├── .gitignore ├── LICENSE ├── README.md ├── file-per-process ├── batch_scripts │ └── archer.pbs └── source │ ├── Makefile │ ├── benchclock.f90 │ ├── benchio_fpp.F90 │ └── multifile.F90 └── shared-file └── source ├── Makefile ├── benchclock.f90 ├── benchio.F90 ├── hdf5.F90 ├── mpiio.F90 ├── netcdf.F90 └── run_scripts └── archer.pbs /.gitignore: -------------------------------------------------------------------------------- 1 | *.mod 2 | *.MOD 3 | *.o 4 | *.x 5 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. By contrast, 15 | the GNU General Public License is intended to guarantee your freedom to 16 | share and change all versions of a program--to make sure it remains free 17 | software for all its users. We, the Free Software Foundation, use the 18 | GNU General Public License for most of our software; it applies also to 19 | any other work released this way by its authors. You can apply it to 20 | your programs, too. 21 | 22 | When we speak of free software, we are referring to freedom, not 23 | price. Our General Public Licenses are designed to make sure that you 24 | have the freedom to distribute copies of free software (and charge for 25 | them if you wish), that you receive source code or can get it if you 26 | want it, that you can change the software or use pieces of it in new 27 | free programs, and that you know you can do these things. 28 | 29 | To protect your rights, we need to prevent others from denying you 30 | these rights or asking you to surrender the rights. Therefore, you have 31 | certain responsibilities if you distribute copies of the software, or if 32 | you modify it: responsibilities to respect the freedom of others. 33 | 34 | For example, if you distribute copies of such a program, whether 35 | gratis or for a fee, you must pass on to the recipients the same 36 | freedoms that you received. You must make sure that they, too, receive 37 | or can get the source code. And you must show them these terms so they 38 | know their rights. 39 | 40 | Developers that use the GNU GPL protect your rights with two steps: 41 | (1) assert copyright on the software, and (2) offer you this License 42 | giving you legal permission to copy, distribute and/or modify it. 43 | 44 | For the developers' and authors' protection, the GPL clearly explains 45 | that there is no warranty for this free software. For both users' and 46 | authors' sake, the GPL requires that modified versions be marked as 47 | changed, so that their problems will not be attributed erroneously to 48 | authors of previous versions. 49 | 50 | Some devices are designed to deny users access to install or run 51 | modified versions of the software inside them, although the manufacturer 52 | can do so. This is fundamentally incompatible with the aim of 53 | protecting users' freedom to change the software. The systematic 54 | pattern of such abuse occurs in the area of products for individuals to 55 | use, which is precisely where it is most unacceptable. Therefore, we 56 | have designed this version of the GPL to prohibit the practice for those 57 | products. If such problems arise substantially in other domains, we 58 | stand ready to extend this provision to those domains in future versions 59 | of the GPL, as needed to protect the freedom of users. 60 | 61 | Finally, every program is threatened constantly by software patents. 62 | States should not allow patents to restrict development and use of 63 | software on general-purpose computers, but in those that do, we wish to 64 | avoid the special danger that patents applied to a free program could 65 | make it effectively proprietary. To prevent this, the GPL assures that 66 | patents cannot be used to render the program non-free. 67 | 68 | The precise terms and conditions for copying, distribution and 69 | modification follow. 70 | 71 | TERMS AND CONDITIONS 72 | 73 | 0. Definitions. 74 | 75 | "This License" refers to version 3 of the GNU General Public License. 76 | 77 | "Copyright" also means copyright-like laws that apply to other kinds of 78 | works, such as semiconductor masks. 79 | 80 | "The Program" refers to any copyrightable work licensed under this 81 | License. Each licensee is addressed as "you". "Licensees" and 82 | "recipients" may be individuals or organizations. 83 | 84 | To "modify" a work means to copy from or adapt all or part of the work 85 | in a fashion requiring copyright permission, other than the making of an 86 | exact copy. The resulting work is called a "modified version" of the 87 | earlier work or a work "based on" the earlier work. 88 | 89 | A "covered work" means either the unmodified Program or a work based 90 | on the Program. 91 | 92 | To "propagate" a work means to do anything with it that, without 93 | permission, would make you directly or secondarily liable for 94 | infringement under applicable copyright law, except executing it on a 95 | computer or modifying a private copy. Propagation includes copying, 96 | distribution (with or without modification), making available to the 97 | public, and in some countries other activities as well. 98 | 99 | To "convey" a work means any kind of propagation that enables other 100 | parties to make or receive copies. Mere interaction with a user through 101 | a computer network, with no transfer of a copy, is not conveying. 102 | 103 | An interactive user interface displays "Appropriate Legal Notices" 104 | to the extent that it includes a convenient and prominently visible 105 | feature that (1) displays an appropriate copyright notice, and (2) 106 | tells the user that there is no warranty for the work (except to the 107 | extent that warranties are provided), that licensees may convey the 108 | work under this License, and how to view a copy of this License. If 109 | the interface presents a list of user commands or options, such as a 110 | menu, a prominent item in the list meets this criterion. 111 | 112 | 1. Source Code. 113 | 114 | The "source code" for a work means the preferred form of the work 115 | for making modifications to it. "Object code" means any non-source 116 | form of a work. 117 | 118 | A "Standard Interface" means an interface that either is an official 119 | standard defined by a recognized standards body, or, in the case of 120 | interfaces specified for a particular programming language, one that 121 | is widely used among developers working in that language. 122 | 123 | The "System Libraries" of an executable work include anything, other 124 | than the work as a whole, that (a) is included in the normal form of 125 | packaging a Major Component, but which is not part of that Major 126 | Component, and (b) serves only to enable use of the work with that 127 | Major Component, or to implement a Standard Interface for which an 128 | implementation is available to the public in source code form. A 129 | "Major Component", in this context, means a major essential component 130 | (kernel, window system, and so on) of the specific operating system 131 | (if any) on which the executable work runs, or a compiler used to 132 | produce the work, or an object code interpreter used to run it. 133 | 134 | The "Corresponding Source" for a work in object code form means all 135 | the source code needed to generate, install, and (for an executable 136 | work) run the object code and to modify the work, including scripts to 137 | control those activities. However, it does not include the work's 138 | System Libraries, or general-purpose tools or generally available free 139 | programs which are used unmodified in performing those activities but 140 | which are not part of the work. For example, Corresponding Source 141 | includes interface definition files associated with source files for 142 | the work, and the source code for shared libraries and dynamically 143 | linked subprograms that the work is specifically designed to require, 144 | such as by intimate data communication or control flow between those 145 | subprograms and other parts of the work. 146 | 147 | The Corresponding Source need not include anything that users 148 | can regenerate automatically from other parts of the Corresponding 149 | Source. 150 | 151 | The Corresponding Source for a work in source code form is that 152 | same work. 153 | 154 | 2. Basic Permissions. 155 | 156 | All rights granted under this License are granted for the term of 157 | copyright on the Program, and are irrevocable provided the stated 158 | conditions are met. This License explicitly affirms your unlimited 159 | permission to run the unmodified Program. The output from running a 160 | covered work is covered by this License only if the output, given its 161 | content, constitutes a covered work. This License acknowledges your 162 | rights of fair use or other equivalent, as provided by copyright law. 163 | 164 | You may make, run and propagate covered works that you do not 165 | convey, without conditions so long as your license otherwise remains 166 | in force. You may convey covered works to others for the sole purpose 167 | of having them make modifications exclusively for you, or provide you 168 | with facilities for running those works, provided that you comply with 169 | the terms of this License in conveying all material for which you do 170 | not control copyright. Those thus making or running the covered works 171 | for you must do so exclusively on your behalf, under your direction 172 | and control, on terms that prohibit them from making any copies of 173 | your copyrighted material outside their relationship with you. 174 | 175 | Conveying under any other circumstances is permitted solely under 176 | the conditions stated below. Sublicensing is not allowed; section 10 177 | makes it unnecessary. 178 | 179 | 3. Protecting Users' Legal Rights From Anti-Circumvention Law. 180 | 181 | No covered work shall be deemed part of an effective technological 182 | measure under any applicable law fulfilling obligations under article 183 | 11 of the WIPO copyright treaty adopted on 20 December 1996, or 184 | similar laws prohibiting or restricting circumvention of such 185 | measures. 186 | 187 | When you convey a covered work, you waive any legal power to forbid 188 | circumvention of technological measures to the extent such circumvention 189 | is effected by exercising rights under this License with respect to 190 | the covered work, and you disclaim any intention to limit operation or 191 | modification of the work as a means of enforcing, against the work's 192 | users, your or third parties' legal rights to forbid circumvention of 193 | technological measures. 194 | 195 | 4. Conveying Verbatim Copies. 196 | 197 | You may convey verbatim copies of the Program's source code as you 198 | receive it, in any medium, provided that you conspicuously and 199 | appropriately publish on each copy an appropriate copyright notice; 200 | keep intact all notices stating that this License and any 201 | non-permissive terms added in accord with section 7 apply to the code; 202 | keep intact all notices of the absence of any warranty; and give all 203 | recipients a copy of this License along with the Program. 204 | 205 | You may charge any price or no price for each copy that you convey, 206 | and you may offer support or warranty protection for a fee. 207 | 208 | 5. Conveying Modified Source Versions. 209 | 210 | You may convey a work based on the Program, or the modifications to 211 | produce it from the Program, in the form of source code under the 212 | terms of section 4, provided that you also meet all of these conditions: 213 | 214 | a) The work must carry prominent notices stating that you modified 215 | it, and giving a relevant date. 216 | 217 | b) The work must carry prominent notices stating that it is 218 | released under this License and any conditions added under section 219 | 7. This requirement modifies the requirement in section 4 to 220 | "keep intact all notices". 221 | 222 | c) You must license the entire work, as a whole, under this 223 | License to anyone who comes into possession of a copy. This 224 | License will therefore apply, along with any applicable section 7 225 | additional terms, to the whole of the work, and all its parts, 226 | regardless of how they are packaged. This License gives no 227 | permission to license the work in any other way, but it does not 228 | invalidate such permission if you have separately received it. 229 | 230 | d) If the work has interactive user interfaces, each must display 231 | Appropriate Legal Notices; however, if the Program has interactive 232 | interfaces that do not display Appropriate Legal Notices, your 233 | work need not make them do so. 234 | 235 | A compilation of a covered work with other separate and independent 236 | works, which are not by their nature extensions of the covered work, 237 | and which are not combined with it such as to form a larger program, 238 | in or on a volume of a storage or distribution medium, is called an 239 | "aggregate" if the compilation and its resulting copyright are not 240 | used to limit the access or legal rights of the compilation's users 241 | beyond what the individual works permit. Inclusion of a covered work 242 | in an aggregate does not cause this License to apply to the other 243 | parts of the aggregate. 244 | 245 | 6. Conveying Non-Source Forms. 246 | 247 | You may convey a covered work in object code form under the terms 248 | of sections 4 and 5, provided that you also convey the 249 | machine-readable Corresponding Source under the terms of this License, 250 | in one of these ways: 251 | 252 | a) Convey the object code in, or embodied in, a physical product 253 | (including a physical distribution medium), accompanied by the 254 | Corresponding Source fixed on a durable physical medium 255 | customarily used for software interchange. 256 | 257 | b) Convey the object code in, or embodied in, a physical product 258 | (including a physical distribution medium), accompanied by a 259 | written offer, valid for at least three years and valid for as 260 | long as you offer spare parts or customer support for that product 261 | model, to give anyone who possesses the object code either (1) a 262 | copy of the Corresponding Source for all the software in the 263 | product that is covered by this License, on a durable physical 264 | medium customarily used for software interchange, for a price no 265 | more than your reasonable cost of physically performing this 266 | conveying of source, or (2) access to copy the 267 | Corresponding Source from a network server at no charge. 268 | 269 | c) Convey individual copies of the object code with a copy of the 270 | written offer to provide the Corresponding Source. This 271 | alternative is allowed only occasionally and noncommercially, and 272 | only if you received the object code with such an offer, in accord 273 | with subsection 6b. 274 | 275 | d) Convey the object code by offering access from a designated 276 | place (gratis or for a charge), and offer equivalent access to the 277 | Corresponding Source in the same way through the same place at no 278 | further charge. You need not require recipients to copy the 279 | Corresponding Source along with the object code. If the place to 280 | copy the object code is a network server, the Corresponding Source 281 | may be on a different server (operated by you or a third party) 282 | that supports equivalent copying facilities, provided you maintain 283 | clear directions next to the object code saying where to find the 284 | Corresponding Source. Regardless of what server hosts the 285 | Corresponding Source, you remain obligated to ensure that it is 286 | available for as long as needed to satisfy these requirements. 287 | 288 | e) Convey the object code using peer-to-peer transmission, provided 289 | you inform other peers where the object code and Corresponding 290 | Source of the work are being offered to the general public at no 291 | charge under subsection 6d. 292 | 293 | A separable portion of the object code, whose source code is excluded 294 | from the Corresponding Source as a System Library, need not be 295 | included in conveying the object code work. 296 | 297 | A "User Product" is either (1) a "consumer product", which means any 298 | tangible personal property which is normally used for personal, family, 299 | or household purposes, or (2) anything designed or sold for incorporation 300 | into a dwelling. In determining whether a product is a consumer product, 301 | doubtful cases shall be resolved in favor of coverage. For a particular 302 | product received by a particular user, "normally used" refers to a 303 | typical or common use of that class of product, regardless of the status 304 | of the particular user or of the way in which the particular user 305 | actually uses, or expects or is expected to use, the product. A product 306 | is a consumer product regardless of whether the product has substantial 307 | commercial, industrial or non-consumer uses, unless such uses represent 308 | the only significant mode of use of the product. 309 | 310 | "Installation Information" for a User Product means any methods, 311 | procedures, authorization keys, or other information required to install 312 | and execute modified versions of a covered work in that User Product from 313 | a modified version of its Corresponding Source. The information must 314 | suffice to ensure that the continued functioning of the modified object 315 | code is in no case prevented or interfered with solely because 316 | modification has been made. 317 | 318 | If you convey an object code work under this section in, or with, or 319 | specifically for use in, a User Product, and the conveying occurs as 320 | part of a transaction in which the right of possession and use of the 321 | User Product is transferred to the recipient in perpetuity or for a 322 | fixed term (regardless of how the transaction is characterized), the 323 | Corresponding Source conveyed under this section must be accompanied 324 | by the Installation Information. But this requirement does not apply 325 | if neither you nor any third party retains the ability to install 326 | modified object code on the User Product (for example, the work has 327 | been installed in ROM). 328 | 329 | The requirement to provide Installation Information does not include a 330 | requirement to continue to provide support service, warranty, or updates 331 | for a work that has been modified or installed by the recipient, or for 332 | the User Product in which it has been modified or installed. Access to a 333 | network may be denied when the modification itself materially and 334 | adversely affects the operation of the network or violates the rules and 335 | protocols for communication across the network. 336 | 337 | Corresponding Source conveyed, and Installation Information provided, 338 | in accord with this section must be in a format that is publicly 339 | documented (and with an implementation available to the public in 340 | source code form), and must require no special password or key for 341 | unpacking, reading or copying. 342 | 343 | 7. Additional Terms. 344 | 345 | "Additional permissions" are terms that supplement the terms of this 346 | License by making exceptions from one or more of its conditions. 347 | Additional permissions that are applicable to the entire Program shall 348 | be treated as though they were included in this License, to the extent 349 | that they are valid under applicable law. If additional permissions 350 | apply only to part of the Program, that part may be used separately 351 | under those permissions, but the entire Program remains governed by 352 | this License without regard to the additional permissions. 353 | 354 | When you convey a copy of a covered work, you may at your option 355 | remove any additional permissions from that copy, or from any part of 356 | it. (Additional permissions may be written to require their own 357 | removal in certain cases when you modify the work.) You may place 358 | additional permissions on material, added by you to a covered work, 359 | for which you have or can give appropriate copyright permission. 360 | 361 | Notwithstanding any other provision of this License, for material you 362 | add to a covered work, you may (if authorized by the copyright holders of 363 | that material) supplement the terms of this License with terms: 364 | 365 | a) Disclaiming warranty or limiting liability differently from the 366 | terms of sections 15 and 16 of this License; or 367 | 368 | b) Requiring preservation of specified reasonable legal notices or 369 | author attributions in that material or in the Appropriate Legal 370 | Notices displayed by works containing it; or 371 | 372 | c) Prohibiting misrepresentation of the origin of that material, or 373 | requiring that modified versions of such material be marked in 374 | reasonable ways as different from the original version; or 375 | 376 | d) Limiting the use for publicity purposes of names of licensors or 377 | authors of the material; or 378 | 379 | e) Declining to grant rights under trademark law for use of some 380 | trade names, trademarks, or service marks; or 381 | 382 | f) Requiring indemnification of licensors and authors of that 383 | material by anyone who conveys the material (or modified versions of 384 | it) with contractual assumptions of liability to the recipient, for 385 | any liability that these contractual assumptions directly impose on 386 | those licensors and authors. 387 | 388 | All other non-permissive additional terms are considered "further 389 | restrictions" within the meaning of section 10. If the Program as you 390 | received it, or any part of it, contains a notice stating that it is 391 | governed by this License along with a term that is a further 392 | restriction, you may remove that term. If a license document contains 393 | a further restriction but permits relicensing or conveying under this 394 | License, you may add to a covered work material governed by the terms 395 | of that license document, provided that the further restriction does 396 | not survive such relicensing or conveying. 397 | 398 | If you add terms to a covered work in accord with this section, you 399 | must place, in the relevant source files, a statement of the 400 | additional terms that apply to those files, or a notice indicating 401 | where to find the applicable terms. 402 | 403 | Additional terms, permissive or non-permissive, may be stated in the 404 | form of a separately written license, or stated as exceptions; 405 | the above requirements apply either way. 406 | 407 | 8. Termination. 408 | 409 | You may not propagate or modify a covered work except as expressly 410 | provided under this License. Any attempt otherwise to propagate or 411 | modify it is void, and will automatically terminate your rights under 412 | this License (including any patent licenses granted under the third 413 | paragraph of section 11). 414 | 415 | However, if you cease all violation of this License, then your 416 | license from a particular copyright holder is reinstated (a) 417 | provisionally, unless and until the copyright holder explicitly and 418 | finally terminates your license, and (b) permanently, if the copyright 419 | holder fails to notify you of the violation by some reasonable means 420 | prior to 60 days after the cessation. 421 | 422 | Moreover, your license from a particular copyright holder is 423 | reinstated permanently if the copyright holder notifies you of the 424 | violation by some reasonable means, this is the first time you have 425 | received notice of violation of this License (for any work) from that 426 | copyright holder, and you cure the violation prior to 30 days after 427 | your receipt of the notice. 428 | 429 | Termination of your rights under this section does not terminate the 430 | licenses of parties who have received copies or rights from you under 431 | this License. If your rights have been terminated and not permanently 432 | reinstated, you do not qualify to receive new licenses for the same 433 | material under section 10. 434 | 435 | 9. Acceptance Not Required for Having Copies. 436 | 437 | You are not required to accept this License in order to receive or 438 | run a copy of the Program. Ancillary propagation of a covered work 439 | occurring solely as a consequence of using peer-to-peer transmission 440 | to receive a copy likewise does not require acceptance. However, 441 | nothing other than this License grants you permission to propagate or 442 | modify any covered work. These actions infringe copyright if you do 443 | not accept this License. Therefore, by modifying or propagating a 444 | covered work, you indicate your acceptance of this License to do so. 445 | 446 | 10. Automatic Licensing of Downstream Recipients. 447 | 448 | Each time you convey a covered work, the recipient automatically 449 | receives a license from the original licensors, to run, modify and 450 | propagate that work, subject to this License. You are not responsible 451 | for enforcing compliance by third parties with this License. 452 | 453 | An "entity transaction" is a transaction transferring control of an 454 | organization, or substantially all assets of one, or subdividing an 455 | organization, or merging organizations. If propagation of a covered 456 | work results from an entity transaction, each party to that 457 | transaction who receives a copy of the work also receives whatever 458 | licenses to the work the party's predecessor in interest had or could 459 | give under the previous paragraph, plus a right to possession of the 460 | Corresponding Source of the work from the predecessor in interest, if 461 | the predecessor has it or can get it with reasonable efforts. 462 | 463 | You may not impose any further restrictions on the exercise of the 464 | rights granted or affirmed under this License. For example, you may 465 | not impose a license fee, royalty, or other charge for exercise of 466 | rights granted under this License, and you may not initiate litigation 467 | (including a cross-claim or counterclaim in a lawsuit) alleging that 468 | any patent claim is infringed by making, using, selling, offering for 469 | sale, or importing the Program or any portion of it. 470 | 471 | 11. Patents. 472 | 473 | A "contributor" is a copyright holder who authorizes use under this 474 | License of the Program or a work on which the Program is based. The 475 | work thus licensed is called the contributor's "contributor version". 476 | 477 | A contributor's "essential patent claims" are all patent claims 478 | owned or controlled by the contributor, whether already acquired or 479 | hereafter acquired, that would be infringed by some manner, permitted 480 | by this License, of making, using, or selling its contributor version, 481 | but do not include claims that would be infringed only as a 482 | consequence of further modification of the contributor version. For 483 | purposes of this definition, "control" includes the right to grant 484 | patent sublicenses in a manner consistent with the requirements of 485 | this License. 486 | 487 | Each contributor grants you a non-exclusive, worldwide, royalty-free 488 | patent license under the contributor's essential patent claims, to 489 | make, use, sell, offer for sale, import and otherwise run, modify and 490 | propagate the contents of its contributor version. 491 | 492 | In the following three paragraphs, a "patent license" is any express 493 | agreement or commitment, however denominated, not to enforce a patent 494 | (such as an express permission to practice a patent or covenant not to 495 | sue for patent infringement). To "grant" such a patent license to a 496 | party means to make such an agreement or commitment not to enforce a 497 | patent against the party. 498 | 499 | If you convey a covered work, knowingly relying on a patent license, 500 | and the Corresponding Source of the work is not available for anyone 501 | to copy, free of charge and under the terms of this License, through a 502 | publicly available network server or other readily accessible means, 503 | then you must either (1) cause the Corresponding Source to be so 504 | available, or (2) arrange to deprive yourself of the benefit of the 505 | patent license for this particular work, or (3) arrange, in a manner 506 | consistent with the requirements of this License, to extend the patent 507 | license to downstream recipients. "Knowingly relying" means you have 508 | actual knowledge that, but for the patent license, your conveying the 509 | covered work in a country, or your recipient's use of the covered work 510 | in a country, would infringe one or more identifiable patents in that 511 | country that you have reason to believe are valid. 512 | 513 | If, pursuant to or in connection with a single transaction or 514 | arrangement, you convey, or propagate by procuring conveyance of, a 515 | covered work, and grant a patent license to some of the parties 516 | receiving the covered work authorizing them to use, propagate, modify 517 | or convey a specific copy of the covered work, then the patent license 518 | you grant is automatically extended to all recipients of the covered 519 | work and works based on it. 520 | 521 | A patent license is "discriminatory" if it does not include within 522 | the scope of its coverage, prohibits the exercise of, or is 523 | conditioned on the non-exercise of one or more of the rights that are 524 | specifically granted under this License. You may not convey a covered 525 | work if you are a party to an arrangement with a third party that is 526 | in the business of distributing software, under which you make payment 527 | to the third party based on the extent of your activity of conveying 528 | the work, and under which the third party grants, to any of the 529 | parties who would receive the covered work from you, a discriminatory 530 | patent license (a) in connection with copies of the covered work 531 | conveyed by you (or copies made from those copies), or (b) primarily 532 | for and in connection with specific products or compilations that 533 | contain the covered work, unless you entered into that arrangement, 534 | or that patent license was granted, prior to 28 March 2007. 535 | 536 | Nothing in this License shall be construed as excluding or limiting 537 | any implied license or other defenses to infringement that may 538 | otherwise be available to you under applicable patent law. 539 | 540 | 12. No Surrender of Others' Freedom. 541 | 542 | If conditions are imposed on you (whether by court order, agreement or 543 | otherwise) that contradict the conditions of this License, they do not 544 | excuse you from the conditions of this License. If you cannot convey a 545 | covered work so as to satisfy simultaneously your obligations under this 546 | License and any other pertinent obligations, then as a consequence you may 547 | not convey it at all. For example, if you agree to terms that obligate you 548 | to collect a royalty for further conveying from those to whom you convey 549 | the Program, the only way you could satisfy both those terms and this 550 | License would be to refrain entirely from conveying the Program. 551 | 552 | 13. Use with the GNU Affero General Public License. 553 | 554 | Notwithstanding any other provision of this License, you have 555 | permission to link or combine any covered work with a work licensed 556 | under version 3 of the GNU Affero General Public License into a single 557 | combined work, and to convey the resulting work. The terms of this 558 | License will continue to apply to the part which is the covered work, 559 | but the special requirements of the GNU Affero General Public License, 560 | section 13, concerning interaction through a network will apply to the 561 | combination as such. 562 | 563 | 14. Revised Versions of this License. 564 | 565 | The Free Software Foundation may publish revised and/or new versions of 566 | the GNU General Public License from time to time. Such new versions will 567 | be similar in spirit to the present version, but may differ in detail to 568 | address new problems or concerns. 569 | 570 | Each version is given a distinguishing version number. If the 571 | Program specifies that a certain numbered version of the GNU General 572 | Public License "or any later version" applies to it, you have the 573 | option of following the terms and conditions either of that numbered 574 | version or of any later version published by the Free Software 575 | Foundation. If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT 593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY 594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, 595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 596 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM 597 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF 598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 599 | 600 | 16. Limitation of Liability. 601 | 602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 610 | SUCH DAMAGES. 611 | 612 | 17. Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | {one line to give the program's name and a brief idea of what it does.} 635 | Copyright (C) {year} {name of author} 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | {project} Copyright (C) {year} {fullname} 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # benchio 2 | EPCC I/O benchmarking application. Tests write bandwidth to a single shared 3 | file for a given problem size per processor (weak scaling). 4 | 5 | Each test is performed 10 times and the minimum, maximum and average bandwidth 6 | returned. It is recommended that the maximum bandwidth be considered in most 7 | cases, due to variations in I/O performance from user contention. 8 | 9 | Data layout is 3D strided - intended to more closely resemble that of a real 10 | world application than 2D sequential. By default, array size is 256x256x256. 11 | 12 | Supports POSIX (serial), MPI-IO, HDF5 and NetCDF backends. A run will test all 13 | backends included at compile time. 14 | 15 | # Compilation 16 | 17 | Tested under all three programming environments on ARCHER: Cray, GNU, and Intel. 18 | 19 | For an ARCHER build: 20 | 21 | `module load cray-netcdf-hdf5parallel/4.4.0` 22 | 23 | `module load cray-hdf5-parallel/1.8.16` 24 | 25 | `make clean` 26 | 27 | `make` 28 | 29 | For other platforms, edit the `Makefile` to point variables `FC` and `CC` to 30 | MPI compilers (e.g. `mpif90` and `mpicc`), and edit `LFLAGS` to the location of 31 | HDF5 and NetCDF libraries. Then `make clean && make`. 32 | 33 | ## Building with selected backends 34 | 35 | POSIX (serial), MPI-IO, HDF5 and NetCDF backends can be disabled by commenting 36 | out the relevant `FFLAGS` lines in the `Makefile`. e.g. Commenting out: 37 | `FFLAGS+= -DWITH_NETCDF` will build the application with only MPI-IO and HDF5 38 | support. 39 | 40 | # Running 41 | 42 | For example, to test performance with maximum striping on Lustre: 43 | 44 | `mkdir -p benchio_files` 45 | 46 | `lfs setstripe -c -1 benchio_files` 47 | 48 | `aprun -n ./benchio.x` 49 | 50 | Explanation of commands follows: 51 | 52 | The application expects a working directory with subdirectory `benchio_files`. 53 | An I/O error will be thrown if this subdirectory is not present. 54 | 55 | Under Lustre, the appropriate striping patterns should be set on this 56 | subdirectory using the `lfs setstripe` command. 57 | 58 | The `benchio.x` executable should be launched with the platform job launcher, 59 | e.g. `aprun` or `mpirun`. Results are written to STDOUT. 60 | 61 | Complete sample run scripts are included in `source/run_scripts`. 62 | 63 | ## Adjusting volume of data 64 | 65 | The array size (per MPI rank) is controlled through the following constants in 66 | `benchio.F90`: 67 | 68 | `integer, parameter :: n1 = 256` 69 | 70 | `integer, parameter :: n2 = 256` 71 | 72 | `integer, parameter :: n3 = 256` 73 | 74 | -------------------------------------------------------------------------------- /file-per-process/batch_scripts/archer.pbs: -------------------------------------------------------------------------------- 1 | #!/bin/bash --login 2 | 3 | #PBS -l select=1 4 | #PBS -l walltime=0:20:00 5 | #PBS -N benchio 6 | #PBS -A z19-cse 7 | 8 | cd $PBS_O_WORKDIR 9 | mkdir -p defstriped 10 | mkdir -p striped 11 | mkdir -p unstriped 12 | lfs setstripe -c -1 striped 13 | lfs setstripe -c 1 unstriped 14 | 15 | # Run tests 16 | aprun -n 24 ./benchio.x 17 | 18 | -------------------------------------------------------------------------------- /file-per-process/source/Makefile: -------------------------------------------------------------------------------- 1 | MF= Makefile 2 | 3 | # Compilers 4 | FC= ftn 5 | CC= cc 6 | # 7 | # 8 | FFLAGS= -g 9 | 10 | # Comment out a line below to disable the named tests 11 | 12 | CFLAGS= $(FFLAGS) 13 | LFLAGS= 14 | # 15 | EXE= benchio_fpp.x 16 | # 17 | FSRC= \ 18 | multifile.F90 \ 19 | benchclock.f90 \ 20 | benchio_fpp.F90 21 | 22 | CSRC= 23 | 24 | # .SUFFIXES: 25 | .SUFFIXES: .F90 .f90 .c .o 26 | 27 | FOBJ= $(FSRC:.F90=.o) 28 | OBJ= $(FOBJ:.f90=.o) $(CSRC:.c=.o) 29 | 30 | FMOD= $(FSRC:.F90=.mod) 31 | MOD= $(FMOD:.f90=.mod) 32 | 33 | .F90.o: 34 | $(FC) $(FFLAGS) -c $< 35 | 36 | .f90.o: 37 | $(FC) $(FFLAGS) -c $< 38 | 39 | .c.o: 40 | $(CC) $(CFLAGS) -c $< 41 | 42 | all: $(EXE) 43 | 44 | $(EXE): $(OBJ) 45 | $(FC) $(FFLAGS) -o $@ $(OBJ) $(LFLAGS) 46 | 47 | $(OBJ): $(MF) 48 | 49 | clean: 50 | rm -f $(OBJ) $(EXE) $(MOD) core 51 | -------------------------------------------------------------------------------- /file-per-process/source/benchclock.f90: -------------------------------------------------------------------------------- 1 | module benchclock 2 | 3 | implicit none 4 | 5 | logical, save, private :: firstcall = .true. 6 | double precision, save, private :: ticktime = 0.0 7 | 8 | integer, parameter :: int32kind = selected_int_kind( 9) 9 | integer, parameter :: int64kind = selected_int_kind(18) 10 | 11 | ! 12 | ! Select high resolution clock 13 | ! 14 | 15 | integer, parameter :: intkind = int64kind 16 | integer(kind = intkind) :: count,rate 17 | 18 | contains 19 | 20 | double precision function benchtime() 21 | 22 | double precision :: dummy 23 | 24 | ! Ensure clock is initialised 25 | 26 | if (firstcall) dummy = benchtick() 27 | 28 | call system_clock(count) 29 | 30 | benchtime = dble(count)*ticktime 31 | 32 | end function benchtime 33 | 34 | 35 | double precision function benchtick() 36 | 37 | if (firstcall) then 38 | 39 | firstcall = .false. 40 | call system_clock(count, rate) 41 | ticktime = 1.0d0/dble(rate) 42 | 43 | end if 44 | 45 | benchtick = ticktime 46 | 47 | end function benchtick 48 | 49 | end module benchclock 50 | 51 | 52 | 53 | -------------------------------------------------------------------------------- /file-per-process/source/benchio_fpp.F90: -------------------------------------------------------------------------------- 1 | program benchio 2 | 3 | use benchclock 4 | use mpi 5 | use mpifile 6 | 7 | implicit none 8 | 9 | integer, parameter :: iolayerstart = 1 10 | integer, parameter :: iolayerend = 1 11 | integer, parameter :: numiolayer = 1 12 | integer, parameter :: numstriping = 3 13 | integer, parameter :: maxlen = 64 14 | integer, parameter :: numrep = 10 15 | 16 | character*(maxlen), dimension(numiolayer) :: iostring, iolayername 17 | character*(maxlen), dimension(numstriping) :: stripestring 18 | 19 | character*(maxlen) :: filename 20 | 21 | integer :: iolayer, istriping, irep 22 | 23 | ! Set local array size - global sizes l1, l2 and l3 are scaled 24 | ! by number of processes in each dimension 25 | 26 | ! Due to Fortran IO agressive buffering you need to 27 | ! make sure that this size is larger than file cache 28 | integer, parameter :: n1 = 512 29 | integer, parameter :: n2 = 512 30 | integer, parameter :: n3 = 512 31 | integer, parameter :: ndim = 3 32 | 33 | integer :: i1, i2, i3, j1, j2, j3, l1, l2, l3, p1, p2, p3 34 | 35 | double precision :: iodata(0:n1+1, 0:n2+1, 0:n3+1) 36 | 37 | integer :: rank, size, ierr, comm, cartcomm, dblesize 38 | integer, dimension(ndim) :: dims, coords 39 | 40 | integer, parameter :: iounit = 12 41 | integer, parameter :: mib = 1024*1024 42 | 43 | logical :: reorder = .false. 44 | logical, dimension(ndim) :: periods = [.false., .false., .false.] 45 | 46 | double precision :: t0, t1, time, iorate, mibdata 47 | double precision :: mintime, maxiorate, avgtime, avgiorate 48 | 49 | iostring(1) = 'File per process' 50 | 51 | iolayername(1) = 'fpp' 52 | 53 | stripestring(1) = 'unstriped' 54 | stripestring(2) = 'striped' 55 | stripestring(3) = 'defstriped' 56 | 57 | call MPI_Init(ierr) 58 | 59 | comm = MPI_COMM_WORLD 60 | 61 | call MPI_Comm_size(comm, size, ierr) 62 | call MPI_Comm_rank(comm, rank, ierr) 63 | 64 | dims(:) = 0 65 | 66 | ! Set 3D processor grid 67 | 68 | call MPI_Dims_create(size, ndim, dims, ierr) 69 | 70 | ! Reverse dimensions as MPI assumes C ordering (this is not essential) 71 | 72 | p1 = dims(3) 73 | p2 = dims(2) 74 | p3 = dims(1) 75 | 76 | ! Compute global sizes 77 | 78 | l1 = p1*n1 79 | l2 = p2*n2 80 | l3 = p3*n3 81 | 82 | call MPI_Type_size(MPI_DOUBLE_PRECISION, dblesize, ierr) 83 | 84 | mibdata = float(dblesize*n1*n2*n3)*float(p1*p2*p3)/float(mib) 85 | 86 | if (rank == 0) then 87 | write(*,*) 88 | write(*,*) 'Simple Parallel IO benchmark' 89 | write(*,*) '----------------------------' 90 | write(*,*) 91 | write(*,*) 'Running on ', size, ' process(es)' 92 | write(*,*) 'Process grid is (', p1, ', ', p2, ', ', p3, ')' 93 | write(*,*) 'Array size is (', n1, ', ', n2, ', ', n3, ')' 94 | write(*,*) 'Global size is (', l1, ', ', l2, ', ', l3, ')' 95 | write(*,*) 96 | write(*,*) 'Total amount of data = ', mibdata, ' MiB' 97 | write(*,*) 98 | write(*,*) 'Clock resolution is ', benchtick()*1.0e6, ', usecs' 99 | end if 100 | 101 | dims(1) = p1 102 | dims(2) = p2 103 | dims(3) = p3 104 | 105 | call MPI_Cart_create(comm, ndim, dims, periods, reorder, cartcomm, ierr) 106 | 107 | ! Set halos to illegal values 108 | 109 | iodata(:,:,:) = -1 110 | 111 | ! Set iodata core to have unique values 1, 2, ..., p1*n1*p2*n2*p3*n3 112 | 113 | call MPI_Cart_coords(cartcomm, rank, ndim, coords, ierr) 114 | 115 | do i3 = 1, n3 116 | do i2 = 1, n2 117 | do i1 = 1, n1 118 | 119 | j1 = coords(1)*n1 + i1 120 | j2 = coords(2)*n2 + i2 121 | j3 = coords(3)*n3 + i3 122 | 123 | iodata(i1,i2,i3) = (j3-1)*l1*l2 + (j2-1)*l1 + j1 124 | 125 | end do 126 | end do 127 | end do 128 | 129 | do iolayer = iolayerstart, iolayerend 130 | 131 | if (rank == 0) then 132 | write(*,*) 133 | write(*,*) '------' 134 | write(*,*) iostring(iolayer) 135 | write(*,*) '------' 136 | write(*,*) 137 | end if 138 | 139 | do istriping = 1, numstriping 140 | 141 | filename = trim(stripestring(istriping))//'/'//trim(iolayername(iolayer)) 142 | 143 | if (rank == 0) then 144 | write(*,*) 'Writing to ', filename 145 | mintime = 0 146 | maxiorate = 0 147 | avgtime = 0 148 | avgiorate = 0 149 | end if 150 | 151 | do irep = 1, numrep 152 | call MPI_Barrier(comm, ierr) 153 | if (rank == 0) then 154 | t0 = benchtime() 155 | end if 156 | 157 | select case (iolayer) 158 | 159 | case(1) 160 | call multiwrite(filename, iodata, n1, n2, n3, cartcomm) 161 | 162 | case default 163 | write(*,*) 'Illegal value of iolayer = ', iolayer 164 | stop 165 | 166 | end select 167 | 168 | call MPI_Barrier(comm, ierr) 169 | if (rank == 0) then 170 | t1 = benchtime() 171 | 172 | time = t1 - t0 173 | iorate = mibdata/time 174 | avgtime = avgtime + time/numrep 175 | avgiorate = avgiorate + iorate/numrep 176 | 177 | if (maxiorate < iorate) then 178 | maxiorate = iorate 179 | mintime = time 180 | end if 181 | 182 | write(*,*) 'time = ', time, ', rate = ', iorate, ' MiB/s' 183 | end if 184 | call multidelete(filename, cartcomm) 185 | end do 186 | if (rank == 0) then 187 | write(*,*) 'mintime = ', mintime, ', maxrate = ', maxiorate, ' MiB/s' 188 | write(*,*) 'avgtime = ', avgtime, ', avgrate = ', avgiorate, ' MiB/s' 189 | write(*,*) 190 | end if 191 | end do 192 | end do 193 | 194 | if (rank == 0) then 195 | write(*,*) 196 | write(*,*) '--------' 197 | write(*,*) 'Finished' 198 | write(*,*) '--------' 199 | write(*,*) 200 | end if 201 | 202 | call MPI_Finalize(ierr) 203 | 204 | end program benchio 205 | -------------------------------------------------------------------------------- /file-per-process/source/multifile.F90: -------------------------------------------------------------------------------- 1 | module mpifile 2 | 3 | use mpi 4 | implicit none 5 | 6 | contains 7 | 8 | ! Write data to multiple files 9 | subroutine multiwrite(filestem, iodata, n1, n2, n3, cartcomm) 10 | 11 | character*(*) :: filestem 12 | 13 | integer :: n1, n2, n3 14 | double precision, dimension(0:n1+1,0:n2+1,0:n3+1) :: iodata 15 | 16 | integer :: cartcomm, ierr, rank, size 17 | integer, parameter :: iounit = 10 18 | character(len=6) :: crank 19 | character(len=50) :: filename 20 | 21 | integer :: i 22 | 23 | call MPI_Comm_size(cartcomm, size, ierr) 24 | call MPI_Comm_rank(cartcomm, rank, ierr) 25 | 26 | write(crank, "(I0.6)") rank 27 | filename = trim(filestem)//crank 28 | open(file=filename, unit=iounit, access='stream') 29 | 30 | write(unit=iounit) iodata(1:n1, 1:n2, 1:n3) 31 | 32 | close(iounit) 33 | 34 | end subroutine multiwrite 35 | 36 | subroutine multidelete(filestem, cartcomm) 37 | 38 | implicit none 39 | 40 | character *(*) :: filestem 41 | integer, parameter :: iounit = 15 42 | integer :: cartcomm, ierr, rank, size 43 | integer :: stat 44 | character(len=6) :: crank 45 | character(len=50) :: filename 46 | 47 | call MPI_Comm_size(cartcomm, size, ierr) 48 | call MPI_Comm_rank(cartcomm, rank, ierr) 49 | 50 | write(crank, "(I0.6)") rank 51 | filename = trim(filestem)//crank 52 | open(unit=iounit, iostat=stat, file=filename, status='old') 53 | if (stat.eq.0) close(unit=iounit, status='delete') 54 | 55 | end subroutine multidelete 56 | 57 | 58 | end module mpifile 59 | -------------------------------------------------------------------------------- /shared-file/source/Makefile: -------------------------------------------------------------------------------- 1 | MF= Makefile 2 | 3 | # Compilers 4 | FC= ftn 5 | CC= cc 6 | # 7 | # 8 | FFLAGS= -g 9 | 10 | # Comment out a line below to disable the named tests 11 | FFLAGS+= -DWITH_SERIAL 12 | FFLAGS+= -DWITH_MPIIO 13 | FFLAGS+= -DWITH_HDF5 14 | FFLAGS+= -DWITH_NETCDF 15 | 16 | CFLAGS= $(FFLAGS) 17 | LFLAGS= 18 | # 19 | EXE= benchio.x 20 | # 21 | FSRC= \ 22 | mpiio.F90 \ 23 | netcdf.F90 \ 24 | hdf5.F90 \ 25 | benchclock.f90 \ 26 | benchio.F90 27 | 28 | CSRC= 29 | 30 | # .SUFFIXES: 31 | .SUFFIXES: .F90 .f90 .c .o 32 | 33 | FOBJ= $(FSRC:.F90=.o) 34 | OBJ= $(FOBJ:.f90=.o) $(CSRC:.c=.o) 35 | 36 | FMOD= $(FSRC:.F90=.mod) 37 | MOD= $(FMOD:.f90=.mod) 38 | 39 | .F90.o: 40 | $(FC) $(FFLAGS) -c $< 41 | 42 | .f90.o: 43 | $(FC) $(FFLAGS) -c $< 44 | 45 | .c.o: 46 | $(CC) $(CFLAGS) -c $< 47 | 48 | all: $(EXE) 49 | 50 | $(EXE): $(OBJ) 51 | $(FC) $(FFLAGS) -o $@ $(OBJ) $(LFLAGS) 52 | 53 | $(OBJ): $(MF) 54 | 55 | clean: 56 | rm -f $(OBJ) $(EXE) $(MOD) core 57 | -------------------------------------------------------------------------------- /shared-file/source/benchclock.f90: -------------------------------------------------------------------------------- 1 | module benchclock 2 | 3 | implicit none 4 | 5 | logical, save, private :: firstcall = .true. 6 | double precision, save, private :: ticktime = 0.0 7 | 8 | integer, parameter :: int32kind = selected_int_kind( 9) 9 | integer, parameter :: int64kind = selected_int_kind(18) 10 | 11 | ! 12 | ! Select high resolution clock 13 | ! 14 | 15 | integer, parameter :: intkind = int64kind 16 | integer(kind = intkind) :: count,rate 17 | 18 | contains 19 | 20 | double precision function benchtime() 21 | 22 | double precision :: dummy 23 | 24 | ! Ensure clock is initialised 25 | 26 | if (firstcall) dummy = benchtick() 27 | 28 | call system_clock(count) 29 | 30 | benchtime = dble(count)*ticktime 31 | 32 | end function benchtime 33 | 34 | 35 | double precision function benchtick() 36 | 37 | if (firstcall) then 38 | 39 | firstcall = .false. 40 | call system_clock(count, rate) 41 | ticktime = 1.0d0/dble(rate) 42 | 43 | end if 44 | 45 | benchtick = ticktime 46 | 47 | end function benchtick 48 | 49 | end module benchclock 50 | 51 | 52 | 53 | -------------------------------------------------------------------------------- /shared-file/source/benchio.F90: -------------------------------------------------------------------------------- 1 | program benchio 2 | 3 | use benchclock 4 | use mpi 5 | use mpiio 6 | use iohdf5 7 | use ionetcdf 8 | 9 | implicit none 10 | 11 | integer, parameter :: numiolayer = 4 12 | integer, parameter :: maxlen = 64 13 | integer, parameter :: numrep = 10 14 | 15 | character*(maxlen), dimension(numiolayer) :: iostring, iolayername 16 | 17 | character*(maxlen) :: filedir, filename 18 | 19 | integer :: iolayer, irep 20 | 21 | ! Set local array size - global sizes l1, l2 and l3 are scaled 22 | ! by number of processes in each dimension 23 | 24 | integer, parameter :: n1 = 256 25 | integer, parameter :: n2 = 256 26 | integer, parameter :: n3 = 256 27 | integer, parameter :: ndim = 3 28 | 29 | integer :: i1, i2, i3, j1, j2, j3, l1, l2, l3, p1, p2, p3 30 | 31 | double precision :: iodata(0:n1+1, 0:n2+1, 0:n3+1) 32 | 33 | integer :: rank, size, ierr, comm, cartcomm, dblesize 34 | integer, dimension(ndim) :: dims, coords 35 | 36 | integer, parameter :: iounit = 12 37 | integer, parameter :: mib = 1024*1024 38 | 39 | logical :: reorder = .false. 40 | logical, dimension(ndim) :: periods = [.false., .false., .false.] 41 | 42 | double precision :: t0, t1, time, iorate, mibdata 43 | double precision :: mintime, maxiorate, avgtime, avgiorate 44 | 45 | iostring(1) = 'Serial' 46 | iostring(2) = 'MPI-IO' 47 | iostring(3) = ' HDF5 ' 48 | iostring(4) = 'NetCDF' 49 | 50 | iolayername(1) = 'serial.dat' 51 | iolayername(2) = 'mpiio.dat' 52 | iolayername(3) = 'hdf5.dat' 53 | iolayername(4) = 'netcdf.dat' 54 | 55 | filedir = 'benchio_files' 56 | 57 | call MPI_Init(ierr) 58 | 59 | comm = MPI_COMM_WORLD 60 | 61 | call MPI_Comm_size(comm, size, ierr) 62 | call MPI_Comm_rank(comm, rank, ierr) 63 | 64 | dims(:) = 0 65 | 66 | ! Set 3D processor grid 67 | 68 | call MPI_Dims_create(size, ndim, dims, ierr) 69 | 70 | ! Reverse dimensions as MPI assumes C ordering (this is not essential) 71 | 72 | p1 = dims(3) 73 | p2 = dims(2) 74 | p3 = dims(1) 75 | 76 | ! Compute global sizes 77 | 78 | l1 = p1*n1 79 | l2 = p2*n2 80 | l3 = p3*n3 81 | 82 | call MPI_Type_size(MPI_DOUBLE_PRECISION, dblesize, ierr) 83 | 84 | mibdata = float(dblesize*n1*n2*n3)*float(p1*p2*p3)/float(mib) 85 | 86 | if (rank == 0) then 87 | write(*,*) 88 | write(*,*) 'Simple Parallel IO benchmark' 89 | write(*,*) '----------------------------' 90 | write(*,*) 91 | write(*,*) 'Running on ', size, ' process(es)' 92 | write(*,*) 'Process grid is (', p1, ', ', p2, ', ', p3, ')' 93 | write(*,*) 'Array size is (', n1, ', ', n2, ', ', n3, ')' 94 | write(*,*) 'Global size is (', l1, ', ', l2, ', ', l3, ')' 95 | write(*,*) 96 | write(*,*) 'Total amount of data = ', mibdata, ' MiB' 97 | write(*,*) 98 | write(*,*) 'Clock resolution is ', benchtick()*1.0e6, ', usecs' 99 | end if 100 | 101 | dims(1) = p1 102 | dims(2) = p2 103 | dims(3) = p3 104 | 105 | call MPI_Cart_create(comm, ndim, dims, periods, reorder, cartcomm, ierr) 106 | 107 | ! Set halos to illegal values 108 | 109 | iodata(:,:,:) = -1 110 | 111 | ! Set iodata core to have unique values 1, 2, ..., p1*n1*p2*n2*p3*n3 112 | 113 | call MPI_Cart_coords(cartcomm, rank, ndim, coords, ierr) 114 | 115 | do i3 = 1, n3 116 | do i2 = 1, n2 117 | do i1 = 1, n1 118 | 119 | j1 = coords(1)*n1 + i1 120 | j2 = coords(2)*n2 + i2 121 | j3 = coords(3)*n3 + i3 122 | 123 | iodata(i1,i2,i3) = (j3-1)*l1*l2 + (j2-1)*l1 + j1 124 | 125 | end do 126 | end do 127 | end do 128 | 129 | do iolayer = 1, numiolayer 130 | 131 | ! Skip layer if support is not compiled in 132 | ! Expects iolayers in order: serial, MPI-IO, HDF5, NetCDF 133 | #ifndef WITH_SERIAL 134 | if (iolayer == 1) then 135 | cycle 136 | endif 137 | #endif 138 | #ifndef WITH_MPIIO 139 | if (iolayer == 2) then 140 | cycle 141 | endif 142 | #endif 143 | #ifndef WITH_HDF5 144 | if (iolayer == 3) then 145 | cycle 146 | endif 147 | #endif 148 | #ifndef WITH_NETCDF 149 | if (iolayer == 4) then 150 | cycle 151 | endif 152 | #endif 153 | 154 | if (rank == 0) then 155 | write(*,*) 156 | write(*,*) '------' 157 | write(*,*) iostring(iolayer) 158 | write(*,*) '------' 159 | write(*,*) 160 | end if 161 | 162 | filename = trim(filedir)//'/'//trim(iolayername(iolayer)) 163 | 164 | if (rank == 0) then 165 | write(*,*) 'Writing to ', filename 166 | mintime = 0 167 | maxiorate = 0 168 | avgtime = 0 169 | avgiorate = 0 170 | end if 171 | 172 | do irep = 1, numrep 173 | call MPI_Barrier(comm, ierr) 174 | if (rank == 0) then 175 | t0 = benchtime() 176 | end if 177 | 178 | select case (iolayer) 179 | 180 | case(1) 181 | call serialwrite(filename, iodata, n1, n2, n3, cartcomm) 182 | 183 | case(2) 184 | call mpiiowrite(filename, iodata, n1, n2, n3, cartcomm) 185 | 186 | case(3) 187 | call hdf5write(filename, iodata, n1, n2, n3, cartcomm) 188 | 189 | case(4) 190 | call netcdfwrite(filename, iodata, n1, n2, n3, cartcomm) 191 | 192 | case default 193 | write(*,*) 'Illegal value of iolayer = ', iolayer 194 | stop 195 | 196 | end select 197 | 198 | call MPI_Barrier(comm, ierr) 199 | if (rank == 0) then 200 | t1 = benchtime() 201 | 202 | time = t1 - t0 203 | iorate = mibdata/time 204 | avgtime = avgtime + time/numrep 205 | avgiorate = avgiorate + iorate/numrep 206 | 207 | if (maxiorate < iorate) then 208 | maxiorate = iorate 209 | mintime = time 210 | end if 211 | 212 | write(*,*) 'time = ', time, ', rate = ', iorate, ' MiB/s' 213 | call fdelete(filename) 214 | end if 215 | end do 216 | if (rank == 0) then 217 | write(*,*) 'mintime = ', mintime, ', maxrate = ', maxiorate, ' MiB/s' 218 | write(*,*) 'avgtime = ', avgtime, ', avgrate = ', avgiorate, ' MiB/s' 219 | write(*,*) 'Deleting: ', filename 220 | write(*,*) 221 | end if 222 | end do 223 | 224 | if (rank == 0) then 225 | write(*,*) 226 | write(*,*) '--------' 227 | write(*,*) 'Finished' 228 | write(*,*) '--------' 229 | write(*,*) 230 | end if 231 | 232 | call MPI_Finalize(ierr) 233 | 234 | end program benchio 235 | 236 | subroutine fdelete(filename) 237 | 238 | implicit none 239 | 240 | character *(*) :: filename 241 | integer, parameter :: iounit = 15 242 | integer :: stat 243 | 244 | open(unit=iounit, iostat=stat, file=filename, status='old') 245 | if (stat.eq.0) close(unit=iounit, status='delete') 246 | 247 | end subroutine fdelete 248 | -------------------------------------------------------------------------------- /shared-file/source/hdf5.F90: -------------------------------------------------------------------------------- 1 | module iohdf5 2 | 3 | #ifdef WITH_HDF5 4 | 5 | use hdf5 6 | use mpi 7 | 8 | implicit none 9 | 10 | contains 11 | 12 | subroutine hdf5write(filename, iodata, n1, n2, n3, cartcomm) 13 | 14 | integer, parameter :: ndim = 3 15 | 16 | character*(*) :: filename 17 | 18 | integer :: n1, n2, n3 19 | double precision, dimension(0:n1+1,0:n2+1,0:n3+1) :: iodata 20 | 21 | integer :: info = MPI_INFO_NULL 22 | integer(hsize_t), dimension(ndim) :: dimsf ! dataset dimensions. 23 | 24 | character(len=8), parameter :: dsetname = "IntArray" ! Dataset name 25 | 26 | integer(hid_t) :: file_id ! file identifier 27 | integer(hid_t) :: dset_id ! dataset identifier 28 | integer(hid_t) :: filespace ! dataspace identifier in file 29 | integer(hid_t) :: memspace ! dataspace identifier in memory 30 | integer(hid_t) :: plist_id ! property list identifier 31 | 32 | integer(hsize_t), dimension(ndim) :: count 33 | integer(hssize_t), dimension(ndim) :: offset 34 | 35 | integer, dimension(ndim) :: arraysize, arraystart 36 | integer, dimension(ndim) :: arraygsize, arraysubsize 37 | 38 | integer :: cartcomm, ierr, rank, size 39 | 40 | integer, dimension(ndim) :: dims, coords 41 | logical, dimension(ndim) :: periods 42 | 43 | integer :: ncid, varid, oldmode, dimids(ndim) 44 | integer :: x_dimid, y_dimid, z_dimid 45 | 46 | call MPI_Comm_size(cartcomm, size, ierr) 47 | call MPI_Comm_rank(cartcomm, rank, ierr) 48 | 49 | call MPI_Cart_get(cartcomm, ndim, dims, periods, coords, ierr) 50 | 51 | arraysize(:) = [n1+2, n2+2, n3+2] 52 | 53 | ! Subtract halos for array subsize 54 | 55 | arraysubsize(:) = [n1, n2, n3] 56 | 57 | ! 58 | ! Define filetype for this process, ie what portion of the global array 59 | ! this process owns; starting positions use C-indexing (ie counting from 0). 60 | ! 61 | 62 | arraygsize(:) = arraysubsize(:) * dims(:) 63 | arraystart(:) = arraysubsize(:) * coords(:) + 1 ! Use Fortran indexing 64 | 65 | dimsf(:) = arraygsize(:) 66 | 67 | ! Initialise the count and offset arrays 68 | count(1) = n1 ! Defines the number of values each proc dumps to 69 | count(2) = n2 70 | count(3) = n3 ! the HDF5 file. 71 | 72 | offset(:) = coords(:) * count(:) ! Defines the offset used in the HDF5 file 73 | 74 | ! Initialize FORTRAN predefined datatypes 75 | CALL h5open_f(ierr) 76 | 77 | ! Setup file access property list with parallel I/O access. 78 | CALL h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, ierr) 79 | CALL h5pset_fapl_mpio_f(plist_id, cartcomm, info, ierr) 80 | 81 | ! Create the file collectively. 82 | CALL h5fcreate_f(filename, H5F_ACC_TRUNC_F, file_id, ierr, & 83 | access_prp = plist_id) 84 | CALL h5pclose_f(plist_id, ierr) 85 | 86 | ! Create the data space for the dataset. 87 | CALL h5screate_simple_f(ndim, dimsf, filespace, ierr) 88 | 89 | ! Create the dataset with default properties. 90 | CALL h5dcreate_f(file_id, dsetname, H5T_NATIVE_DOUBLE, filespace, & 91 | dset_id, ierr) 92 | CALL h5sclose_f(filespace, ierr) 93 | ! Each process defines dataset in memory and writes it to the hyperslab 94 | ! in the file. 95 | CALL h5screate_simple_f(ndim, count, memspace, ierr) 96 | 97 | ! Select hyperslab in the file. 98 | CALL h5dget_space_f(dset_id, filespace, ierr) 99 | CALL h5sselect_hyperslab_f (filespace, H5S_SELECT_SET_F, offset, & 100 | count, ierr) 101 | 102 | ! Create property list for collective dataset write 103 | CALL h5pcreate_f(H5P_DATASET_XFER_F, plist_id, ierr) 104 | CALL h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, ierr) 105 | 106 | ! Write the dataset collectively. 107 | CALL h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, iodata(1:n1, 1:n2, 1:n3), & 108 | dimsf, ierr, file_space_id = filespace, mem_space_id = memspace, & 109 | xfer_prp = plist_id) 110 | ! Write the dataset independently. Comment out the collective 111 | ! and use the following call to investigate non-collective performance. 112 | ! CALL h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, data, arraygsize, ierr, & 113 | ! file_space_id = filespace, mem_space_id = memspace) 114 | 115 | ! Close dataspaces. 116 | CALL h5sclose_f(filespace, ierr) 117 | CALL h5sclose_f(memspace, ierr) 118 | 119 | ! Close the dataset and property list. 120 | CALL h5dclose_f(dset_id, ierr) 121 | CALL h5pclose_f(plist_id, ierr) 122 | 123 | ! Close the file. 124 | CALL h5fclose_f(file_id, ierr) 125 | 126 | ! Close FORTRAN predefined datatypes. 127 | CALL h5close_f(ierr) 128 | 129 | end subroutine hdf5write 130 | 131 | ! WITH_HDF5 not defined. Dummy subroutine. 132 | #else 133 | 134 | contains 135 | subroutine hdf5write(filename, iodata, n1, n2, n3, cartcomm) 136 | character*(*) :: filename 137 | integer :: n1, n2, n3, cartcomm 138 | double precision, dimension(0:n1+1,0:n2+1,0:n3+1) :: iodata 139 | end subroutine hdf5write 140 | 141 | #endif 142 | 143 | end module iohdf5 144 | -------------------------------------------------------------------------------- /shared-file/source/mpiio.F90: -------------------------------------------------------------------------------- 1 | module mpiio 2 | 3 | #ifdef WITH_MPIIO 4 | 5 | use mpi 6 | implicit none 7 | 8 | contains 9 | 10 | subroutine mpiiowrite(filename, iodata, n1, n2, n3, cartcomm) 11 | 12 | integer, parameter :: ndim = 3 13 | 14 | character*(*) :: filename 15 | 16 | integer :: n1, n2, n3 17 | double precision, dimension(0:n1+1,0:n2+1,0:n3+1) :: iodata 18 | 19 | integer, dimension(ndim) :: arraysize, arraystart 20 | integer, dimension(ndim) :: arraygsize, arraysubsize 21 | 22 | integer :: cartcomm, ierr, rank, size 23 | 24 | integer :: filetype, mpi_subarray, fh 25 | integer (kind=MPI_OFFSET_KIND) :: disp = 0 26 | integer, dimension(MPI_STATUS_SIZE) :: status 27 | 28 | integer, dimension(ndim) :: dims, coords 29 | logical, dimension(ndim) :: periods 30 | 31 | call MPI_Comm_size(cartcomm, size, ierr) 32 | call MPI_Comm_rank(cartcomm, rank, ierr) 33 | 34 | call MPI_Cart_get(cartcomm, ndim, dims, periods, coords, ierr) 35 | 36 | arraysize(:) = [n1+2, n2+2, n3+2] 37 | 38 | ! Subtract halos for array subsize 39 | 40 | arraysubsize(:) = [n1, n2, n3] 41 | 42 | ! 43 | ! Define filetype for this process, ie what portion of the global array 44 | ! this process owns; starting positions use C-indexing (ie counting from 0). 45 | ! 46 | 47 | arraygsize(:) = arraysubsize(:) * dims(:) 48 | arraystart(:) = arraysubsize(:) * coords(:) 49 | 50 | call MPI_Type_create_subarray(ndim, arraygsize, arraysubsize, arraystart, & 51 | MPI_ORDER_FORTRAN, MPI_DOUBLE_PRECISION, & 52 | filetype, ierr) 53 | 54 | call MPI_Type_commit(filetype, ierr) 55 | 56 | ! 57 | ! Define subarray for this process, ie what portion of the local array 58 | ! is to be written (excludes halos); starting positions use C-indexing. 59 | ! 60 | 61 | arraystart(:) = 1 62 | 63 | call MPI_Type_create_subarray(ndim, arraysize, arraysubsize, arraystart, & 64 | MPI_ORDER_FORTRAN, MPI_DOUBLE_PRECISION, & 65 | mpi_subarray, ierr) 66 | 67 | call MPI_Type_commit(mpi_subarray, ierr) 68 | 69 | ! 70 | ! Open the file for reading only and attach to file handle fh 71 | ! No IO hints are passed since MPI_INFO_NULL is specified 72 | ! 73 | 74 | call MPI_File_open(cartcomm, filename, MPI_MODE_WRONLY+MPI_MODE_CREATE, & 75 | MPI_INFO_NULL, fh, ierr) 76 | 77 | if (ierr /= MPI_SUCCESS) write(*,*) 'Open error on rank ', rank 78 | 79 | ! 80 | ! Set view for this process using appropriate datatype 81 | ! 82 | 83 | call MPI_File_set_view(fh, disp, MPI_DOUBLE_PRECISION, filetype, 'native', & 84 | MPI_INFO_NULL, ierr) 85 | if (ierr /= MPI_SUCCESS) write(*,*) 'View error on rank ', rank 86 | 87 | ! 88 | ! Write all the data for this process. 89 | ! Remove halo data by passing an MPI subarray type 90 | ! 91 | 92 | call MPI_File_write_all(fh, iodata, 1, mpi_subarray, status, ierr) 93 | 94 | if (ierr /= MPI_SUCCESS) write(*,*) 'Write error on rank ', rank 95 | 96 | ! Alternative: remove halo data by passing an explicit Fortran subarray 97 | ! This should give an identical file to the above call with mpi_subaray 98 | ! 99 | ! call MPI_File_write_all(fh, & 100 | ! array(1:arraysubsize(1), 1:arraysubsize(2), 1:arraysubsize(3)), & 101 | ! arraysubsize(1)*arraysubsize(2)*arraysubsize(3), & 102 | ! MPI_DOUBLE_PRECISION, status, ierr) 103 | 104 | 105 | ! 106 | ! Close file 107 | ! 108 | 109 | call MPI_File_close(fh, ierr) 110 | 111 | if (ierr /= MPI_SUCCESS) write(*,*) 'Close error on rank ', rank 112 | 113 | call MPI_Type_free(filetype, ierr) 114 | call MPI_Type_free(mpi_subarray, ierr) 115 | 116 | end subroutine mpiiowrite 117 | 118 | ! WITH_MPIIO not defined. Dummy subroutine. 119 | #else 120 | 121 | contains 122 | subroutine mpiiowrite(filename, iodata, n1, n2, n3, cartcomm) 123 | character*(*) :: filename 124 | integer :: n1, n2, n3, cartcomm 125 | double precision, dimension(0:n1+1,0:n2+1,0:n3+1) :: iodata 126 | end subroutine mpiiowrite 127 | 128 | #endif 129 | 130 | ! Serial write is unconditionally compiled 131 | subroutine serialwrite(filename, iodata, n1, n2, n3, cartcomm) 132 | 133 | character*(*) :: filename 134 | 135 | integer :: n1, n2, n3 136 | double precision, dimension(0:n1+1,0:n2+1,0:n3+1) :: iodata 137 | 138 | integer :: cartcomm, ierr, rank, size 139 | integer, parameter :: iounit = 10 140 | 141 | integer :: i 142 | 143 | call MPI_Comm_size(cartcomm, size, ierr) 144 | call MPI_Comm_rank(cartcomm, rank, ierr) 145 | 146 | ! Write same amount of data as the parallel write but do it all from rank 0 147 | ! This is just to get a baseline figure for serial IO performance - note 148 | ! that the contents of the file will be differnent from the parallel calls 149 | 150 | if (rank == 0) then 151 | 152 | open(file=filename, unit=iounit, access='stream') 153 | 154 | do i = 1, size 155 | write(unit=iounit) iodata(1:n1, 1:n2, 1:n3) 156 | end do 157 | 158 | close(iounit) 159 | 160 | end if 161 | 162 | end subroutine serialwrite 163 | 164 | end module mpiio 165 | -------------------------------------------------------------------------------- /shared-file/source/netcdf.F90: -------------------------------------------------------------------------------- 1 | module ionetcdf 2 | 3 | #ifdef WITH_NETCDF 4 | 5 | use netcdf 6 | use mpi 7 | 8 | implicit none 9 | 10 | contains 11 | 12 | subroutine netcdfwrite(filename, iodata, n1, n2, n3, cartcomm) 13 | 14 | integer, parameter :: ndim = 3 15 | 16 | character*(*) :: filename 17 | 18 | integer :: n1, n2, n3 19 | double precision, dimension(0:n1+1,0:n2+1,0:n3+1) :: iodata 20 | 21 | integer, dimension(ndim) :: arraysize, arraystart 22 | integer, dimension(ndim) :: arraygsize, arraysubsize 23 | 24 | integer :: cartcomm, ierr, rank, size 25 | 26 | integer, dimension(ndim) :: dims, coords 27 | logical, dimension(ndim) :: periods 28 | 29 | integer :: ncid, varid, oldmode, dimids(ndim) 30 | integer :: x_dimid, y_dimid, z_dimid 31 | 32 | call MPI_Comm_size(cartcomm, size, ierr) 33 | call MPI_Comm_rank(cartcomm, rank, ierr) 34 | 35 | call MPI_Cart_get(cartcomm, ndim, dims, periods, coords, ierr) 36 | 37 | arraysize(:) = [n1+2, n2+2, n3+2] 38 | 39 | ! Subtract halos for array subsize 40 | 41 | arraysubsize(:) = [n1, n2, n3] 42 | 43 | ! 44 | ! Define filetype for this process, ie what portion of the global array 45 | ! this process owns; starting positions use C-indexing (ie counting from 0). 46 | ! 47 | 48 | arraygsize(:) = arraysubsize(:) * dims(:) 49 | arraystart(:) = arraysubsize(:) * coords(:) + 1 ! Use Fortran indexing 50 | 51 | ! Create (i.e. open) the netCDF file. The NF90_NETCDF4 flag causes a 52 | ! HDF5/netCDF-4 type file to be created. The comm and info parameters 53 | ! cause parallel I/O to be enabled. 54 | call check( nf90_create(filename, ior(nf90_netcdf4,nf90_mpiio), ncid, comm=cartcomm, info=MPI_INFO_NULL)) 55 | ! Define the dimensions. NetCDF returns an ID for each. Any 56 | ! metadata operations must take place on ALL processors 57 | call check( nf90_def_dim(ncid, "x", arraygsize(1), x_dimid) ) 58 | call check( nf90_def_dim(ncid, "y", arraygsize(2), y_dimid) ) 59 | call check( nf90_def_dim(ncid, "z", arraygsize(3), z_dimid) ) 60 | ! The dimids array is used to pass the ID's of the dimensions of 61 | ! the variables. 62 | dimids = (/ x_dimid , y_dimid, z_dimid /) 63 | ! Define the variable. The type of the variable in this case is 64 | ! NF90_DOUBLE (8-byte float). 65 | call check( nf90_def_var(ncid, "data", NF90_DOUBLE, dimids, varid) ) 66 | ! Make sure file it not filled with default values which doubles wrote volume 67 | ! Below line modified on 8th March 2016 68 | call check ( nf90_def_var_fill(ncid, varid, 1, 1) ) 69 | ! End define mode. This tells netCDF we are done defining 70 | ! metadata. This operation is collective and all processors will 71 | ! write their metadata to disk. 72 | call check( nf90_enddef(ncid) ) 73 | ! This appears also to write out all the data which is not what we want 74 | ! Have commented this out - appears to give exactly the same output 75 | ! file without this callm but at a faster rate overall. DSH 09/12/15 76 | 77 | ! Parallel access 78 | call check( nf90_var_par_access(ncid, varid, nf90_collective) ) 79 | 80 | ! Write the data to file, start will equal the displacement from the 81 | ! start of the file and count is the number of points each proc writes. 82 | call check( nf90_put_var(ncid, varid, iodata(1:n1, 1:n2, 1:n3), & 83 | start = arraystart, count = arraysubsize) ) 84 | ! Close the file. This frees up any internal netCDF resources 85 | ! associated with the file, and flushes any buffers. 86 | call check( nf90_close(ncid) ) 87 | 88 | end subroutine netcdfwrite 89 | 90 | subroutine check(status) 91 | integer, intent ( in) :: status 92 | if(status /= nf90_noerr) then 93 | print *, trim(nf90_strerror(status)) 94 | stop 95 | end if 96 | end subroutine check 97 | 98 | ! WITH_NETCDF not defined. Dummy subroutine. 99 | #else 100 | 101 | contains 102 | subroutine netcdfwrite(filename, iodata, n1, n2, n3, cartcomm) 103 | character*(*) :: filename 104 | integer :: n1, n2, n3, cartcomm 105 | double precision, dimension(0:n1+1,0:n2+1,0:n3+1) :: iodata 106 | end subroutine netcdfwrite 107 | 108 | #endif 109 | 110 | end module ionetcdf 111 | -------------------------------------------------------------------------------- /shared-file/source/run_scripts/archer.pbs: -------------------------------------------------------------------------------- 1 | #!/bin/bash --login 2 | 3 | #PBS -l select=1 4 | #PBS -l walltime=0:20:00 5 | #PBS -N benchio 6 | #PBS -A z19-cse 7 | 8 | cd $PBS_O_WORKDIR 9 | mkdir -p defstriped 10 | mkdir -p striped 11 | mkdir -p unstriped 12 | lfs setstripe -c -1 striped 13 | lfs setstripe -c 1 unstriped 14 | 15 | # Run tests 16 | aprun -n 24 ./benchio.x 17 | 18 | --------------------------------------------------------------------------------