK_LIBRARY=REPLACEME_TK_LIBRARY 29 | export LD_LIBRARY_PATH=REPLACEME_TCLTK_SO_PATH:$LD_LIBRARY_PATH 30 | 31 | # vtk additions 32 | case "$SV_OS" in 33 | "windows" ) 34 | export LD_LIBRARY_PATH=REPLACEME_VTK_SO_PATH:$LD_LIBRARY_PATH 35 | # leave VTK_RENDERER blank for win32 36 | ;; 37 | "linux" ) 38 | export LD_LIBRARY_PATH=REPLACEME_VTK_SO_PATH:$LD_LIBRARY_PATH 39 | export VTK_RENDERER=OpenGL 40 | ;; 41 | * ) 42 | export LD_LIBRARY_PATH=REPLACEME_VTK_SO_PATH:$LD_LIBRARY_PATH 43 | ;; 44 | esac 45 | # Vtk Tcl path additions 46 | export TCLLIBPATH=REPLACEME_VTK_TCL_LIB_PATH 47 | # Vtk Python additions (included above with python site-packages) 48 | 49 | # MPICH2 additions 50 | export LD_LIBRARY_PATH=REPLACEME_MPICH_SO_PATH:$LD_LIBRARY_PATH 51 | 52 | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:REPLACEME_INTEL_COMPILER_SO_PATH 53 | 54 | # needed for macosx 55 | export DYLD_LIBRARY_PATH=$LD_LIBRARY_PATH 56 | 57 | # need to convert to dos style paths on windows 58 | case "$SV_OS" in 59 | "windows" ) 60 | export OPEN_SOFTWARE_BINARIES_TOPLEVEL=`cygpath --windows -t mixed $OPEN_SOFTWARE_BINARIES_TOPLEVEL` 61 | export SV_HOME=`cygpath --windows -t mixed $SV_HOME` 62 | export TCL_LIBRARY=`cygpath --windows -t mixed $TCL_LIBRARY` 63 | export TK_LIBRARY=`cygpath --windows -t mixed $TK_LIBRARY` 64 | export PATH=$LD_LIBRARY_PATH:$PATH 65 | ;; 66 | esac 67 | -------------------------------------------------------------------------------- /BuildWithMake/Release/developer_wrapper_scripts/developer-svpost-script: -------------------------------------------------------------------------------- 1 | 2 | # run the executable 3 | case "$*" in 4 | "") 5 | $SV_HOME/BuildWithMake/Bin/svpost.exe 6 | ;; 7 | *) 8 | $SV_HOME/BuildWithMake/Bin/svpost.exe $* 9 | ;; 10 | esac 11 | 12 | -------------------------------------------------------------------------------- /BuildWithMake/Release/developer_wrapper_scripts/developer-svpre-script: -------------------------------------------------------------------------------- 1 | 2 | # run the executable 3 | case "$*" in 4 | "") 5 | $SV_HOME/BuildWithMake/Bin/svpre.exe 6 | ;; 7 | *) 8 | $SV_HOME/BuildWithMake/Bin/svpre.exe $* 9 | ;; 10 | esac 11 | 12 | -------------------------------------------------------------------------------- /BuildWithMake/Release/developer_wrapper_scripts/developer-svsolver-mpi-linux-script: -------------------------------------------------------------------------------- 1 | #!/bin/bash -f 2 | 3 | # NOTE: in the past, needed to use tcsh to set unlimited 4 | # stack size. Using tcsh seems to die when using 5 | # ubuntu and mpich2 6 | # 7 | #/bin/tcsh -f 8 | # limit stacksize unlimited 9 | 10 | # simvascular specific additions 11 | 12 | export SOFTWARE_PLATFORM=REPLACEME_SOFTWARE_PLATFORM 13 | export COMPILER_VERSION=REPLACEME_COMPILER_VERSION 14 | export OPEN_SOFTWARE_BINARIES_TOPLEVEL=REPLACEME_OPEN_SOFTWARE_BINARIES_TOPLEVEL 15 | export LICENSED_SOFTWARE_TOPLEVEL=REPLACEME_LICENSED_SOFTWARE_TOPLEVEL 16 | export SV_HOME=REPLACEME_SV_HOME 17 | export LES_LICENSE_SERVER=REPLACEME_LES_LICENSE_SERVER 18 | 19 | ############################################################ 20 | # YOU SHOULDN'T NEED TO CHANGE ANYTHING BELOW THIS LINE!! # 21 | ############################################################ 22 | 23 | # 3-D solver environment variables 24 | export FLOWSOLVER_CONFIG=$SV_HOME/Code/FlowSolvers/ThreeDSolver/svSolver 25 | 26 | # simvascular addition 27 | export LD_LIBRARY_PATH=$SV_HOME/Code/Lib:$LD_LIBRARY_PATH 28 | 29 | # MPICH2 additions 30 | export LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH 31 | 32 | # intel compiler additions 33 | export LD_LIBRARY_PATH=$OPEN_SOFTWARE_BINARIES_TOPLEVEL/intel_compiler_libs/intel64:$LD_LIBRARY_PATH 34 | 35 | $SV_HOME/BuildWithMake/Bin/svsolver-REPLACE_MPI_NAME.exe $* 36 | -------------------------------------------------------------------------------- /BuildWithMake/Release/developer_wrapper_scripts/developer-svsolver-mpi-macosx-script: -------------------------------------------------------------------------------- 1 | 2 | #!/bin/bash -f 3 | 4 | # NOTE: in the past, needed to use tcsh to set unlimited 5 | # stack size. Using tcsh seems to die when using 6 | # ubuntu and mpich2 7 | # 8 | #/bin/tcsh -f 9 | # limit stacksize unlimited 10 | 11 | # simvascular specific additions 12 | 13 | export SOFTWARE_PLATFORM=REPLACEME_SOFTWARE_PLATFORM 14 | export COMPILER_VERSION=REPLACEME_COMPILER_VERSION 15 | export OPEN_SOFTWARE_BINARIES_TOPLEVEL=REPLACEME_OPEN_SOFTWARE_BINARIES_TOPLEVEL 16 | export LICENSED_SOFTWARE_TOPLEVEL=REPLACEME_LICENSED_SOFTWARE_TOPLEVEL 17 | export SV_HOME=REPLACEME_SV_HOME 18 | export LES_LICENSE_SERVER=REPLACEME_LES_LICENSE_SERVER 19 | 20 | ############################################################ 21 | # YOU SHOULDN'T NEED TO CHANGE ANYTHING BELOW THIS LINE!! # 22 | ############################################################ 23 | 24 | # 3-D solver environment variables 25 | export FLOWSOLVER_CONFIG=$SV_HOME/Code/FlowSolvers/ThreeDSolver/svSolver 26 | 27 | # simvascular addition 28 | export LD_LIBRARY_PATH=$SV_HOME/Code/Lib:$LD_LIBRARY_PATH 29 | 30 | # MPICH2 additions 31 | export LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH 32 | 33 | # intel compiler additions 34 | export LD_LIBRARY_PATH=$OPEN_SOFTWARE_BINARIES_TOPLEVEL/intel_compiler_libs/intel64:$LD_LIBRARY_PATH 35 | 36 | $SV_HOME/BuildWithMake/Bin/svsolver-REPLACE_MPI_NAME.exe $* 37 | -------------------------------------------------------------------------------- /BuildWithMake/Release/developer_wrapper_scripts/developer-svsolver-mpi-windows-script: -------------------------------------------------------------------------------- 1 | #!/bin/bash -f 2 | 3 | # simvascular specific additions 4 | 5 | export SOFTWARE_PLATFORM=REPLACEME_SOFTWARE_PLATFORM 6 | export COMPILER_VERSION=REPLACEME_COMPILER_VERSION 7 | export SV_OS=REPLACEME_SV_OS 8 | 9 | # must specify paths in unix style 10 | export OPEN_SOFTWARE_BINARIES_TOPLEVEL=REPLACEME_OPEN_SOFTWARE_BINARIES_TOPLEVEL 11 | export LICENSED_SOFTWARE_TOPLEVEL=REPLACEME_LICENSED_SOFTWARE_TOPLEVEL 12 | export SV_HOME=REPLACEME_SV_HOME 13 | 14 | # MeshSim license file 15 | export SIM_LICENSE_FILE=REPLACEME_LICENSE_FILE 16 | export SIM_LICENSE_FILE=$SV_HOME/Licenses/MeshSim/license.dat 17 | 18 | # 3-D solver environment variables 19 | export FLOWSOLVER_CONFIG=$SV_HOME/Code/FlowSolvers/ThreeDSolver/svSolver 20 | export LES_LICENSE_SERVER=$SV_HOME/Licenses/LesLib/license.dat 21 | #export LES_LICENSE_SERVER=foo.bar.edu 22 | 23 | ################################################################ 24 | # YOU PROBABLY DON'T NEED TO CHANGE ANYTHING BELOW THIS LINE. # 25 | # # 26 | # NOTE: This file needs to be kept current with changes in # 27 | # paths found in include.mk # 28 | # # 29 | ################################################################ 30 | 31 | # simvascular addition 32 | export LD_LIBRARY_PATH=$SV_HOME/Code/Lib:$LD_LIBRARY_PATH 33 | 34 | # need to convert to dos style paths on windows 35 | case "$SV_OS" in 36 | "windows" ) 37 | export SV_HOME=`cygpath --windows -t mixed $SV_HOME` 38 | export OPEN_SOFTWARE_BINARIES_TOPLEVEL=`cygpath --windows -t mixed $OPEN_SOFTWARE_BINARIES_TOPLEVEL` 39 | export LICENSED_SOFTWARE_TOPLEVEL=`cygpath --windows -t mixed $OPEN_SOFTWARE_BINARIES_TOPLEVEL` 40 | export FLOWSOLVER_CONFIG=`cygpath --windows -t mixed $FLOWSOLVER_CONFIG` 41 | export LES_LICENSE_SERVER=`cygpath --windows -t mixed $LES_LICENSE_SERVER` 42 | export PATH=$LD_LIBRARY_PATH:$PATH 43 | ;; 44 | esac 45 | 46 | # run the executable 47 | /cygdrive/c/Program\ Files/Microsoft\ MPI/Bin/mpiexec.exe -np $1 -env FLOWSOLVER_CONFIG $FLOWSOLVER_CONFIG $SV_HOME/BuildWithMake/Bin/svsolver-mpi.exe $2 $3 $4 48 | -------------------------------------------------------------------------------- /BuildWithMake/Release/developer_wrapper_scripts/developer-svsolver-nompi-linux-script: -------------------------------------------------------------------------------- 1 | #!/bin/bash -f 2 | 3 | # NOTE: in the past, needed to use tcsh to set unlimited 4 | # stack size. Using tcsh seems to die when using 5 | # ubuntu and mpich2 6 | # 7 | #/bin/tcsh -f 8 | # limit stacksize unlimited 9 | 10 | # simvascular specific additions 11 | 12 | export SOFTWARE_PLATFORM=REPLACEME_SOFTWARE_PLATFORM 13 | export COMPILER_VERSION=REPLACEME_COMPILER_VERSION 14 | export OPEN_SOFTWARE_BINARIES_TOPLEVEL=REPLACEME_OPEN_SOFTWARE_BINARIES_TOPLEVEL 15 | export LICENSED_SOFTWARE_TOPLEVEL=REPLACEME_LICENSED_SOFTWARE_TOPLEVEL 16 | export SV_HOME=REPLACEME_SV_HOME 17 | export LES_LICENSE_SERVER=REPLACEME_LES_LICENSE_SERVER 18 | 19 | ############################################################ 20 | # YOU SHOULDN'T NEED TO CHANGE ANYTHING BELOW THIS LINE!! # 21 | ############################################################ 22 | 23 | # 3-D solver environment variables 24 | export FLOWSOLVER_CONFIG=$SV_HOME/Code/FlowSolvers/ThreeDSolver/svSolver 25 | 26 | # simvascular addition 27 | export LD_LIBRARY_PATH=$SV_HOME/Code/Lib:$LD_LIBRARY_PATH 28 | 29 | # MPICH2 additions 30 | export LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH 31 | 32 | # intel compiler additions 33 | export LD_LIBRARY_PATH=$OPEN_SOFTWARE_BINARIES_TOPLEVEL/intel_compiler_libs/intel64:$LD_LIBRARY_PATH 34 | 35 | $SV_HOME/BuildWithMake/Bin/svsolver-nompi.exe $* 36 | -------------------------------------------------------------------------------- /BuildWithMake/Release/developer_wrapper_scripts/developer-svsolver-nompi-macosx-script: -------------------------------------------------------------------------------- 1 | 2 | #!/bin/bash -f 3 | 4 | # NOTE: in the past, needed to use tcsh to set unlimited 5 | # stack size. Using tcsh seems to die when using 6 | # ubuntu and mpich2 7 | # 8 | #/bin/tcsh -f 9 | # limit stacksize unlimited 10 | 11 | # simvascular specific additions 12 | 13 | export SOFTWARE_PLATFORM=REPLACEME_SOFTWARE_PLATFORM 14 | export COMPILER_VERSION=REPLACEME_COMPILER_VERSION 15 | export OPEN_SOFTWARE_BINARIES_TOPLEVEL=REPLACEME_OPEN_SOFTWARE_BINARIES_TOPLEVEL 16 | export LICENSED_SOFTWARE_TOPLEVEL=REPLACEME_LICENSED_SOFTWARE_TOPLEVEL 17 | export SV_HOME=REPLACEME_SV_HOME 18 | export LES_LICENSE_SERVER=REPLACEME_LES_LICENSE_SERVER 19 | 20 | ############################################################ 21 | # YOU SHOULDN'T NEED TO CHANGE ANYTHING BELOW THIS LINE!! # 22 | ############################################################ 23 | 24 | # 3-D solver environment variables 25 | export FLOWSOLVER_CONFIG=$SV_HOME/Code/FlowSolvers/ThreeDSolver/svSolver 26 | 27 | # simvascular addition 28 | export LD_LIBRARY_PATH=$SV_HOME/Code/Lib:$LD_LIBRARY_PATH 29 | 30 | # MPICH2 additions 31 | export LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH 32 | 33 | # intel compiler additions 34 | export LD_LIBRARY_PATH=$OPEN_SOFTWARE_BINARIES_TOPLEVEL/intel_compiler_libs/intel64:$LD_LIBRARY_PATH 35 | 36 | $SV_HOME/BuildWithMake/Bin/svsolver-nompi.exe $* 37 | -------------------------------------------------------------------------------- /BuildWithMake/Release/developer_wrapper_scripts/developer-svsolver-nompi-windows-script: -------------------------------------------------------------------------------- 1 | #!/bin/bash -f 2 | 3 | # simvascular specific additions 4 | 5 | export SOFTWARE_PLATFORM=REPLACEME_SOFTWARE_PLATFORM 6 | export COMPILER_VERSION=REPLACEME_COMPILER_VERSION 7 | export SV_OS=REPLACEME_SV_OS 8 | 9 | # must specify paths in unix style 10 | export OPEN_SOFTWARE_BINARIES_TOPLEVEL=REPLACEME_OPEN_SOFTWARE_BINARIES_TOPLEVEL 11 | export LICENSED_SOFTWARE_TOPLEVEL=REPLACEME_LICENSED_SOFTWARE_TOPLEVEL 12 | export SV_HOME=REPLACEME_SV_HOME 13 | 14 | # MeshSim license file 15 | export SIM_LICENSE_FILE=REPLACEME_LICENSE_FILE 16 | export SIM_LICENSE_FILE=$SV_HOME/Licenses/MeshSim/license.dat 17 | 18 | # 3-D solver environment variables 19 | export FLOWSOLVER_CONFIG=$SV_HOME/Code/FlowSolvers/ThreeDSolver/svSolver 20 | export LES_LICENSE_SERVER=$SV_HOME/Licenses/LesLib/license.dat 21 | #export LES_LICENSE_SERVER=foo.bar.edu 22 | 23 | ################################################################ 24 | # YOU PROBABLY DON'T NEED TO CHANGE ANYTHING BELOW THIS LINE. # 25 | # # 26 | # NOTE: This file needs to be kept current with changes in # 27 | # paths found in include.mk # 28 | # # 29 | ################################################################ 30 | 31 | # simvascular addition 32 | export LD_LIBRARY_PATH=$SV_HOME/Code/Lib:$LD_LIBRARY_PATH 33 | 34 | # need to convert to dos style paths on windows 35 | case "$SV_OS" in 36 | "windows" ) 37 | export SV_HOME=`cygpath --windows -t mixed $SV_HOME` 38 | export OPEN_SOFTWARE_BINARIES_TOPLEVEL=`cygpath --windows -t mixed $OPEN_SOFTWARE_BINARIES_TOPLEVEL` 39 | export LICENSED_SOFTWARE_TOPLEVEL=`cygpath --windows -t mixed $OPEN_SOFTWARE_BINARIES_TOPLEVEL` 40 | export FLOWSOLVER_CONFIG=`cygpath --windows -t mixed $FLOWSOLVER_CONFIG` 41 | export LES_LICENSE_SERVER=`cygpath --windows -t mixed $LES_LICENSE_SERVER` 42 | export PATH=$LD_LIBRARY_PATH:$PATH 43 | ;; 44 | esac 45 | 46 | # run the executable 47 | /cygdrive/c/Program\ Files/Microsoft\ MPI/Bin/mpiexec.exe -np $1 -env FLOWSOLVER_CONFIG $FLOWSOLVER_CONFIG $SV_HOME/BuildWithMake/Bin/svsolver-nompi.exe $2 $3 $4 48 | -------------------------------------------------------------------------------- /BuildWithMake/Release/linux_wrapper_scripts/linux-dist-core-script: -------------------------------------------------------------------------------- 1 | #!/bin/bash -f 2 | 3 | export SV_HOME=/usr/local/package/REPLACE_SV_VERSION/REPLACE_TIMESTAMP 4 | export SV_RELEASE_BUILD=REPLACE_SV_PLATFORM 5 | 6 | ################################################################ 7 | # YOU PROBABLY DON'T NEED TO CHANGE ANYTHING BELOW THIS LINE. # 8 | ################################################################ 9 | 10 | export SV_STATIC_BUILD=1 11 | export SV_RELEASED_MODE=1 12 | 13 | # SV additions (parasolid, tcltk, etc.) 14 | export LD_LIBRARY_PATH=$SV_HOME:$LD_LIBRARY_PATH 15 | 16 | # MeshSim license file 17 | export SIM_LICENSE_FILE=$SV_HOME/meshsim-license.dat 18 | 19 | # Tcl/Tk additions 20 | export TCL_LIBRARY=$SV_HOME/lib/REPLACE_TCL_VERSION_NO 21 | export TK_LIBRARY=$SV_HOME/lib/REPLACE_TK_VERSION_NO 22 | export LD_LIBRARY_PATH=$SV_HOME/lib:$LD_LIBRARY_PATH 23 | 24 | # PARASOLID additions 25 | export P_SCHEMA=$SV_HOME/schema 26 | 27 | # MPICH2 additions 28 | export LD_LIBRARY_PATH=$SV_HOME/mpi/lib:$LD_LIBRARY_PATH 29 | 30 | # intel additions 31 | export LD_LIBRARY_PATH=$SV_HOME/intel_compiler_runtime_libs:$LD_LIBRARY_PATH 32 | 33 | -------------------------------------------------------------------------------- /BuildWithMake/Release/linux_wrapper_scripts/linux-dist-svpost-script: -------------------------------------------------------------------------------- 1 | 2 | # run the executable 3 | case "$*" in 4 | "") 5 | $SV_HOME/postsolver-bin.exe 6 | ;; 7 | *) 8 | $SV_HOME/postsolver-bin.exe $* 9 | ;; 10 | esac 11 | 12 | 13 | -------------------------------------------------------------------------------- /BuildWithMake/Release/linux_wrapper_scripts/linux-dist-svpre-script: -------------------------------------------------------------------------------- 1 | 2 | $SV_HOME/presolver-bin.exe $* 3 | 4 | -------------------------------------------------------------------------------- /BuildWithMake/Release/linux_wrapper_scripts/linux-dist-svsolver-mpi-script: -------------------------------------------------------------------------------- 1 | 2 | # on windows, use a file 3 | #export LES_LICENSE_SERVER=$SV_HOME/Licenses/LesLib/license.dat 4 | # on linux, point to a server 5 | #export LES_LICENSE_SERVER=foo.bar.edu 6 | 7 | # config file for solver 8 | export FLOWSOLVER_CONFIG=$SV_HOME 9 | 10 | $SV_HOME/flowsolver-bin.exe $* 11 | -------------------------------------------------------------------------------- /BuildWithMake/Release/linux_wrapper_scripts/linux-dist-svsolver-nompi-script: -------------------------------------------------------------------------------- 1 | 2 | # on windows, use a file 3 | #export LES_LICENSE_SERVER=$SV_HOME/Licenses/LesLib/license.dat 4 | # on linux, point to a server 5 | #export LES_LICENSE_SERVER=foo.bar.edu 6 | 7 | # config file for solver 8 | export FLOWSOLVER_CONFIG=$SV_HOME 9 | 10 | $SV_HOME/flowsolver-bin.exe $* 11 | -------------------------------------------------------------------------------- /BuildWithMake/Release/platform_independent_scripts/generic-launch-script: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | # the next line restarts using tclsh \ 3 | exec /usr/bin/tclsh "$0" $0 $* 4 | 5 | set lexec [lindex $argv 0] 6 | set myexec [file tail $lexec] 7 | set allvers [glob -nocomplain [file dirname $lexec]/../package/svsolver/*] 8 | set dirnames {} 9 | foreach i $allvers { 10 | if [file isdirectory $i] { 11 | lappend dirnames [file tail $i] 12 | } 13 | } 14 | if {[llength $dirnames] == 0} { 15 | return -code error "ERROR: installation of simvascular not found!" 16 | } 17 | 18 | set dirnames [lsort -integer $dirnames] 19 | set mostrecent [lindex $dirnames end] 20 | 21 | exec bash -c "[file dirname $lexec]/../package/svsolver/$mostrecent/$myexec [lrange $argv 1 end]" >&@ stdout 22 | 23 | exit 24 | -------------------------------------------------------------------------------- /BuildWithMake/Release/platform_independent_scripts/post-install.sh: -------------------------------------------------------------------------------- 1 | #/bin/sh 2 | rm -f /usr/local/bin/REPLACE_SV_VERSION 3 | rm -f /usr/local/bin/REPLACE_SV_VERSION-cmdline 4 | rm -f /usr/local/bin/adaptorREPLACE_SV_POSTFIX 5 | rm -f /usr/local/bin/tetadaptorREPLACE_SV_POSTFIX 6 | rm -f /usr/local/bin/presolverREPLACE_SV_POSTFIX 7 | rm -f /usr/local/bin/postsolverREPLACE_SV_POSTFIX 8 | rm -f /usr/local/bin/xfsvREPLACE_SV_POSTFIX 9 | cp /usr/local/package/REPLACE_SV_VERSION/REPLACE_TIMESTAMP/generic_launch_script /usr/local/bin/REPLACE_SV_VERSION 10 | cp /usr/local/package/REPLACE_SV_VERSION/REPLACE_TIMESTAMP/generic_launch_script /usr/local/bin/REPLACE_SV_VERSION-cmdline 11 | cp /usr/local/package/REPLACE_SV_VERSION/REPLACE_TIMESTAMP/generic_launch_script /usr/local/bin/adaptorREPLACE_SV_POSTFIX 12 | cp /usr/local/package/REPLACE_SV_VERSION/REPLACE_TIMESTAMP/generic_launch_script /usr/local/bin/tetadaptorREPLACE_SV_POSTFIX 13 | cp /usr/local/package/REPLACE_SV_VERSION/REPLACE_TIMESTAMP/generic_launch_script /usr/local/bin/presolverREPLACE_SV_POSTFIX 14 | cp /usr/local/package/REPLACE_SV_VERSION/REPLACE_TIMESTAMP/generic_launch_script /usr/local/bin/postsolverREPLACE_SV_POSTFIX 15 | cp /usr/local/package/REPLACE_SV_VERSION/REPLACE_TIMESTAMP/generic_launch_script /usr/local/bin/xfsvREPLACE_SV_POSTFIX 16 | chmod a+rx /usr/local/bin/simvascularREPLACE_SV_POSTFIX 17 | chmod a+rx /usr/local/bin/simvascularREPLACE_SV_POSTFIX-cmdline 18 | chmod a+rx /usr/local/bin/adaptorREPLACE_SV_POSTFIX 19 | chmod a+rx /usr/local/bin/tetadaptorREPLACE_SV_POSTFIX 20 | chmod a+rx /usr/local/bin/presolverREPLACE_SV_POSTFIX 21 | chmod a+rx /usr/local/bin/postsolverREPLACE_SV_POSTFIX 22 | chmod a+rx /usr/local/bin/xfsvREPLACE_SV_POSTFIX 23 | 24 | 25 | -------------------------------------------------------------------------------- /BuildWithMake/Release/platform_independent_scripts/post-solver-install.sh: -------------------------------------------------------------------------------- 1 | #/bin/sh 2 | rm -f /usr/local/bin/flowsolverREPLACE_SV_POSTFIX 3 | cp /usr/local/package/REPLACE_SV_VERSION/REPLACE_TIMESTAMP/generic_launch_script /usr/local/bin/flowsolverREPLACE_SV_POSTFIX 4 | chmod a+rx /usr/local/bin/flowsolverREPLACE_SV_POSTFIX 5 | 6 | 7 | -------------------------------------------------------------------------------- /BuildWithMake/Release/platform_independent_scripts/post-svsolver-install.sh: -------------------------------------------------------------------------------- 1 | #/bin/sh 2 | rm -f /usr/local/bin/svsolver-nompi 3 | cp /usr/local/package/REPLACE_SV_VERSION/REPLACE_TIMESTAMP/generic_launch_script /usr/local/bin/svsolver-nompi 4 | chmod a+rx /usr/local/bin/svsolver-nompi 5 | rm -f /usr/local/bin/svsolver-REPLACE_MPI_NAME 6 | cp /usr/local/package/REPLACE_SV_VERSION/REPLACE_TIMESTAMP/generic_launch_script /usr/local/bin/svsolver-REPLACE_MPI_NAME 7 | chmod a+rx /usr/local/bin/svsolver-REPLACE_MPI_NAME 8 | -------------------------------------------------------------------------------- /BuildWithMake/Release/tcl_helper_scripts/create_tclIndex.tcl: -------------------------------------------------------------------------------- 1 | # 2 | # Copyright (c) 2014-2015 The Regents of the University of California. 3 | # All Rights Reserved. 4 | # 5 | # Portions of the code Copyright (c) 2009-2011 Open Source Medical 6 | # Software Corporation, University of California, San Diego. 7 | # All rights reserved. 8 | # 9 | # Copyright (c) 2007 Stanford University, 10 | # Charles Taylor, Nathan Wilson, Bill Katz. 11 | # 12 | # Permission is hereby granted, free of charge, to any person obtaining 13 | # a copy of this software and associated documentation files (the 14 | # "Software"), to deal in the Software without restriction, including 15 | # without limitation the rights to use, copy, modify, merge, publish, 16 | # distribute, sublicense, and/or sell copies of the Software, and to 17 | # permit persons to whom the Software is furnished to do so, subject 18 | # to the following conditions: 19 | # 20 | # The above copyright notice and this permission notice shall be included 21 | # in all copies or substantial portions of the Software. 22 | # 23 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 24 | # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 25 | # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 26 | # IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 27 | # CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 28 | # TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 29 | # SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 30 | 31 | proc check_for_dirs {mydir} { 32 | foreach fn [glob -nocomplain [file join $mydir *]] { 33 | puts "$fn" 34 | if [file isdirectory $fn] { 35 | puts "found directory $fn" 36 | if {[llength [glob -nocomplain [file join $fn *.tcl]]] > 0} { 37 | puts "indexing $fn *.tcl" 38 | catch {auto_mkindex $fn *.tcl} 39 | } 40 | check_for_dirs $fn 41 | } 42 | } 43 | puts "Finished check for dirs" 44 | } 45 | 46 | check_for_dirs $argv 47 | -------------------------------------------------------------------------------- /BuildWithMake/Release/tcl_helper_scripts/d2u_files.tcl: -------------------------------------------------------------------------------- 1 | # 2 | # Copyright (c) 2014-2015 The Regents of the University of California. 3 | # All Rights Reserved. 4 | # 5 | # Portions of the code Copyright (c) 2009-2011 Open Source Medical 6 | # Software Corporation, University of California, San Diego. 7 | # All rights reserved. 8 | # 9 | # Permission is hereby granted, free of charge, to any person obtaining 10 | # a copy of this software and associated documentation files (the 11 | # "Software"), to deal in the Software without restriction, including 12 | # without limitation the rights to use, copy, modify, merge, publish, 13 | # distribute, sublicense, and/or sell copies of the Software, and to 14 | # permit persons to whom the Software is furnished to do so, subject 15 | # to the following conditions: 16 | # 17 | # The above copyright notice and this permission notice shall be included 18 | # in all copies or substantial portions of the Software. 19 | # 20 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 22 | # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 23 | # IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 24 | # CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 25 | # TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 26 | # SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 27 | # 28 | 29 | foreach fileext {.cxx .c .h .tcl .txt .f Makefile ACKNOWLEDGEMENTS .mk} { 30 | 31 | foreach i [file_find .. *$fileext] { 32 | 33 | if {![file isdirectory $i]} { 34 | 35 | if {[regexp .svn $i]} { 36 | 37 | puts "Skipping svn hidden file ($i)." 38 | 39 | } else { 40 | 41 | file_dos2unix $i $i.tmp 42 | if [catch {exec diff $i $i.tmp} msg] { 43 | puts "File $i has changed after d2u!!" 44 | } 45 | file delete $i 46 | file rename $i.tmp $i 47 | 48 | } 49 | 50 | } else { 51 | 52 | puts "skipping directory $i" 53 | 54 | } 55 | 56 | } 57 | 58 | } 59 | 60 | -------------------------------------------------------------------------------- /BuildWithMake/Release/windows_installer_packages/msi-logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/BuildWithMake/Release/windows_installer_packages/msi-logo.png -------------------------------------------------------------------------------- /BuildWithMake/Release/windows_installer_packages/w_fcompxe_redist_intel64_2013_sp1.5.239.msi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/BuildWithMake/Release/windows_installer_packages/w_fcompxe_redist_intel64_2013_sp1.5.239.msi -------------------------------------------------------------------------------- /BuildWithMake/Release/windows_installer_packages/wix-simvascular-svsolver-bundle.wxs: -------------------------------------------------------------------------------- 1 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 22 | 23 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | -------------------------------------------------------------------------------- /BuildWithMake/Release/windows_msi_helpers/msi-banner.bmp: -------------------------------------------------------------------------------- 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/BuildWithMake/Release/windows_msi_helpers/msi-dialog.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/BuildWithMake/Release/windows_msi_helpers/msi-dialog.jpg -------------------------------------------------------------------------------- /BuildWithMake/Release/windows_msi_helpers/simvascular.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/BuildWithMake/Release/windows_msi_helpers/simvascular.ico -------------------------------------------------------------------------------- /BuildWithMake/Release/windows_msi_helpers/uuidgen.c: -------------------------------------------------------------------------------- 1 | /* Copyright (c) 2014-2015 The Regents of the University of California. 2 | * All Rights Reserved. 3 | * 4 | * Portions of the code Copyright (c) 2009-2011 Open Source Medical 5 | * Software Corporation, University of California, San Diego. 6 | * All rights reserved. 7 | * 8 | * Permission is hereby granted, free of charge, to any person obtaining 9 | * a copy of this software and associated documentation files (the 10 | * "Software"), to deal in the Software without restriction, including 11 | * without limitation the rights to use, copy, modify, merge, publish, 12 | * distribute, sublicense, and/or sell copies of the Software, and to 13 | * permit persons to whom the Software is furnished to do so, subject 14 | * to the following conditions: 15 | * 16 | * The above copyright notice and this permission notice shall be included 17 | * in all copies or substantial portions of the Software. 18 | * 19 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 20 | * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 21 | * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 22 | * IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 23 | * CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 24 | * TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 25 | * SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 26 | */ 27 | 28 | #define _OLEAUT32_ 29 | 30 | #include 31 | #include 32 | 33 | GUID guid; 34 | WORD* wstrGUID[100]; 35 | char strGUID[100]; 36 | int count, i; 37 | 38 | int main (int argc, char* argv[]) { 39 | if (argc != 2) { 40 | fprintf (stderr, "SYNTAX: UUIDGEN \n"); 41 | return 1; 42 | } 43 | count = atoi (argv[1]); 44 | for (i = 0; i < count; i++) { 45 | CoCreateGuid (&guid); 46 | StringFromCLSID (&guid, wstrGUID); 47 | WideCharToMultiByte (CP_ACP, 0, *wstrGUID, -1, strGUID, MAX_PATH, NULL, NULL); 48 | printf ("%s\n", strGUID); 49 | } 50 | return 0; 51 | } 52 | -------------------------------------------------------------------------------- /BuildWithMake/Release/windows_wrapper_scripts/windows-dist-core-script: -------------------------------------------------------------------------------- 1 | #!/bin/bash -f 2 | 3 | export SV_HOME=/usr/local/package/svsolver/REPLACE_TIMESTAMP 4 | export SV_RELEASE_BUILD=REPLACE_SV_PLATFORM 5 | export SV_OS=REPLACE_SV_OS 6 | 7 | ################################################################ 8 | # YOU PROBABLY DON'T NEED TO CHANGE ANYTHING BELOW THIS LINE. # 9 | ################################################################ 10 | 11 | export SV_STATIC_BUILD=1 12 | export SV_RELEASED_MODE=1 13 | 14 | # SV additions (parasolid, tcltk, etc.) 15 | export LD_LIBRARY_PATH=$SV_HOME:$LD_LIBRARY_PATH 16 | 17 | # Tcl/Tk additions 18 | export TCL_LIBRARY=$SV_HOME/lib/REPLACE_TCL_VERSION_NO 19 | export TK_LIBRARY=$SV_HOME/lib/REPLACE_TK_VERSION_NO 20 | export LD_LIBRARY_PATH=$SV_HOME/lib:$LD_LIBRARY_PATH 21 | 22 | # MPICH2 additions 23 | export LD_LIBRARY_PATH=$SV_HOME/mpi/lib:$LD_LIBRARY_PATH 24 | 25 | # intel additions 26 | export LD_LIBRARY_PATH=$SV_HOME/intel_compiler_libs:$LD_LIBRARY_PATH 27 | 28 | # need to convert to dos style paths on windows 29 | case "$SV_OS" in 30 | "windows" ) 31 | export SV_HOME=`cygpath --windows -t mixed "$SV_HOME"` 32 | export TCL_LIBRARY=`cygpath --windows -t mixed "$TCL_LIBRARY"` 33 | export TK_LIBRARY=`cygpath --windows -t mixed "$TK_LIBRARY"` 34 | export PATH=$LD_LIBRARY_PATH:$PATH 35 | ;; 36 | esac 37 | -------------------------------------------------------------------------------- /BuildWithMake/Release/windows_wrapper_scripts/windows-dist-svpost-script: -------------------------------------------------------------------------------- 1 | 2 | # run the executable 3 | case "$*" in 4 | "") 5 | "$SV_HOME/svpost-bin.exe" 6 | ;; 7 | *) 8 | "$SV_HOME/svpost-bin.exe" $* 9 | ;; 10 | esac 11 | -------------------------------------------------------------------------------- /BuildWithMake/Release/windows_wrapper_scripts/windows-dist-svpre-script: -------------------------------------------------------------------------------- 1 | 2 | $SV_HOME/svpre-bin.exe $* 3 | 4 | -------------------------------------------------------------------------------- /BuildWithMake/Release/windows_wrapper_scripts/windows-dist-svsolver-mpi-script: -------------------------------------------------------------------------------- 1 | 2 | # 3-D solver environment variables 3 | export FLOWSOLVER_CONFIG=$SV_HOME 4 | 5 | #export LES_LICENSE_SERVER=$SV_HOME/license.dat 6 | 7 | $SV_HOME/mpiexec.exe -noprompt -user 1 -localroot -localonly -env FLOWSOLVER_CONFIG $FLOWSOLVER_CONFIG -n $1 $SV_HOME/svsolver-REPLACE_MPI_NAME-bin.exe $2 $3 8 | -------------------------------------------------------------------------------- /BuildWithMake/Release/windows_wrapper_scripts/windows-dist-svsolver-nompi-script: -------------------------------------------------------------------------------- 1 | 2 | # 3-D solver environment variables 3 | export FLOWSOLVER_CONFIG=$SV_HOME 4 | 5 | #export LES_LICENSE_SERVER=$SV_HOME/license.dat 6 | 7 | $SV_HOME/mpiexec.exe -noprompt -user 1 -localroot -localonly -env FLOWSOLVER_CONFIG $FLOWSOLVER_CONFIG -n $1 $SV_HOME/svsolver-nompi-bin.exe $2 $3 8 | -------------------------------------------------------------------------------- /BuildWithMake/SampleOverrides/centos_6/global_overrides.mk: -------------------------------------------------------------------------------- 1 | # 2 | # external location for installed vtk libs 3 | # 4 | # * can be built using scripts in "../Externals" 5 | # * pre-built binaries for centos 6.8, gnu 4.4.7 compilers 6 | # can be downloaded using the "get-vtk-binaries.sh" script: 7 | # i.e. % ./get-vtk-binaries.sh centos_6 8 | 9 | OPEN_SOFTWARE_BINARIES_TOPLEVEL=${HOME}/svsolver/externals/bin/gnu-4.4/x64 10 | 11 | # 12 | # licensed is only needed if using leslib 13 | # 14 | 15 | LICENSED_SOFTWARE_TOPLEVEL= 16 | 17 | # 18 | # Notes on MPI: 19 | # * default is to use dummy mpi 20 | # * can only build one at a time 21 | # * use modules on centos: 22 | # e.g. % module add openmpi-x86_64 23 | # e.g. % module add mpich-x864_64 24 | # 25 | 26 | SV_USE_DUMMY_MPI=1 27 | SV_USE_OPENMPI=0 28 | SV_USE_MPICH=0 29 | -------------------------------------------------------------------------------- /BuildWithMake/SampleOverrides/macosx_11/global_overrides.mk: -------------------------------------------------------------------------------- 1 | # 2 | # Override default cluster to build on Mac OSX 3 | # with clang and intel fortran compiler 4 | # 5 | 6 | CLUSTER = x64_macosx 7 | CXX_COMPILER_VERSION = clang 8 | FORTRAN_COMPILER_VERSION = ifort 9 | 10 | # 11 | # external location for installed vtk libs 12 | # 13 | # * can be built using scripts in "../Externals" 14 | # * pre-built binaries for macosx clang 7.3 compilers 15 | # can be downloaded using the "get-vtk-binaries.sh" script: 16 | # i.e. % ./get-vtk-binaries.sh macosx_11 17 | 18 | SVEXTERN_COMPILER_VERSION = clang-7.3 19 | OPEN_SOFTWARE_BINARIES_TOPLEVEL=${HOME}/svsolver/externals/bin/$(SVEXTERN_COMPILER_VERSION)/x64 20 | 21 | # 22 | # licensed is only needed if using leslib 23 | # 24 | 25 | LICENSED_SOFTWARE_TOPLEVEL= 26 | 27 | # 28 | # Notes on MPI: 29 | # * default is to use dummy mpi 30 | # * can only build one at a time 31 | # 32 | 33 | SV_USE_DUMMY_MPI=1 34 | SV_USE_OPENMPI=0 35 | SV_USE_MPICH=0 36 | -------------------------------------------------------------------------------- /BuildWithMake/SampleOverrides/ubuntu_14/global_overrides.mk: -------------------------------------------------------------------------------- 1 | # 2 | # external location for installed vtk libs 3 | # 4 | # * can be built using scripts in "../Externals" 5 | # * pre-built binaries for ubuntu 14.04 and gnu 4.8 compilers 6 | # can be downloaded using the "get-vtk-binaries.sh" script: 7 | # i.e. % ./get-vtk-binaries.sh ubuntu_14 8 | 9 | OPEN_SOFTWARE_BINARIES_TOPLEVEL=${HOME}/svsolver/externals/bin/gnu-4.8/x64 10 | 11 | # 12 | # licensed is only needed if using leslib 13 | # 14 | 15 | LICENSED_SOFTWARE_TOPLEVEL= 16 | 17 | # 18 | # Notes on MPI: 19 | # * default is to use dummy mpi 20 | # * can only build one at a time 21 | # 22 | 23 | SV_USE_DUMMY_MPI=1 24 | SV_USE_OPENMPI=0 25 | SV_USE_MPICH=0 26 | -------------------------------------------------------------------------------- /BuildWithMake/SampleOverrides/windows/global_overrides.mk: -------------------------------------------------------------------------------- 1 | # 2 | # Override default cluster to build on Windows 3 | # with msvc 2013 compiler 4 | # 5 | 6 | CLUSTER = x64_cygwin 7 | CXX_COMPILER_VERSION = msvc-12.5 8 | FORTRAN_COMPILER_VERSION = ifort 9 | 10 | # 11 | # external location for installed vtk libs 12 | # 13 | # * can be built using scripts in "../Externals" 14 | # * pre-built binaries for Windows 10, vs2013 compilers 15 | # can be downloaded using the "get-vtk-binaries.sh" script: 16 | # i.e. % ./get-vtk-binaries.sh msvc-12.5 17 | 18 | SVEXTERN_COMPILER_VERSION = $(CXX_COMPILER_VERSION) 19 | OPEN_SOFTWARE_BINARIES_TOPLEVEL =C:/cygwin64/${HOME}/svsolver/externals/bin/$(SVEXTERN_COMPILER_VERSION)/x64 20 | LICENSED_SOFTWARE_TOPLEVEL = 21 | 22 | # 23 | # licensed is only needed if using leslib 24 | # 25 | 26 | LICENSED_SOFTWARE_TOPLEVEL= 27 | 28 | # 29 | # Notes on MPI: 30 | # * default is to use msmpi 31 | # * can only build one at a time 32 | 33 | SV_USE_DUMMY_MPI=0 34 | -------------------------------------------------------------------------------- /BuildWithMake/get-vtk-binaries.sh: -------------------------------------------------------------------------------- 1 | #/bin/sh -f 2 | 3 | if [ "$1" == "centos_6" ]; then 4 | rm -Rf $HOME/svsolver/externals/bin/gnu-4.4/x64 5 | mkdir -p $HOME/svsolver/externals/bin/gnu-4.4/x64 6 | pushd $HOME/svsolver/externals/bin/gnu-4.4/x64 7 | wget http://simvascular.stanford.edu/downloads/public/svsolver/externals/linux/centos_6/gnu-4.4/latest/linux.gnu-4.4.x64.vtk-6.2.0-latest.tar.gz 8 | tar xvzf linux.gnu-4.4.x64.vtk-6.2.0-latest.tar.gz 9 | popd 10 | elif [ "$1" == "ubuntu_14" ]; then 11 | rm -Rf $HOME/svsolver/externals/bin/gnu-4.8/x64 12 | mkdir -p $HOME/svsolver/externals/bin/gnu-4.8/x64 13 | pushd $HOME/svsolver/externals/bin/gnu-4.8/x64 14 | wget http://simvascular.stanford.edu/downloads/public/svsolver/externals/linux/ubuntu_14/gnu-4.8/latest/linux.gnu-4.8.x64.vtk-6.2.0-latest.tar.gz 15 | tar xvzf linux.gnu-4.8.x64.vtk-6.2.0-latest.tar.gz 16 | popd 17 | elif [ "$1" == "macosx_11" ]; then 18 | rm -Rf $HOME/svsolver/externals/bin/clang-7.3/x64 19 | mkdir -p $HOME/svsolver/externals/bin/clang-7.3/x64 20 | pushd $HOME/svsolver/externals/bin/clang-7.3/x64 21 | wget http://simvascular.stanford.edu/downloads/public/svsolver/externals/mac_osx/10.11/clang-7.3/latest/mac_osx.clang-7.3.x64.vtk-6.2.0-latest.tar.gz 22 | tar xvzf mac_osx.clang-7.3.x64.vtk-6.2.0-latest.tar.gz 23 | popd 24 | elif [ "$1" == "msvc-12.5" ]; then 25 | rm -Rf $HOME/svsolver/externals/bin/msvc-12.5/x64 26 | mkdir -p $HOME/svsolver/externals/bin/msvc-12.5/x64 27 | pushd $HOME/svsolver/externals/bin/msvc-12.5/x64 28 | wget http://simvascular.stanford.edu/downloads/public/svsolver/externals/windows/10/msvc_2013/latest/windows.msvc-12.5.x64.vtk-6.2.0-latest.tar.gz 29 | tar xvzf windows.msvc-12.5.x64.vtk-6.2.0-latest.tar.gz 30 | popd 31 | fi 32 | 33 | 34 | -------------------------------------------------------------------------------- /Code/CMake/SVFSILSConfig.cmake: -------------------------------------------------------------------------------- 1 | 2 | 3 | set(SVFSILS_DEFINITIONS "") 4 | set(SVFSILS_NEEDED_LIBS SVFSILS) 5 | 6 | if(IS64 AND (WIN32 OR CYGWIN)) 7 | unset(SVFSILS_INCLUDE_DIR) 8 | set(SVFSILS_PATH_PREFIX "SVFSILS-2013.08.10/win/x64") 9 | set(SVFSILS_FULL_PATH "${LicensedLibs_Bin_Directory}${SVFSILS_PATH_PREFIX}") 10 | set(SVFSILS_LIB_DIR "${SVFSILS_FULL_PATH}" CACHE TYPE PATH) 11 | set(SVFSILS_POSSIBLE_INCLUDE_DIR "${SVFSILS_FULL_PATH}" CACHE TYPE PATH) 12 | endif() 13 | 14 | find_path(SVFSILS_INCLUDE_DIR SVFSILS.h HINTS ${SVFSILS_POSSIBLE_INCLUDE_DIR}) 15 | 16 | GENLIBS(SVFSILS_LIBRARY "${SVFSILS_NEEDED_LIBS}" "SVFSILS" "${SVFSILS_LIB_DIR}") 17 | set(SVFSILS_LIBRARY ${SVFSILS_SVFSILS_LIBRARY}) 18 | 19 | include_directories(${SVFSILS_INCLUDE_DIR}) 20 | link_directories(${SVFSILS_LIB_DIR}) 21 | add_definitions(${SVFSILS_DEFINITIONS}) 22 | 23 | 24 | -------------------------------------------------------------------------------- /Code/CMake/SimVascularInternals.cmake: -------------------------------------------------------------------------------- 1 | set(SV_LIBS 2 | THIRDPARTY_METIS_SVFSI 3 | THIRDPARTY_PARMETIS_SVFSI 4 | THIRDPARTY_TETGEN 5 | THIRDPARTY_ZLIB 6 | SVFSILS) 7 | 8 | foreach(lib ${SV_LIBS}) 9 | string(TOLOWER "_SIMVASCULAR_${lib}" SV_LIB_${lib}_NAME) 10 | endforeach() 11 | -------------------------------------------------------------------------------- /Code/CMake/SimVascularThirdParty.cmake: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | # ZLIB 3 | if(SV_USE_ZLIB) 4 | set(USE_ZLIB ON) 5 | simvascular_third_party(zlib) 6 | if(NOT SV_USE_SYSTEM_ZLIB) 7 | set(ZLIB_LIBRARY ${SV_LIB_THIRDPARTY_ZLIB_NAME}) 8 | else() 9 | find_package(ZLIB) 10 | endif() 11 | else() 12 | unset(ZLIB_LIBRARY CACHE) 13 | endif() 14 | 15 | #----------------------------------------------------------------------------- 16 | # METIS_SVFSI 17 | if(SV_USE_METIS_SVFSI) 18 | set(USE_METIS_SVFSI ON) 19 | simvascular_third_party(metis_svfsi) 20 | # require to be built here 21 | set(METIS_SVFSI_LIBRARY ${SV_LIB_THIRDPARTY_METIS_SVFSI_NAME}) 22 | endif() 23 | 24 | #----------------------------------------------------------------------------- 25 | # PARMETIS_SVFSI 26 | if(SV_USE_PARMETIS_SVFSI) 27 | set(USE_PARMETIS_SVFSI ON) 28 | simvascular_third_party(parmetis_svfsi) 29 | # require to be built here 30 | set(PARMETIS_SVFSI_LIBRARY ${SV_LIB_THIRDPARTY_PARMETIS_SVFSI_NAME}) 31 | endif() 32 | 33 | #----------------------------------------------------------------------------- 34 | # TETGEN 35 | if(SV_USE_TETGEN) 36 | set(USE_TETGEN ON) 37 | simvascular_third_party(tetgen) 38 | # require to be built here 39 | set(TETGEN_LIBRARY ${SV_LIB_THIRDPARTY_TETGEN_NAME}) 40 | endif() 41 | -------------------------------------------------------------------------------- /Code/Scripts/README-install: -------------------------------------------------------------------------------- 1 | You may need to install libxss, mpich2, or libgfortran. 2 | If you're on linux these may work: 3 | 4 | sudo apt-get install libxss 5 | sudo apt-get install mpich2 6 | sudo apt-get install gfortran 7 | 8 | -------- 9 | 10 | To use Meshim on linux copy your license file into the simvascular directory and rename it meshsim-license.dat 11 | 12 | -------- 13 | 14 | To add SimVascular to your path (this is very helpful with using svsolver), you will need to run the post-install script: 15 | 16 | sudo bash setup-symlinks.sh 17 | 18 | This script places symbolic links in /usr/local/bin to the simvascular executable scripts. 19 | You may wish to edit the symbolic links. 20 | 21 | Note that the solver can be run with mpiexec. 22 | For example to run on two processors: 23 | cd /folder/with/input 24 | mpiexec -np 2 svsolver 25 | 26 | -- -------------------------------------------------------------------------------- /Code/Scripts/README-postinstall: -------------------------------------------------------------------------------- 1 | 2 | To add SimVascular to your path, you will need to run the post-install script. 3 | This script places symbolic links in /usr/local/bin to the simvascular executables. -------------------------------------------------------------------------------- /Code/Scripts/executable/developer/locate-linux-script.in: -------------------------------------------------------------------------------- 1 | SOURCE="${BASH_SOURCE[0]}" 2 | while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink 3 | TARGET="$(readlink "$SOURCE")" 4 | if [[ $SOURCE == /* ]]; then 5 | SOURCE="$TARGET" 6 | else 7 | DIR="$( dirname "$SOURCE" )" 8 | SOURCE="$DIR/$TARGET" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located 9 | fi 10 | done 11 | RDIR="$( dirname "$SOURCE" )" 12 | DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" 13 | -------------------------------------------------------------------------------- /Code/Scripts/executable/developer/svFSI-linux.in: -------------------------------------------------------------------------------- 1 | $SV_HOME/bin/@SV_SVFSI_EXE@ $* 2 | -------------------------------------------------------------------------------- /Code/Scripts/executable/developer/svpost-linux.in: -------------------------------------------------------------------------------- 1 | 2 | # run the executable 3 | case "$*" in 4 | "") 5 | $SV_HOME/bin/@SV_POSTSOLVER_EXE@ 6 | ;; 7 | *) 8 | $SV_HOME/bin/@SV_POSTSOLVER_EXE@ $* 9 | ;; 10 | esac 11 | 12 | -------------------------------------------------------------------------------- /Code/Scripts/executable/developer/svpost-windows.in: -------------------------------------------------------------------------------- 1 | 2 | "%SV_HOME%\Bin\@SV_POSTSOLVER_EXE@@WIN_EXE@$ * 3 | -------------------------------------------------------------------------------- /Code/Scripts/executable/developer/svpre-linux.in: -------------------------------------------------------------------------------- 1 | $SV_HOME/bin/@SV_PRESOLVER_EXE@ $* 2 | -------------------------------------------------------------------------------- /Code/Scripts/executable/developer/svpre-windows.in: -------------------------------------------------------------------------------- 1 | 2 | 3 | "%SV_HOME%\Bin\@SV_PRESOLVER_EXE@@WIN_EXE@$ * 4 | -------------------------------------------------------------------------------- /Code/Scripts/executable/developer/svsolver-linux.in: -------------------------------------------------------------------------------- 1 | export LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ 2 | export FLOWSOLVER_CONFIG=@ENV_SV_HOME@/bin/ 3 | $SV_HOME/bin/@SV_FLOWSOLVER_EXE@ $* 4 | -------------------------------------------------------------------------------- /Code/Scripts/executable/developer/svsolver-nompi-linux.in: -------------------------------------------------------------------------------- 1 | export LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ 2 | export FLOWSOLVER_CONFIG=@ENV_SV_HOME@/Bin/ 3 | $SV_HOME/bin/@SV_FLOWSOLVER_EXE@-nompi $* 4 | -------------------------------------------------------------------------------- /Code/Scripts/executable/developer/svsolver-nompi-windows.in: -------------------------------------------------------------------------------- 1 | set LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ 2 | set FLOWSOLVER_CONFIG=@ENV_SV_HOME@\Bin\ 3 | 4 | %SV_HOME%\Bin\@SV_FLOWSOLVER_EXE@-nompi@WIN_EXE@ 5 | -------------------------------------------------------------------------------- /Code/Scripts/executable/developer/svsolver-windows.in: -------------------------------------------------------------------------------- 1 | set LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ 2 | set FLOWSOLVER_CONFIG=@ENV_SV_HOME@\Bin\ 3 | 4 | "@MPIEXEC@" -np %1 "%SV_HOME%\Bin\@SV_FLOWSOLVER_EXE@@WIN_EXE@" %2 %3 %4 5 | -------------------------------------------------------------------------------- /Code/Scripts/executable/install/svFSI-linux.in: -------------------------------------------------------------------------------- 1 | $SV_HOME/@SV_INSTALL_RUNTIME_DIR@/@SV_SVFSI_EXE@@CMAKE_EXECUTABLE_SUFFIX@ $* 2 | -------------------------------------------------------------------------------- /Code/Scripts/executable/install/svpost-linux.in: -------------------------------------------------------------------------------- 1 | 2 | # run the executable 3 | case "$*" in 4 | "") 5 | $SV_HOME/@SV_INSTALL_RUNTIME_DIR@/@SV_POSTSOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@ 6 | ;; 7 | *) 8 | $SV_HOME/@SV_INSTALL_RUNTIME_DIR@/@SV_POSTSOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@ $* 9 | ;; 10 | esac 11 | 12 | -------------------------------------------------------------------------------- /Code/Scripts/executable/install/svpost-windows.in: -------------------------------------------------------------------------------- 1 | 2 | "%SV_HOME%\@SV_INSTALL_RUNTIME_DIR@\@SV_POSTSOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@ * 3 | -------------------------------------------------------------------------------- /Code/Scripts/executable/install/svpre-linux.in: -------------------------------------------------------------------------------- 1 | $SV_HOME/@SV_INSTALL_RUNTIME_DIR@/@SV_PRESOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@ $* 2 | -------------------------------------------------------------------------------- /Code/Scripts/executable/install/svpre-windows.in: -------------------------------------------------------------------------------- 1 | 2 | 3 | "%SV_HOME%\@SV_INSTALL_RUNTIME_DIR@\@SV_PRESOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@ $* 4 | -------------------------------------------------------------------------------- /Code/Scripts/executable/install/svsolver-linux.in: -------------------------------------------------------------------------------- 1 | export LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ 2 | export FLOWSOLVER_CONFIG=@ENV_SV_HOME@/@SV_INSTALL_RUNTIME_DIR@/ 3 | $SV_HOME/@SV_INSTALL_RUNTIME_DIR@/@SV_FLOWSOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@ $* 4 | -------------------------------------------------------------------------------- /Code/Scripts/executable/install/svsolver-nompi-linux.in: -------------------------------------------------------------------------------- 1 | export LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ 2 | export FLOWSOLVER_CONFIG=@ENV_SV_HOME@/@SV_INSTALL_RUNTIME_DIR@/ 3 | $SV_HOME/@SV_INSTALL_RUNTIME_DIR@/@SV_FLOWSOLVER_EXE@-nompi@CMAKE_EXECUTABLE_SUFFIX@ $* 4 | -------------------------------------------------------------------------------- /Code/Scripts/executable/install/svsolver-nompi-windows.in: -------------------------------------------------------------------------------- 1 | set LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ 2 | set FLOWSOLVER_CONFIG=@ENV_SV_HOME@\@SV_INSTALL_RUNTIME_DIR@\ 3 | 4 | %SV_HOME%\@SV_INSTALL_RUNTIME_DIR@\@SV_FLOWSOLVER_EXE@-nompi@CMAKE_EXECUTABLE_SUFFIX@" %2 %3 %4 5 | -------------------------------------------------------------------------------- /Code/Scripts/executable/install/svsolver-windows.in: -------------------------------------------------------------------------------- 1 | set LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ 2 | set FLOWSOLVER_CONFIG=@ENV_SV_HOME@\@SV_INSTALL_RUNTIME_DIR@\ 3 | 4 | %SV_HOME%\mpiexec@CMAKE_EXECUTABLE_SUFFIX@ -np %1 "%SV_HOME%\@SV_INSTALL_RUNTIME_DIR@\@SV_FLOWSOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@" %2 %3 %4 5 | -------------------------------------------------------------------------------- /Code/Scripts/home-locate-linux.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -f 2 | # Copyright (c) 2014-2015 The Regents of the University of California. 3 | # All Rights Reserved. 4 | # 5 | # Permission is hereby granted, free of charge, to any person obtaining 6 | # a copy of this software and associated documentation files (the 7 | # "Software"), to deal in the Software without restriction, including 8 | # without limitation the rights to use, copy, modify, merge, publish, 9 | # distribute, sublicense, and/or sell copies of the Software, and to 10 | # permit persons to whom the Software is furnished to do so, subject 11 | # to the following conditions: 12 | # 13 | # The above copyright notice and this permission notice shall be included 14 | # in all copies or substantial portions of the Software. 15 | # 16 | # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS 17 | # IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED 18 | # TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 19 | # PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER 20 | # OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 21 | # EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 22 | # PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 23 | # PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 24 | # LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 25 | # NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 26 | # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 27 | 28 | SOURCE="${BASH_SOURCE[0]}" 29 | while [ -h "$SOURCE" ]; do 30 | TARGET="$(readlink "$SOURCE")" 31 | if [[ $SOURCE == /* ]]; then 32 | SOURCE="$TARGET" 33 | else 34 | DIR="$( dirname "$SOURCE" )" 35 | SOURCE="$DIR/$TARGET" 36 | fi 37 | done 38 | RDIR="$( dirname "$SOURCE" )" 39 | DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" -------------------------------------------------------------------------------- /Code/Source/Include/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | configure_file(simvascular_version.h.in ${CMAKE_CURRENT_BINARY_DIR}/simvascular_version.h) 3 | configure_file(simvascular_options.h.in ${CMAKE_CURRENT_BINARY_DIR}/simvascular_options.h) 4 | -------------------------------------------------------------------------------- /Code/Source/Include/cvFlowsolverOptions.h.in: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright (c) 2014-2015 The Regents of the University of California. 4 | * All Rights Reserved. 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining 7 | * a copy of this software and associated documentation files (the 8 | * "Software"), to deal in the Software without restriction, including 9 | * without limitation the rights to use, copy, modify, merge, publish, 10 | * distribute, sublicense, and/or sell copies of the Software, and to 11 | * permit persons to whom the Software is furnished to do so, subject 12 | * to the following conditions: 13 | * 14 | * The above copyright notice and this permission notice shall be included 15 | * in all copies or substantial portions of the Software. 16 | * 17 | * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS 18 | * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED 19 | * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 20 | * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER 21 | * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 22 | * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 23 | * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 24 | * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 25 | * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 26 | * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 27 | * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 28 | * 29 | *=========================================================================*/ 30 | 31 | /* Simvascular Version defines */ 32 | #define SV_VERSION "@SV_VERSION@" 33 | #define SV_MAJOR_VERSION "@SV_MAJOR_VERSION@" 34 | #define SV_MINOR_VERSION "@SV_MINOR_VERSION@" 35 | #define SV_PATCH_VERSION "@SV_PATCH_VERSION@" 36 | #define SV_FULL_VERSION "@SV_FULL_VERSION@" 37 | 38 | /* Our Version defines */ 39 | #define SV_MAJOR_VER_NO "@SV_MAJOR_VERSION@" 40 | #define SV_FULL_VER_NO "@SV_MAJOR_VERSION@.@SV_MINOR_VERSION@" 41 | 42 | #cmakedefine SV_USE_ZLIB 43 | #cmakedefine SV_USE_LESLIB 44 | #cmakedefine SV_USE_NSPCG 45 | #cmakedefine SV_USE_METIS 46 | #cmakedefine SV_USE_SPARSE 47 | #cmakedefine SV_USE_SVLS 48 | 49 | 50 | /* Flowsolver defines */ 51 | #define VER_CORONARY @VER_CORONARY@ 52 | #define VER_CLOSEDLOOP @VER_CLOSEDLOOP@ 53 | #define VER_VARWALL @VER_VARWALL@ 54 | #define VER_USE_VTK @VER_USE_VTK@ 55 | -------------------------------------------------------------------------------- /Code/Source/Include/simvascular_version.h.in: -------------------------------------------------------------------------------- 1 | /* Copyright (c) 2014-2015 The Regents of the University of California. 2 | * All Rights Reserved. 3 | * 4 | * Permission is hereby granted, free of charge, to any person obtaining 5 | * a copy of this software and associated documentation files (the 6 | * "Software"), to deal in the Software without restriction, including 7 | * without limitation the rights to use, copy, modify, merge, publish, 8 | * distribute, sublicense, and/or sell copies of the Software, and to 9 | * permit persons to whom the Software is furnished to do so, subject 10 | * to the following conditions: 11 | * 12 | * The above copyright notice and this permission notice shall be included 13 | * in all copies or substantial portions of the Software. 14 | * 15 | * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS 16 | * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED 17 | * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 18 | * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER 19 | * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 20 | * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 21 | * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 22 | * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 23 | * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 24 | * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 25 | * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 26 | */ 27 | 28 | /* Standard Version defines */ 29 | #define SV_VERSION "@SV_VERSION@" 30 | #define SV_MAJOR_VERSION "@SV_MAJOR_VERSION@" 31 | #define SV_MINOR_VERSION "@SV_MINOR_VERSION@" 32 | #define SV_PATCH_VERSION "@SV_PATCH_VERSION@" 33 | #define SV_FULL_VERSION "@SV_FULL_VERSION@" 34 | 35 | /* Our Version defines */ 36 | #define SV_MAJOR_VER_NO "@SV_MAJOR_VERSION@" 37 | #define SV_FULL_VER_NO "@SV_MAJOR_VERSION@.@SV_MINOR_VERSION@" 38 | -------------------------------------------------------------------------------- /Code/Source/svFSILS/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | include_directories(${MPI_C_INCLUDE_PATH}) 2 | 3 | if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU") 4 | set(CMAKE_Fortran_FLAGS "-O3 -DNDEBUG -march=native") 5 | set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -cpp -pthread -std=legacy") 6 | 7 | # Use below flags for debugging 8 | # set(CMAKE_Fortran_FLAGS "-O0") 9 | # set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -cpp -pthread -std=legacy") 10 | # set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -Wall -Wconversion -Wline-truncation -pedantic -fimplicit-none -fbacktrace -fbounds-check -p -fcheck=all -ffpe-trap=invalid,zero,overflow,underflow") 11 | elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel") 12 | set(CMAKE_Fortran_FLAGS "-O3 -march=native") 13 | set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fpp -pthread") 14 | else() 15 | # nothing for now 16 | # may need to set for other compilers 17 | endif() 18 | 19 | set(lib ${SV_LIB_SVFSILS_NAME}${SV_MPI_NAME_EXT}) 20 | 21 | set(FSRCS ADDBCMUL.f 22 | BCAST.f 23 | CGRAD.f 24 | CPUT.f 25 | FSISOLVER.f 26 | GMRES.f 27 | LHS.f 28 | NORM.f 29 | OMPLA.f 30 | PRECOND.f 31 | SPARMUL.f 32 | BC.f 33 | BICGS.f 34 | COMMU.f 35 | DOT.f 36 | GE.f 37 | INCOMMU.f 38 | LS.f 39 | NSSOLVER.f 40 | PCGMRES.f 41 | SOLVE.f) 42 | 43 | set(CSRCS HRCPUT.c) 44 | 45 | add_library(${lib} ${SV_LIBRARY_TYPE} ${FSRCS} ${CSRCS}) 46 | 47 | target_link_libraries(${lib} ${MPI_LIBRARY} ${MPI_Fortran_LIBRARIES}) 48 | 49 | # extra MPI libraries only if there are not set to NOT_FOUND or other null 50 | if(SV_MPI_EXTRA_LIBRARY) 51 | target_link_libraries(${lib} ${SV_MPI_EXTRA_LIBRARY}) 52 | endif() 53 | 54 | if(SV_INSTALL_LIBS) 55 | install(TARGETS ${lib} 56 | RUNTIME DESTINATION ${SV_INSTALL_RUNTIME_DIR} COMPONENT CoreExecutables 57 | LIBRARY DESTINATION ${SV_INSTALL_LIBRARY_DIR} COMPONENT CoreLibraries 58 | ARCHIVE DESTINATION ${SV_INSTALL_ARCHIVE_DIR} COMPONENT CoreLibraries 59 | ) 60 | endif() 61 | if(SV_INSTALL_HEADERS) 62 | install(FILES ${HDRS} 63 | DESTINATION ${SV_INSTALL_INCLUDE_DIR}/core COMPONENT CoreHeaders 64 | ) 65 | endif() 66 | -------------------------------------------------------------------------------- /Code/Source/svFSILS/FSILS.h: -------------------------------------------------------------------------------- 1 | !-------------------------------------------------------------------- 2 | ! Created by Mahdi Esmaily Moghadam 3 | ! contact memt63@gmail.com for reporting the bugs. 4 | !-------------------------------------------------------------------- 5 | ! 6 | ! UC Copyright Notice 7 | ! This software is Copyright ©2012 The Regents of the University of 8 | ! California. All Rights Reserved. 9 | ! 10 | ! Permission to copy and modify this software and its documentation 11 | ! for educational, research and non-profit purposes, without fee, 12 | ! and without a written agreement is hereby granted, provided that 13 | ! the above copyright notice, this paragraph and the following three 14 | ! paragraphs appear in all copies. 15 | ! 16 | ! Permission to make commercial use of this software may be obtained 17 | ! by contacting: 18 | ! Technology Transfer Office 19 | ! 9500 Gilman Drive, Mail Code 0910 20 | ! University of California 21 | ! La Jolla, CA 92093-0910 22 | ! (858) 534-5815 23 | ! invent@ucsd.edu 24 | ! 25 | ! This software program and documentation are copyrighted by The 26 | ! Regents of the University of California. The software program and 27 | ! documentation are supplied "as is", without any accompanying 28 | ! services from The Regents. The Regents does not warrant that the 29 | ! operation of the program will be uninterrupted or error-free. The 30 | ! end-user understands that the program was developed for research 31 | ! purposes and is advised not to rely exclusively on the program for 32 | ! any reason. 33 | ! 34 | ! IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY 35 | ! PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL 36 | ! DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS 37 | ! SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE UNIVERSITY OF 38 | ! CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 39 | ! THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY 40 | ! WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES 41 | ! OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 42 | ! SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE 43 | ! UNIVERSITY OF CALIFORNIA HAS NO OBLIGATIONS TO PROVIDE 44 | ! MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. 45 | ! 46 | !-------------------------------------------------------------------- 47 | ! This is the main header that needs to be included in your solver 48 | ! to get access to the FSILS_API and data structures 49 | !-------------------------------------------------------------------- 50 | 51 | INCLUDE "FSILS_STRUCT.h" 52 | INCLUDE "FSILS_API.h" 53 | -------------------------------------------------------------------------------- /Code/Source/svFSILS/FSILS_TYPEDEF.h: -------------------------------------------------------------------------------- 1 | ! 2 | ! Copyright (c) Stanford University, The Regents of the University of 3 | ! California, and others. 4 | ! 5 | ! All Rights Reserved. 6 | ! 7 | ! See Copyright-SimVascular.txt for additional details. 8 | ! 9 | ! Permission is hereby granted, free of charge, to any person obtaining 10 | ! a copy of this software and associated documentation files (the 11 | ! "Software"), to deal in the Software without restriction, including 12 | ! without limitation the rights to use, copy, modify, merge, publish, 13 | ! distribute, sublicense, and/or sell copies of the Software, and to 14 | ! permit persons to whom the Software is furnished to do so, subject 15 | ! to the following conditions: 16 | ! 17 | ! The above copyright notice and this permission notice shall be included 18 | ! in all copies or substantial portions of the Software. 19 | ! 20 | ! THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS 21 | ! IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED 22 | ! TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 23 | ! PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER 24 | ! OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 25 | ! EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 26 | ! PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 27 | ! PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 28 | ! LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 29 | ! NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 30 | ! SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 31 | ! 32 | !-------------------------------------------------------------------- 33 | ! 34 | ! Data types are defined here 35 | ! 36 | !-------------------------------------------------------------------- 37 | 38 | ! Integer, 8 bits 39 | INTEGER, PARAMETER :: LSIP1 = SELECTED_INT_KIND(2) 40 | ! Integer, 16 bits 41 | INTEGER, PARAMETER :: LSIP2 = SELECTED_INT_KIND(4) 42 | ! Integer, 32 bits 43 | INTEGER, PARAMETER :: LSIP4 = SELECTED_INT_KIND(9) 44 | ! Integer, 64 bits 45 | INTEGER, PARAMETER :: LSIP8 = SELECTED_INT_KIND(18) 46 | 47 | ! Real 32 bits (single) 48 | INTEGER, PARAMETER :: LSRP4 = SELECTED_REAL_KIND(6, 37) 49 | ! Real 64 bits (double) 50 | INTEGER, PARAMETER :: LSRP8 = SELECTED_REAL_KIND(15, 307) 51 | ! Real 128 bits (long double) 52 | INTEGER, PARAMETER :: LSRP16 = SELECTED_REAL_KIND(33, 4931) 53 | 54 | ! Default integer precision 55 | INTEGER, PARAMETER :: LSIP = LSIP4 56 | ! Default real precision 57 | INTEGER, PARAMETER :: LSRP = LSRP8 58 | 59 | !#################################################################### 60 | -------------------------------------------------------------------------------- /Code/Source/svFSILS/HRCPUT.c: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include 4 | #ifdef __MACH__ 5 | #include 6 | #include 7 | #endif 8 | 9 | double fsils_hrcput_() 10 | { 11 | struct timespec time; 12 | double res; 13 | 14 | #ifdef __MACH__ // OSX does not have clock_gettime 15 | clock_serv_t cclock; 16 | mach_timespec_t mts; 17 | host_get_clock_service(mach_host_self(), CALENDAR_CLOCK, &cclock); 18 | clock_get_time(cclock, &mts); 19 | mach_port_deallocate(mach_task_self(), cclock); 20 | time.tv_sec = mts.tv_sec; 21 | time.tv_nsec = mts.tv_nsec; 22 | #else 23 | clock_gettime(CLOCK_THREAD_CPUTIME_ID, &time); 24 | #endif 25 | 26 | res = ((double)time.tv_nsec)/1000000000.0 + (double)(time.tv_sec%1000000); 27 | 28 | return res; 29 | } 30 | 31 | -------------------------------------------------------------------------------- /Code/ThirdParty/README: -------------------------------------------------------------------------------- 1 | The files in this directory are included only for convience when compiling SimVascular. They have their own license agreements. Only minimal changes have been made to allow their use in SimVascular. 2 | Please see README.simvascular in each directory for more details. -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | simvascular_third_party(metis_svfsi) 2 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi.h.in: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright (c) 2014-2015 The Regents of the University of California. 4 | * All Rights Reserved. 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining 7 | * a copy of this software and associated documentation files (the 8 | * "Software"), to deal in the Software without restriction, including 9 | * without limitation the rights to use, copy, modify, merge, publish, 10 | * distribute, sublicense, and/or sell copies of the Software, and to 11 | * permit persons to whom the Software is furnished to do so, subject 12 | * to the following conditions: 13 | * 14 | * The above copyright notice and this permission notice shall be included 15 | * in all copies or substantial portions of the Software. 16 | * 17 | * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS 18 | * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED 19 | * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 20 | * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER 21 | * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 22 | * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 23 | * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 24 | * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 25 | * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 26 | * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 27 | * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 28 | * 29 | *=========================================================================*/ 30 | 31 | #ifndef __simvascular_metis_svfsi_h 32 | #define __simvascular_metis_svfsi_h 33 | 34 | # hardcoded to build, update if want to allow system version 35 | #include 36 | 37 | #endif 38 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8.8) 2 | project(METIS_SVFSI) 3 | if (NOT METIS_SVFSI_LIBRARY_NAME) 4 | set(METIS_SVFSI_LIBRARY_NAME metis_svfsi) 5 | endif() 6 | 7 | if (NOT PARMETIS_SVFSI_LIBRARY_NAME) 8 | set(PARMETIS_SVFSI_LIBRARY_NAME parmetis_svfsi) 9 | endif() 10 | 11 | #set default build type to relwithdebinfo, also sets flags O2 on linux 12 | if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES) 13 | message(STATUS "Setting build type to 'RelWithDebInfo' as none was specified.") 14 | set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build." FORCE) 15 | mark_as_advanced(CMAKE_BUILD_TYPE) 16 | # Set the possible values of build type for cmake-gui 17 | set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" 18 | "MinSizeRel" "RelWithDebInfo") 19 | endif() 20 | 21 | if(WIN32) 22 | add_definitions("/Zi") 23 | add_definitions("-DWINDOWS") 24 | endif() 25 | 26 | add_subdirectory(METISLib) 27 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/LICENSE.txt: -------------------------------------------------------------------------------- 1 | Copyright & License Notice 2 | -------------------------- 3 | 4 | The ParMETIS/METIS package is copyrighted by the Regents of the 5 | University of Minnesota. It can be freely used for educational and 6 | research purposes by non-profit institutions and US government 7 | agencies only. Other organizations are allowed to use ParMETIS/METIS 8 | only for evaluation purposes, and any further uses will require prior 9 | approval. The software may not be sold or redistributed without prior 10 | approval. One may make copies of the software for their use provided 11 | that the copies, are not sold or distributed, are used under the same 12 | terms and conditions. 13 | 14 | As unestablished research software, this code is provided on an 15 | ``as is'' basis without warranty of any kind, either expressed or 16 | implied. The downloading, or executing any part of this software 17 | constitutes an implicit agreement to these terms. These terms and 18 | conditions are subject to change at any time without prior notice. 19 | 20 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/METISLib/Makefile: -------------------------------------------------------------------------------- 1 | include ../../../Makefile.in 2 | include ../Makefile.in 3 | 4 | 5 | CFLAGS = $(COPTIONS) $(OPTFLAGS) -I. $(INCDIR) 6 | 7 | 8 | OBJS = coarsen.o fm.o initpart.o match.o ccgraph.o \ 9 | pmetis.o pqueue.o refine.o util.o timing.o debug.o \ 10 | bucketsort.o graph.o stat.o kmetis.o kwayrefine.o \ 11 | kwayfm.o balance.o ometis.o srefine.o sfm.o separator.o \ 12 | mincover.o mmd.o mesh.o meshpart.o frename.o fortran.o \ 13 | myqsort.o compress.o parmetis.o estmem.o \ 14 | mpmetis.o mcoarsen.o mmatch.o minitpart.o mbalance.o \ 15 | mutil.o mkmetis.o mkwayrefine.o mkwayfmh.o \ 16 | mrefine2.o minitpart2.o mbalance2.o mfm2.o \ 17 | kvmetis.o kwayvolrefine.o kwayvolfm.o subdomains.o \ 18 | mfm.o memory.o mrefine.o checkgraph.o 19 | 20 | .c.o: 21 | $(CC) $(CFLAGS) -c $*.c 22 | 23 | ../libmetis.a: $(OBJS) 24 | $(AR) $@ $(OBJS) 25 | $(RANLIB) $@ 26 | 27 | clean: 28 | rm -f *.o 29 | 30 | realclean: 31 | rm -f *.o ; rm -f ../libmetis.a 32 | 33 | 34 | checkin: 35 | @for file in *.[c,h]; \ 36 | do \ 37 | ci -u -m'Maintance' $$file;\ 38 | done 39 | 40 | checkin2: 41 | @for file in *.[c,h]; \ 42 | do \ 43 | ci $$file;\ 44 | rcs -U $$file;\ 45 | co $$file;\ 46 | done 47 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/METISLib/bucketsort.c: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 1997, Regents of the University of Minnesota 3 | * 4 | * bucketsort.c 5 | * 6 | * This file contains code that implement a variety of counting sorting 7 | * algorithms 8 | * 9 | * Started 7/25/97 10 | * George 11 | * 12 | * $Id: bucketsort.c,v 1.1 2003/07/16 15:55:00 karypis Exp $ 13 | * 14 | */ 15 | 16 | #include 17 | 18 | 19 | 20 | /************************************************************************* 21 | * This function uses simple counting sort to return a permutation array 22 | * corresponding to the sorted order. The keys are assumed to start from 23 | * 0 and they are positive. This sorting is used during matching. 24 | **************************************************************************/ 25 | void BucketSortKeysInc(int n, int max, idxtype *keys, idxtype *tperm, idxtype *perm) 26 | { 27 | int i, ii; 28 | idxtype *counts; 29 | 30 | counts = idxsmalloc(max+2, 0, "BucketSortKeysInc: counts"); 31 | 32 | for (i=0; i 14 | 15 | 16 | /************************************************************************* 17 | * This function takes a graph and creates a sequence of coarser graphs 18 | **************************************************************************/ 19 | GraphType *Coarsen2Way(CtrlType *ctrl, GraphType *graph) 20 | { 21 | int clevel; 22 | GraphType *cgraph; 23 | 24 | IFSET(ctrl->dbglvl, DBG_TIME, starttimer(ctrl->CoarsenTmr)); 25 | 26 | cgraph = graph; 27 | 28 | /* The following is ahack to allow the multiple bisections to go through with correct 29 | coarsening */ 30 | if (ctrl->CType > 20) { 31 | clevel = 1; 32 | ctrl->CType -= 20; 33 | } 34 | else 35 | clevel = 0; 36 | 37 | do { 38 | IFSET(ctrl->dbglvl, DBG_COARSEN, printf("%6d %7d [%d] [%d %d]\n", 39 | cgraph->nvtxs, cgraph->nedges, ctrl->CoarsenTo, ctrl->maxvwgt, 40 | (cgraph->vwgt ? idxsum(cgraph->nvtxs, cgraph->vwgt) : cgraph->nvtxs))); 41 | 42 | if (cgraph->adjwgt) { 43 | switch (ctrl->CType) { 44 | case MATCH_RM: 45 | Match_RM(ctrl, cgraph); 46 | break; 47 | case MATCH_HEM: 48 | if (clevel < 1 || cgraph->nedges == 0) 49 | Match_RM(ctrl, cgraph); 50 | else 51 | Match_HEM(ctrl, cgraph); 52 | break; 53 | case MATCH_SHEM: 54 | if (clevel < 1 || cgraph->nedges == 0) 55 | Match_RM(ctrl, cgraph); 56 | else 57 | Match_SHEM(ctrl, cgraph); 58 | break; 59 | case MATCH_SHEMKWAY: 60 | if (cgraph->nedges == 0) 61 | Match_RM(ctrl, cgraph); 62 | else 63 | Match_SHEM(ctrl, cgraph); 64 | break; 65 | default: 66 | errexit("Unknown CType: %d\n", ctrl->CType); 67 | } 68 | } 69 | else { 70 | Match_RM_NVW(ctrl, cgraph); 71 | } 72 | 73 | cgraph = cgraph->coarser; 74 | clevel++; 75 | 76 | } while (cgraph->nvtxs > ctrl->CoarsenTo && cgraph->nvtxs < COARSEN_FRACTION2*cgraph->finer->nvtxs && cgraph->nedges > cgraph->nvtxs/2); 77 | 78 | IFSET(ctrl->dbglvl, DBG_COARSEN, printf("%6d %7d [%d] [%d %d]\n", 79 | cgraph->nvtxs, cgraph->nedges, ctrl->CoarsenTo, ctrl->maxvwgt, 80 | (cgraph->vwgt ? idxsum(cgraph->nvtxs, cgraph->vwgt) : cgraph->nvtxs))); 81 | 82 | IFSET(ctrl->dbglvl, DBG_TIME, stoptimer(ctrl->CoarsenTmr)); 83 | 84 | return cgraph; 85 | } 86 | 87 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/METISLib/metis.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 1997, Regents of the University of Minnesota 3 | * 4 | * metis.h 5 | * 6 | * This file includes all necessary header files 7 | * 8 | * Started 8/27/94 9 | * George 10 | * 11 | * $Id: metis.h,v 1.3 2003/07/25 13:52:00 karypis Exp $ 12 | */ 13 | 14 | /* 15 | #define DEBUG 1 16 | #define DMALLOC 1 17 | */ 18 | 19 | #include 20 | 21 | #ifdef DMALLOC 22 | #include 23 | #endif 24 | 25 | // moved this to metis_svfsi directory 26 | // #include "../parmetis.h" /* Get the idxtype definition */ 27 | #include /* Get the idxtype definition */ 28 | #include 29 | #include 30 | #include 31 | #include 32 | #include 33 | 34 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/METISLib/mrefine2.c: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 1997, Regents of the University of Minnesota 3 | * 4 | * mrefine2.c 5 | * 6 | * This file contains the driving routines for multilevel refinement 7 | * 8 | * Started 7/24/97 9 | * George 10 | * 11 | * $Id: mrefine2.c,v 1.1 2003/07/16 15:55:12 karypis Exp $ 12 | */ 13 | 14 | #include 15 | 16 | 17 | /************************************************************************* 18 | * This function is the entry point of refinement 19 | **************************************************************************/ 20 | void MocRefine2Way2(CtrlType *ctrl, GraphType *orggraph, GraphType *graph, float *tpwgts, 21 | float *ubvec) 22 | { 23 | 24 | IFSET(ctrl->dbglvl, DBG_TIME, starttimer(ctrl->UncoarsenTmr)); 25 | 26 | /* Compute the parameters of the coarsest graph */ 27 | MocCompute2WayPartitionParams(ctrl, graph); 28 | 29 | for (;;) { 30 | ASSERT(CheckBnd(graph)); 31 | 32 | IFSET(ctrl->dbglvl, DBG_TIME, starttimer(ctrl->RefTmr)); 33 | switch (ctrl->RType) { 34 | case RTYPE_FM: 35 | MocBalance2Way2(ctrl, graph, tpwgts, ubvec); 36 | MocFM_2WayEdgeRefine2(ctrl, graph, tpwgts, ubvec, 8); 37 | break; 38 | default: 39 | errexit("Unknown refinement type: %d\n", ctrl->RType); 40 | } 41 | IFSET(ctrl->dbglvl, DBG_TIME, stoptimer(ctrl->RefTmr)); 42 | 43 | if (graph == orggraph) 44 | break; 45 | 46 | graph = graph->finer; 47 | IFSET(ctrl->dbglvl, DBG_TIME, starttimer(ctrl->ProjectTmr)); 48 | MocProject2WayPartition(ctrl, graph); 49 | IFSET(ctrl->dbglvl, DBG_TIME, stoptimer(ctrl->ProjectTmr)); 50 | } 51 | 52 | IFSET(ctrl->dbglvl, DBG_TIME, stoptimer(ctrl->UncoarsenTmr)); 53 | } 54 | 55 | 56 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/METISLib/stats.c: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 1997, Regents of the University of Minnesota 3 | * 4 | * stat.c 5 | * 6 | * This file computes various statistics 7 | * 8 | * Started 7/25/97 9 | * George 10 | * 11 | * $Id: stats.c,v 1.1 2003/03/13 06:33:20 karypis Exp $ 12 | * 13 | */ 14 | 15 | #include 16 | 17 | 18 | /************************************************************************* 19 | * This function computes the balance of the partitioning 20 | **************************************************************************/ 21 | void Moc_ComputePartitionBalance(GraphType *graph, int nparts, idxtype *where, float *ubvec) 22 | { 23 | int i, j, nvtxs, ncon; 24 | float *kpwgts, *nvwgt; 25 | float balance; 26 | 27 | nvtxs = graph->nvtxs; 28 | ncon = graph->ncon; 29 | nvwgt = graph->nvwgt; 30 | 31 | kpwgts = fmalloc(nparts, "ComputePartitionInfo: kpwgts"); 32 | 33 | for (j=0; jnvtxs; i++) 36 | kpwgts[where[i]] += nvwgt[i*ncon+j]; 37 | 38 | ubvec[j] = (float)nparts*kpwgts[samax(nparts, kpwgts)]/ssum(nparts, kpwgts); 39 | } 40 | 41 | free(kpwgts); 42 | 43 | } 44 | 45 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/METISLib/stdheaders.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 1997, Regents of the University of Minnesota 3 | * 4 | * stdheaders.h 5 | * 6 | * This file includes all necessary header files 7 | * 8 | * Started 8/27/94 9 | * George 10 | * 11 | * $Id: stdheaders.h,v 1.2 2003/07/25 14:31:45 karypis Exp $ 12 | */ 13 | 14 | 15 | #include 16 | #ifdef __STDC__ 17 | #include 18 | #else 19 | #include 20 | #endif 21 | #include 22 | #include 23 | #include 24 | #include 25 | #include 26 | #include 27 | 28 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/METISLib/temp/metis.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 1997, Regents of the University of Minnesota 3 | * 4 | * metis.h 5 | * 6 | * This file includes all necessary header files 7 | * 8 | * Started 8/27/94 9 | * George 10 | * 11 | * $Id: metis.h,v 1.3 2003/07/25 13:52:00 karypis Exp $ 12 | */ 13 | 14 | /* 15 | #define DEBUG 1 16 | #define DMALLOC 1 17 | */ 18 | 19 | #include 20 | 21 | #ifdef DMALLOC 22 | #include 23 | #endif 24 | 25 | // moved this to metis_svfsi directory 26 | // #include "../metis_svfsi_parmetis.h" /* Get the idxtype definition */ 27 | #include /* Get the idxtype definition */ 28 | #include 29 | #include 30 | #include 31 | #include 32 | #include 33 | 34 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/Makefile: -------------------------------------------------------------------------------- 1 | 2 | default: 3 | (cd METISLib ; make ) 4 | (cd ParMETISLib ; make ) 5 | 6 | clean: 7 | (cd METISLib ; make clean ) 8 | (cd ParMETISLib ; make clean ) 9 | 10 | realclean: 11 | (cd METISLib ; make realclean ) 12 | (cd ParMETISLib ; make realclean ) 13 | 14 | 15 | checkin: 16 | (cd METISLib ; make checkin ) 17 | (cd ParMETISLib ; make checkin ) 18 | 19 | checkin2: 20 | (cd METISLib ; make checkin2 ) 21 | (cd ParMETISLib ; make checkin2 ) 22 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/Makefile.in: -------------------------------------------------------------------------------- 1 | # Which compiler to use 2 | # This is included from ../../Makefile.in 3 | #CC = mpicc 4 | 5 | 6 | # What optimization level to use 7 | #OPTFLAGS = -g 8 | OPTFLAGS = -O3 9 | 10 | # Include directories for the compiler 11 | INCDIR = 12 | 13 | # What options to be used by the compiler 14 | #COPTIONS = -g 15 | COPTIONS = -DNDEBUG 16 | 17 | # Which loader to use 18 | LD = $(CC) 19 | 20 | # In which directories to look for any additional libraries 21 | LIBDIR = 22 | 23 | # What additional libraries to link the programs with (eg., -lmpi) 24 | #XTRALIBS = -lefence 25 | #XTRALIBS = -ldmalloc 26 | 27 | # What archiving to use 28 | # This is included from ../../Makefile.in 29 | #AR = ar rv 30 | 31 | # What to use for indexing the archive 32 | # This is included from ../../Makefile.in 33 | #RANLIB = ranlib 34 | #RANLIB = ar -ts 35 | 36 | VERNUM = 3.2.0 37 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/README: -------------------------------------------------------------------------------- 1 | This is ParMetis version 3.2.0. You can find the manual describing the 2 | various routines in the directory 'Manual'. Also, the file called 3 | INSTALL contains instructions on how to build and test ParMetis. 4 | 5 | 6 | Please let me know of any problems that you have found with it. 7 | 8 | George Karypis 9 | karypis@cs.umn.edu 10 | -------------------------------------------------------------------------------- /Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/VERSION: -------------------------------------------------------------------------------- 1 | ParMetis Version 3.2.0 Wed Apr 6 13:28:15 CDT 2011 2 | ParMetis Version 3.1.1 Mon Nov 17 16:41:47 CST 2008 3 | ParMetis Version 3.1.0 Fri Aug 15 13:59:41 CDT 2003 4 | ParMetis Version 3.0.0 Wed Mar 27 23:56:38 CST 2002 5 | ParMetis Version 2.0.0 Tue Sep 22 18:58:31 CDT 1998 6 | ParMetis Version 1.0.2 Wed Apr 15 13:14:50 CDT 1998 7 | 8 | -------------------------------------------------------------------------------- /Code/ThirdParty/msmpi/Include/mpi.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Code/ThirdParty/msmpi/Include/mpi.f90 -------------------------------------------------------------------------------- /Code/ThirdParty/msmpi/Include/mpi.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Code/ThirdParty/msmpi/Include/mpi.h -------------------------------------------------------------------------------- /Code/ThirdParty/msmpi/Include/mpi.h.org: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Code/ThirdParty/msmpi/Include/mpi.h.org -------------------------------------------------------------------------------- /Code/ThirdParty/msmpi/Include/mpif.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Code/ThirdParty/msmpi/Include/mpif.h -------------------------------------------------------------------------------- /Code/ThirdParty/msmpi/Include/mpif.h.org: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Code/ThirdParty/msmpi/Include/mpif.h.org -------------------------------------------------------------------------------- /Code/ThirdParty/msmpi/Include/mpio.h: -------------------------------------------------------------------------------- 1 | 2 | #error do not include mpio.h, use mpi.h 3 | 4 | -------------------------------------------------------------------------------- /Code/ThirdParty/msmpi/Include/x64/mpifptr.h: -------------------------------------------------------------------------------- 1 | ! -*- Mode: F77; F90; -*- 2 | ! 3 | ! (C) Microsoft Corporation. 4 | ! 5 | INTEGER MPI_AINT 6 | PARAMETER (MPI_AINT=z'4c00083b') 7 | -------------------------------------------------------------------------------- /Code/ThirdParty/msmpi/Include/x86/mpifptr.h: -------------------------------------------------------------------------------- 1 | ! -*- Mode: F77; F90; -*- 2 | ! 3 | ! (C) Microsoft Corporation. 4 | ! 5 | INTEGER MPI_AINT 6 | PARAMETER (MPI_AINT=z'4c00043b') 7 | -------------------------------------------------------------------------------- /Code/ThirdParty/msmpi/Installers/msmpisdk.msi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Code/ThirdParty/msmpi/Installers/msmpisdk.msi -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | simvascular_third_party(parmetis_svfsi) 2 | -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi.h.in: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright (c) 2014-2015 The Regents of the University of California. 4 | * All Rights Reserved. 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining 7 | * a copy of this software and associated documentation files (the 8 | * "Software"), to deal in the Software without restriction, including 9 | * without limitation the rights to use, copy, modify, merge, publish, 10 | * distribute, sublicense, and/or sell copies of the Software, and to 11 | * permit persons to whom the Software is furnished to do so, subject 12 | * to the following conditions: 13 | * 14 | * The above copyright notice and this permission notice shall be included 15 | * in all copies or substantial portions of the Software. 16 | * 17 | * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS 18 | * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED 19 | * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 20 | * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER 21 | * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 22 | * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 23 | * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 24 | * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 25 | * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 26 | * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 27 | * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 28 | * 29 | *=========================================================================*/ 30 | 31 | #ifndef __simvascular_parmetis_svfsi_h 32 | #define __simvascular_parmetis_svfsi_h 33 | 34 | # hardcoded to build, update if want to allow system version 35 | # check paths on this, this shuold maybe be 36 | #include 37 | 38 | #endif 39 | 40 | -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8.8) 2 | 3 | if (NOT PARMETIS_SVFSI_LIBRARY_NAME) 4 | set(PARMETIS_SVFSI_LIBRARY_NAME parmetis_svfsi) 5 | endif() 6 | 7 | #set default build type to relwithdebinfo, also sets flags O2 on linux 8 | if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES) 9 | message(STATUS "Setting build type to 'RelWithDebInfo' as none was specified.") 10 | set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build." FORCE) 11 | mark_as_advanced(CMAKE_BUILD_TYPE) 12 | # Set the possible values of build type for cmake-gui 13 | set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" 14 | "MinSizeRel" "RelWithDebInfo") 15 | endif() 16 | 17 | if(WIN32) 18 | add_definitions("/Zi") 19 | add_definitions("-DWINDOWS") 20 | endif() 21 | 22 | add_subdirectory(ParMETISLib) 23 | -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/LICENSE.txt: -------------------------------------------------------------------------------- 1 | Copyright & License Notice 2 | -------------------------- 3 | 4 | The ParMETIS/METIS package is copyrighted by the Regents of the 5 | University of Minnesota. It can be freely used for educational and 6 | research purposes by non-profit institutions and US government 7 | agencies only. Other organizations are allowed to use ParMETIS/METIS 8 | only for evaluation purposes, and any further uses will require prior 9 | approval. The software may not be sold or redistributed without prior 10 | approval. One may make copies of the software for their use provided 11 | that the copies, are not sold or distributed, are used under the same 12 | terms and conditions. 13 | 14 | As unestablished research software, this code is provided on an 15 | ``as is'' basis without warranty of any kind, either expressed or 16 | implied. The downloading, or executing any part of this software 17 | constitutes an implicit agreement to these terms. These terms and 18 | conditions are subject to change at any time without prior notice. 19 | 20 | -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/Makefile: -------------------------------------------------------------------------------- 1 | 2 | default: 3 | (cd METISLib ; make ) 4 | (cd ParMETISLib ; make ) 5 | 6 | clean: 7 | (cd METISLib ; make clean ) 8 | (cd ParMETISLib ; make clean ) 9 | 10 | realclean: 11 | (cd METISLib ; make realclean ) 12 | (cd ParMETISLib ; make realclean ) 13 | 14 | 15 | checkin: 16 | (cd METISLib ; make checkin ) 17 | (cd ParMETISLib ; make checkin ) 18 | 19 | checkin2: 20 | (cd METISLib ; make checkin2 ) 21 | (cd ParMETISLib ; make checkin2 ) 22 | -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/Makefile.in: -------------------------------------------------------------------------------- 1 | # Which compiler to use 2 | # This is included from ../../Makefile.in 3 | #CC = mpicc 4 | 5 | 6 | # What optimization level to use 7 | #OPTFLAGS = -g 8 | OPTFLAGS = -O3 9 | 10 | # Include directories for the compiler 11 | INCDIR = 12 | 13 | # What options to be used by the compiler 14 | #COPTIONS = -g 15 | COPTIONS = -DNDEBUG 16 | 17 | # Which loader to use 18 | LD = $(CC) 19 | 20 | # In which directories to look for any additional libraries 21 | LIBDIR = 22 | 23 | # What additional libraries to link the programs with (eg., -lmpi) 24 | #XTRALIBS = -lefence 25 | #XTRALIBS = -ldmalloc 26 | 27 | # What archiving to use 28 | # This is included from ../../Makefile.in 29 | #AR = ar rv 30 | 31 | # What to use for indexing the archive 32 | # This is included from ../../Makefile.in 33 | #RANLIB = ranlib 34 | #RANLIB = ar -ts 35 | 36 | VERNUM = 3.2.0 37 | -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/ParMETISLib/Makefile: -------------------------------------------------------------------------------- 1 | include ../../../Makefile.in 2 | include ../Makefile.in 3 | 4 | 5 | CFLAGS = $(COPTIONS) $(OPTFLAGS) -I. $(INCDIR) 6 | 7 | 8 | OBJS = comm.o util.o debug.o setup.o grsetup.o timer.o \ 9 | node_refine.o initmsection.o \ 10 | xyzpart.o pspases.o frename.o \ 11 | iintsort.o iidxsort.o ikeysort.o ikeyvalsort.o \ 12 | kmetis.o gkmetis.o ometis.o \ 13 | initpart.o match.o \ 14 | kwayfm.o kwayrefine.o kwaybalance.o \ 15 | remap.o stat.o fpqueue.o \ 16 | ametis.o rmetis.o initbalance.o \ 17 | mdiffusion.o diffutil.o wave.o \ 18 | csrmatch.o redomylink.o balancemylink.o \ 19 | selectq.o akwayfm.o serial.o move.o \ 20 | mmetis.o mesh.o memory.o weird.o backcompat.o 21 | 22 | .c.o: 23 | $(CC) $(CFLAGS) -c $*.c 24 | 25 | 26 | ../libparmetis.a: $(OBJS) 27 | $(AR) $@ $(OBJS) 28 | $(RANLIB) $@ 29 | 30 | clean: 31 | rm -f *.o 32 | 33 | realclean: 34 | rm -f *.o ; rm -f ../libparmetis.a 35 | 36 | 37 | checkin: 38 | @for file in *.[c,h]; \ 39 | do \ 40 | ci -u -m'Maintance' $$file;\ 41 | done 42 | 43 | checkin2: 44 | @for file in *.[c,h]; \ 45 | do \ 46 | ci $$file;\ 47 | rcs -U $$file;\ 48 | co $$file;\ 49 | done 50 | -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/ParMETISLib/csrmatch.c: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 1997, Regents of the University of Minnesota 3 | * 4 | * csrmatch.c 5 | * 6 | * This file contains the code that computes matchings 7 | * 8 | * Started 7/23/97 9 | * George 10 | * 11 | * $Id: csrmatch.c,v 1.2 2003/07/21 17:18:48 karypis Exp $ 12 | * 13 | */ 14 | 15 | #include 16 | 17 | 18 | 19 | 20 | /************************************************************************* 21 | * This function finds a matching using the HEM heuristic 22 | **************************************************************************/ 23 | void CSR_Match_SHEM(MatrixType *matrix, idxtype *match, idxtype *mlist, 24 | idxtype *skip, int ncon) 25 | { 26 | int h, i, ii, j; 27 | int nrows, edge, maxidx, count; 28 | float maxwgt; 29 | idxtype *rowptr, *colind; 30 | float *transfer; 31 | KVType *links; 32 | 33 | nrows = matrix->nrows; 34 | rowptr = matrix->rowptr; 35 | colind = matrix->colind; 36 | transfer = matrix->transfer; 37 | 38 | idxset(nrows, UNMATCHED, match); 39 | 40 | links = (KVType *)GKmalloc(sizeof(KVType)*nrows, "links"); 41 | for (i=0; i 20 | 21 | // updated to place in current directory 22 | #include 23 | // #include "../parmetis.h" 24 | 25 | #ifdef DMALLOC 26 | #include 27 | #endif 28 | 29 | #include 30 | #include 31 | #include 32 | #include 33 | #include 34 | 35 | -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/ParMETISLib/stdheaders.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 1997, Regents of the University of Minnesota 3 | * 4 | * stdheaders.h 5 | * 6 | * This file includes all necessary header files 7 | * 8 | * Started 8/27/94 9 | * George 10 | * 11 | * $Id: stdheaders.h,v 1.4 2003/07/25 14:31:47 karypis Exp $ 12 | */ 13 | 14 | 15 | #include 16 | #include 17 | #include 18 | #include 19 | #include 20 | #include 21 | #include 22 | #include 23 | #include 24 | #include 25 | 26 | -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/ParMETISLib/temp/metis.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/ParMETISLib/temp/metis.h -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/ParMETISLib/temp/parmetislib.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 1997, Regents of the University of Minnesota 3 | * 4 | * par_metis.h 5 | * 6 | * This file includes all necessary header files 7 | * 8 | * Started 8/27/94 9 | * George 10 | * 11 | * $Id: parmetislib.h,v 1.2 2003/07/21 17:50:22 karypis Exp $ 12 | */ 13 | 14 | /* 15 | #define DEBUG 1 16 | #define DMALLOC 1 17 | */ 18 | 19 | #include 20 | 21 | // updated to place in current directory 22 | #include 23 | // #include "../parmetis_svfsi_parmetis.h" 24 | 25 | #ifdef DMALLOC 26 | #include 27 | #endif 28 | 29 | #include 30 | #include 31 | #include 32 | #include 33 | #include 34 | 35 | -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/README: -------------------------------------------------------------------------------- 1 | This is ParMetis version 3.2.0. You can find the manual describing the 2 | various routines in the directory 'Manual'. Also, the file called 3 | INSTALL contains instructions on how to build and test ParMetis. 4 | 5 | 6 | Please let me know of any problems that you have found with it. 7 | 8 | George Karypis 9 | karypis@cs.umn.edu 10 | -------------------------------------------------------------------------------- /Code/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/VERSION: -------------------------------------------------------------------------------- 1 | ParMetis Version 3.2.0 Wed Apr 6 13:28:15 CDT 2011 2 | ParMetis Version 3.1.1 Mon Nov 17 16:41:47 CST 2008 3 | ParMetis Version 3.1.0 Fri Aug 15 13:59:41 CDT 2003 4 | ParMetis Version 3.0.0 Wed Mar 27 23:56:38 CST 2002 5 | ParMetis Version 2.0.0 Tue Sep 22 18:58:31 CDT 1998 6 | ParMetis Version 1.0.2 Wed Apr 15 13:14:50 CDT 1998 7 | 8 | -------------------------------------------------------------------------------- /Code/ThirdParty/tetgen/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | simvascular_third_party(tetgen) 2 | -------------------------------------------------------------------------------- /Code/ThirdParty/tetgen/Makefile: -------------------------------------------------------------------------------- 1 | # Hey emacs, this is a -*- makefile -*- 2 | 3 | # Copyright (c) 2015 Open Source Medical Software Corporation, 4 | # University of California, San Diego. 5 | # 6 | # All rights reserved. 7 | # 8 | # Permission is hereby granted, free of charge, to any person obtaining 9 | # a copy of this software and associated documentation files (the 10 | # "Software"), to deal in the Software without restriction, including 11 | # without limitation the rights to use, copy, modify, merge, publish, 12 | # distribute, sublicense, and/or sell copies of the Software, and to 13 | # permit persons to whom the Software is furnished to do so, subject 14 | # to the following conditions: 15 | # 16 | # The above copyright notice and this permission notice shall be included 17 | # in all copies or substantial portions of the Software. 18 | # 19 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 20 | # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 21 | # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 22 | # IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 23 | # CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 24 | # TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 25 | # SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 26 | 27 | TOP=../../../BuildWithMake 28 | 29 | include $(TOP)/include.mk 30 | 31 | TETGEN_SUBDIRS = simvascular_tetgen 32 | 33 | lib: createHeaderFile libsubdirs 34 | 35 | shared: 36 | 37 | libsubdirs: 38 | @for i in ${TETGEN_SUBDIRS}; do ( \ 39 | cd $$i; \ 40 | $(MAKE)) ; done 41 | 42 | clean: 43 | for i in ${TETGEN_SUBDIRS}; do ( \ 44 | cd $$i; \ 45 | $(MAKE) clean ) ; done 46 | 47 | veryclean: clean 48 | rm -f simvascular_tetgen.h 49 | for i in ${TETGEN_SUBDIRS}; do ( \ 50 | cd $$i; \ 51 | $(MAKE) veryclean ) ; done 52 | 53 | createHeaderFile: 54 | rm -f simvascular_tetgen.h 55 | @echo "#ifndef __simvascular_tetgen_h" > simvascular_tetgen.h 56 | @echo "#define __simvascular_tetgen_h" >> simvascular_tetgen.h 57 | @echo "#include " >> simvascular_tetgen.h 58 | @echo "#endif" >> simvascular_tetgen.h 59 | 60 | 61 | -------------------------------------------------------------------------------- /Code/ThirdParty/tetgen/simvascular_tetgen.h.in: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright (c) 2014-2015 The Regents of the University of California. 4 | * All Rights Reserved. 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining 7 | * a copy of this software and associated documentation files (the 8 | * "Software"), to deal in the Software without restriction, including 9 | * without limitation the rights to use, copy, modify, merge, publish, 10 | * distribute, sublicense, and/or sell copies of the Software, and to 11 | * permit persons to whom the Software is furnished to do so, subject 12 | * to the following conditions: 13 | * 14 | * The above copyright notice and this permission notice shall be included 15 | * in all copies or substantial portions of the Software. 16 | * 17 | * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS 18 | * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED 19 | * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 20 | * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER 21 | * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 22 | * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 23 | * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 24 | * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 25 | * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 26 | * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 27 | * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 28 | * 29 | *=========================================================================*/ 30 | 31 | #ifndef __simvascular_tetgen_h 32 | #define __simvascular_tetgen_h 33 | 34 | /* Use the tetgen library configured for SimVascular. */ 35 | #cmakedefine SV_USE_SYSTEM_TETGEN 36 | #ifdef SV_USE_SYSTEM_TETGEN 37 | #include 38 | #else 39 | #include 40 | #endif 41 | 42 | #endif 43 | -------------------------------------------------------------------------------- /Code/ThirdParty/tetgen/simvascular_tetgen/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # THIS FILE WAS EDITED BY Jameson Merkow (jmerkow@eng.ucsd.edu) to include install support - March 25 2011 2 | 3 | # Set the minimum required version of cmake for a project. 4 | cmake_minimum_required(VERSION 2.6) 5 | project(TETGEN) 6 | # message(STATUS "TETGEN_INSTALL_DIR: ${TETGEN_INSTALL_DIR}") 7 | # Add an executable to the project using the specified source files. 8 | ###SIMVASCULAR_CHANGE 9 | # add_executable(tetgen tetgen.cxx predicates.cxx) 10 | 11 | #Add a library to the project using the specified source files. 12 | # In Linux/Unix, it will creates the libtet.a 13 | ###SIMVASCULAR_CHANGE 14 | set(lib ${SV_LIB_THIRDPARTY_TETGEN_NAME}) 15 | if(SV_USE_THIRDPARTY_SHARED_LIBRARIES) 16 | add_library(${lib} SHARED tetgen.cxx predicates.cxx) 17 | else() 18 | add_library(${lib} STATIC tetgen.cxx predicates.cxx) 19 | endif() 20 | 21 | #Set properties on a target. 22 | #We use this here to set -DTETLIBRARY for when compiling the 23 | #library 24 | ###SIMVASCULAR_CHANGE 25 | set_target_properties(${lib} PROPERTIES "COMPILE_DEFINITIONS" TETLIBRARY) 26 | 27 | if(SV_INSTALL_LIBS) 28 | install(TARGETS ${lib} 29 | RUNTIME DESTINATION ${SV_INSTALL_RUNTIME_DIR} COMPONENT ThirdPartyExecutables 30 | LIBRARY DESTINATION ${SV_INSTALL_LIBRARY_DIR} COMPONENT ThirdPartyLibraries 31 | ARCHIVE DESTINATION ${SV_INSTALL_ARCHIVE_DIR} COMPONENT ThirdPartyLibraries 32 | ) 33 | endif() 34 | if(SV_INSTALL_HEADERS) 35 | install(FILES tetgen.h 36 | DESTINATION ${SV_INSTALL_INCLUDE_DIR}/thirdparty/tetgen COMPONENT ThirdPartyHeaders 37 | ) 38 | endif() 39 | -------------------------------------------------------------------------------- /Code/ThirdParty/tetgen/simvascular_tetgen/Makefile: -------------------------------------------------------------------------------- 1 | # Hey emacs, this is a -*- makefile -*- 2 | 3 | # Copyright (c) 2015 Open Source Medical Software Corporation, 4 | # University of California, San Diego. 5 | # 6 | # All rights reserved. 7 | # 8 | # Permission is hereby granted, free of charge, to any person obtaining 9 | # a copy of this software and associated documentation files (the 10 | # "Software"), to deal in the Software without restriction, including 11 | # without limitation the rights to use, copy, modify, merge, publish, 12 | # distribute, sublicense, and/or sell copies of the Software, and to 13 | # permit persons to whom the Software is furnished to do so, subject 14 | # to the following conditions: 15 | # 16 | # The above copyright notice and this permission notice shall be included 17 | # in all copies or substantial portions of the Software. 18 | # 19 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 20 | # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 21 | # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 22 | # IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 23 | # CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 24 | # TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 25 | # SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 26 | 27 | TOP=../../../../BuildWithMake 28 | 29 | include $(TOP)/include.mk 30 | 31 | CXXFLAGS = $(GLOBAL_CXXFLAGS) $(LOCAL_INCDIR) 32 | 33 | HDRS = tetgen.h 34 | 35 | CXXSRCS = predicates.cxx tetgen.cxx 36 | 37 | TARGET_LIB_NAME = $(SV_LIB_THIRDPARTY_TETGEN_NAME) 38 | 39 | include $(TOP)/targetlib.mk 40 | 41 | -------------------------------------------------------------------------------- /Code/ThirdParty/tetgen/simvascular_tetgen/README: -------------------------------------------------------------------------------- 1 | This is TetGen version 1.5.1 (released on March, 2013) 2 | 3 | Please see the documentation of TetGen for compiling and using TetGen. 4 | It is available at the following link: 5 | 6 | http://www.tetgen.org 7 | 8 | For more information on this product, contact : 9 | 10 | Hang Si 11 | Research Group of Numerical Mathematics and Scientific Computing 12 | Weierstrass Institute for Applied Analysis and Stochastics 13 | Mohrenstr. 39 14 | 10117 Berlin, Germany 15 | 16 | Phone: +49 (0) 30-20372-446 Fax: +49 (0) 30-2044975 17 | EMail: 18 | Web Site: http://www.wias-berlin.de/~si 19 | 20 | ------------------- IMPORTANCE NOTICE ----------------------------- 21 | 22 | BEFORE INTALLING OR USING TetGen(R) READ the 23 | GENERAL LICENSE TERMS AND CONDITIONS 24 | 25 | ------------------------------------------------------------------- 26 | -------------------------------------------------------------------------------- /Code/ThirdParty/tetgen/simvascular_tetgen/README.simvascular: -------------------------------------------------------------------------------- 1 | This contains tetgen 1.5.1 with few custom changes for use in simvascular. 2 | 3 | 4 | Chnaged Files 5 | ------------- 6 | CMakeList.txt 7 | -Install support was added. 8 | 9 | tetgen.cxx 10 | 11 | diff --git a/Code/ThirdParty/tetgen/simvascular_tetgen/tetgen.cxx b/Code/ThirdParty/tetgen/simvascular_tetgen/tetgen.cxx 12 | index d36f03b..90522c1 100644 13 | --- a/Code/ThirdParty/tetgen/simvascular_tetgen/tetgen.cxx 14 | +++ b/Code/ThirdParty/tetgen/simvascular_tetgen/tetgen.cxx 15 | 16 | @@ -29546,7 +29546,7 @@ void tetgenmesh::outsubfaces(tetgenio* out) 17 | int *elist = NULL; 18 | int *emlist = NULL; 19 | int index = 0, index1 = 0, index2 = 0; 20 | - triface abuttingtet; 21 | + triface abuttingtet, abuttingtet2; 22 | face faceloop; 23 | point torg, tdest, tapex; 24 | int marker = 0; 25 | @@ -29664,11 +29664,18 @@ void tetgenmesh::outsubfaces(tetgenio* out) 26 | neigh1 = -1; 27 | neigh2 = -1; 28 | stpivot(faceloop, abuttingtet); 29 | + 30 | if (abuttingtet.tet != NULL) { 31 | - neigh1 = elemindex(abuttingtet.tet); 32 | - fsymself(abuttingtet); 33 | if (!ishulltet(abuttingtet)) { 34 | - neigh2 = elemindex(abuttingtet.tet); 35 | + neigh1 = elemindex(abuttingtet.tet); 36 | + } 37 | + } 38 | + 39 | + fsym(abuttingtet, abuttingtet2); 40 | + 41 | + if (abuttingtet2.tet != NULL) { 42 | + if (!ishulltet(abuttingtet2)) { 43 | + neigh2 = elemindex(abuttingtet2.tet); 44 | } 45 | } 46 | } 47 | -------------------------------------------------------------------------------- /Code/ThirdParty/tetgen/simvascular_tetgen/example.poly: -------------------------------------------------------------------------------- 1 | 28 3 0 1 2 | 1 0 0 0 1 3 | 2 2 0 0 1 4 | 3 2 2 0 1 5 | 4 0 2 0 1 6 | 5 0 0 4 9 7 | 6 2 0 4 9 8 | 7 2 2 3 9 9 | 8 0 2 3 9 10 | 9 0 0 5 2 11 | 10 2 0 5 2 12 | 11 2 2 5 2 13 | 12 0 2 5 2 14 | 13 0.25 0.25 0.5 4 15 | 14 1.75 0.25 0.5 4 16 | 15 1.75 1.5 0.5 4 17 | 16 0.25 1.5 0.5 4 18 | 17 0.25 0.25 1 4 19 | 18 1.75 0.25 1 4 20 | 19 1.75 1.5 1 4 21 | 20 0.25 1.5 1 4 22 | 21 0.25 0 2 4 23 | 22 1.75 0 2 4 24 | 23 1.75 1.5 2 4 25 | 24 0.25 1.5 2 4 26 | 25 0.25 0 2.5 4 27 | 26 1.75 0 2.5 4 28 | 27 1.75 1.5 2.5 4 29 | 28 0.25 1.5 2.5 4 30 | 23 1 31 | 1 0 1 # 1 32 | 4 1 2 3 4 33 | 1 0 9 # 2 34 | 4 5 6 7 8 35 | 2 1 3 # 3 36 | 4 1 2 6 5 37 | 4 21 22 26 25 38 | 1 1 0 2.25 39 | 1 0 3 # 4 40 | 4 2 3 7 6 41 | 1 0 3 # 5 42 | 4 3 4 8 7 43 | 1 0 3 # 6 44 | 4 4 1 5 8 45 | 1 0 2 # 7 46 | 4 9 10 11 12 47 | 1 0 3 # 8 48 | 4 9 10 6 5 49 | 1 0 3 # 9 50 | 4 10 11 7 6 51 | 1 0 3 # 10 52 | 4 11 12 8 7 53 | 1 0 3 # 11 54 | 4 12 9 5 8 55 | 1 0 4 # 12 56 | 4 13 14 15 16 57 | 1 0 4 # 13 58 | 4 17 18 19 20 59 | 1 0 4 # 14 60 | 4 13 14 18 17 61 | 1 0 4 # 15 62 | 4 14 15 19 18 63 | 1 0 4 # 16 64 | 4 15 16 20 19 65 | 1 0 4 # 17 66 | 4 16 13 17 20 67 | 1 0 4 # 18 68 | 4 21 22 23 24 69 | 1 0 4 # 19 70 | 4 25 26 27 28 71 | 1 0 4 # 20 72 | 4 21 22 26 25 73 | 1 0 4 # 21 74 | 4 22 23 27 26 75 | 1 0 4 # 22 76 | 4 23 24 28 27 77 | 1 0 4 # 23 78 | 4 24 21 25 28 79 | 2 80 | 1 1 0.4 2.25 81 | 2 1 0.4 0.75 82 | 2 83 | 1 1 0.25 0.1 10 0.001 84 | 2 1 0.5 4 20 0.01 85 | -------------------------------------------------------------------------------- /Code/ThirdParty/tetgen/simvascular_tetgen/makefile.tetgen.org: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # # 3 | # makefile for TetGen # 4 | # # 5 | # Type "make" to compile TetGen into an executable program (tetgen). # 6 | # Type "make tetlib" to compile TetGen into a library (libtet.a). # 7 | # Type "make distclean" to delete all object (*.o) files. # 8 | # # 9 | ############################################################################### 10 | 11 | # CXX should be set to the name of your favorite C++ compiler. 12 | # =========================================================== 13 | 14 | CXX = g++ 15 | #CXX = icpc 16 | #CXX = CC 17 | 18 | # CXXFLAGS is the level of optimiztion, default is -O. One should try 19 | # -O2, -O3 ... to find the best optimization level. 20 | # =================================================================== 21 | 22 | CXXFLAGS = -O3 23 | 24 | # PREDCXXFLAGS is for compiling J. Shewchuk's predicates. 25 | 26 | PREDCXXFLAGS = -O0 27 | 28 | # SWITCHES is a list of switches to compile TetGen. 29 | # ================================================= 30 | # 31 | # By default, TetGen uses double precision floating point numbers. If you 32 | # prefer single precision, use the -DSINGLE switch. 33 | # 34 | # The source code of TetGen includes a lot of assertions, which are mainly 35 | # used for catching bugs at that places. These assertions somewhat slow 36 | # down the speed of TetGen. They can be skipped by define the -DNDEBUG 37 | # switch. 38 | 39 | SWITCHES = 40 | 41 | # RM should be set to the name of your favorite rm (file deletion program). 42 | 43 | RM = /bin/rm 44 | 45 | # The action starts here. 46 | 47 | tetgen: tetgen.cxx predicates.o 48 | $(CXX) $(CXXFLAGS) $(SWITCHES) -o tetgen tetgen.cxx predicates.o -lm 49 | 50 | tetlib: tetgen.cxx predicates.o 51 | $(CXX) $(CXXFLAGS) $(SWITCHES) -DTETLIBRARY -c tetgen.cxx 52 | ar r libtet.a tetgen.o predicates.o 53 | 54 | predicates.o: predicates.cxx 55 | $(CXX) $(PREDCXXFLAGS) -c predicates.cxx 56 | 57 | clean: 58 | $(RM) *.o *.a tetgen *~ 59 | 60 | 61 | 62 | 63 | -------------------------------------------------------------------------------- /Code/ThirdParty/zlib/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | #simvascular_third_party(zlib) 2 | -------------------------------------------------------------------------------- /Code/ThirdParty/zlib/Makefile: -------------------------------------------------------------------------------- 1 | # Hey emacs, this is a -*- makefile -*- 2 | 3 | # Copyright (c) 2015 Open Source Medical Software Corporation, 4 | # University of California, San Diego. 5 | # 6 | # All rights reserved. 7 | # 8 | # Permission is hereby granted, free of charge, to any person obtaining 9 | # a copy of this software and associated documentation files (the 10 | # "Software"), to deal in the Software without restriction, including 11 | # without limitation the rights to use, copy, modify, merge, publish, 12 | # distribute, sublicense, and/or sell copies of the Software, and to 13 | # permit persons to whom the Software is furnished to do so, subject 14 | # to the following conditions: 15 | # 16 | # The above copyright notice and this permission notice shall be included 17 | # in all copies or substantial portions of the Software. 18 | # 19 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 20 | # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 21 | # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 22 | # IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 23 | # CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 24 | # TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 25 | # SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 26 | 27 | TOP=../../../BuildWithMake 28 | 29 | include $(TOP)/include.mk 30 | 31 | ZLIB_SUBDIRS = simvascular_zlib 32 | 33 | lib: createHeaderFile libsubdirs 34 | 35 | shared: 36 | 37 | libsubdirs: 38 | @for i in ${ZLIB_SUBDIRS}; do ( \ 39 | cd $$i; \ 40 | $(MAKE)) ; done 41 | 42 | clean: 43 | for i in ${ZLIB_SUBDIRS}; do ( \ 44 | cd $$i; \ 45 | $(MAKE) clean ) ; done 46 | 47 | veryclean: clean 48 | rm -f simvascular_zlib.h 49 | for i in ${ZLIB_SUBDIRS}; do ( \ 50 | cd $$i; \ 51 | $(MAKE) veryclean ) ; done 52 | 53 | createHeaderFile: 54 | rm -f simvascular_zlib.h 55 | @echo "#ifndef __simvascular_zlib_h" > simvascular_zlib.h 56 | @echo "#define __simvascular_zlib_h" >> simvascular_zlib.h 57 | @echo "#include " >> simvascular_zlib.h 58 | @echo "#endif" >> simvascular_zlib.h 59 | 60 | 61 | -------------------------------------------------------------------------------- /Code/ThirdParty/zlib/simvascular_zlib.h.in: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright (c) 2014-2015 The Regents of the University of California. 4 | * All Rights Reserved. 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining 7 | * a copy of this software and associated documentation files (the 8 | * "Software"), to deal in the Software without restriction, including 9 | * without limitation the rights to use, copy, modify, merge, publish, 10 | * distribute, sublicense, and/or sell copies of the Software, and to 11 | * permit persons to whom the Software is furnished to do so, subject 12 | * to the following conditions: 13 | * 14 | * The above copyright notice and this permission notice shall be included 15 | * in all copies or substantial portions of the Software. 16 | * 17 | * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS 18 | * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED 19 | * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 20 | * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER 21 | * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 22 | * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 23 | * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 24 | * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 25 | * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 26 | * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 27 | * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 28 | * 29 | *=========================================================================*/ 30 | 31 | #ifndef __simvascular_zlib_h 32 | #define __simvascular_zlib_h 33 | 34 | /* Use the zlib library configured for SimVascular. */ 35 | #cmakedefine SV_USE_SYSTEM_ZLIB 36 | #ifdef SV_USE_SYSTEM_ZLIB 37 | # include 38 | #else 39 | # include 40 | #endif 41 | 42 | #endif 43 | -------------------------------------------------------------------------------- /Code/ThirdParty/zlib/simvascular_zlib/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | project(SimVascularZLIB) 2 | 3 | include_directories(BEFORE ${SimVascularZLIB_SOURCE_DIR}) 4 | 5 | # source files for zlib 6 | set(SRCS 7 | adler32.c compress.c crc32.c deflate.c gzio.c inffast.c 8 | inflate.c inftrees.c trees.c uncompr.c zutil.c 9 | ) 10 | set(HDRS crc32.h deflate.h inffast.h inffixed.h inflate.h inftrees.h 11 | trees.h zconf.h zlib.h zutil.h) 12 | 13 | if(WIN32) 14 | if(BUILD_SHARED_LIBS) 15 | set(ZLIB_DLL 1) 16 | endif(BUILD_SHARED_LIBS) 17 | endif(WIN32) 18 | 19 | set(lib ${SV_LIB_THIRDPARTY_ZLIB_NAME}) 20 | if(SV_USE_THIRDPARTY_SHARED_LIBRARIES) 21 | add_library(${lib} SHARED ${SRCS}) 22 | else() 23 | add_library(${lib} STATIC ${SRCS}) 24 | endif() 25 | 26 | if(SV_INSTALL_LIBS) 27 | install(TARGETS ${lib} 28 | RUNTIME DESTINATION ${SV_INSTALL_RUNTIME_DIR} COMPONENT ThirdPartyExecutables 29 | LIBRARY DESTINATION ${SV_INSTALL_LIBRARY_DIR} COMPONENT ThirdPartyLibraries 30 | ARCHIVE DESTINATION ${SV_INSTALL_ARCHIVE_DIR} COMPONENT ThirdPartyLibraries 31 | ) 32 | endif() 33 | if(SV_INSTALL_HEADERS) 34 | install(FILES ${HDRS} 35 | DESTINATION ${SV_INSTALL_INCLUDE_DIR}/thirdparty/zlib COMPONENT ThirdPartyHeaders 36 | ) 37 | endif() 38 | -------------------------------------------------------------------------------- /Code/ThirdParty/zlib/simvascular_zlib/Makefile: -------------------------------------------------------------------------------- 1 | # Hey emacs, this is a -*- makefile -*- 2 | 3 | # Copyright (c) 2015 Open Source Medical Software Corporation, 4 | # University of California, San Diego. 5 | # 6 | # All rights reserved. 7 | # 8 | # Permission is hereby granted, free of charge, to any person obtaining 9 | # a copy of this software and associated documentation files (the 10 | # "Software"), to deal in the Software without restriction, including 11 | # without limitation the rights to use, copy, modify, merge, publish, 12 | # distribute, sublicense, and/or sell copies of the Software, and to 13 | # permit persons to whom the Software is furnished to do so, subject 14 | # to the following conditions: 15 | # 16 | # The above copyright notice and this permission notice shall be included 17 | # in all copies or substantial portions of the Software. 18 | # 19 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 20 | # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 21 | # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 22 | # IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 23 | # CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 24 | # TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 25 | # SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 26 | 27 | TOP=../../../../BuildWithMake 28 | 29 | include $(TOP)/include.mk 30 | 31 | CCFLAGS = $(GLOBAL_CCFLAGS) 32 | 33 | HDRS = crc32.h deflate.h inffast.h inflate.h inftrees.h \ 34 | trees.h zlib.h zutil.h 35 | 36 | CSRCS = adler32.c compress.c crc32.c deflate.c gzio.c inffast.c \ 37 | inflate.c inftrees.c trees.c uncompr.c zutil.c 38 | 39 | TARGET_LIB_NAME = simvascular_thirdparty_zlib 40 | 41 | include $(TOP)/targetlib.mk 42 | 43 | 44 | -------------------------------------------------------------------------------- /Code/ThirdParty/zlib/simvascular_zlib/READ.simvascular: -------------------------------------------------------------------------------- 1 | This directory contains a subset of the zlib library (1.2.3) and 2 | some custom changes. 3 | 4 | We only include enough of the distribution to provide the functionalities 5 | required. 6 | 7 | We would like to thank the zlib team for distributing this library. 8 | http://www.zlib.net 9 | 10 | Added Files 11 | ----------- 12 | 13 | CMakeLists.txt 14 | -Support building with CMake. 15 | 16 | zlib.def 17 | -For MS Windows only: used to explicitly list the exports from dll builds. 18 | 19 | simvascular_zlib_mangle.h 20 | -Mangles symbols exported from the zlib library for use by simvascular. 21 | 22 | 23 | Changed Files 24 | ------------- 25 | You can search the code for "KITWARE_ZLIB_CHANGE" to find modifications 26 | vs the original zlib code 27 | 28 | zconf.h 29 | -Include simvascular_zlib_mangle.h (at the top) 30 | -Changed an #if 0 to #ifdef HAVE_UNISTD_H (near middle) 31 | -Suppress selected compiler warnings (at the bottom) -------------------------------------------------------------------------------- /Code/ThirdParty/zlib/simvascular_zlib/compress.c: -------------------------------------------------------------------------------- 1 | /* compress.c -- compress a memory buffer 2 | * Copyright (C) 1995-2003 Jean-loup Gailly. 3 | * For conditions of distribution and use, see copyright notice in zlib.h 4 | */ 5 | 6 | /* @(#) $Id$ */ 7 | 8 | #define ZLIB_INTERNAL 9 | #include "zlib.h" 10 | 11 | /* =========================================================================== 12 | Compresses the source buffer into the destination buffer. The level 13 | parameter has the same meaning as in deflateInit. sourceLen is the byte 14 | length of the source buffer. Upon entry, destLen is the total size of the 15 | destination buffer, which must be at least 0.1% larger than sourceLen plus 16 | 12 bytes. Upon exit, destLen is the actual size of the compressed buffer. 17 | 18 | compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough 19 | memory, Z_BUF_ERROR if there was not enough room in the output buffer, 20 | Z_STREAM_ERROR if the level parameter is invalid. 21 | */ 22 | int ZEXPORT compress2 (dest, destLen, source, sourceLen, level) 23 | Bytef *dest; 24 | uLongf *destLen; 25 | const Bytef *source; 26 | uLong sourceLen; 27 | int level; 28 | { 29 | z_stream stream; 30 | int err; 31 | 32 | stream.next_in = (Bytef*)source; 33 | stream.avail_in = (uInt)sourceLen; 34 | #ifdef MAXSEG_64K 35 | /* Check for source > 64K on 16-bit machine: */ 36 | if ((uLong)stream.avail_in != sourceLen) return Z_BUF_ERROR; 37 | #endif 38 | stream.next_out = dest; 39 | stream.avail_out = (uInt)*destLen; 40 | if ((uLong)stream.avail_out != *destLen) return Z_BUF_ERROR; 41 | 42 | stream.zalloc = (alloc_func)0; 43 | stream.zfree = (free_func)0; 44 | stream.opaque = (voidpf)0; 45 | 46 | err = deflateInit(&stream, level); 47 | if (err != Z_OK) return err; 48 | 49 | err = deflate(&stream, Z_FINISH); 50 | if (err != Z_STREAM_END) { 51 | deflateEnd(&stream); 52 | return err == Z_OK ? Z_BUF_ERROR : err; 53 | } 54 | *destLen = stream.total_out; 55 | 56 | err = deflateEnd(&stream); 57 | return err; 58 | } 59 | 60 | /* =========================================================================== 61 | */ 62 | int ZEXPORT compress (dest, destLen, source, sourceLen) 63 | Bytef *dest; 64 | uLongf *destLen; 65 | const Bytef *source; 66 | uLong sourceLen; 67 | { 68 | return compress2(dest, destLen, source, sourceLen, Z_DEFAULT_COMPRESSION); 69 | } 70 | 71 | /* =========================================================================== 72 | If the default memLevel or windowBits for deflateInit() is changed, then 73 | this function needs to be updated. 74 | */ 75 | uLong ZEXPORT compressBound (sourceLen) 76 | uLong sourceLen; 77 | { 78 | return sourceLen + (sourceLen >> 12) + (sourceLen >> 14) + 11; 79 | } 80 | -------------------------------------------------------------------------------- /Code/ThirdParty/zlib/simvascular_zlib/inffast.h: -------------------------------------------------------------------------------- 1 | /* inffast.h -- header to use inffast.c 2 | * Copyright (C) 1995-2003 Mark Adler 3 | * For conditions of distribution and use, see copyright notice in zlib.h 4 | */ 5 | 6 | /* WARNING: this file should *not* be used by applications. It is 7 | part of the implementation of the compression library and is 8 | subject to change. Applications should only use zlib.h. 9 | */ 10 | 11 | void inflate_fast OF((z_streamp strm, unsigned start)); 12 | -------------------------------------------------------------------------------- /Code/ThirdParty/zlib/simvascular_zlib/inftrees.h: -------------------------------------------------------------------------------- 1 | /* inftrees.h -- header to use inftrees.c 2 | * Copyright (C) 1995-2005 Mark Adler 3 | * For conditions of distribution and use, see copyright notice in zlib.h 4 | */ 5 | 6 | /* WARNING: this file should *not* be used by applications. It is 7 | part of the implementation of the compression library and is 8 | subject to change. Applications should only use zlib.h. 9 | */ 10 | 11 | /* Structure for decoding tables. Each entry provides either the 12 | information needed to do the operation requested by the code that 13 | indexed that table entry, or it provides a pointer to another 14 | table that indexes more bits of the code. op indicates whether 15 | the entry is a pointer to another table, a literal, a length or 16 | distance, an end-of-block, or an invalid code. For a table 17 | pointer, the low four bits of op is the number of index bits of 18 | that table. For a length or distance, the low four bits of op 19 | is the number of extra bits to get after the code. bits is 20 | the number of bits in this code or part of the code to drop off 21 | of the bit buffer. val is the actual byte to output in the case 22 | of a literal, the base length or distance, or the offset from 23 | the current table to the next table. Each entry is four bytes. */ 24 | typedef struct { 25 | unsigned char op; /* operation, extra bits, table bits */ 26 | unsigned char bits; /* bits in this part of the code */ 27 | unsigned short val; /* offset in table or code value */ 28 | } code; 29 | 30 | /* op values as set by inflate_table(): 31 | 00000000 - literal 32 | 0000tttt - table link, tttt != 0 is the number of table index bits 33 | 0001eeee - length or distance, eeee is the number of extra bits 34 | 01100000 - end of block 35 | 01000000 - invalid code 36 | */ 37 | 38 | /* Maximum size of dynamic tree. The maximum found in a long but non- 39 | exhaustive search was 1444 code structures (852 for length/literals 40 | and 592 for distances, the latter actually the result of an 41 | exhaustive search). The true maximum is not known, but the value 42 | below is more than safe. */ 43 | #define ENOUGH 2048 44 | #define MAXD 592 45 | 46 | /* Type of code to build for inftable() */ 47 | typedef enum { 48 | CODES, 49 | LENS, 50 | DISTS 51 | } codetype; 52 | 53 | extern int inflate_table OF((codetype type, unsigned short FAR *lens, 54 | unsigned codes, code FAR * FAR *table, 55 | unsigned FAR *bits, unsigned short FAR *work)); 56 | -------------------------------------------------------------------------------- /Code/ThirdParty/zlib/simvascular_zlib/uncompr.c: -------------------------------------------------------------------------------- 1 | /* uncompr.c -- decompress a memory buffer 2 | * Copyright (C) 1995-2003 Jean-loup Gailly. 3 | * For conditions of distribution and use, see copyright notice in zlib.h 4 | */ 5 | 6 | /* @(#) $Id$ */ 7 | 8 | #define ZLIB_INTERNAL 9 | #include "zlib.h" 10 | 11 | /* =========================================================================== 12 | Decompresses the source buffer into the destination buffer. sourceLen is 13 | the byte length of the source buffer. Upon entry, destLen is the total 14 | size of the destination buffer, which must be large enough to hold the 15 | entire uncompressed data. (The size of the uncompressed data must have 16 | been saved previously by the compressor and transmitted to the decompressor 17 | by some mechanism outside the scope of this compression library.) 18 | Upon exit, destLen is the actual size of the compressed buffer. 19 | This function can be used to decompress a whole file at once if the 20 | input file is mmap'ed. 21 | 22 | uncompress returns Z_OK if success, Z_MEM_ERROR if there was not 23 | enough memory, Z_BUF_ERROR if there was not enough room in the output 24 | buffer, or Z_DATA_ERROR if the input data was corrupted. 25 | */ 26 | int ZEXPORT uncompress (dest, destLen, source, sourceLen) 27 | Bytef *dest; 28 | uLongf *destLen; 29 | const Bytef *source; 30 | uLong sourceLen; 31 | { 32 | z_stream stream; 33 | int err; 34 | 35 | stream.next_in = (Bytef*)source; 36 | stream.avail_in = (uInt)sourceLen; 37 | /* Check for source > 64K on 16-bit machine: */ 38 | if ((uLong)stream.avail_in != sourceLen) return Z_BUF_ERROR; 39 | 40 | stream.next_out = dest; 41 | stream.avail_out = (uInt)*destLen; 42 | if ((uLong)stream.avail_out != *destLen) return Z_BUF_ERROR; 43 | 44 | stream.zalloc = (alloc_func)0; 45 | stream.zfree = (free_func)0; 46 | 47 | err = inflateInit(&stream); 48 | if (err != Z_OK) return err; 49 | 50 | err = inflate(&stream, Z_FINISH); 51 | if (err != Z_STREAM_END) { 52 | inflateEnd(&stream); 53 | if (err == Z_NEED_DICT || (err == Z_BUF_ERROR && stream.avail_in == 0)) 54 | return Z_DATA_ERROR; 55 | return err; 56 | } 57 | *destLen = stream.total_out; 58 | 59 | err = inflateEnd(&stream); 60 | return err; 61 | } 62 | -------------------------------------------------------------------------------- /Code/ThirdParty/zlib/simvascular_zlib/zlib.def: -------------------------------------------------------------------------------- 1 | LIBRARY 2 | ; zlib data compression library 3 | 4 | EXPORTS 5 | ; basic functions 6 | zlibVersion 7 | deflate 8 | deflateEnd 9 | inflate 10 | inflateEnd 11 | ; advanced functions 12 | deflateSetDictionary 13 | deflateCopy 14 | deflateReset 15 | deflateParams 16 | deflateBound 17 | deflatePrime 18 | inflateSetDictionary 19 | inflateSync 20 | inflateCopy 21 | inflateReset 22 | inflateBack 23 | inflateBackEnd 24 | zlibCompileFlags 25 | ; utility functions 26 | compress 27 | compress2 28 | compressBound 29 | uncompress 30 | gzopen 31 | gzdopen 32 | gzsetparams 33 | gzread 34 | gzwrite 35 | gzprintf 36 | gzputs 37 | gzgets 38 | gzputc 39 | gzgetc 40 | gzungetc 41 | gzflush 42 | gzseek 43 | gzrewind 44 | gztell 45 | gzeof 46 | gzclose 47 | gzerror 48 | gzclearerr 49 | ; checksum functions 50 | adler32 51 | crc32 52 | ; various hacks, don't look :) 53 | deflateInit_ 54 | deflateInit2_ 55 | inflateInit_ 56 | inflateInit2_ 57 | inflateBackInit_ 58 | inflateSyncPoint 59 | get_crc_table 60 | zError 61 | -------------------------------------------------------------------------------- /Code/ThirdParty/zlib/simvascular_zlib/ztest2978.c: -------------------------------------------------------------------------------- 1 | #include 2 | int main() { return 0; } 3 | -------------------------------------------------------------------------------- /Distribution/OSX/Info.plist.in: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | CFBundleDevelopmentRegion 6 | en 7 | CFBundleExecutable 8 | SimVascular 9 | CFBundleGetInfoString 10 | @SV_FULL_VERSION@, Copyright (C) 2014 11 | CFBundleIdentifier 12 | org.simvascular.simvascular 13 | CFBundleInfoDictionaryVersion 14 | 6.0 15 | CFBundlePackageType 16 | APPL 17 | CFBundleShortVersionString 18 | @SV_FULL_VERSION@ 19 | CFBundleSignature 20 | simvascular 21 | CFBundleVersion 22 | @SV_FULL_VERSION@ 23 | CFBundleIconFile 24 | SimVascular.icns 25 | LSMinimumSystemVersion 26 | 10.5 27 | 28 | 29 | -------------------------------------------------------------------------------- /Distribution/OSX/cpmview.icns: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Distribution/OSX/cpmview.icns -------------------------------------------------------------------------------- /Distribution/OSX/simvascular.icns: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Distribution/OSX/simvascular.icns -------------------------------------------------------------------------------- /Distribution/OSX/simvascular.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -f 2 | #/bin/tcsh -f 3 | # limit stacksize unlimited 4 | 5 | if [ "$BASH_SOURCE" == "$0" ];then 6 | BUNDLE=`echo "$0" | sed -e 's/\/Contents\/MacOS\/.*//'` 7 | else 8 | BUNDLE=`echo "$BASH_SOURCE" | sed -e 's/\/Contents\/MacOS\/.*//'` 9 | fi 10 | 11 | RESOURCES=$BUNDLE/Contents/Resources 12 | 13 | echo "BUNDLE: $BUNDLE" 14 | echo "RESOURCES: $RESOURCES" 15 | 16 | sh $RESOURCES/simvascular -------------------------------------------------------------------------------- /Distribution/OSX/simvascular.sh.in: -------------------------------------------------------------------------------- 1 | #!/bin/bash -f 2 | #/bin/tcsh -f 3 | # limit stacksize unlimited 4 | 5 | export SOFTWARE_PLATFORM=@CLUSTER@ 6 | export COMPILER_VERSION=@COMPILER_VERSION@ 7 | export OPEN_SOFTWARE_BINARIES_TOPLEVEL=@OpenLibs_Bin_Directory@ 8 | export LICENSED_SOFTWARE_TOPLEVEL=@LicensedLibs_Bin_Directory@ 9 | export SV_HOME=@SimVascular_HOME@ 10 | export LES_LICENSE_SERVER= 11 | 12 | ############################################################ 13 | # YOU SHOULDN'T NEED TO CHANGE ANYTHING BELOW THIS LINE!! # 14 | ############################################################ 15 | 16 | # 3-D solver environment variables 17 | export FLOWSOLVER_CONFIG=@FLOWSOLVER_CONFIG@/ 18 | 19 | # simvascular addition 20 | export LD_LIBRARY_PATH=$SV_HOME/Lib:$LD_LIBRARY_PATH 21 | 22 | # MPICH2 additions 23 | export LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH 24 | 25 | # intel compiler additions 26 | export LD_LIBRARY_PATH=@INTELRUNTIME_LIB_DIR@:$LD_LIBRARY_PATH 27 | 28 | @OUTBIN_DIR@/@FLOWSOLVER_EXE@ $* 29 | # run the executable 30 | case "$SV_BATCH_MODE" in 31 | "1") 32 | case "$*" in 33 | "") 34 | @OUTBIN_DIR@/@SV_EXE@ 35 | ;; 36 | *) 37 | @OUTBIN_DIR@/@SV_EXE@ $* 38 | ;; 39 | esac 40 | ;; 41 | *) 42 | @GDB@ @GDB_FLAGS@ @OUTBIN_DIR@/@SV_EXE@ @SimVascular_HOME@/Tcl/SimVascular_2.0/simvascular_startup.tcl $* 43 | ;; 44 | -------------------------------------------------------------------------------- /Distribution/license.txt: -------------------------------------------------------------------------------- 1 | # Copyright (c) Stanford University, The Regents of the University of 2 | # California, and others. 3 | # 4 | # All Rights Reserved. 5 | # 6 | # See Copyright-SimVascular.txt for additional details. 7 | # 8 | # Permission is hereby granted, free of charge, to any person obtaining 9 | # a copy of this software and associated documentation files (the 10 | # "Software"), to deal in the Software without restriction, including 11 | # without limitation the rights to use, copy, modify, merge, publish, 12 | # distribute, sublicense, and/or sell copies of the Software, and to 13 | # permit persons to whom the Software is furnished to do so, subject 14 | # to the following conditions: 15 | # 16 | # The above copyright notice and this permission notice shall be included 17 | # in all copies or substantial portions of the Software. 18 | # 19 | # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS 20 | # IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED 21 | # TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 22 | # PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER 23 | # OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 24 | # EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 25 | # PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 26 | # PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 27 | # LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 28 | # NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 29 | # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 30 | -------------------------------------------------------------------------------- /Distribution/windows/msi-banner.bmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Distribution/windows/msi-banner.bmp -------------------------------------------------------------------------------- /Distribution/windows/msi-banner.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Distribution/windows/msi-banner.jpg -------------------------------------------------------------------------------- /Distribution/windows/msi-dialog.bmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Distribution/windows/msi-dialog.bmp -------------------------------------------------------------------------------- /Distribution/windows/msi-dialog.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Distribution/windows/msi-dialog.jpg -------------------------------------------------------------------------------- /Distribution/windows/registry-patch-notargets.xml.in: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | @FRAGMENT_INJECTION_STRING@ 10 | 11 | 12 | -------------------------------------------------------------------------------- /Distribution/windows/registry-patch.xml.in: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | @FRAGMENT_INJECTION_STRING@ 10 | 11 | 12 | -------------------------------------------------------------------------------- /Distribution/windows/simvascular.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimVascular/svFSI/7bdb74cdd517310d6bf32c0bb7d42072aeac8658/Distribution/windows/simvascular.ico -------------------------------------------------------------------------------- /Docker/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM ubuntu:18.04 2 | 3 | ENV DEBIAN_FRONTEND=noninteractive 4 | 5 | # Install supporting packages 6 | RUN apt-get update 7 | RUN apt-get install -yq --no-install-recommends apt-utils 8 | RUN apt-get install -yq git make cmake 9 | RUN apt-get install -yq libblas-dev liblapack-dev 10 | RUN apt-get install -yq gcc g++ gfortran 11 | RUN apt-get install -yq openmpi-bin libopenmpi-dev 12 | 13 | # Create directory 14 | RUN mkdir -p /home/test 15 | 16 | # Add non-root user and set up home directory 17 | RUN useradd testuser -u 1000 -g 100 -m -s /bin/bash 18 | RUN chown testuser /home/test 19 | USER testuser 20 | WORKDIR /home/test 21 | 22 | # Obtain source code 23 | RUN git clone https://github.com/SimVascular/svFSI 24 | 25 | # Compile svFSI source code 26 | RUN mkdir Build && \ 27 | cd Build && \ 28 | cmake ../svFSI && \ 29 | make 30 | 31 | ENV PATH=$PATH:/home/test/Build/svFSI-build/bin 32 | -------------------------------------------------------------------------------- /Docker/README.md: -------------------------------------------------------------------------------- 1 | # Docker-svFSI 2 | This Dockerfile will build [`svFSI`](https://github.com/SimVascular/svFSI) executable from the most recent source code in the main repository. This procedure has been successfully tested on MacOS Big Sur, Ubuntu 18.04 and Windows 10 with WSL 2. Assuming you already have [Docker](https://docs.docker.com/get-docker/) installed, please follow the steps below to run `svFSI`. 3 | 4 | 1. Build Docker image. In the current directory (Path_to_svFSI/Docker), run the following command. 5 | 6 | ```bash 7 | docker build -t svfsi-image . 8 | ``` 9 | 10 | This may take a while. Afterwards, run the command `docker images`, and you should see `svfsi-image`. 11 | 12 | 3. Download the examples. 13 | 14 | ```bash 15 | git clone https://github.com/SimVascular/svFSI-Tests 16 | ``` 17 | 18 | 4. Run the container in interactive mode. 19 | 20 | ```bash 21 | docker container run --cap-add=SYS_PTRACE -v "$PWD"/svFSI-Tests:/home/test/svFSI-Tests -it --rm --name svfsi-demo svfsi-image 22 | ``` 23 | 24 | This will open a shell prompt and you can proceed as usual. Here, `--cap-add=SYS_PTRACE` fixes a known [issue](https://github.com/open-mpi/ompi/issues/4948) of running openmpi in Docker. 25 | 26 | 5. Let's take `04-fluid/06-channel-flow-2D` for example. In the shell prompt, run the following commands to generate the simulation results. 27 | 28 | ```bash 29 | cd svFSI-Tests/04-fluid/06-channel-flow-2D && \ 30 | mpiexec -n 4 svFSI ./svFSI_Taylor-Hood.inp 31 | ``` 32 | 33 | The results will be stored in `4-procs` in vtu format, and can be viewed with [Paraview](https://www.paraview.org). 34 | 35 | 6. After all tests are done, execute the following commands to exit the docker and delete the image. 36 | 37 | ```bash 38 | exit && \ 39 | docker rmi 40 | ``` 41 | 42 | 43 | 44 | ### Known Issues 45 | 46 | `svFSI` built with this Dockerfile won't work with any example that requires Trilinos. Trilinos takes too long to build within the Docker image, and we encourage any user that needs it to build `svFSI` from source. Please report any other issue through the GitHub page. -------------------------------------------------------------------------------- /Externals/BuildHelpers/CompileScripts/compile-cmake-vtk-generic.sh: -------------------------------------------------------------------------------- 1 | # 2 | # vtk 3 | # 4 | 5 | REPLACEME_SV_SPECIAL_COMPILER_SCRIPT 6 | 7 | export CC=REPLACEME_CC 8 | export CXX=REPLACEME_CXX 9 | 10 | rm -Rf REPLACEME_SV_TOP_BIN_DIR_VTK 11 | mkdir -p REPLACEME_SV_TOP_BIN_DIR_VTK 12 | chmod u+w,a+rx REPLACEME_SV_TOP_BIN_DIR_VTK 13 | 14 | rm -Rf REPLACEME_SV_TOP_BLD_DIR_VTK 15 | mkdir -p REPLACEME_SV_TOP_BLD_DIR_VTK 16 | cd REPLACEME_SV_TOP_BLD_DIR_VTK 17 | 18 | REPLACEME_SV_CMAKE_CMD -G REPLACEME_SV_CMAKE_GENERATOR \ 19 | -DCMAKE_INSTALL_PREFIX=REPLACEME_SV_TOP_BIN_DIR_VTK \ 20 | -DCMAKE_BUILD_TYPE=REPLACEME_SV_CMAKE_BUILD_TYPE \ 21 | -DBUILD_EXAMPLES=0 \ 22 | -DBUILD_SHARED_LIBS=0 \ 23 | -DVTK_Group_Imaging=0 \ 24 | -DVTK_Group_Qt=0 \ 25 | -DVTK_Group_Tk=0 \ 26 | -DVTK_Group_Rendering=0 \ 27 | -DVTK_WRAP_PYTHON=0 \ 28 | -DVTK_WRAP_TCL=0 \ 29 | -DVTK_QT_VERSION=5 \ 30 | -DModule_vtkTestingRendering=0 \ 31 | -DTCL_INCLUDE_PATH=REPLACEME_SV_TOP_BIN_DIR_TCL/include \ 32 | -DTCL_LIBRARY=REPLACEME_SV_TOP_BIN_DIR_TCL/lib/REPLACEME_SV_TCL_LIB_NAME \ 33 | -DTCL_TCLSH=REPLACEME_SV_TOP_BIN_DIR_TCL/bin/REPLACEME_SV_TCLSH_EXECUTABLE \ 34 | -DTK_INCLUDE_PATH=REPLACEME_SV_TOP_BIN_DIR_TK/include \ 35 | -DTK_LIBRARY=REPLACEME_SV_TOP_BIN_DIR_TK/lib/REPLACEME_SV_TK_LIB_NAME \ 36 | -DTK_WISH=REPLACEME_SV_TOP_BIN_DIR_TK/bin/REPLACEME_SV_WISH_EXECUTABLE \ 37 | -DTK_XLIB_PATH=REPLACEME_SV_TOP_BIN_DIR_TK/include \ 38 | REPLACEME_SV_TOP_SRC_DIR_VTK 39 | 40 | REPLACEME_SV_MAKE_CMD REPLACEME_SV_VTK_MAKE_FILENAME REPLACEME_SV_MAKE_BUILD_PARAMETERS 41 | 42 | REPLACEME_SV_MAKE_CMD REPLACEME_SV_VTK_MAKE_FILENAME REPLACEME_SV_MAKE_INSTALL_PARAMETERS 43 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/CompileScripts/compile-make-tcl-generic.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -f 2 | 3 | REPLACEME_SV_SPECIAL_COMPILER_SCRIPT 4 | 5 | export CC=REPLACEME_CC 6 | export CXX=REPLACEME_CXX 7 | 8 | CompileScripts/tcl-REPLACEME_SV_PLATFORM-generic.sh REPLACEME_SV_TCL_VERSION REPLACEME_SV_COMPILER_BIN_DIR 9 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/CompileScripts/tcl-linux-generic.sh: -------------------------------------------------------------------------------- 1 | #/bin/bash -f 2 | 3 | # Copyright (c) 2015 Open Source Medical Software Corporation. 4 | # All Rights Reserved. 5 | 6 | REPLACEME_SV_SPECIAL_COMPILER_SCRIPT 7 | 8 | export CC=gcc 9 | 10 | rm -Rf REPLACEME_SV_TOP_BIN_DIR_TCL 11 | mkdir -p REPLACEME_SV_TOP_BIN_DIR_TCL 12 | chmod u+w,a+rx REPLACEME_SV_TOP_BIN_DIR_TCL 13 | 14 | 15 | cd ../REPLACEME_SV_TCL_DIR/unix 16 | ./configure --prefix=REPLACEME_SV_TOP_BIN_DIR_TCL --enable-threads --disable-shared 17 | make -j8 clean 18 | make -j8 release 19 | make -j8 install 20 | 21 | cd ../.. 22 | cd REPLACEME_SV_TK_DIR/unix 23 | ./configure --prefix=REPLACEME_SV_TOP_BIN_DIR_TK \ 24 | --with-tcl=REPLACEME_SV_TOP_BIN_DIR_TCL/lib \ 25 | --enable-threads --disable-shared 26 | make -j8 clean 27 | make -j8 release 28 | make -j8 install 29 | make -j8 clean 30 | 31 | cd ../.. 32 | cd REPLACEME_SV_TCL_DIR/unix 33 | make -j8 clean 34 | 35 | cd ../../BuildHelpers 36 | 37 | cd ../tcllib-1.17 38 | REPLACEME_SV_TOP_BIN_DIR_TCL/bin/tclsh8.? installer.tcl 39 | cd ../BuildHelpers 40 | 41 | cd ../tklib-0.6 42 | REPLACEME_SV_TOP_BIN_DIR_TCL/bin/tclsh8.? installer.tcl 43 | cd ../BuildHelpers 44 | 45 | 46 | 47 | 48 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/CompileScripts/tcl-mac_osx-generic.sh: -------------------------------------------------------------------------------- 1 | #/bin/bash -f 2 | 3 | # Copyright (c) 2015 Open Source Medical Software Corporation. 4 | # All Rights Reserved. 5 | 6 | REPLACEME_SV_SPECIAL_COMPILER_SCRIPT 7 | 8 | export CC=clang 9 | 10 | rm -Rf REPLACEME_SV_TOP_BIN_DIR_TCL 11 | mkdir -p REPLACEME_SV_TOP_BIN_DIR_TCL 12 | chmod u+w,a+rx REPLACEME_SV_TOP_BIN_DIR_TCL 13 | 14 | 15 | cd ../REPLACEME_SV_TCL_DIR/unix 16 | ./configure --prefix=REPLACEME_SV_TOP_BIN_DIR_TCL --enable-threads --enable-shared \ 17 | --enable-corefoundation 18 | make -j8 clean 19 | make -j8 release 20 | make -j8 install 21 | 22 | cd ../.. 23 | cd REPLACEME_SV_TK_DIR/unix 24 | ./configure --prefix=REPLACEME_SV_TOP_BIN_DIR_TK \ 25 | --with-tcl=REPLACEME_SV_TOP_BIN_DIR_TCL/lib \ 26 | --enable-threads --enable-shared --enable-corefoundation \ 27 | --enable-aqua 28 | make -j8 clean 29 | make -j8 release 30 | make -j8 install 31 | make -j8 clean 32 | 33 | cd ../.. 34 | cd REPLACEME_SV_TCL_DIR/unix 35 | make -j8 clean 36 | 37 | cd ../../BuildHelpers 38 | 39 | cd ../tcllib-1.17 40 | REPLACEME_SV_TOP_BIN_DIR_TCL/bin/tclsh8.? installer.tcl 41 | cd ../BuildHelpers 42 | 43 | cd ../tklib-0.6 44 | REPLACEME_SV_TOP_BIN_DIR_TCL/bin/tclsh8.? installer.tcl 45 | cd ../BuildHelpers 46 | 47 | chmod u+w,a+rx REPLACEME_SV_TOP_BIN_DIR_TCL/lib/REPLACEME_SV_TCL_LIB_NAME 48 | install_name_tool -id REPLACEME_SV_TCL_LIB_NAME REPLACEME_SV_TOP_BIN_DIR_TCL/lib/REPLACEME_SV_TCL_LIB_NAME 49 | 50 | chmod u+w,a+rx REPLACEME_SV_TOP_BIN_DIR_TCL/bin/REPLACEME_SV_TCLSH_EXECUTABLE 51 | install_name_tool -change REPLACEME_SV_TOP_BIN_DIR_TCL/lib/REPLACEME_SV_TCL_LIB_NAME REPLACEME_SV_TCL_LIB_NAME REPLACEME_SV_TOP_BIN_DIR_TCL/bin/REPLACEME_SV_TCLSH_EXECUTABLE 52 | 53 | chmod u+w,a+rx REPLACEME_SV_TOP_BIN_DIR_TCL/lib/REPLACEME_SV_TK_LIB_NAME 54 | install_name_tool -id REPLACEME_SV_TK_LIB_NAME REPLACEME_SV_TOP_BIN_DIR_TCL/lib/REPLACEME_SV_TK_LIB_NAME 55 | 56 | chmod u+w,a+rx REPLACEME_SV_TOP_BIN_DIR_TCL/bin/REPLACEME_SV_WISH_EXECUTABLE 57 | install_name_tool -change REPLACEME_SV_TOP_BIN_DIR_TCL/lib/REPLACEME_SV_TCL_LIB_NAME REPLACEME_SV_TCL_LIB_NAME REPLACEME_SV_TOP_BIN_DIR_TCL/bin/REPLACEME_SV_WISH_EXECUTABLE 58 | install_name_tool -change REPLACEME_SV_TOP_BIN_DIR_TCL/lib/REPLACEME_SV_TK_LIB_NAME REPLACEME_SV_TK_LIB_NAME REPLACEME_SV_TOP_BIN_DIR_TCL/bin/REPLACEME_SV_WISH_EXECUTABLE 59 | 60 | 61 | 62 | 63 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/CompileScripts/tcl-mingw64-generic.sh: -------------------------------------------------------------------------------- 1 | 2 | #/bin/bash -f 3 | 4 | # Copyright (c) 2015 Open Source Medical Software Corporation. 5 | # All Rights Reserved. 6 | 7 | export SV_TCL_VERSION=$1 8 | export SV_COMPILER_DIR=$2 9 | 10 | export SV_TOPLEVEL_SRCDIR=/usr/local/sv/ext/src 11 | export SV_TOPLEVEL_BINDIR=/usr/local/sv/ext/bin 12 | 13 | export SV_ARCH_DIR=x64 14 | 15 | export SV_TCL_INSTALL_SHORT_DIR_NAME=tcltk-$SV_TCL_VERSION 16 | export SV_TCL_INSTALL_FULL_DIR_NAME=${SV_TOPLEVEL_BINDIR}/${SV_COMPILER_DIR}/${SV_ARCH_DIR}/${SV_TCL_INSTALL_SHORT_DIR_NAME} 17 | 18 | mkdir -p $SV_TCL_INSTALL_FULL_DIR_NAME 19 | 20 | chmod a+rx $SV_TCL_INSTALL_FULL_DIR_NAME 21 | cd ../tcl-$SV_TCL_VERSION/win 22 | ./configure --prefix=${SV_TCL_INSTALL_FULL_DIR_NAME} --enable-threads --disable-shared --enable-64bit 23 | 24 | make clean 25 | make binaries libraries 26 | make install-binaries install-libraries 27 | 28 | chmod -R a+rx $SV_TCL_INSTALL_FULL_DIR_NAME 29 | cd ../.. 30 | cd tk-$SV_TCL_VERSION/win 31 | ./configure --prefix=${SV_TCL_INSTALL_FULL_DIR_NAME} \ 32 | --with-tcl=${SV_TCL_INSTALL_FULL_DIR_NAME}/lib \ 33 | --enable-threads --disable-shared --enable-64bit 34 | make clean 35 | make binaries libraries 36 | make install-binaries install-libraries 37 | make clean 38 | #chmod -R a+rx $SV_TCL_INSTALL_FULL_DIR_NAME 39 | cd ../.. 40 | cd tcl-$SV_TCL_VERSION/win 41 | make clean 42 | 43 | cd ../../BuildHelpers 44 | 45 | cd ../tcllib-1.17 46 | $SV_TCL_INSTALL_FULL_DIR_NAME/bin/tclsh8?.exe installer.tcl 47 | cd ../BuildHelpers 48 | #chmod -R a+rx $SV_TCL_INSTALL_FULL_DIR_NAME 49 | 50 | cd ../tklib-0.6 51 | $SV_TCL_INSTALL_FULL_DIR_NAME/bin/tclsh8?.exe installer.tcl 52 | cd ../BuildHelpers 53 | #chmod -R a+rx $SV_TCL_INSTALL_FULL_DIR_NAME 54 | 55 | 56 | 57 | 58 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/CompileScripts/tcl-windows-generic.sh: -------------------------------------------------------------------------------- 1 | #/bin/bash -f 2 | 3 | # Copyright (c) 2015 Open Source Medical Software Corporation. 4 | # All Rights Reserved. 5 | 6 | REPLACEME_SV_SPECIAL_COMPILER_SCRIPT 7 | 8 | export CC=CL 9 | 10 | rm -Rf REPLACEME_SV_TOP_BIN_DIR_TCL 11 | mkdir -p REPLACEME_SV_TOP_BIN_DIR_TCL 12 | chmod u+w,a+rx REPLACEME_SV_TOP_BIN_DIR_TCL 13 | 14 | 15 | cd ../REPLACEME_SV_TCL_DIR/win 16 | nmake -f makefile.vc MACHINE=AMD64 INSTALLDIR="REPLACEME_SV_TOP_BIN_DIR_TCL" OPTS=msvcrt,static,threads hose 17 | nmake -f makefile.vc MACHINE=AMD64 INSTALLDIR="REPLACEME_SV_TOP_BIN_DIR_TCL" OPTS=msvcrt,static,threads release 18 | nmake -f makefile.vc MACHINE=AMD64 INSTALLDIR="REPLACEME_SV_TOP_BIN_DIR_TCL" OPTS=msvcrt,static,threads install 19 | chmod -R a+rwx REPLACEME_SV_TOP_BIN_DIR_TCL 20 | cd ../.. 21 | cd REPLACEME_SV_TK_DIR/win 22 | nmake -f makefile.vc MACHINE=AMD64 TCLDIR="REPLACEME_SV_TOP_SRC_DIR_TCL" INSTALLDIR="REPLACEME_SV_TOP_BIN_DIR_TK" OPTS=msvcrt,static,threads hose 23 | nmake -f makefile.vc MACHINE=AMD64 TCLDIR="REPLACEME_SV_TOP_SRC_DIR_TCL" INSTALLDIR="REPLACEME_SV_TOP_BIN_DIR_TK" OPTS=msvcrt,static,threads release 24 | nmake -f makefile.vc MACHINE=AMD64 TCLDIR="REPLACEME_SV_TOP_SRC_DIR_TCL" INSTALLDIR="REPLACEME_SV_TOP_BIN_DIR_TK" OPTS=msvcrt,static,threads install 25 | chmod -R a+rwx REPLACEME_SV_TOP_BIN_DIR_TK 26 | nmake -f makefile.vc MACHINE=AMD64 TCLDIR="REPLACEME_SV_TOP_SRC_DIR_TCL" INSTALLDIR= OPTS=msvcrt,static,threads hose 27 | cd ../.. 28 | cd REPLACEME_SV_TCL_DIR/win 29 | nmake -f makefile.vc MACHINE=AMD64 INSTALLDIR="REPLACEME_SV_TOP_BIN_DIR_TCL" OPTS=msvcrt,static,threads hose 30 | 31 | cd ../../BuildHelpers 32 | 33 | export SV_TOPLEVEL_BINDIR_CYGWIN=`cygpath "REPLACEME_SV_TOP_BIN_DIR_TCL"` 34 | 35 | cd ../tcllib-1.17 36 | $SV_TOPLEVEL_BINDIR_CYGWIN/bin/REPLACEME_SV_TCLSH_EXECUTABLE installer.tcl 37 | cd ../BuildHelpers 38 | chmod -R a+rx $SV_TOPLEVEL_BINDIR_CYGWIN 39 | 40 | cd ../tklib-0.6 41 | $SV_TOPLEVEL_BINDIR_CYGWIN/bin/REPLACEME_SV_TCLSH_EXECUTABLE installer.tcl 42 | cd ../BuildHelpers 43 | chmod -R a+rx $SV_TOPLEVEL_BINDIR_CYGWIN 44 | 45 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/CygwinHelpers/clean-env.sh: -------------------------------------------------------------------------------- 1 | # visual studio 2010 defines 2 | export VS100COMNTOOLS= 3 | export VSINSTALLDIR= 4 | export VCINSTALLDIR= 5 | export FrameworkDir= 6 | export FrameworkVersion= 7 | export WindowsSdkDir= 8 | export Platform= 9 | export CommandPromptType= 10 | export INCLUDE= 11 | export LIB= 12 | export PATH=/usr/bin:/bin:/cygdrive/c/Windows/system32/reg:/cygdrive/c/Windows/system32:/cygdrive/c/Windows/SysWOW64 13 | export LIBPATH= 14 | # visual studio 2013 defines 15 | export VisualStudioVersion= 16 | export Framework40Version= 17 | export WindowsSdkDir= 18 | export ExtensionSdkDir= 19 | export WindowsSDK_ExecutablePath_x64= 20 | export VS120COMNTOOLS= 21 | export VSINSTALLDIR= 22 | export VCINSTALLDIR= 23 | export FrameworkDir= 24 | export FrameworkVersion= 25 | export Platform= 26 | export CommandPromptType= 27 | export INCLUDE= 28 | export LIB= 29 | export PATH=/usr/bin:/bin:/cygdrive/c/Windows/system32/reg:/cygdrive/c/Windows/system32:/cygdrive/c/Windows/SysWOW64 30 | export LIBPATH= 31 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/Patches/patch-source-tcltk-8.5.sh: -------------------------------------------------------------------------------- 1 | cp -f Patches/tk-8.5.18-win-ttkWinXPTheme.c ../tk-8.5.18/win/ttkWinXPTheme.c 2 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/Patches/patch-source-vtk-6.2.sh: -------------------------------------------------------------------------------- 1 | cp -f Patches/vtk-6.2.0-IO-Video-vtkWin32VideoSource.cxx.from-master-2015-07-20 ../vtk-6.2.0/IO/Video/vtkWin32VideoSource.cxx 2 | cp -f Patches/vtk-6.2.0-ThirdParty-hdf5-vtkhdf5-src-H5system.c ../vtk-6.2.0/ThirdParty/hdf5/vtkhdf5/src/H5system.c 3 | cp -f Patches/vtk-6.2.0-ThirdParty-hdf5-vtkhdf5-src-H5win32defs.h ../vtk-6.2.0/ThirdParty/hdf5/vtkhdf5/src/H5win32defs.h 4 | cp -f Patches/vtk-6.2.0-ThirdParty-TclTk-internals-tk8.5-tkWinPort.h ../vtk-6.2.0/ThirdParty/TclTk/internals/tk8.5/tkWinPort.h 5 | 6 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/Patches/patch-source-vtk-6.3.sh: -------------------------------------------------------------------------------- 1 | #cp Patches/vtk-6.2.0-IO-Video-vtkWin32VideoSource.cxx.from-master-2015-07-20 ../vtk-6.2.0/IO/Video/vtkWin32VideoSource.cxx 2 | cp -f Patches/vtk-6.3.0-ThirdParty-hdf5-vtkhdf5-src-H5system.c ../vtk-6.3.0/ThirdParty/hdf5/vtkhdf5/src/H5system.c 3 | cp -f Patches/vtk-6.3.0-ThirdParty-hdf5-vtkhdf5-src-H5win32defs.h ../vtk-6.3.0/ThirdParty/hdf5/vtkhdf5/src/H5win32defs.h 4 | cp -f Patches/vtk-6.3.0-ThirdParty-TclTk-internals-tk8.5-tkWinPort.h ../vtk-6.3.0/ThirdParty/TclTk/internals/tk8.5/tkWinPort.h 5 | 6 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/Scripts/create-archives-generic.sh: -------------------------------------------------------------------------------- 1 | BUILDDATE=`date +%F` 2 | mkdir -p tar_output 3 | 4 | #pushd REPLACEME_SV_TOPLEVEL_BINDIR/REPLACEME_SV_COMPILER_BIN_DIR/REPLACEME_SV_ARCH_DIR 5 | #REPLACEME_TAR -cvzf REPLACEME_SV_PLATFORM.REPLACEME_SV_COMPILER_BIN_DIR.REPLACEME_SV_ARCH_DIR.REPLACEME_SV_TCLTK_DIR-BUILD${BUILDDATE}.tar.gz REPLACEME_SV_TCLTK_DIR 6 | #popd 7 | #mv REPLACEME_SV_TOPLEVEL_BINDIR/REPLACEME_SV_COMPILER_BIN_DIR/REPLACEME_SV_ARCH_DIR/REPLACEME_SV_PLATFORM.REPLACEME_SV_COMPILER_BIN_DIR.REPLACEME_SV_ARCH_DIR.REPLACEME_SV_TCLTK_DIR-BUILD${BUILDDATE}.tar.gz tar_output 8 | 9 | pushd REPLACEME_SV_TOPLEVEL_BINDIR/REPLACEME_SV_COMPILER_BIN_DIR/REPLACEME_SV_ARCH_DIR 10 | REPLACEME_TAR -cvzf REPLACEME_SV_PLATFORM.REPLACEME_SV_COMPILER_BIN_DIR.REPLACEME_SV_ARCH_DIR.REPLACEME_SV_VTK_DIR-BUILD${BUILDDATE}.tar.gz REPLACEME_SV_VTK_DIR 11 | popd 12 | mv REPLACEME_SV_TOPLEVEL_BINDIR/REPLACEME_SV_COMPILER_BIN_DIR/REPLACEME_SV_ARCH_DIR/REPLACEME_SV_PLATFORM.REPLACEME_SV_COMPILER_BIN_DIR.REPLACEME_SV_ARCH_DIR.REPLACEME_SV_VTK_DIR-BUILD${BUILDDATE}.tar.gz tar_output 13 | 14 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/Scripts/superbuild-linux-gcc.sh: -------------------------------------------------------------------------------- 1 | # 2 | # unpack all of the source code 3 | # 4 | 5 | source Scripts/untar-unzip-source-all.sh 6 | mkdir -p tmp 7 | 8 | # 9 | # make build scripts 10 | # 11 | 12 | 13 | # tcl/tk 8.6 14 | #sed -f CompileScripts/sed-script-x64_linux-options-gcc.sh CompileScripts/tcl-linux-generic.sh > tmp/compile.make.tcl.gcc.sh 15 | #chmod a+rx ./tmp/compile.make.tcl.gcc.sh 16 | 17 | # vtk 18 | sed -f CompileScripts/sed-script-x64_linux-options-gcc.sh CompileScripts/compile-cmake-vtk-generic.sh > tmp/compile.cmake.vtk.gcc.sh 19 | chmod a+rx ./tmp/compile.cmake.vtk.gcc.sh 20 | 21 | # create script to create tar files 22 | sed -f CompileScripts/sed-script-x64_linux-options-gcc.sh Scripts/create-archives-generic.sh > tmp/create-archives-all.gcc.sh 23 | chmod a+rx ./tmp/create-archives-all.gcc.sh 24 | 25 | # create script to create zip files 26 | sed -f CompileScripts/sed-script-x64_linux-options-gcc.sh Scripts/tar-to-zip-all.sh > tmp/tar-to-zip-all.gcc.sh 27 | chmod a+rx ./tmp/tar-to-zip-all.gcc.sh 28 | 29 | # 30 | # compile code 31 | # 32 | 33 | # tcl/tk 8.6 34 | #./tmp/compile.make.tcl.gcc.sh >& ./tmp/stdout.tcl.txt 35 | 36 | # vtk 37 | ./tmp/compile.cmake.vtk.gcc.sh >& ./tmp/stdout.vtk.gcc.txt 38 | 39 | # 40 | # create tar files for distrution 41 | # 42 | 43 | ./tmp/create-archives-all.gcc.sh >& ./tmp/stdout.create-archives-all.gcc.txt 44 | 45 | ./tmp/tar-to-zip-all.gcc.sh >& ./tmp/stdout.tar-to-zip-all.gcc.txt 46 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/Scripts/superbuild-mac_osx-clang.sh: -------------------------------------------------------------------------------- 1 | # 2 | # unpack all of the source code 3 | # 4 | 5 | source Scripts/untar-unzip-source-all.sh 6 | mkdir -p tmp 7 | 8 | # 9 | # make build scripts 10 | # 11 | 12 | 13 | # tcl/tk 8.6 14 | #sed -f CompileScripts/sed-script-x64_mac_osx-options-clang.sh CompileScripts/tcl-mac_osx-generic.sh > tmp/compile.make.tcl.clang.sh 15 | #chmod a+rx ./tmp/compile.make.tcl.clang.sh 16 | 17 | # vtk 18 | sed -f CompileScripts/sed-script-x64_mac_osx-options-clang.sh CompileScripts/compile-cmake-vtk-generic.sh > tmp/compile.cmake.vtk.clang.sh 19 | chmod a+rx ./tmp/compile.cmake.vtk.clang.sh 20 | 21 | # create script to create tar files 22 | sed -f CompileScripts/sed-script-x64_mac_osx-options-clang.sh Scripts/create-archives-generic.sh > tmp/create-archives-mac_osx.clang.sh 23 | chmod a+rx ./tmp/create-archives-mac_osx.clang.sh 24 | 25 | # create script to create zip files 26 | sed -f CompileScripts/sed-script-x64_mac_osx-options-clang.sh Scripts/tar-to-zip-all.sh > tmp/tar-to-zip-all.clang.sh 27 | chmod a+rx ./tmp/tar-to-zip-all.clang.sh 28 | 29 | # 30 | # compile code 31 | # 32 | 33 | # tcl/tk 8.6 34 | #./tmp/compile.make.tcl.clang.sh >& ./tmp/stdout.tcl.txt 35 | 36 | # vtk 37 | ./tmp/compile.cmake.vtk.clang.sh >& ./tmp/stdout.vtk.clang.txt 38 | 39 | # 40 | # create tar files for distrution 41 | # 42 | 43 | ./tmp/create-archives-mac_osx.clang.sh >& ./tmp/stdout.create-archives-mac_osx.clang.txt 44 | 45 | ./tmp/tar-to-zip-all.clang.sh >& ./tmp/stdout.tar-to-zip-all.clang.txt 46 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/Scripts/superbuild-windows-cl.sh: -------------------------------------------------------------------------------- 1 | # 2 | # unpack all of the source code 3 | # 4 | 5 | source Scripts/untar-unzip-source-all.sh 6 | mkdir -p tmp 7 | 8 | # 9 | # make build scripts 10 | # 11 | 12 | # tcl/tk 8.6 13 | #sed -f CompileScripts/sed-script-x64_cygwin-options-cl.sh CompileScripts/tcl-windows-generic.sh > tmp/compile.make.tcl.cl.sh 14 | #chmod a+rx ./tmp/compile.make.tcl.cl.sh 15 | 16 | # vtk 17 | sed -f CompileScripts/sed-script-x64_cygwin-options-cl.sh CompileScripts/compile-cmake-vtk-generic.sh > tmp/compile.cmake.vtk.cl.sh 18 | chmod a+rx ./tmp/compile.cmake.vtk.cl.sh 19 | 20 | # create script to create tar files 21 | sed -f CompileScripts/sed-script-x64_cygwin-options-cl.sh Scripts/create-archives-generic.sh > tmp/create-archives-windows.cl.sh 22 | chmod a+rx ./tmp/create-archives-windows.cl.sh 23 | 24 | # create script to create zip files 25 | sed -f CompileScripts/sed-script-x64_cygwin-options-cl.sh Scripts/tar-to-zip-all.sh > tmp/tar-to-zip-all.windows.cl.sh 26 | chmod a+rx ./tmp/tar-to-zip-all.windows.cl.sh 27 | 28 | # 29 | # compile code 30 | # 31 | 32 | # tcl/tk 8.6 33 | #./tmp/compile.make.tcl.cl.sh >& ./tmp/stdout.tcl.txt 34 | 35 | # vtk 36 | ./tmp/compile.cmake.vtk.cl.sh >& ./tmp/stdout.vtk.cl.txt 37 | 38 | # 39 | # create tar files for distrution 40 | # 41 | 42 | ./tmp/create-archives-windows.cl.sh >& ./tmp/stdout.create-archives-windows.cl.txt 43 | 44 | ./tmp/tar-to-zip-all.windows.cl.sh >& ./tmp/stdout.tar-to-zip-all.windows.cl.txt 45 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/Scripts/tar-to-zip-all.sh: -------------------------------------------------------------------------------- 1 | BUILDDATE=`date +%F` 2 | 3 | rm -Rf zip_output 4 | mkdir -p zip_output 5 | 6 | rm -Rf zip_output_tmp 7 | mkdir -p zip_output_tmp 8 | 9 | #REPLACEME_TAR -C zip_output_tmp/ -xvzf tar_output/REPLACEME_SV_PLATFORM.REPLACEME_SV_COMPILER_BIN_DIR.REPLACEME_SV_ARCH_DIR.REPLACEME_SV_TCLTK_DIR-BUILD${BUILDDATE}.tar.gz 10 | #pushd zip_output_tmp 11 | #REPLACEME_ZIP -r ../zip_output/REPLACEME_SV_PLATFORM.REPLACEME_SV_COMPILER_BIN_DIR.REPLACEME_SV_ARCH_DIR.REPLACEME_SV_TCLTK_DIR-BUILD${BUILDDATE}.zip REPLACEME_SV_TCLTK_DIR 12 | #popd 13 | 14 | rm -Rf zip_output_tmp 15 | mkdir -p zip_output_tmp 16 | 17 | REPLACEME_TAR -C zip_output_tmp/ -xvzf tar_output/REPLACEME_SV_PLATFORM.REPLACEME_SV_COMPILER_BIN_DIR.REPLACEME_SV_ARCH_DIR.REPLACEME_SV_VTK_DIR-BUILD${BUILDDATE}.tar.gz 18 | pushd zip_output_tmp 19 | REPLACEME_ZIP -r ../zip_output/REPLACEME_SV_PLATFORM.REPLACEME_SV_COMPILER_BIN_DIR.REPLACEME_SV_ARCH_DIR.REPLACEME_SV_VTK_DIR-BUILD${BUILDDATE}.zip REPLACEME_SV_VTK_DIR 20 | popd 21 | 22 | rm -Rf zip_output_tmp 23 | -------------------------------------------------------------------------------- /Externals/BuildHelpers/Scripts/untar-unzip-source-all.sh: -------------------------------------------------------------------------------- 1 | # 2 | # untar tcl/tk 3 | # 4 | 5 | #tar xvf Originals/tcltk/tcl8.5.18-src.tar.gz 6 | #tar xvf Originals/tcltk/tk8.5.18-src.tar.gz 7 | #tar xvf Originals/tcltk/tcl8.6.4-src.tar.gz 8 | #tar xvf Originals/tcltk/tk8.6.4-src.tar.gz 9 | #tar xvf Originals/tcltk/tcllib-1.17.tar.gz 10 | #tar xvf Originals/tcltk/tklib-0.6.tar.tgz 11 | 12 | # 13 | # move and rename tcl/tk 14 | # 15 | 16 | #mv tcl8.5.18 ../tcl-8.5.18 17 | #mv tk8.5.18 ../tk-8.5.18 18 | #mv tcl8.6.4 ../tcl-8.6.4 19 | #mv tk8.6.4 ../tk-8.6.4 20 | #mv tcllib-1.17 ../tcllib-1.17 21 | #mv tklib-0.6 ../tklib-0.6 22 | #source Patches/patch-source-tcltk-8.5.sh 23 | 24 | # 25 | # vtk 26 | # 27 | 28 | tar xvf Originals/vtk/VTK-6.2.0.tar.gz 29 | mv VTK-6.2.0 ../vtk-6.2.0 30 | source Patches/patch-source-vtk-6.2.sh 31 | #tar xvf Originals/vtk/VTK-6.3.0.tar.gz 32 | #mv VTK-6.3.0 ../vtk-6.3.0 33 | #source Patches/patch-source-vtk-6.3.sh 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /Externals/build-sv-externals-helper-wget-generic.sh: -------------------------------------------------------------------------------- 1 | export PARENT_URL=http://simvascular.stanford.edu/downloads/public/simvascular/externals/src/originals/ 2 | 3 | mkdir Originals 4 | pushd Originals 5 | 6 | #mkdir -p tcltk 7 | #pushd tcltk 8 | #wget $PARENT_URL/tcltk/tcl8.5.18-src.tar.gz 9 | #wget $PARENT_URL/tcltk/tcl8.6.4-src.tar.gz 10 | #wget $PARENT_URL/tcltk/tcllib-1.17.tar.gz 11 | #wget $PARENT_URL/tcltk/tk8.5.18-src.tar.gz 12 | #wget $PARENT_URL/tcltk/tk8.6.4-src.tar.gz 13 | #wget $PARENT_URL/tcltk/tklib-0.6.tar.tgz 14 | #popd 15 | 16 | mkdir -p vtk 17 | pushd vtk 18 | wget $PARENT_URL/vtk/VTK-6.2.0.tar.gz 19 | #wget $PARENT_URL/vtk/VTK-6.3.0.tar.gz 20 | popd 21 | 22 | popd 23 | -------------------------------------------------------------------------------- /Externals/build-sv-externals-linux.sh: -------------------------------------------------------------------------------- 1 | EXTERNALS_TOP=/usr/local/svsolver/externals 2 | EXTERNALS_BUILD_TOP=$EXTERNALS_TOP/build 3 | 4 | # 5 | # must have write permissions to dirs! 6 | # 7 | 8 | sudo mkdir -p /usr/local/package 9 | sudo chmod a+rwx /usr/local/package 10 | 11 | sudo mkdir -p /usr/local/svsolver 12 | sudo chmod a+rwx /usr/local/svsolver 13 | 14 | # 15 | # initial setup 16 | # 17 | 18 | echo "Deleting previous build dir ($EXTERNALS_BUILD_TOP)" 19 | rm -Rf $EXTERNALS_BUILD_TOP 20 | mkdir $EXTERNALS_BUILD_TOP 21 | 22 | echo "Deleting previous src+bin dir ($EXTERNALS_TOP)" 23 | rm -Rf $EXTERNALS_TOP 24 | mkdir -p $EXTERNALS_TOP 25 | mkdir -p $EXTERNALS_TOP/src 26 | cp -Rf BuildHelpers $EXTERNALS_TOP/src 27 | 28 | # 29 | # wget the original src files 30 | # 31 | 32 | source build-sv-externals-helper-wget-generic.sh 33 | mv Originals $EXTERNALS_TOP/src/BuildHelpers 34 | 35 | # 36 | # let's do it 37 | # 38 | 39 | pushd $EXTERNALS_TOP/src/BuildHelpers 40 | 41 | echo "Starting build in ($EXTERNALS_TOP)..." 42 | echo " note: see logs in stdout.superbuild.txt, tmp/stdout*, etc." 43 | source Scripts/superbuild-linux-gcc.sh >& stdout.superbuild.txt 44 | 45 | popd 46 | 47 | 48 | -------------------------------------------------------------------------------- /Externals/build-sv-externals-mac_osx.sh: -------------------------------------------------------------------------------- 1 | EXTERNALS_TOP=/usr/local/svsolver/externals 2 | EXTERNALS_BUILD_TOP=$EXTERNALS_TOP/build 3 | 4 | # 5 | # must have write permissions to dirs! 6 | # 7 | 8 | sudo mkdir -p /usr/local/package 9 | sudo chmod a+rwx /usr/local/package 10 | 11 | sudo mkdir -p /usr/local/svsolver 12 | sudo chmod a+rwx /usr/local/svsolver 13 | 14 | # 15 | # initial setup 16 | # 17 | 18 | echo "Deleting previous build dir ($EXTERNALS_BUILD_TOP)" 19 | rm -Rf $EXTERNALS_BUILD_TOP 20 | mkdir $EXTERNALS_BUILD_TOP 21 | 22 | echo "Deleting previous src+bin dir ($EXTERNALS_TOP)" 23 | rm -Rf $EXTERNALS_TOP 24 | mkdir -p $EXTERNALS_TOP 25 | mkdir -p $EXTERNALS_TOP/src 26 | cp -Rf BuildHelpers $EXTERNALS_TOP/src 27 | 28 | # 29 | # wget the original src files 30 | # 31 | 32 | source build-sv-externals-helper-wget-generic.sh 33 | mv Originals $EXTERNALS_TOP/src/BuildHelpers 34 | 35 | # 36 | # let's do it 37 | # 38 | 39 | pushd $EXTERNALS_TOP/src/BuildHelpers 40 | 41 | echo "Starting build in ($EXTERNALS_TOP)..." 42 | echo " note: see logs in stdout.superbuild.txt, tmp/stdout*, etc." 43 | source Scripts/superbuild-mac_osx-clang.sh >& stdout.superbuild.txt 44 | 45 | popd 46 | 47 | 48 | -------------------------------------------------------------------------------- /Externals/build-sv-externals-windows.sh: -------------------------------------------------------------------------------- 1 | EXTERNALS_TOP=/usr/local/svsolver/externals 2 | EXTERNALS_BUILD_TOP=$EXTENALS_TOP 3 | #EXTERNALS_BUILD_TOP=/cygdrive/c/svsolver 4 | 5 | # 6 | # initial setup 7 | # 8 | 9 | echo "Deleting previous build dir ($EXTERNALS_BUILD_TOP)" 10 | rm -Rf $EXTERNALS_BUILD_TOP 11 | mkdir $EXTERNALS_BUILD_TOP 12 | 13 | echo "Deleting previous src+bin dir ($EXTERNALS_TOP)" 14 | rm -Rf $EXTERNALS_TOP 15 | mkdir -p $EXTERNALS_TOP 16 | mkdir -p $EXTERNALS_TOP/src 17 | cp -Rf BuildHelpers $EXTERNALS_TOP/src 18 | 19 | # 20 | # wget the original src files 21 | # 22 | 23 | source build-sv-externals-helper-wget-generic.sh 24 | mv Originals $EXTERNALS_TOP/src/BuildHelpers 25 | 26 | # 27 | # let's do it 28 | # 29 | 30 | pushd $EXTERNALS_TOP/src/BuildHelpers 31 | 32 | echo "Starting build in ($EXTERNALS_TOP)..." 33 | echo " note: see logs in stdout.superbuild.txt, tmp/stdout*, etc." 34 | echo " note: see individual build logs as well" 35 | source Scripts/superbuild-windows-cl.sh >& stdout.superbuild.txt 36 | 37 | popd 38 | 39 | 40 | -------------------------------------------------------------------------------- /Licenses/ExternalOpenSourcePackages/README-external-licenses-lgpl.txt: -------------------------------------------------------------------------------- 1 | 1. NSPCG (LGPL) 2 | 3 | *************************************************************** 4 | *************************************************************** 5 | NSPCG (as of version 2007) 6 | *************************************************************** 7 | *************************************************************** 8 | 9 | Email correspondence with David Kincaid confirmed LGPL 10 | license (March 12, 2007). 11 | -------------------------------------------------------------------------------- /Licenses/LesLib/README-LESLIB.txt: -------------------------------------------------------------------------------- 1 | Put your LesLib license file in this directory. 2 | It should be named "license.dat" 3 | 4 | -------------------------------------------------------------------------------- /travis/travis_build.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | set -e 4 | 5 | if $WITH_CMAKE; then 6 | MAKE="make --jobs=$NUM_THREADS --keep-going" 7 | mkdir -p $BUILD_DIR 8 | cd $BUILD_DIR 9 | SV_EXTERNALS_ARGS="" 10 | if $BUILD_VTK; then 11 | SV_EXTERNALS_ARGS="-DSV_EXTERNALS_DOWNLOAD_VTK:BOOL=OFF" 12 | fi 13 | export SV_EXTERNALS_ARGS=$SV_EXTERNALS_ARGS 14 | source $SCRIPTS/travis_cmake_config.sh 15 | pushd $BUILD_DIR 16 | $MAKE 17 | popd 18 | fi 19 | 20 | -------------------------------------------------------------------------------- /travis/travis_cmake_config.sh: -------------------------------------------------------------------------------- 1 | ### install more recent version of CMake for Ubuntu 14.04 2 | if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then 3 | wget http://simvascular.stanford.edu/downloads/public/open_source/linux/cmake/cmake-3.6.1-Linux-x86_64.sh 4 | chmod a+rx ./cmake-3.6.1-Linux-x86_64.sh 5 | sudo mkdir -p /usr/local/package/cmake-3.6.1 6 | sudo ./cmake-3.6.1-Linux-x86_64.sh --prefix=/usr/local/package/cmake-3.6.1 --skip-license 7 | sudo ln -s /usr/local/package/cmake-3.6.1/bin/ccmake /usr/local/bin/ccmake 8 | sudo ln -s /usr/local/package/cmake-3.6.1/bin/cmake /usr/local/bin/cmake 9 | sudo ln -s /usr/local/package/cmake-3.6.1/bin/cmake-gui /usr/local/bin/cmake-gui 10 | sudo ln -s /usr/local/package/cmake-3.6.1/bin/cpack /usr/local/bin/cpack 11 | sudo ln -s /usr/local/package/cmake-3.6.1/bin/ctest /usr/local/bin/ctest 12 | fi 13 | 14 | #compilers 15 | if [[ "$TRAVIS_OS_NAME" == "linux" ]] 16 | then 17 | export CC="gcc" 18 | export CXX="g++" 19 | elif [[ "$TRAVIS_OS_NAME" == "osx" ]] 20 | then 21 | export CC="clang" 22 | export CXX="clang++" 23 | fi 24 | 25 | pushd $BUILD_DIR 26 | 27 | echo SV_EXTERNALS_ARGS: $SV_EXTERNALS_ARGS 28 | #cmake 29 | export REPLACEME_SV_CMAKE_CMD="cmake" 30 | export REPLACEME_SV_CMAKE_GENERATOR="Unix Makefiles" 31 | export REPLACEME_SV_CMAKE_BUILD_TYPE="RelWithDebInfo" 32 | export REPLACEME_SV_MAKE_CMD="make -j8" 33 | export REPLACEME_SV_TOP_SRC_DIR_SV=$SV_TOP_DIR 34 | 35 | "$REPLACEME_SV_CMAKE_CMD" \ 36 | \ 37 | -G "$REPLACEME_SV_CMAKE_GENERATOR" \ 38 | \ 39 | -DCMAKE_BUILD_TYPE="$REPLACEME_SV_CMAKE_BUILD_TYPE" \ 40 | -DBUILD_SHARED_LIBS=OFF \ 41 | -DBUILD_TESTING=OFF \ 42 | -DSV_EXTERNALS_ADDITIONAL_CMAKE_ARGS="$SV_EXTERNALS_ARGS" \ 43 | \ 44 | "$REPLACEME_SV_TOP_SRC_DIR_SV" 45 | 46 | popd 47 | --------------------------------------------------------------------------------