├── .github └── workflows │ └── Languages-Python-Example1.yml ├── .gitignore ├── AI ├── Anthropic │ ├── .gitignore │ ├── README.md │ ├── claude_quickstart.py │ ├── install_claude.sh │ └── run_claude.sh ├── OpenAI │ ├── README.md │ ├── Whisper │ │ ├── README.md │ │ ├── harvard.wav │ │ └── openai-whisper-test.py │ └── openai-test.py ├── PyTorch │ ├── Images │ │ ├── pytorch-chart.png │ │ └── pytorch-logo.png │ ├── README.md │ ├── check_gpu.py │ ├── local.conf │ ├── pytorch_gpu_test.sh │ ├── pytorch_interactive.sh │ ├── pytorch_with_cuda.sh │ ├── run.sbatch │ └── setup_environment.sh ├── README.md ├── TensorFlow │ ├── Example1 │ │ ├── README.md │ │ ├── run.sbatch │ │ ├── tf_mnist.ipynb │ │ ├── tf_mnist.out │ │ └── tf_mnist.py │ ├── Example2 │ │ ├── README.md │ │ └── get_started.ipynb │ ├── Example3 │ │ ├── README.md │ │ ├── run.sbatch │ │ ├── tf_multi.out │ │ └── tf_multi_gpu.py │ ├── Example4 │ │ ├── README.md │ │ ├── run.sbatch │ │ ├── tf_test.out │ │ └── tf_test_multi_gpu.py │ ├── Images │ │ └── tensorflow-logo.png │ ├── README.md │ ├── tf-2.12.def │ └── tf_test.py └── heavyAI │ ├── README.md │ ├── heavyAI.err │ ├── heavyAI.out │ ├── run_heavyAI.sh │ └── setup_heavyAI.sh ├── Applications ├── AlphaFold │ ├── 5ZE6_1.fasta │ ├── README.md │ ├── T1083_T1084.fasta │ ├── alphafold3_input.json │ ├── alphafold_v3.def │ ├── run_af3_all.sh │ ├── run_af3_data_pipeline.sh │ ├── run_af3_inference.sh │ ├── run_alphafold.sh │ └── run_alphafold_multi.sh ├── CryoSPARC │ ├── README.md │ ├── bashrc_additions.sh │ └── configure.sh ├── Dynamite │ └── README.md ├── Gurobi │ ├── CurveFitting.lp │ ├── Images │ │ ├── ExtraModules.png │ │ └── gurobi_env_kernel.png │ ├── README.md │ ├── gurobi_test.py │ ├── runscript.sh │ └── test.out ├── KHARMA │ ├── README.md │ └── kharma_v2.def ├── Knitro │ ├── C │ │ ├── README.md │ │ ├── knitro.opt │ │ ├── knitro_test.c │ │ ├── knitro_test.out │ │ └── run.sbatch │ ├── Images │ │ └── knitro-logo.png │ ├── Matlab │ │ ├── README.md │ │ ├── knitro_test.m │ │ ├── knitro_test.out │ │ └── run.sbatch │ ├── Python │ │ ├── README.md │ │ ├── knitro_test_python.out │ │ ├── knitro_test_python.py │ │ └── run_python.sbatch │ └── README.md ├── LANDIS │ ├── Dockerfile │ ├── Images │ │ └── landis-logo.jpeg │ ├── README.md │ ├── Singularity.def │ └── test │ │ ├── Landis-log.txt │ │ ├── Metadata │ │ ├── Base Fire │ │ │ ├── Base Fire.xml │ │ │ ├── FireEventsLog_Metadata.xml │ │ │ └── FireSummaryLog_Metadata.xml │ │ └── Output Max Species Age │ │ │ └── Output Max Species Age.xml │ │ ├── age-only-succession_DynamicInputs_s1e1.txt │ │ ├── age-only-succession_InitialCommunities_s1e1.gis │ │ ├── age-only-succession_InitialCommunities_s1e1.txt │ │ ├── age-only-succession_SetUp_s1e1.txt │ │ ├── base-fire_SetUp_s1e1.txt │ │ ├── ecoregions_s1e1.gis │ │ ├── ecoregions_s1e1.txt │ │ ├── fire │ │ ├── base-fire-log.csv │ │ ├── base-fire-severity-10.img │ │ ├── base-fire-severity-100.img │ │ ├── base-fire-severity-15.img │ │ ├── base-fire-severity-20.img │ │ ├── base-fire-severity-25.img │ │ ├── base-fire-severity-30.img │ │ ├── base-fire-severity-35.img │ │ ├── base-fire-severity-40.img │ │ ├── base-fire-severity-45.img │ │ ├── base-fire-severity-5.img │ │ ├── base-fire-severity-50.img │ │ ├── base-fire-severity-55.img │ │ ├── base-fire-severity-60.img │ │ ├── base-fire-severity-65.img │ │ ├── base-fire-severity-70.img │ │ ├── base-fire-severity-75.img │ │ ├── base-fire-severity-80.img │ │ ├── base-fire-severity-85.img │ │ ├── base-fire-severity-90.img │ │ ├── base-fire-severity-95.img │ │ └── base-fire-summary-log.csv │ │ ├── landis_test.err │ │ ├── landis_test.out │ │ ├── output_MaxSppAge.txt │ │ ├── outputs │ │ └── max-age-selected-spp │ │ │ ├── AllSppMaxAge-0.gis │ │ │ ├── AllSppMaxAge-10.gis │ │ │ ├── AllSppMaxAge-100.gis │ │ │ ├── AllSppMaxAge-15.gis │ │ │ ├── AllSppMaxAge-20.gis │ │ │ ├── AllSppMaxAge-25.gis │ │ │ ├── AllSppMaxAge-30.gis │ │ │ ├── AllSppMaxAge-35.gis │ │ │ ├── AllSppMaxAge-40.gis │ │ │ ├── AllSppMaxAge-45.gis │ │ │ ├── AllSppMaxAge-5.gis │ │ │ ├── AllSppMaxAge-50.gis │ │ │ ├── AllSppMaxAge-55.gis │ │ │ ├── AllSppMaxAge-60.gis │ │ │ ├── AllSppMaxAge-65.gis │ │ │ ├── AllSppMaxAge-70.gis │ │ │ ├── AllSppMaxAge-75.gis │ │ │ ├── AllSppMaxAge-80.gis │ │ │ ├── AllSppMaxAge-85.gis │ │ │ ├── AllSppMaxAge-90.gis │ │ │ ├── AllSppMaxAge-95.gis │ │ │ ├── abiebals-0.gis │ │ │ ├── abiebals-10.gis │ │ │ ├── abiebals-100.gis │ │ │ ├── abiebals-15.gis │ │ │ ├── abiebals-20.gis │ │ │ ├── abiebals-25.gis │ │ │ ├── abiebals-30.gis │ │ │ ├── abiebals-35.gis │ │ │ ├── abiebals-40.gis │ │ │ ├── abiebals-45.gis │ │ │ ├── abiebals-5.gis │ │ │ ├── abiebals-50.gis │ │ │ ├── abiebals-55.gis │ │ │ ├── abiebals-60.gis │ │ │ ├── abiebals-65.gis │ │ │ ├── abiebals-70.gis │ │ │ ├── abiebals-75.gis │ │ │ ├── abiebals-80.gis │ │ │ ├── abiebals-85.gis │ │ │ ├── abiebals-90.gis │ │ │ └── abiebals-95.gis │ │ ├── run.sbatch │ │ ├── scenario_s1e1.txt │ │ └── species_s1e1.txt ├── PariGP │ ├── Images │ │ └── parigp.png │ ├── README.md │ ├── par_pari.gp │ ├── runscript_par.sh │ ├── runscript_seq.sh │ └── seq_pari.gp ├── README.md ├── Schrodinger │ ├── H2O.in │ ├── README.md │ └── run.sbatch ├── TotalView │ ├── README.md │ ├── figures │ │ ├── totalview-logo.jpeg │ │ ├── tv1.png │ │ ├── tv2.png │ │ ├── tv3.png │ │ └── tv4.png │ └── wave_mpi.f90 └── WRF_Model │ ├── README.md │ ├── WRF_logo.jpeg │ ├── compile_wps.log │ └── compile_wrf.log ├── Courses ├── AC290 │ ├── Example1 │ │ ├── Makefile │ │ ├── mpi_hello.cpp │ │ ├── mpi_hello.dat │ │ └── sbatch.run │ ├── Example2 │ │ ├── Makefile │ │ ├── mpi_dot.cpp │ │ ├── mpi_dot.dat │ │ └── sbatch.run │ ├── Example3 │ │ ├── Makefile │ │ ├── mpi_pi.cpp │ │ ├── mpi_pi.dat │ │ ├── sbatch.run │ │ └── speedup.py │ ├── Example4 │ │ ├── Makefile │ │ ├── mmult.c │ │ ├── mmult.out │ │ └── sbatch.run │ ├── Example5 │ │ ├── Makefile │ │ ├── README.md │ │ ├── external_libs.f90 │ │ ├── planczos.dat │ │ ├── planczos2.f90 │ │ └── sbatch.run │ └── README.md ├── CS205 │ ├── MPI │ │ ├── Example1 │ │ │ ├── Makefile │ │ │ ├── mpi_hello.err │ │ │ ├── mpi_hello.out │ │ │ ├── mpi_hello_world.c │ │ │ └── sbatch.run │ │ ├── Example2 │ │ │ ├── Makefile │ │ │ ├── prime_mpi.c │ │ │ ├── prime_mpi.err │ │ │ ├── prime_mpi.out │ │ │ └── sbatch.run │ │ ├── Example3 │ │ │ ├── Makefile │ │ │ ├── mmult.c │ │ │ ├── mmult.err │ │ │ ├── mmult.out │ │ │ └── sbatch.run │ │ ├── Example4 │ │ │ ├── Makefile │ │ │ ├── poisson_mpi.c │ │ │ ├── poisson_mpi.err │ │ │ ├── poisson_mpi.out │ │ │ └── sbatch.run │ │ ├── Example5 │ │ │ ├── Makefile │ │ │ ├── communicator_mpi.c │ │ │ ├── communicator_mpi.err │ │ │ ├── communicator_mpi.out │ │ │ └── sbatch.run │ │ └── README.md │ ├── MPI_2021 │ │ ├── Example1 │ │ │ ├── Makefile │ │ │ ├── build.sh │ │ │ ├── clean.sh │ │ │ ├── mpi_hello.cpp │ │ │ ├── sbatch.run │ │ │ └── sbatch.run.multinode │ │ ├── Example2 │ │ │ ├── Makefile │ │ │ ├── build.sh │ │ │ ├── clean.sh │ │ │ ├── mpi_dot.cpp │ │ │ └── sbatch.run │ │ ├── Example3 │ │ │ ├── Makefile │ │ │ ├── build.sh │ │ │ ├── clean.sh │ │ │ ├── mpi_pi.cpp │ │ │ ├── mpi_pi.dat │ │ │ ├── mpi_pi.err │ │ │ ├── mpi_pi.out │ │ │ ├── sbatch.run │ │ │ ├── scaling_results.txt │ │ │ ├── speedup.png │ │ │ └── speedup.py │ │ ├── Example4 │ │ │ ├── Makefile │ │ │ ├── build.sh │ │ │ ├── clean.sh │ │ │ ├── mmult.c │ │ │ ├── sbatch.run │ │ │ └── sbatch.run.multinode │ │ ├── Example5 │ │ │ ├── Makefile │ │ │ ├── README.md │ │ │ ├── build.sh │ │ │ ├── clean.sh │ │ │ ├── external_libs.f90 │ │ │ ├── planczos2.f90 │ │ │ └── sbatch.run │ │ └── README.md │ └── OpenMP │ │ ├── Example1 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_hello.c │ │ └── sbatch.run │ │ ├── Example10 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_md.c │ │ ├── omp_md.dat │ │ └── sbatch.run │ │ ├── Example2 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_loop.c │ │ └── sbatch.run │ │ ├── Example3 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_sections.c │ │ └── sbatch.run │ │ ├── Example4 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_dot.c │ │ └── sbatch.run │ │ ├── Example5 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_dot2.c │ │ └── sbatch.run │ │ ├── Example6 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_pi.c │ │ ├── sbatch.run │ │ ├── speedup.png │ │ └── speedup.py │ │ ├── Example7 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_mm.c │ │ └── sbatch.run │ │ ├── Example8 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_helmholtz.c │ │ ├── omp_helmholtz.dat │ │ └── sbatch.run │ │ ├── Example9 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_poisson.c │ │ ├── omp_poisson.dat │ │ └── sbatch.run │ │ └── README.md ├── README.md └── numpy-talk │ ├── .gitignore │ ├── MANIFEST.in │ ├── README.md │ ├── bin │ └── main │ ├── cpp │ ├── README.md │ └── operators.cpp │ ├── docker │ ├── Dockerfile │ └── entrypoint.sh │ ├── notebook.ipynb │ ├── notebook.pdf │ ├── setup-requirements.txt │ ├── setup.py │ └── src │ └── kuramoto │ ├── __init__.py │ ├── base.py │ └── solvers.py ├── Example_Recipes ├── Images │ └── recipes-logo.png ├── Job_Arrays │ ├── job_arrays_1 │ │ ├── README.md │ │ ├── pro.c │ │ └── test.py │ └── job_arrays_2 │ │ ├── Makefile │ │ ├── README.md │ │ ├── main_program.cpp │ │ └── run.sbatch ├── README.md ├── Recipe1 │ ├── README.md │ ├── pso_rosenbrock.R │ ├── pso_rosenbrock.Rout │ └── run.sbatch ├── Recipe2 │ ├── pso_rosenbrock_v2.R │ └── run.sbatch ├── Recipe3 │ ├── README.md │ ├── drive_sum.py │ ├── run.sbatch │ ├── sum.f90 │ └── test.out ├── high_precision │ ├── Makefile │ ├── README.md │ ├── mpfuna.f90 │ ├── mpfunf.f90 │ ├── mpfung1.f90 │ ├── mpint_lib.f90 │ ├── mpint_test_v1.f90 │ ├── mpint_test_v2.f90 │ ├── mpinterface.c │ ├── mpmodule.f90 │ ├── run.sbatch │ └── secondu.f90 ├── image_processing │ ├── README.md │ ├── image_process.m │ ├── images_in │ │ ├── image_in_1.tif │ │ ├── image_in_2.tif │ │ ├── image_in_3.tif │ │ ├── image_in_4.tif │ │ └── image_in_5.tif │ ├── images_out │ │ ├── image_out_1.tif │ │ ├── image_out_2.tif │ │ ├── image_out_3.tif │ │ ├── image_out_4.tif │ │ └── image_out_5.tif │ ├── images_png │ │ ├── image_in_2.png │ │ └── image_out_2.png │ └── run.sbatch ├── image_processing_matlab │ ├── README.md │ ├── run.sbatch │ ├── test_mv_1.mp4 │ ├── test_mv_2.mp4 │ ├── test_mv_3.mp4 │ └── video_test.m ├── matlab_cpp │ ├── Makefile │ ├── README.md │ ├── bessel_test.cpp │ ├── mex_test.m │ └── mex_test.sbatch ├── matrix_diag │ ├── Makefile │ ├── README.md │ ├── matrix_diag.f90 │ └── run.sbatch ├── movie_processing │ ├── README.md │ ├── movie_info.csv │ └── process_movies.sh ├── parallel_job_arrays │ ├── README.md │ ├── input_1 │ ├── input_2 │ ├── input_3 │ ├── parallel_sum.m │ └── run.sbatch ├── parameters_1 │ ├── README.md │ ├── file_1.txt │ ├── file_2.txt │ ├── file_3.txt │ ├── file_4.txt │ ├── file_5.txt │ ├── ran_array.py │ ├── run.sbatch │ ├── test.py │ └── test.sh └── pytorch │ ├── README.md │ └── pytorch.slurm ├── GPU_Computing ├── CUDA │ ├── README.md │ ├── cuda-logo.jpeg │ ├── run.sbatch │ ├── run_fort.sbatch │ ├── saxpy.cu │ └── saxpy.cuf ├── Dist_GPU_Computing │ ├── MPI_and_CUDA │ │ ├── Makefile │ │ ├── README.md │ │ ├── mpi_cuda.cu │ │ ├── output.out │ │ ├── run_4.sbatch │ │ └── run_8.sbatch │ ├── NCCL_and_CUDA │ │ ├── MultiNode │ │ │ ├── README.md │ │ │ ├── ncclAllGather_mpi.cu │ │ │ ├── ncclAllGather_nompi.cu │ │ │ ├── ncclAllGather_pmix.cu │ │ │ ├── ncclBcast_mpi.cu │ │ │ ├── ncclReduceScatter_mpi.cu │ │ │ ├── ncclReduce_mpi.cu │ │ │ ├── nccl_allgather_mpi.out │ │ │ ├── nccl_allgather_nompi.out │ │ │ ├── nccl_allgather_pmix.out │ │ │ ├── nccl_bcast_mpi.out │ │ │ ├── nccl_reduce_mpi.out │ │ │ ├── nccl_reduce_scatter_mpi.out │ │ │ ├── run_allgather_mpi.sbatch │ │ │ ├── run_bcast_mpi.sbatch │ │ │ ├── run_nccl_allgather_nompi.sbatch │ │ │ ├── run_nccl_allgather_pmix.sbatch │ │ │ ├── run_reduce_mpi.sbatch │ │ │ └── run_reduce_scatter_mpi.sbatch │ │ └── SingleNode │ │ │ ├── README.md │ │ │ ├── mpiAllGather.cpp │ │ │ ├── mpiBcast.cpp │ │ │ ├── mpiGather.cpp │ │ │ ├── mpiReduce.cpp │ │ │ ├── ncclAllGather.cu │ │ │ ├── ncclAllGather.out │ │ │ ├── ncclBcast.cu │ │ │ ├── ncclReduce.cu │ │ │ ├── ncclReduceScatter.cu │ │ │ ├── run_ncclAllGather.slurm │ │ │ └── test_if_gpu_is_available.py │ └── README.md ├── Images │ └── GPU-logo.jpeg ├── Libs │ ├── README.md │ ├── gpu-libs-logo.png │ ├── run.sbtach │ ├── saxpy_blas.c │ ├── saxpy_cublas.c │ └── saxpy_example.out ├── Numba │ ├── README.md │ ├── numba-logo.svg │ ├── run.sbatch │ ├── run_nb.sbatch │ ├── saxpy.py │ └── saxpy_nb.py ├── OpenACC │ ├── README.md │ ├── example_acc.f90 │ ├── mod_saxpy.mod │ ├── openacc-logo.jpeg │ └── run.sbatch └── README.md ├── Globus ├── README.md └── transfer_globus.py ├── IQSS-slurm-examples ├── README.md ├── basicbatch.slurm ├── hello.R ├── hello.R.slurm ├── hello.jl ├── hello.julia.slurm ├── hello.m ├── hello.math ├── hello.mathematica.slurm ├── hello.matlab.slurm ├── hello.py ├── hello.py2 ├── hello.python2.slurm ├── hello.python3.slurm ├── hello.sas ├── hello.sas.slurm ├── hello.sh ├── hello.sh.slurm ├── multicore.slurm ├── multiprocess.slurm ├── multitask.example.R ├── multitask.example.R.slurm └── template.slurm ├── Images ├── README.md └── rc-logo-text_2017-88.png ├── Languages ├── BASH │ ├── Example1 │ │ ├── README.md │ │ ├── bash_sum.out │ │ ├── run.sbatch │ │ └── sum.sh │ ├── Images │ │ └── bash-logo.png │ └── README.md ├── C │ ├── Example │ │ ├── run.sbatch │ │ └── sum.c │ ├── Images │ │ └── c-logo.png │ └── README.md ├── Cpp │ ├── Example1 │ │ ├── README.md │ │ └── sum.cpp │ ├── Example2 │ │ ├── README.md │ │ └── sum2.cpp │ ├── Example3 │ │ ├── README.md │ │ └── allocate.cpp │ ├── Example4 │ │ ├── README.md │ │ └── matvec.cpp │ ├── Example5 │ │ ├── README.md │ │ ├── dot_prod.cpp │ │ └── runscript.sh │ ├── Example6 │ │ ├── README.md │ │ ├── arrays_and_pointers.cpp │ │ └── runscript.sh │ ├── Example7 │ │ ├── README.md │ │ ├── runscript.sh │ │ └── void_point.cpp │ ├── Example8 │ │ ├── README.md │ │ └── function_factorial.cpp │ ├── Example9 │ │ ├── README.md │ │ ├── point_func.cpp │ │ └── runscript.sh │ └── README.md ├── Fortran │ ├── Deriv │ │ ├── README.md │ │ ├── deriv_tab.f90 │ │ └── deriv_test.f90 │ ├── Example1 │ │ ├── README.md │ │ ├── lanczos.f90 │ │ ├── lanczos_job.out │ │ └── run.sbatch │ ├── Example2 │ │ ├── README.md │ │ ├── run.sbatch │ │ ├── sum.f90 │ │ └── sum_job.out │ ├── Images │ │ └── fortran-logo.png │ ├── Interp │ │ ├── README.md │ │ ├── interp_test.f90 │ │ └── lagint.f90 │ └── README.md ├── IDL │ ├── README.md │ ├── pi_monte_carlo.pro │ └── run.sbatch ├── Julia │ ├── Example1 │ │ ├── README.md │ │ ├── pi_monte_carlo.jl │ │ └── run.sbatch │ ├── Example2 │ │ ├── README.md │ │ ├── figure.py │ │ ├── ode_test.jl │ │ └── run.sbatch │ ├── Images │ │ ├── figure.png │ │ ├── gadfly-demo.png │ │ ├── julia-logo.png │ │ ├── julia-vdi-1.png │ │ └── julia-vdi-2.png │ ├── Montepi-Julia.ipynb │ ├── Notebook.md │ └── README.md ├── MATLAB │ ├── Example1 │ │ ├── README.md │ │ ├── pi_monte_carlo.m │ │ ├── pi_monte_carlo.out │ │ └── run.sbatch │ ├── Example2 │ │ ├── README.md │ │ ├── run.sbatch │ │ ├── serial_sum.m │ │ └── serial_sum.out │ ├── Example3 │ │ ├── README.md │ │ ├── figure.png │ │ ├── multi_fig.m │ │ └── run.sbatch │ ├── Example4 │ │ ├── README.md │ │ ├── run.sbatch │ │ └── serial_sum.m │ ├── Example5 │ │ ├── README.md │ │ ├── rnd_test.m │ │ └── run.sbatch │ ├── Images │ │ └── matlab-logo.png │ └── README.md ├── Mathematica │ ├── README.md │ ├── pi_monte_carlo.m │ └── run.sbatch ├── Perl │ ├── Example1 │ │ ├── README.md │ │ ├── run.sbatch │ │ └── sum_array.pl │ └── README.md ├── Python │ ├── .gitignore │ ├── Docs │ │ ├── conda-cheatsheet.pdf │ │ ├── conda-cheatsheet_Page_1.png │ │ └── conda-cheatsheet_Page_2.png │ ├── Example1 │ │ ├── README.md │ │ ├── mc_pi.py │ │ ├── run.sbatch │ │ └── test_mc_pi.py │ ├── Example2 │ │ ├── README.md │ │ ├── build_env.sh │ │ ├── np_pandas.out │ │ ├── numpy_pandas_ex.py │ │ └── run.sbatch │ ├── Images │ │ ├── anaconda-logo.png │ │ ├── mamba-logo.png │ │ └── python-logo.png │ ├── README.md │ └── myscript.py ├── R │ ├── Example1 │ │ ├── README.md │ │ ├── count_down.R │ │ ├── count_down.Rout │ │ └── run.sbatch │ ├── Example2 │ │ ├── README.md │ │ ├── count_down.R │ │ ├── count_down.Rout │ │ ├── count_down.out │ │ └── run.sbatch │ ├── Images │ │ ├── R-kernel.png │ │ ├── R-logo.png │ │ ├── R-notebook.png │ │ ├── R-packages.png │ │ ├── R_setup_script.png │ │ ├── rpy2-R_setup_script.png │ │ └── rpy2-kernel.png │ ├── README.md │ ├── R_with_Jupyter │ │ ├── README.md │ │ ├── rpy2-test.ipynb │ │ └── rpy2_setup.sh │ ├── R_with_Singularity │ │ ├── README.md │ │ └── bioconductor_3.14.def │ ├── R_with_Spack │ │ ├── README.md │ │ ├── r_spack_load_libs.R │ │ └── runscript_r_spack.sh │ └── Rstan │ │ └── README.md ├── README.md └── STATA │ ├── README.md │ ├── hello_mp.do │ ├── hello_se.do │ ├── run.sbatch │ ├── run_hello_mp.sbatch │ ├── run_hello_se.sbatch │ └── test.do ├── Libraries ├── Armadillo │ ├── Makefile │ ├── README.md │ ├── armadillo_test.cpp │ └── run.sbatch ├── BLAS │ ├── Makefile │ ├── README.md │ ├── blas_test.f90 │ └── blas_test.sbatch ├── FFTW │ ├── Makefile │ ├── README.md │ ├── fftw_test.f90 │ └── fftw_test.sbatch ├── GSL │ ├── Makefile │ ├── README.md │ ├── gsl_int_test.c │ └── gsl_int_test.sbatch ├── HDF5 │ ├── Makefile │ ├── README.md │ ├── hdf5_test.f90 │ └── run_hdf5_test.sh ├── LAPACK │ ├── Makefile │ ├── README.md │ ├── lapack_test.f90 │ └── run.sbatch ├── MKL │ ├── Makefile │ ├── README.md │ ├── mkltest.f90 │ └── mkltest.sbatch ├── NETCDF │ ├── Makefile │ ├── README.md │ ├── netcdf_test.f90 │ └── netcdf_test.sbatch ├── OpenBLAS │ ├── Makefile │ ├── README.md │ ├── openblas_test.f90 │ └── run.sbatch └── README.md ├── Notebooks ├── Classification pipeline in Python.ipynb ├── Data_Classification.ipynb ├── Data_Clustering.ipynb ├── Data_Exploration.Rmd ├── README.md └── iris.data ├── Notes ├── Dash-Cannon.pdf ├── Devtools-R-terminal.pdf ├── Flask-Cannon.pdf ├── INLA_R.md ├── JAX.md ├── JobArrays │ ├── Exercise_nonsequential │ │ ├── array_job_nonsequence.sh │ │ ├── main.sh │ │ └── masks │ │ │ ├── MNI05 │ │ │ └── test.txt │ │ │ ├── sub-blasta001 │ │ │ └── test1.txt │ │ │ ├── sub-blasta002 │ │ │ └── test2.txt │ │ │ ├── sub-blasta004 │ │ │ └── test4.txt │ │ │ ├── sub-blasta005 │ │ │ └── test5.txt │ │ │ ├── sub-blasta006 │ │ │ └── test6.txt │ │ │ ├── sub-blasta007 │ │ │ └── test7.txt │ │ │ ├── sub-blasta008 │ │ │ └── test8.txt │ │ │ ├── sub-blasta010 │ │ │ └── test10.txt │ │ │ ├── sub-blasta011 │ │ │ └── test11.txt │ │ │ ├── sub-blasta012 │ │ │ └── test12.txt │ │ │ └── sub-blasta013 │ │ │ └── test13.txt │ ├── Exercise_nonsequential_maxarray │ │ ├── README.txt │ │ ├── array_script.sh │ │ ├── directories │ │ │ ├── C1 │ │ │ │ └── job.sh │ │ │ ├── C2 │ │ │ │ └── job.sh │ │ │ ├── en1 │ │ │ │ └── job.sh │ │ │ └── en2 │ │ │ │ └── job.sh │ │ └── main.sh │ ├── Exercise_recursive │ │ ├── recursive-array.sh │ │ └── test_function_script.py │ ├── Exercise_sequential_basic │ │ ├── d1 │ │ │ └── a.txt │ │ ├── d2 │ │ │ └── a.txt │ │ ├── d3 │ │ │ └── a.txt │ │ ├── d4 │ │ │ └── a.txt │ │ └── sample_array_job.bash │ ├── Exercise_sequential_fastqc │ │ ├── fastqc_arrayjob.slurm.sh │ │ ├── wgEncode1_Sub.fq │ │ ├── wgEncode2_Sub.fq │ │ └── wgEncode3_Sub.fq │ ├── Exercise_sequential_python │ │ ├── all-lists │ │ ├── getMax.py │ │ ├── list1 │ │ ├── list2 │ │ ├── list3 │ │ ├── list4 │ │ ├── submit.bash │ │ └── submit_inputfile.bash │ ├── README.md │ └── commands_for_exercises.txt ├── OpenFoam │ ├── README.md │ └── of90.def ├── README.md ├── R_in_Jupyter.md ├── Stata-Python-Instructions.pdf ├── Tidyverse-R-CLI.pdf ├── alphapose.md ├── amber.md ├── augustus-install.md ├── cutlass.md ├── gReLU │ ├── gReLU-test.ipynb │ └── grelu.md ├── jax_logo_250px.png ├── mmpose.md ├── ollama.md ├── plotly_test.ipynb ├── qchem.md ├── recursive-array.sh └── vscode_remote_tunnel.md ├── Parallel_Computing ├── EP │ ├── Example1 │ │ ├── README.md │ │ ├── output_100.out │ │ ├── output_200.out │ │ ├── output_300.out │ │ ├── run.sbatch │ │ └── serial_sum.py │ ├── Example2 │ │ ├── README.md │ │ ├── output_100.out │ │ ├── output_200.out │ │ ├── output_300.out │ │ ├── run.sbatch │ │ └── serial_sum.py │ └── README.md ├── MATLAB │ ├── Example1 │ │ ├── README.md │ │ ├── parallel_monte_carlo.m │ │ └── run.sbatch │ ├── Example2 │ │ ├── README.md │ │ ├── run.sbatch │ │ ├── speedup.png │ │ └── thread_test.m │ ├── Example3 │ │ ├── README.md │ │ ├── fig_1.png │ │ ├── fig_2.png │ │ ├── fig_3.png │ │ ├── fig_4.png │ │ ├── prun.m │ │ ├── run.sbatch │ │ ├── se_fdm.m │ │ └── simpson1d.m │ └── README.md ├── MPI │ ├── Example1 │ │ ├── Makefile │ │ ├── README.md │ │ ├── pi_monte_carlo.f90 │ │ ├── pi_monte_carlo.out │ │ └── run.sbatch │ ├── Example2 │ │ ├── Makefile │ │ ├── README.md │ │ ├── ptrap.f90 │ │ ├── ptrap.out │ │ └── run.sbatch │ ├── Example3 │ │ ├── Makefile │ │ ├── README.md │ │ ├── external_libs.f90 │ │ ├── planczos.out │ │ ├── planczos2.f90 │ │ └── run.sbatch │ ├── README.md │ ├── mpitest.c │ ├── mpitest.cpp │ ├── mpitest.f │ ├── mpitest.f90 │ ├── run.sbtach │ └── run_intelmpi.sbatch ├── MPI_IO │ ├── Example1 │ │ ├── Makefile │ │ ├── README.md │ │ ├── mpi_IO_test1.f90 │ │ └── run.sbatch │ └── README.md ├── Mathematica │ ├── README.md │ ├── parallel_pi.m │ └── run.sbtach ├── OpenMP │ ├── Example1 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_hello.c │ │ ├── omp_hello.dat │ │ └── run.sbatch │ ├── Example2 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_diag.f90 │ │ ├── omp_diag.out │ │ └── run.sbatch │ ├── Example3 │ │ ├── Makefile │ │ ├── README.md │ │ ├── omp_pi.c │ │ ├── omp_pi.dat │ │ ├── omp_pi.out │ │ ├── run.sbatch │ │ ├── scaling_results.txt │ │ ├── speedup.png │ │ └── speedup.py │ ├── Images │ │ └── openmp-logo.png │ └── README.md ├── Parallel_HDF5 │ ├── Example1 │ │ ├── Makefile │ │ ├── README.md │ │ ├── parallel_hdf5.f90 │ │ └── run.sbatch │ ├── Example2 │ │ ├── Makefile │ │ ├── README.md │ │ ├── parallel_hdf5_2d.f90 │ │ └── run.sbatch │ ├── Example3 │ │ ├── Makefile │ │ ├── README.md │ │ ├── parallel_hdf5_3d.f90 │ │ └── run.sbatch │ └── README.md ├── Parallel_NetCDF │ ├── Example1 │ │ ├── Makefile │ │ ├── README.md │ │ ├── f90tst_parallel.f90 │ │ └── run.sbatch │ ├── Example2 │ │ ├── Makefile │ │ ├── README.md │ │ ├── run.sbatch │ │ └── simple_xy_par_wr.f90 │ ├── Example3 │ │ ├── Makefile │ │ ├── README.md │ │ ├── run.sbatch │ │ ├── simple_xy_par.nc │ │ └── simple_xy_par_rd.f90 │ └── README.md ├── PnetCDF │ ├── Example1 │ │ ├── Makefile │ │ ├── README.md │ │ ├── parallel_netcdf.err │ │ ├── parallel_netcdf.out │ │ ├── run.sbatch │ │ ├── testfile.nc │ │ ├── transpose.f90 │ │ ├── transpose.o │ │ ├── transpose.x │ │ ├── utils.F90 │ │ └── utils.o │ ├── Example2 │ │ ├── Makefile │ │ ├── README.md │ │ ├── column_wise.f90 │ │ ├── run.sbatch │ │ └── utils.F90 │ ├── Example3 │ │ ├── Makefile │ │ ├── README.md │ │ ├── block_cyclic.f90 │ │ ├── run.sbatch │ │ └── utils.F90 │ └── README.md ├── Python │ ├── Python-Multiprocessing-Tutorial │ │ ├── .ipynb_checkpoints │ │ │ └── multiprocessing-checkpoint.ipynb │ │ ├── cpu-count.py │ │ ├── multiprocbuild_env.sh │ │ ├── multiprocessing.ipynb │ │ ├── multiprocessing_basic.py │ │ ├── multiprocessing_pool.py │ │ ├── run_multiproc.sbatch │ │ └── sample_data.pkl │ ├── README.md │ └── mpi4py │ │ ├── Example1 │ │ ├── README.md │ │ ├── mpi4py_test.py │ │ ├── run.sbatch │ │ └── run_ompi.sbatch │ │ ├── Example2 │ │ ├── README.md │ │ ├── optimize_mpi.py │ │ ├── run.sbatch │ │ └── run_ompi.sbatch │ │ └── README.md ├── R │ ├── Large_Data_Processing_R │ │ ├── README.md │ │ ├── R_Big_Data_April7_NK.pdf │ │ ├── data_format │ │ │ ├── NYC_lyft.Rmd │ │ │ ├── NYC_lyft.md │ │ │ └── figures │ │ │ │ └── png │ │ │ │ ├── file_format.png │ │ │ │ └── nyc-tlc-logo.png │ │ ├── figures │ │ │ └── png │ │ │ │ ├── R_and_wrappers.png │ │ │ │ └── computing_systems.png │ │ └── parallel_computation │ │ │ ├── R │ │ │ ├── 0_helper_functions.R │ │ │ ├── 1_compute_pi_lapply.R │ │ │ ├── 2_compute_pi_parLapply.R │ │ │ ├── mpi_data.csv │ │ │ ├── parLapply_mpi.R │ │ │ ├── plot_scaling_data.R │ │ │ └── run.sh │ │ │ ├── R_embarrassingly_parallel.md │ │ │ ├── R_parLapply_vdi.md │ │ │ └── figures │ │ │ └── png │ │ │ ├── monte_carlo.png │ │ │ ├── monte_carlo_computation.png │ │ │ ├── mpi_run_scaling.png │ │ │ ├── vdi_1.png │ │ │ ├── vdi_2.png │ │ │ ├── vdi_3.png │ │ │ ├── vdi_4.png │ │ │ ├── vdi_5.png │ │ │ ├── vdi_6.png │ │ │ ├── vdi_7.png │ │ │ └── vdi_8.png │ ├── README.md │ ├── Rmpi │ │ ├── README.md │ │ ├── mpi_test.R │ │ ├── mpi_test.Rout │ │ └── run.sbatch │ ├── figures │ │ └── png │ │ │ ├── HPCschematic.png │ │ │ └── HPCschematicTypes.png │ ├── future │ │ ├── README.md │ │ ├── Rhybrid.log │ │ ├── future_hybrid.R │ │ ├── future_hybrid.Rout │ │ ├── future_slow_square.R │ │ ├── future_slow_square.Rout │ │ ├── future_slurm.tmpl │ │ ├── run_future.sbatch │ │ └── run_hybrid.sbatch │ └── pbdMPI │ │ ├── README.md │ │ ├── pbdApply.R │ │ ├── pbdApply.Rout │ │ ├── pbdLapply.R │ │ ├── pbdLapply.Rout │ │ ├── run_Lapply.sbatch │ │ ├── run_apply.sbatch │ │ ├── run_scatter.sbatch │ │ ├── scatter.R │ │ └── scatter.Rout ├── README.md ├── STATA │ ├── Example1 │ │ ├── README.md │ │ ├── run.sbatch │ │ └── test.do │ └── README.md └── ScaLAPACK │ ├── Example1 │ ├── Makefile │ ├── README.md │ ├── psgesv.f90 │ └── run.sbatch │ └── README.md ├── Performance └── TAU │ ├── Example1 │ ├── README.md │ ├── mpi4py_test.py │ ├── profile.0.0.0 │ ├── profile.1.0.0 │ ├── profile.2.0.0 │ ├── profile.3.0.0 │ ├── run.sbatch │ ├── tau01.gif │ ├── tau02.gif │ ├── tau03.gif │ ├── tau04.gif │ ├── tau05.gif │ └── tau07.gif │ ├── Images │ └── tau-logo.png │ └── README.md ├── README.md ├── Singularity_Containers ├── MPI_Apps │ ├── README.md │ ├── compile_openmpi.sh │ ├── mpi_test.out │ ├── mpich_test.def │ ├── mpitest.f90 │ ├── openmpi_test_centos7.def │ ├── run.sbatch.mpich │ └── run.sbatch.ompi ├── OMP_Apps │ ├── README.md │ ├── omp_dot.c │ ├── omp_dot.dat │ ├── omp_dot.def │ └── run.sbatch └── README.md └── Training └── Advanced_Cluster_Usage ├── Exercise1 ├── C │ ├── Makefile │ ├── README.md │ ├── mem_test.c │ └── run.sbatch ├── Cpp │ ├── Makefile │ ├── README.md │ ├── mem_test.cpp │ └── run.sbatch ├── Fortran │ ├── Makefile │ ├── README.md │ ├── mem_test.f90 │ └── run.sbatch ├── Python │ ├── README.md │ ├── mem_test.py │ └── run_python.sbatch ├── R │ ├── README.md │ ├── mem_test.R │ └── run_r.sbatch └── README.md ├── Exercise2 ├── C │ ├── Makefile │ ├── README.md │ ├── omp_mem_test.c │ └── run.sbatch ├── Cpp │ ├── Makefile │ ├── README.md │ ├── omp_mem_test.cpp │ └── run.sbatch ├── Fortran │ ├── Makefile │ ├── README.md │ ├── omp_mem_test.f90 │ ├── rng_module.mod │ └── run.sbatch ├── Python │ ├── README.md │ ├── mp_mem_test.py │ └── run.sbatch ├── R │ ├── README.md │ ├── mp_mem_test.R │ └── run.sbatch └── README.md ├── Exercise3 ├── C │ ├── Makefile │ ├── README.md │ ├── omp_pi.c │ ├── run.sbatch │ ├── run_speedup.sbatch │ ├── scaling_results.txt │ ├── speedup.png │ └── speedup.py ├── Cpp │ ├── Makefile │ ├── README.md │ ├── omp_pi.cpp │ ├── run.sbatch │ ├── run_speedup.sbatch │ ├── scaling_results.txt │ ├── speedup.png │ └── speedup.py ├── Fortran │ ├── Makefile │ ├── README.md │ ├── omp_pi.f90 │ ├── run.sbatch │ ├── run_speedup.sbatch │ ├── scaling_results.txt │ ├── speedup.png │ └── speedup.py ├── Python │ ├── README.md │ ├── mp_pi.py │ ├── run.sbatch │ ├── run_speedup.sbatch │ ├── scaling_results.txt │ ├── speedup.png │ └── speedup.py ├── R │ ├── README.md │ ├── mp_pi.R │ ├── run.sbatch │ ├── run_speedup.sbatch │ ├── scaling_results.txt │ ├── speedup.png │ └── speedup.py ├── README.md └── run_speedup.sbatch ├── Exercise4 ├── Makefile ├── README.md ├── pi_monte_carlo.f90 ├── pi_monte_carlo.out ├── run.sbatch ├── run2.sbatch ├── run_speedup.sbatch ├── run_speedup2.sbatch ├── scaling_results.txt ├── scaling_results2.txt ├── speedup.png ├── speedup2.png ├── speedup_figure.out ├── speedup_mpi.py └── speedup_mpi2.py ├── Exercise5 ├── Makefile ├── README.md ├── external_libs.f90 ├── planczos.out ├── planczos2.f90 └── run.sbatch ├── Exercise6 ├── Makefile ├── 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