├── .gitignore ├── COPYING ├── README.md ├── Singularity.def ├── example_slurm_job.sh ├── requirements.txt └── run_singularity.py /.gitignore: -------------------------------------------------------------------------------- 1 | Dockerfile 2 | -------------------------------------------------------------------------------- /COPYING: -------------------------------------------------------------------------------- 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 | 635 | Copyright (C) 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 | Copyright (C) 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 | # alphafold_singularity 2 | 3 | **NOTICE: THIS CODEBASE IS NOT ACTIVELY MAINTAINTED; NO ISSUES WILL BE ADDRESSED** 4 | 5 | Singularity recipe for [AlphaFold](https://github.com/deepmind/alphafold/), with example Slurm job script. 6 | 7 | This splits off my pull request https://github.com/deepmind/alphafold/pull/166 8 | 9 | Disclaimer: this project is not affiliated with DeepMind. 10 | 11 | ## IMPORTANT - `main` branch not usable directly 12 | The `main` branch here is not directly usable with the `main` branch of AlphaFold. This Singularity recipe 13 | works only with the matching release of AlphaFold. Please use one of the releases here, with a matching 14 | release of AlphaFold (ignoring the bugfix number). 15 | 16 | ### Unfixed bug in Alphafold tagged release 2.2.2 17 | N.B. https://github.com/deepmind/alphafold/issues/510#issuecomment-1159062272 18 | 19 | ## Prebuilt Singularity image 20 | A prebuilt image is hosted on cloud.sylabs.io: [https://cloud.sylabs.io/library/prehensilecode/alphafold_singularity/alphafold](https://cloud.sylabs.io/library/prehensilecode/alphafold_singularity/alphafold) 21 | 22 | ## What This Code Contains 23 | * `Singularity.def` which is the recipe to build the Singularity image. This is a port of the [Dockerfile](https://github.com/deepmind/alphafold/blob/main/docker/Dockerfile) provided by AlphaFold. 24 | * `run_singularity.py` which is a port of the [`run_docker.py`](https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py) script provided by AlphaFold. It is a wrapper to provide a friendly interface for running the container. 25 | 26 | ## Installation Instructions 27 | ### Download AlphaFold and alphafold_singularity: 28 | N.B. The AlphaFold version and the alphafold_singularity versions must match, 29 | except for the bugfix number in alphafold_singularity. E.g. alphafold_singularity 2.3.2-1 30 | goes with AlphaFold 2.3.2 31 | 32 | ``` 33 | $ export ALPHAFOLD_VERSION=2.3.2 34 | $ wget https://github.com/deepmind/alphafold/archive/refs/tags/v${ALPHAFOLD_VERSION}.tar.gz -O alphafold-${ALPHAFOLD_VERSION}.tar.gz 35 | ... 36 | 2023-02-08 17:28:50 (1.24 MB/s) - ‘alphafold-x.x.x.tar.gz’ saved [5855095] 37 | $ tar -xvf alphafold-${ALPHAFOLD_VERSION}.tar.gz 38 | $ cd alphafold-${ALPHAFOLD_VERSION} 39 | $ wget https://github.com/prehensilecode/alphafold_singularity/archive/refs/tags/v${ALPHAFOLD_VERSION}.tar.gz -O alphafold_singularity-${ALPHAFOLD_VERSION}.tar.gz 40 | ... 41 | 2023-02-08 17:42:18 (1.58 MB/s) - ‘alphafold_singularity-x.x.x.tar.gz’ saved [10148] 42 | $ tar -xf alphafold_singularity-${ALPHAFOLD_VERSION}.tar.gz 43 | $ mv alphafold_singularity-${ALPHAFOLD_VERSION} singularity 44 | $ python3 -m pip install -r singularity/requirements.txt 45 | $ sudo singularity build alphafold.sif singularity/Singularity.def 46 | ``` 47 | 48 | ### Build the Singularity image 49 | First install the Python requirements: 50 | ``` 51 | $ python3 -m pip install -r singularity/requirements.txt 52 | ``` 53 | 54 | Then, build the Singularity image: 55 | ``` 56 | $ sudo singularity build alphafold.sif singularity/Singularity.def 57 | ``` 58 | 59 | If your `/tmp` directory is small, you may need to set the [`SINGULARITY_TMPDIR` 60 | environment variable](https://sylabs.io/guides/3.3/user-guide/build_env.html#temporary-folders) to a directory on a filesystem with more free space. 61 | My builds have consumed up to 15 GiB of space. The resulting image file may be up to 10 GiB. 62 | 63 | ### Download genetic databases 64 | See [AlphaFold 2.3.2 README](https://github.com/deepmind/alphafold/tree/v2.3.2) 65 | for instructions on downloading genetic databases. These are necessary 66 | to run AlphaFold. 67 | 68 | This step requires [aria2c](https://aria2.github.io/). 69 | 70 | N.B. The difference between downloading the "reduced databases" as opposed 71 | to the "full databases" is that the reduced databases download "small BFD" 72 | instead of "BFD". 73 | 74 | ### Modify run script, install, and run 75 | To run, modify the `$ALPHAFOLD_SRC/singularity/run_singularity.py` and change the 76 | section marked `USER CONFIGURATION`. At the least, you will need to modify the values 77 | of: 78 | - `singularity_image` - absolute path to the `alphafold.sif` Singularity image 79 | 80 | E.g. 81 | ``` 82 | #### USER CONFIGURATION #### 83 | # AlphaFold Singularity image. 84 | singularity_image = Client.load(os.path.join(os.environ['ALPHAFOLD_DIR'], 'alphafold.sif')) 85 | ``` 86 | 87 | ## Running on an HPC cluster 88 | Currently, this project only supports Slurm. Please open an issue to request 89 | support for other job schedulers/resource managers. 90 | 91 | 92 | ### Run as a Slurm job on a cluster 93 | See the example job script [`example_slurm_job.sh`](https://github.com/prehensilecode/alphafold_singularity/blob/main/example_slurm_job.sh). 94 | N.B. this example must be modified to suit your specific HPC environment. 95 | 96 | The `run_singularity.py` script will use all GPUs available to the job. If 97 | Slurm has been set up with [`cgroups`](https://en.wikipedia.org/wiki/Cgroups), 98 | the job may request fewer than the total number of GPUs installed on a node. 99 | E.g. if the GPU nodes in the cluster have 4 GPU devices each, the job can 100 | do 101 | ```bash 102 | #SBATCH --gpus=2 103 | ``` 104 | and AlphaFold Singularity will use only two of the four GPUs. This is 105 | because the `cgroup` for the job only shows 2 GPUs to the job. 106 | -------------------------------------------------------------------------------- /Singularity.def: -------------------------------------------------------------------------------- 1 | Bootstrap: docker 2 | From: nvidia/cuda:11.1.1-cudnn8-runtime-ubuntu18.04 3 | Stage: spython-base 4 | 5 | %files 6 | . /app/alphafold 7 | %post 8 | # Copyright 2023 David Chin 9 | # 10 | # This file is part of alphafold_singularity. 11 | # 12 | # alphafold_singularity is free software: you can redistribute it and/or 13 | # modify it under the terms of the GNU General Public License as 14 | # published by the Free Software Foundation, either version 3 of the 15 | # License, or (at your option) any later version. 16 | # 17 | # alphafold_singularity is distributed in the hope that it will be 18 | # useful, but WITHOUT ANY WARRANTY; without even the implied warranty 19 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 20 | # General Public License for more details. 21 | # 22 | # You should have received a copy of the GNU General Public License 23 | # along with alphafold_singularity. If not, see . 24 | 25 | 26 | # FROM directive resets ARGS, so we specify again (the value is retained if 27 | # previously set). 28 | 29 | apt-get update \ 30 | && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \ 31 | build-essential \ 32 | cmake \ 33 | cuda-command-line-tools-11-1 \ 34 | git \ 35 | hmmer \ 36 | kalign \ 37 | tzdata \ 38 | wget \ 39 | && rm -rf /var/lib/apt/lists/* \ 40 | && apt-get autoremove -y \ 41 | && apt-get clean 42 | 43 | # Compile HHsuite from source. 44 | /bin/rm -rf /tmp/hh-suite \ 45 | && git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite \ 46 | && mkdir /tmp/hh-suite/build \ 47 | && cd /tmp/hh-suite/build \ 48 | && cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \ 49 | && make -j 4 && make install \ 50 | && ln -s /opt/hhsuite/bin/* /usr/bin \ 51 | && cd / \ 52 | && /bin/rm -rf /tmp/hh-suite 53 | 54 | # Install Miniconda package manager. 55 | wget -q -P /tmp \ 56 | https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \ 57 | && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \ 58 | && rm /tmp/Miniconda3-latest-Linux-x86_64.sh 59 | 60 | # Install conda packages. 61 | PATH="/opt/conda/bin:/usr/local/cuda-11.1/bin:$PATH" 62 | conda install -qy conda==23.5.2 \ 63 | && conda install -y -c conda-forge \ 64 | openmm=7.7.0 \ 65 | cudatoolkit==11.1.1 \ 66 | pdbfixer \ 67 | pip \ 68 | python=3.10 \ 69 | && conda clean --all --force-pkgs-dirs --yes 70 | 71 | ### /bin/cp -r . /app/alphafold 72 | 73 | wget -q -P /app/alphafold/alphafold/common/ \ 74 | https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt 75 | 76 | # Install pip packages. 77 | # N.B. The URL specifies the list of jaxlib releases. 78 | pip3 install --upgrade pip --no-cache-dir \ 79 | && pip3 install -r /app/alphafold/requirements.txt --no-cache-dir \ 80 | && pip3 install --upgrade --no-cache-dir \ 81 | jax==0.3.25 \ 82 | jaxlib==0.3.25+cuda11.cudnn805 \ 83 | -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html 84 | 85 | # Add SETUID bit to the ldconfig binary so that non-root users can run it. 86 | chmod u+s /sbin/ldconfig.real 87 | 88 | ### SETUID bit does not matter: Apptainer does not allow suid commands 89 | ### Workaround below is to use /mnt/out/ld.so.cache for the ld cache file 90 | 91 | %environment 92 | export PATH="/opt/conda/bin:/usr/local/cuda-11.1/bin:$PATH" 93 | %runscript 94 | cd /app/alphafold 95 | ldconfig -C /mnt/output/ld.so.cache 96 | exec python /app/alphafold/run_alphafold.py "$@" 97 | # %startscript 98 | # cd /app/alphafold 99 | # exec python /app/alphafold/run_alphafold.py "$@" 100 | -------------------------------------------------------------------------------- /example_slurm_job.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # Copyright 2023 David Chin 4 | # 5 | # This file is part of alphafold_singularity. 6 | # 7 | # alphafold_singularity is free software: you can redistribute it and/or 8 | # modify it under the terms of the GNU General Public License as 9 | # published by the Free Software Foundation, either version 3 of the 10 | # License, or (at your option) any later version. 11 | # 12 | # alphafold_singularity is distributed in the hope that it will be 13 | # useful, but WITHOUT ANY WARRANTY; without even the implied warranty 14 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 15 | # General Public License for more details. 16 | # 17 | # You should have received a copy of the GNU General Public License 18 | # along with alphafold_singularity. If not, see . 19 | 20 | #SBATCH --partition=gpu 21 | #SBATCH --time=2:00:00 22 | #SBATCH --gpus=4 23 | #SBATCH --cpus-per-gpu=12 24 | #SBATCH --mem-per-gpu=36G 25 | 26 | ### NOTE 27 | ### This job script cannot be used without modification for your specific environment. 28 | 29 | module load python/gcc/3.11 30 | module load alphafold/2.3.2-1 31 | 32 | ### Check values of some environment variables 33 | echo INFO: SLURM_GPUS_ON_NODE=$SLURM_GPUS_ON_NODE 34 | echo INFO: SLURM_JOB_GPUS=$SLURM_JOB_GPUS 35 | echo INFO: SLURM_STEP_GPUS=$SLURM_STEP_GPUS 36 | echo INFO: ALPHAFOLD_DIR=$ALPHAFOLD_DIR 37 | echo INFO: ALPHAFOLD_DATADIR=$ALPHAFOLD_DATADIR 38 | echo INFO: TMP=$TMP 39 | 40 | ### 41 | ### README This runs AlphaFold 2.3.2 on the T1050.fasta file 42 | ### 43 | 44 | # AlphaFold should use all GPU devices available to the job by default. 45 | # 46 | # To run the CASP14 evaluation, use: 47 | # --model_preset=monomer_casp14 48 | # --db_preset=full_dbs (or delete the line; default is "full_dbs") 49 | # 50 | # On a test system with 4x Tesla V100-SXM2, this took about 50 minutes. 51 | # 52 | # To benchmark, running multiple JAX model evaluations (NB this 53 | # significantly increases run time): 54 | # --benchmark 55 | # 56 | # On a test system with 4x Tesla V100-SXM2, this took about 6 hours. 57 | 58 | # Create output directory in $TMP (which is cleaned up by Slurm at end 59 | # of job). 60 | output_dir=$TMP/output 61 | mkdir -p $output_dir 62 | 63 | echo INFO: output_dir=$output_dir 64 | 65 | # Run AlphaFold; default is to use GPUs 66 | python3 ${ALPHAFOLD_DIR}/singularity/run_singularity.py \ 67 | --use_gpu \ 68 | --output_dir=$output_dir \ 69 | --data_dir=${ALPHAFOLD_DATADIR} \ 70 | --fasta_paths=T1050.fasta \ 71 | --max_template_date=2020-05-14 \ 72 | --model_preset=monomer \ 73 | --db_preset=reduced_dbs 74 | 75 | echo INFO: AlphaFold returned $? 76 | 77 | ### Copy Alphafold output back to directory where "sbatch" command was issued. 78 | mkdir $SLURM_SUBMIT_DIR/Output-$SLURM_JOB_ID 79 | cp -R $output_dir $SLURM_SUBMIT_DIR/Output-$SLURM_JOB_ID 80 | 81 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | # Copyright 2023 David Chin 2 | # 3 | # This file is part of alphafold_singularity. 4 | # 5 | # alphafold_singularity is free software: you can redistribute it and/or 6 | # modify it under the terms of the GNU General Public License as 7 | # published by the Free Software Foundation, either version 3 of the 8 | # License, or (at your option) any later version. 9 | # 10 | # alphafold_singularity is distributed in the hope that it will be 11 | # useful, but WITHOUT ANY WARRANTY; without even the implied warranty 12 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | # General Public License for more details. 14 | # 15 | # You should have received a copy of the GNU General Public License 16 | # along with alphafold_singularity. If not, see . 17 | # 18 | # Dependencies necessary to execute run_singularity.py 19 | # absl-py version to match deepmind/alphafold 20 | absl-py==1.0.0 21 | spython==0.3.0 22 | -------------------------------------------------------------------------------- /run_singularity.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | # Copyright 2023 David Chin 3 | # 4 | # This file is part of alphafold_singularity. 5 | # 6 | # alphafold_singularity is free software: you can redistribute it and/or 7 | # modify it under the terms of the GNU General Public License as 8 | # published by the Free Software Foundation, either version 3 of the 9 | # License, or (at your option) any later version. 10 | # 11 | # alphafold_singularity is distributed in the hope that it will be 12 | # useful, but WITHOUT ANY WARRANTY; without even the implied warranty 13 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 14 | # General Public License for more details. 15 | # 16 | # You should have received a copy of the GNU General Public License 17 | # along with alphafold_singularity. If not, see . 18 | 19 | """Singularity launch script for Alphafold Singularity image.""" 20 | 21 | import os 22 | import sys 23 | import pathlib 24 | import signal 25 | from typing import Tuple 26 | 27 | from absl import app 28 | from absl import flags 29 | from absl import logging 30 | from spython.main import Client 31 | 32 | import tempfile 33 | import subprocess 34 | 35 | 36 | #### USER CONFIGURATION #### 37 | 38 | # Path to AlphaFold Singularity image. This relies on 39 | # the environment variable ALPHAFOLD_DIR which is the 40 | # directory where AlphaFold is installed. 41 | singularity_image = Client.load(os.path.join(os.environ['ALPHAFOLD_DIR'], 'alphafold.sif')) 42 | 43 | # tmp directory 44 | if 'TMP' in os.environ: 45 | tmp_dir = os.environ['TMP'] 46 | elif 'TMPDIR' in os.environ: 47 | tmp_dir = os.environ['TMPDIR'] 48 | else: 49 | tmp_dir = '/tmp' 50 | 51 | # Default path to a directory that will store the results. 52 | output_dir_default = tempfile.mkdtemp(dir=tmp_dir, prefix='alphafold') 53 | 54 | logging.info(f'INFO: tmp_dir = {tmp_dir}') 55 | logging.info(f'INFO: output_dir_default = {output_dir_default}') 56 | 57 | #### END USER CONFIGURATION #### 58 | 59 | ### These flags correspond to the flags defined in ../run_alphafold.py 60 | flags.DEFINE_bool( 61 | 'use_gpu', True, 'Enable NVIDIA runtime to run with GPUs.') 62 | flags.DEFINE_enum( 63 | 'models_to_relax', 'best', ['best', 'all', 'none'], 64 | 'The models to run the final relaxation step on. ' 65 | 'If `all`, all models are relaxed, which may be time ' 66 | 'consuming. If `best`, only the most confident model is ' 67 | 'relaxed. If `none`, relaxation is not run. Turning off ' 68 | 'relaxation might result in predictions with ' 69 | 'distracting stereochemical violations but might help ' 70 | 'in case you are having issues with the relaxation ' 71 | 'stage.') 72 | flags.DEFINE_bool( 73 | 'enable_gpu_relax', True, 'Run relax on GPU if GPU is enabled.') 74 | flags.DEFINE_string( 75 | 'gpu_devices', 'all', 76 | 'Comma separated list of devices to pass to NVIDIA_VISIBLE_DEVICES.') 77 | flags.DEFINE_list( 78 | 'fasta_paths', None, 'Paths to FASTA files, each containing a prediction ' 79 | 'target that will be folded one after another. If a FASTA file contains ' 80 | 'multiple sequences, then it will be folded as a multimer. Paths should be ' 81 | 'separated by commas. All FASTA paths must have a unique basename as the ' 82 | 'basename is used to name the output directories for each prediction.') 83 | flags.DEFINE_string( 84 | 'output_dir', output_dir_default, 85 | 'Path to a directory that will store the results.') 86 | flags.DEFINE_string( 87 | 'data_dir', None, 88 | 'Path to directory with supporting data: AlphaFold parameters and genetic ' 89 | 'and template databases. Set to the target of download_all_databases.sh.') 90 | flags.DEFINE_string( 91 | 'docker_image_name', 'alphafold', 'Name of the AlphaFold Docker image.') 92 | flags.DEFINE_string( 93 | 'max_template_date', None, 94 | 'Maximum template release date to consider (ISO-8601 format: YYYY-MM-DD). ' 95 | 'Important if folding historical test sets.') 96 | flags.DEFINE_enum( 97 | 'db_preset', 'full_dbs', ['full_dbs', 'reduced_dbs'], 98 | 'Choose preset MSA database configuration - smaller genetic database ' 99 | 'config (reduced_dbs) or full genetic database config (full_dbs)') 100 | flags.DEFINE_enum( 101 | 'model_preset', 'monomer', 102 | ['monomer', 'monomer_casp14', 'monomer_ptm', 'multimer'], 103 | 'Choose preset model configuration - the monomer model, the monomer model ' 104 | 'with extra ensembling, monomer model with pTM head, or multimer model') 105 | flags.DEFINE_integer('num_multimer_predictions_per_model', 5, 'How many ' 106 | 'predictions (each with a different random seed) will be ' 107 | 'generated per model. E.g. if this is 2 and there are 5 ' 108 | 'models then there will be 10 predictions per input. ' 109 | 'Note: this FLAG only applies if model_preset=multimer') 110 | flags.DEFINE_boolean( 111 | 'benchmark', False, 112 | 'Run multiple JAX model evaluations to obtain a timing that excludes the ' 113 | 'compilation time, which should be more indicative of the time required ' 114 | 'for inferencing many proteins.') 115 | flags.DEFINE_boolean( 116 | 'use_precomputed_msas', False, 117 | 'Whether to read MSAs that have been written to disk instead of running ' 118 | 'the MSA tools. The MSA files are looked up in the output directory, so it ' 119 | 'must stay the same between multiple runs that are to reuse the MSAs. ' 120 | 'WARNING: This will not check if the sequence, database or configuration ' 121 | 'have changed.') 122 | flags.DEFINE_string( 123 | 'docker_user', f'{os.geteuid()}:{os.getegid()}', 124 | 'UID:GID with which to run the Docker container. The output directories ' 125 | 'will be owned by this user:group. By default, this is the current user. ' 126 | 'Valid options are: uid or uid:gid, non-numeric values are not recognised ' 127 | 'by Docker unless that user has been created within the container.') 128 | 129 | FLAGS = flags.FLAGS 130 | 131 | _ROOT_MOUNT_DIRECTORY = '/mnt/' 132 | 133 | 134 | def _create_bind(bind_name: str, path: str) -> Tuple[str, str]: 135 | """Create a bind point for each file and directory used by the model.""" 136 | path = os.path.abspath(path) 137 | source_path = os.path.dirname(path) if bind_name != 'data_dir' else path 138 | target_path = os.path.join(_ROOT_MOUNT_DIRECTORY, bind_name) 139 | 140 | logging.info('Binding %s -> %s', source_path, target_path) 141 | 142 | # NOTE singularity binds are read-only by default 143 | if bind_name == 'data_dir': 144 | data_path = target_path 145 | else: 146 | data_path = f'{os.path.join(target_path, os.path.basename(path))}' 147 | 148 | return (f'{source_path}:{target_path}', f'{data_path}') 149 | 150 | 151 | def main(argv): 152 | if len(argv) > 1: 153 | raise app.UsageError('Too many command-line arguments.') 154 | 155 | # You can individually override the following paths if you have placed the 156 | # data in locations other than the FLAGS.data_dir. 157 | 158 | # Path to the Uniref90 database for use by JackHMMER. 159 | uniref90_database_path = os.path.join( 160 | FLAGS.data_dir, 'uniref90', 'uniref90.fasta') 161 | 162 | # Path to the Uniprot database for use by JackHMMER. 163 | uniprot_database_path = os.path.join( 164 | FLAGS.data_dir, 'uniprot', 'uniprot.fasta') 165 | 166 | # Path to the MGnify database for use by JackHMMER. 167 | mgnify_database_path = os.path.join( 168 | FLAGS.data_dir, 'mgnify', 'mgy_clusters_2022_05.fa') 169 | 170 | # Path to the BFD database for use by HHblits. 171 | bfd_database_path = os.path.join( 172 | FLAGS.data_dir, 'bfd', 173 | 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt') 174 | 175 | # Path to the Small BFD database for use by JackHMMER. 176 | small_bfd_database_path = os.path.join( 177 | FLAGS.data_dir, 'small_bfd', 'bfd-first_non_consensus_sequences.fasta') 178 | 179 | # Path to the Uniref30 database for use by HHblits. 180 | uniref30_database_path = os.path.join( 181 | FLAGS.data_dir, 'uniref30', 'UniRef30_2021_03') 182 | 183 | # Path to the PDB70 database for use by HHsearch. 184 | pdb70_database_path = os.path.join(FLAGS.data_dir, 'pdb70', 'pdb70') 185 | 186 | # Path to the PDB seqres database for use by hmmsearch. 187 | pdb_seqres_database_path = os.path.join( 188 | FLAGS.data_dir, 'pdb_seqres', 'pdb_seqres.txt') 189 | 190 | # Path to a directory with template mmCIF structures, each named .cif. 191 | template_mmcif_dir = os.path.join(FLAGS.data_dir, 'pdb_mmcif', 'mmcif_files') 192 | 193 | # Path to a file mapping obsolete PDB IDs to their replacements. 194 | obsolete_pdbs_path = os.path.join(FLAGS.data_dir, 'pdb_mmcif', 'obsolete.dat') 195 | 196 | alphafold_path = pathlib.Path(__file__).parent.parent 197 | data_dir_path = pathlib.Path(FLAGS.data_dir) 198 | if alphafold_path == data_dir_path or alphafold_path in data_dir_path.parents: 199 | raise app.UsageError( 200 | f'The download directory {FLAGS.data_dir} should not be a subdirectory ' 201 | f'in the AlphaFold repository directory. If it is, the Singularity build is ' 202 | f'slow since the large databases are copied during the image creation.') 203 | 204 | binds = [] 205 | command_args = [] 206 | 207 | # Mount each fasta path as a unique target directory. 208 | target_fasta_paths = [] 209 | for i, fasta_path in enumerate(FLAGS.fasta_paths): 210 | bind, target_path = _create_bind(f'fasta_path_{i}', fasta_path) 211 | binds.append(bind) 212 | target_fasta_paths.append(target_path) 213 | command_args.append(f'--fasta_paths={",".join(target_fasta_paths)}') 214 | 215 | database_paths = [ 216 | ('uniref90_database_path', uniref90_database_path), 217 | ('mgnify_database_path', mgnify_database_path), 218 | ('data_dir', FLAGS.data_dir), 219 | ('template_mmcif_dir', template_mmcif_dir), 220 | ('obsolete_pdbs_path', obsolete_pdbs_path), 221 | ] 222 | 223 | if FLAGS.model_preset == 'multimer': 224 | database_paths.append(('uniprot_database_path', uniprot_database_path)) 225 | database_paths.append(('pdb_seqres_database_path', 226 | pdb_seqres_database_path)) 227 | else: 228 | database_paths.append(('pdb70_database_path', pdb70_database_path)) 229 | 230 | if FLAGS.db_preset == 'reduced_dbs': 231 | database_paths.append(('small_bfd_database_path', small_bfd_database_path)) 232 | else: 233 | database_paths.extend([ 234 | ('uniref30_database_path', uniref30_database_path), 235 | ('bfd_database_path', bfd_database_path), 236 | ]) 237 | 238 | # NB for binds: 239 | # - first arg = path on host 240 | # - second arg = path in container 241 | for name, path in database_paths: 242 | if path: 243 | bind, target_path = _create_bind(name, path) 244 | binds.append(bind) 245 | command_args.append(f'--{name}={target_path}') 246 | 247 | output_target_path = os.path.join(_ROOT_MOUNT_DIRECTORY, 'output') 248 | binds.append(f'{FLAGS.output_dir}:{output_target_path}') 249 | logging.info('Binding %s -> %s', FLAGS.output_dir, output_target_path) 250 | 251 | tmp_target_path = '/tmp' 252 | binds.append(f'{tmp_dir}:{tmp_target_path}') 253 | logging.info('Binding %s -> %s', tmp_dir, tmp_target_path) 254 | 255 | use_gpu_relax = FLAGS.enable_gpu_relax and FLAGS.use_gpu 256 | 257 | command_args.extend([ 258 | f'--output_dir={output_target_path}', 259 | f'--max_template_date={FLAGS.max_template_date}', 260 | f'--db_preset={FLAGS.db_preset}', 261 | f'--model_preset={FLAGS.model_preset}', 262 | f'--benchmark={FLAGS.benchmark}', 263 | f'--use_precomputed_msas={FLAGS.use_precomputed_msas}', 264 | f'--num_multimer_predictions_per_model={FLAGS.num_multimer_predictions_per_model}', 265 | f'--models_to_relax={FLAGS.models_to_relax}', 266 | f'--use_gpu_relax={use_gpu_relax}', 267 | '--logtostderr', 268 | ]) 269 | 270 | options = [ 271 | '--bind', f'{",".join(binds)}', 272 | '--env', f'NVIDIA_VISIBLE_DEVICES={FLAGS.gpu_devices}', 273 | # The following flags allow us to make predictions on proteins that 274 | # would typically be too long to fit into GPU memory. 275 | '--env', 'TF_FORCE_UNIFIED_MEMORY=1', 276 | '--env', 'XLA_PYTHON_CLIENT_MEM_FRACTION=4.0', 277 | ] 278 | 279 | # Run the container. 280 | # Result is a dict with keys "message" (value = all output as a single string), 281 | # and "return_code" (value = integer return code) 282 | result = Client.run( 283 | singularity_image, 284 | command_args, 285 | nv=True if FLAGS.use_gpu else None, 286 | return_result=True, 287 | options=options 288 | ) 289 | 290 | 291 | if __name__ == '__main__': 292 | flags.mark_flags_as_required([ 293 | 'data_dir', 294 | 'fasta_paths', 295 | 'max_template_date', 296 | ]) 297 | app.run(main) 298 | --------------------------------------------------------------------------------