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8f21aa22 | 1 | ;;; GNU Guix --- Functional package management for GNU |
f7a4757a | 2 | ;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com> |
8f21aa22 PG |
3 | ;;; |
4 | ;;; This file is part of GNU Guix. | |
5 | ;;; | |
6 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
7 | ;;; under the terms of the GNU General Public License as published by | |
8 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
9 | ;;; your option) any later version. | |
10 | ;;; | |
11 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
12 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
13 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
14 | ;;; GNU General Public License for more details. | |
15 | ;;; | |
16 | ;;; You should have received a copy of the GNU General Public License | |
17 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
18 | ||
19 | (define-module (gnu packages simulation) | |
20 | #:use-module (gnu packages) | |
0ace6c0b | 21 | #:use-module (gnu packages algebra) |
8f21aa22 PG |
22 | #:use-module (gnu packages base) |
23 | #:use-module (gnu packages bash) | |
24 | #:use-module (gnu packages bison) | |
25 | #:use-module (gnu packages boost) | |
f7a4757a | 26 | #:use-module (gnu packages check) |
0ace6c0b | 27 | #:use-module (gnu packages cmake) |
8f21aa22 PG |
28 | #:use-module (gnu packages compression) |
29 | #:use-module (gnu packages flex) | |
30 | #:use-module (gnu packages gettext) | |
31 | #:use-module (gnu packages gcc) | |
32 | #:use-module (gnu packages gl) | |
33 | #:use-module (gnu packages graphics) | |
34 | #:use-module (gnu packages gtk) | |
35 | #:use-module (gnu packages linux) | |
36 | #:use-module (gnu packages m4) | |
37 | #:use-module (gnu packages maths) | |
38 | #:use-module (gnu packages mpi) | |
39 | #:use-module (gnu packages multiprecision) | |
40 | #:use-module (gnu packages ncurses) | |
0ace6c0b | 41 | #:use-module (gnu packages pkg-config) |
f7a4757a | 42 | #:use-module (gnu packages python) |
44d10b1f | 43 | #:use-module (gnu packages python-xyz) |
8f21aa22 PG |
44 | #:use-module (gnu packages readline) |
45 | #:use-module (gnu packages tls) | |
46 | #:use-module (gnu packages version-control) | |
47 | #:use-module (gnu packages xml) | |
48 | #:use-module (gnu packages xorg) | |
49 | #:use-module (guix download) | |
0ace6c0b | 50 | #:use-module (guix build-system cmake) |
8f21aa22 | 51 | #:use-module (guix build-system gnu) |
f7a4757a | 52 | #:use-module (guix build-system python) |
8f21aa22 PG |
53 | #:use-module ((guix licenses) #:prefix license:) |
54 | #:use-module (guix packages) | |
55 | #:use-module (guix utils) | |
56 | #:use-module (ice-9 ftw) | |
57 | #:use-module (ice-9 regex) | |
58 | #:use-module (srfi srfi-1)) | |
59 | ||
60 | (define-public openfoam | |
61 | (package | |
62 | (name "openfoam") | |
63 | (version "4.1") | |
64 | (source | |
65 | (origin | |
66 | (method url-fetch) | |
67 | (uri (string-append | |
68 | "http://dl.openfoam.org/source/" | |
69 | (string-map (lambda (x) (if (eq? x #\.) #\- x)) version))) | |
70 | (file-name (string-append name "-" version ".tar.gz")) | |
71 | (sha256 | |
72 | (base32 "0cgxh4h2hf50qbvvdg5miwc2nympb0nrv3md96vb3gbs9vk8vq9d")) | |
886d833e LC |
73 | (patches (search-patches "openfoam-4.1-cleanup.patch")) |
74 | (modules '((guix build utils))) | |
75 | (snippet | |
76 | '(begin | |
77 | ;; Include <sys/sysmacros.h>, which is where glibc >= 2.28 provides | |
78 | ;; 'major' and 'minor'. | |
79 | (substitute* "src/OSspecific/POSIX/fileStat.C" | |
80 | (("#include <unistd\\.h>") | |
81 | "#include <unistd.h>\n#include <sys/sysmacros.h>\n")) | |
82 | #t)))) | |
8f21aa22 PG |
83 | (build-system gnu-build-system) |
84 | (inputs | |
85 | `(("boost" ,boost) | |
86 | ("cgal" ,cgal) | |
87 | ("flex" ,flex) | |
88 | ("git" ,git) | |
89 | ("gmp" ,gmp) | |
90 | ("libxt" ,libxt) | |
91 | ("metis" ,metis) | |
92 | ("mpfr" ,mpfr) | |
93 | ("ncurses" ,ncurses) | |
94 | ("readline" ,readline) | |
95 | ("scotch" ,pt-scotch32) | |
96 | ("zlib" ,zlib))) | |
97 | (native-inputs | |
98 | `(("bison" ,bison))) | |
99 | (propagated-inputs | |
100 | `(("gzip" ,gzip) | |
101 | ("gnuplot" ,gnuplot) | |
102 | ("openmpi" ,openmpi))) | |
f1de0e37 DL |
103 | (outputs '("debug" ;~60MB |
104 | "out")) | |
8f21aa22 PG |
105 | (arguments |
106 | `( ;; Executable files and shared libraries are located in the 'platforms' | |
107 | ;; subdirectory. | |
108 | #:strip-directories (list (string-append | |
109 | "lib/OpenFOAM-" ,version | |
110 | "/platforms/linux64GccDPInt32Opt/bin") | |
111 | (string-append | |
112 | "lib/OpenFOAM-" ,version | |
113 | "/platforms/linux64GccDPInt32Opt/lib")) | |
114 | #:tests? #f ; no tests to run | |
115 | ||
116 | #:modules ((ice-9 ftw) | |
117 | (ice-9 regex) | |
118 | (guix build gnu-build-system) | |
119 | (guix build utils)) | |
120 | ||
121 | #:phases (modify-phases %standard-phases | |
122 | (add-after 'unpack 'rename-build-directory | |
123 | (lambda _ | |
124 | (chdir "..") | |
125 | ;; Use 'OpenFOAM-version' convention to match the file | |
126 | ;; name expectations in the build phase. | |
127 | (let ((unpack-dir (string-append | |
128 | (getcwd) "/" | |
129 | (list-ref (scandir (getcwd) (lambda (name) | |
130 | (string-match "^OpenFOAM" name))) 0))) | |
131 | (build-dir (string-append | |
132 | (getcwd) "/OpenFOAM-" ,version))) | |
133 | (rename-file unpack-dir build-dir) ; rename build directory | |
134 | (chdir (basename build-dir))) ; move to build directory | |
135 | #t)) | |
136 | (delete 'configure) ; no configure phase | |
137 | (replace 'build | |
138 | (lambda _ | |
139 | (let ((libraries '("boost" "cgal" "gmp" "metis" "mpfr" "scotch"))) | |
140 | ;; set variables to define store paths | |
141 | (for-each (lambda (library) | |
142 | (setenv (string-append | |
143 | (string-upcase library) "_ROOT") | |
144 | (assoc-ref %build-inputs library))) libraries)) | |
145 | ;; set variables to define package versions | |
146 | (setenv "SCOTCHVERSION" ,(package-version scotch)) | |
147 | (setenv "METISVERSION" ,(package-version metis)) | |
148 | ;; set variable to pass extra 'rpath' arguments to linker | |
149 | (setenv "LDFLAGS" | |
150 | (string-append | |
151 | "-Wl," | |
152 | "-rpath=" %output "/lib/OpenFOAM-" ,version | |
153 | "/platforms/linux64GccDPInt32Opt/lib," | |
154 | "-rpath=" %output "/lib/OpenFOAM-" ,version | |
155 | "/platforms/linux64GccDPInt32Opt/lib/dummy")) | |
156 | ;; compile OpenFOAM libraries and applications | |
157 | (zero? (system (format #f | |
158 | "source ./etc/bashrc && ./Allwmake -j~a" | |
159 | (parallel-job-count)))))) | |
160 | (add-after 'build 'update-configuration-files | |
161 | (lambda _ | |
162 | ;; record store paths and package versions in | |
163 | ;; configuration files | |
164 | (substitute* "etc/config.sh/CGAL" | |
165 | (("$BOOST_ROOT") (getenv "BOOST_ROOT"))) | |
166 | (substitute* "etc/config.sh/CGAL" | |
167 | (("$CGAL_ROOT") (getenv "CGAL_ROOT"))) | |
168 | (substitute* "etc/config.sh/metis" | |
169 | (("$METIS_ROOT") (getenv "METIS_ROOT"))) | |
170 | (substitute* "etc/config.sh/metis" | |
171 | (("$METISVERSION") (getenv "METISVERSION"))) | |
172 | (substitute* "etc/config.sh/scotch" | |
173 | (("$SCOTCH_ROOT") (getenv "SCOTCH_ROOT"))) | |
174 | (substitute* "etc/config.sh/scotch" | |
175 | (("$SCOTCHVERSION") (getenv "SCOTCHVERSION"))) | |
176 | (substitute* "etc/config.sh/settings" | |
177 | (("$GMP_ROOT") (getenv "GMP_ROOT"))) | |
178 | (substitute* "etc/config.sh/settings" | |
179 | (("$MPFR_ROOT") (getenv "MPFR_ROOT"))) | |
180 | ;; reset lockDir variable to refer to write-enabled | |
181 | ;; directory | |
182 | (substitute* "wmake/wmake" | |
183 | ((" lockDir=.*$") | |
184 | " lockDir=$HOME/.$WM_PROJECT/.wmake\n")) | |
185 | (substitute* "wmake/wmakeScheduler" | |
186 | (("lockDir=.*$") | |
187 | "lockDir=$HOME/.$WM_PROJECT/.wmake\n")) | |
188 | (substitute* "wmake/wmakeSchedulerUptime" | |
189 | (("lockDir=.*$") | |
190 | "lockDir=$HOME/.$WM_PROJECT/.wmake\n")) | |
191 | #t)) | |
f1de0e37 DL |
192 | (add-after 'build 'cleanup |
193 | ;; Avoid unncessary, voluminous object and dep files. | |
194 | (lambda _ | |
195 | (delete-file-recursively | |
196 | "platforms/linux64GccDPInt32Opt/src") | |
197 | (delete-file-recursively | |
198 | "platforms/linux64GccDPInt32OptSYSTEMOPENMPI") | |
199 | (for-each delete-file (find-files "." "\\.o$")) | |
200 | #t)) | |
8f21aa22 PG |
201 | (replace 'install |
202 | (lambda _ | |
203 | ;; use 'OpenFOAM-version' convention | |
204 | (let ((install-dir (string-append | |
205 | %output "/lib/OpenFOAM-" ,version))) | |
206 | (mkdir-p install-dir) ; create install directory | |
207 | ;; move contents of build directory to install directory | |
208 | (copy-recursively "." install-dir)))) | |
209 | (add-after 'install 'add-symbolic-link | |
210 | (lambda _ | |
211 | ;; add symbolic link for standard 'bin' directory | |
212 | (symlink | |
213 | (string-append "./lib/OpenFOAM-" ,version | |
214 | "/platforms/linux64GccDPInt32Opt/bin") | |
215 | (string-append %output "/bin")) | |
216 | #t))))) | |
217 | ;; Note: | |
218 | ;; Tutorial files are installed read-only in /gnu/store. | |
219 | ;; To allow write permissions on files copied from the store a | |
220 | ;; 'chmod' step is needed before running the applications. For | |
221 | ;; example, from a user's login: | |
222 | ;; $ source $GUIX_PROFILE/lib/OpenFOAM-4.1/etc/bashrc | |
223 | ;; $ mkdir -p $FOAM_RUN | |
224 | ;; $ cd $FOAM_RUN | |
a836e9f5 PG |
225 | ;; $ cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily . |
226 | ;; $ cd pitzDaily | |
8f21aa22 PG |
227 | ;; $ chmod -R u+w . |
228 | ;; $ blockMesh | |
229 | (synopsis "Framework for numerical simulation of fluid flow") | |
230 | (description "OpenFOAM provides a set of solvers and methods for tackling | |
231 | problems in the field of Computational Fluid Dynamics (CFD). It is written in | |
232 | C++. Governing equations such as the Navier-Stokes equations can be solved in | |
233 | integral form. Physical processes such as phase change, droplet transport and | |
234 | chemical reaction can be modelled. Numerical methods are included to deal with | |
235 | sharp gradients, such as those encountered in flows with shock waves and flows | |
236 | with gas/liquid interfaces. Large problems may be split into smaller, connected | |
b6598237 | 237 | problems for efficient solution on parallel systems.") |
8f21aa22 PG |
238 | (license license:gpl3+) |
239 | (home-page "https://openfoam.org"))) | |
f7a4757a PG |
240 | |
241 | (define-public python-fenics-dijitso | |
242 | (package | |
243 | (name "python-fenics-dijitso") | |
244 | (version "2018.1.0") | |
245 | (source | |
246 | (origin | |
247 | (method url-fetch) | |
248 | (uri (pypi-uri "fenics-dijitso" version)) | |
249 | (sha256 | |
250 | (base32 | |
251 | "1qax2f52qsjbd1h5lk5i5shp448qlakxabjjybrfc1w823p0yql9")))) | |
252 | (build-system python-build-system) | |
253 | (inputs | |
254 | `(("openmpi" ,openmpi) | |
255 | ("python-numpy" ,python-numpy))) | |
256 | (native-inputs | |
257 | `(("python-pytest-cov" ,python-pytest-cov))) | |
258 | (propagated-inputs | |
259 | `(("python-mpi4py" ,python-mpi4py))) | |
260 | (arguments | |
261 | `(#:phases | |
262 | (modify-phases %standard-phases | |
263 | (add-after 'build 'mpi-setup | |
264 | ,%openmpi-setup) | |
265 | (replace 'check | |
266 | (lambda _ | |
267 | (setenv "HOME" "/tmp") | |
268 | (setenv "PYTHONPATH" | |
269 | (string-append (getcwd) ":" (getenv "PYTHONPATH"))) | |
270 | (with-directory-excursion "test" | |
7a82074c PG |
271 | ;; Disable parallel tests to avoid race condition. See |
272 | ;; https://github.com/pytest-dev/pytest-cov/issues/237. | |
273 | (substitute* "runtests.sh" | |
274 | (("for p in 1 4 8 16; do") | |
275 | "for p in 1; do")) | |
f7a4757a PG |
276 | (invoke "./runtests.sh")) |
277 | #t))))) | |
278 | (home-page "https://bitbucket.org/fenics-project/dijitso/") | |
279 | (synopsis "Distributed just-in-time building of shared libraries") | |
280 | (description | |
281 | "Dijitso provides a core component of the @code{FEniCS} framework, | |
282 | namely the just-in-time compilation of C++ code that is generated from | |
283 | Python modules. It is called from within a C++ library, using ctypes | |
284 | to import the dynamic shared library directly. | |
285 | ||
286 | As long as the compiled code can provide a simple factory function to | |
287 | a class implementing a predefined C++ interface, there is no limit to | |
288 | the complexity of that interface. Parallel support depends on the | |
289 | @code{mpi4py} interface.") | |
290 | (license license:lgpl3+))) | |
3941cf5a PG |
291 | |
292 | (define-public python-fenics-ufl | |
293 | (package | |
294 | (name "python-fenics-ufl") | |
295 | (version "2018.1.0") | |
296 | (source | |
297 | (origin | |
298 | (method url-fetch) | |
299 | (uri (pypi-uri "fenics-ufl" version)) | |
300 | (sha256 | |
301 | (base32 | |
302 | "1fq8yc86s1s3c8c0b1rc2vf265q0hrkzg57100fg1nghcz0p4vla")))) | |
303 | (build-system python-build-system) | |
304 | (inputs | |
305 | `(("python-numpy" ,python-numpy))) | |
306 | (native-inputs | |
307 | `(("python-pytest" ,python-pytest))) | |
308 | (arguments | |
309 | '(#:phases | |
310 | (modify-phases %standard-phases | |
311 | (replace 'check | |
312 | (lambda _ | |
313 | (setenv "PYTHONPATH" | |
314 | (string-append (getcwd) ":" (getenv "PYTHONPATH"))) | |
315 | (with-directory-excursion "test" | |
316 | (invoke "py.test")) | |
317 | #t))))) | |
318 | (home-page "https://bitbucket.org/fenics-project/ufl/") | |
319 | (synopsis "Unified language for form-compilers") | |
320 | (description "The Unified Form Language (UFL) is a domain specific | |
321 | language for declaration of finite element discretizations of | |
322 | variational forms. More precisely, it defines a flexible interface | |
323 | for choosing finite element spaces and defining expressions for weak | |
324 | forms in a notation close to mathematical notation. | |
325 | ||
326 | UFL is part of the FEniCS Project.") | |
327 | (license license:lgpl3+))) | |
0fc49983 PG |
328 | |
329 | (define-public python-fenics-fiat | |
330 | (package | |
331 | (name "python-fenics-fiat") | |
332 | (version "2018.1.0") | |
333 | (source | |
334 | (origin | |
335 | (method url-fetch) | |
336 | (uri (pypi-uri "fenics-fiat" version)) | |
337 | (sha256 | |
338 | (base32 | |
339 | "0fmjd93r6bwf6xs8csw86qzphrnr66xwv7f372w59gmq8mg6rljc")))) | |
340 | (build-system python-build-system) | |
341 | (native-inputs | |
342 | `(("python-pytest" ,python-pytest))) | |
343 | (propagated-inputs | |
344 | `(("python-numpy" ,python-numpy) | |
345 | ("python-sympy" ,python-sympy))) | |
346 | (arguments | |
347 | '(#:phases | |
348 | (modify-phases %standard-phases | |
349 | (replace 'check | |
350 | (lambda _ | |
351 | (setenv "PYTHONPATH" | |
352 | (string-append (getcwd) ":" (getenv "PYTHONPATH"))) | |
353 | (with-directory-excursion "test" | |
354 | (invoke "py.test" "unit/")) | |
355 | #t))))) | |
356 | (home-page "https://bitbucket.org/fenics-project/fiat/") | |
357 | (synopsis "Tabulation of finite element function spaces") | |
358 | (description | |
359 | "The FInite element Automatic Tabulator (FIAT) supports | |
360 | generation of arbitrary order instances of the Lagrange elements on | |
361 | lines, triangles, and tetrahedra. It is also capable of generating | |
362 | arbitrary order instances of Jacobi-type quadrature rules on the same | |
363 | element shapes. Further, H(div) and H(curl) conforming finite element | |
364 | spaces such as the families of Raviart-Thomas, Brezzi-Douglas-Marini | |
365 | and Nedelec are supported on triangles and tetrahedra. Upcoming | |
366 | versions will also support Hermite and nonconforming elements. | |
367 | ||
368 | FIAT is part of the FEniCS Project.") | |
369 | (license license:lgpl3+))) | |
6b7f1f8a PG |
370 | |
371 | (define-public python-fenics-ffc | |
372 | (package | |
373 | (name "python-fenics-ffc") | |
374 | (version "2018.1.0") | |
375 | (source | |
376 | (origin | |
377 | (method url-fetch) | |
378 | (uri (pypi-uri "fenics-ffc" version)) | |
379 | (sha256 | |
380 | (base32 | |
381 | "1b2ia5vlkw298x7rf0k2p3ihlpwkwgc98p3s6sbpds3hqmfrzdz9")))) | |
382 | (build-system python-build-system) | |
383 | (native-inputs | |
384 | `(("python-pytest" ,python-pytest))) | |
385 | (propagated-inputs | |
386 | `(("python-fenics-dijitso" ,python-fenics-dijitso) | |
387 | ("python-fenics-fiat" ,python-fenics-fiat) | |
388 | ("python-fenics-ufl" ,python-fenics-ufl))) | |
389 | (arguments | |
390 | '(#:phases | |
391 | (modify-phases %standard-phases | |
392 | (replace 'check | |
393 | (lambda _ | |
394 | (setenv "HOME" (getcwd)) | |
395 | (setenv "PYTHONPATH" | |
396 | (string-append (getcwd) ":" (getenv "PYTHONPATH"))) | |
397 | (with-directory-excursion "test" | |
398 | ;; FIXME: the tests in subdirectory | |
399 | ;; 'unit/ufc/finite_element' require the ffc_factory | |
400 | ;; extension module. This module, located in the 'libs' | |
401 | ;; subdirectory, needs to be built and made accessible | |
402 | ;; prior to running the tests. | |
403 | (invoke "py.test" "unit/" "--ignore=unit/ufc/") | |
404 | (with-directory-excursion "uflacs" | |
405 | (invoke "py.test" "unit/"))) | |
406 | #t))))) | |
407 | (home-page "https://bitbucket.org/fenics-project/ffc/") | |
408 | (synopsis "Compiler for finite element variational forms") | |
409 | (description "The FEniCS Form Compiler (FFC) is a compiler for | |
410 | finite element variational forms. From a high-level description of | |
411 | the form, it generates efficient low-level C++ code that can be used | |
412 | to assemble the corresponding discrete operator (tensor). In | |
413 | particular, a bilinear form may be assembled into a matrix and a | |
414 | linear form may be assembled into a vector. FFC may be used either | |
415 | from the command line (by invoking the @code{ffc} command) or as a | |
416 | Python module (@code{import ffc}). | |
417 | ||
418 | FFC is part of the FEniCS Project.") | |
419 | ;; There are two files released with a public domain licence; | |
420 | ;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'. | |
421 | (license (list license:public-domain license:lgpl3+)))) | |
0ace6c0b PG |
422 | |
423 | (define-public fenics-dolfin | |
424 | (package | |
425 | (name "fenics-dolfin") | |
426 | (version "2018.1.0.post1") | |
427 | (source | |
428 | (origin | |
429 | (method url-fetch) | |
430 | (uri (string-append | |
431 | "https://bitbucket.org/fenics-project/dolfin/get/" | |
432 | version ".tar.gz")) | |
433 | (file-name (string-append name "-" version ".tar.gz")) | |
434 | (sha256 | |
435 | (base32 | |
436 | "12zkk8j3xsg6l8p0ggwsl03084vlcivw4h99b7z9kndg7k89b3ya")) | |
437 | (modules '((guix build utils))) | |
438 | (snippet | |
439 | '(begin | |
440 | ;; Make sure we don't use the bundled test framework. | |
441 | (delete-file-recursively "test/unit/cpp/catch") | |
442 | (substitute* "test/unit/cpp/main.cpp" | |
443 | ;; Use standard search paths for 'catch' header file. | |
444 | (("#include.*") | |
445 | "#include <catch.hpp>\n")) | |
446 | (substitute* "test/unit/cpp/CMakeLists.txt" | |
447 | ;; Add extra include directories required by the unit tests. | |
448 | (("(^target_link_libraries.*)" line) | |
449 | (string-append line "\n" | |
450 | "target_include_directories(" | |
451 | "unittests PRIVATE " | |
452 | "${DOLFIN_SOURCE_DIR} " | |
453 | "${DOLFIN_SOURCE_DIR}/dolfin " | |
454 | "${DOLFIN_BINARY_DIR})\n")) | |
455 | (("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back) | |
456 | (string-append front | |
457 | "$ENV{CATCH_DIR}" | |
458 | "/include" back "\n"))) | |
459 | (substitute* "demo/CMakeLists.txt" | |
460 | ;; Add extra include directories required by the demo tests. | |
461 | (("(^#find_package.*)" line) | |
462 | (string-append line "\n" | |
463 | "include_directories(" | |
464 | "${DOLFIN_SOURCE_DIR} " | |
465 | "${DOLFIN_SOURCE_DIR}/dolfin " | |
466 | "${DOLFIN_BINARY_DIR})\n"))) | |
3a261950 PG |
467 | (substitute* "dolfin/nls/PETScSNESSolver.cpp" |
468 | ;; Remove SNESTEST mapping. The SNESTEST symbol was removed | |
469 | ;; from PETSc at version 3.10.3. | |
470 | ((".*SNESTEST.*") "" )) | |
0ace6c0b PG |
471 | #t)))) |
472 | (build-system cmake-build-system) | |
473 | (inputs | |
474 | `(("blas" ,openblas) | |
475 | ("boost" ,boost) | |
476 | ("eigen" ,eigen) | |
477 | ("hdf5" ,hdf5-parallel-openmpi) | |
478 | ("lapack" ,lapack) | |
479 | ("libxml2" ,libxml2) | |
480 | ("openmpi" ,openmpi) | |
481 | ("python" ,python-3) | |
482 | ("scotch" ,pt-scotch32) | |
483 | ("suitesparse" ,suitesparse) | |
484 | ("sundials" ,sundials-openmpi) | |
485 | ("zlib" ,zlib))) | |
486 | (native-inputs | |
487 | `(("catch" ,catch-framework2) | |
488 | ("pkg-config" ,pkg-config))) | |
489 | (propagated-inputs | |
490 | `(("ffc" ,python-fenics-ffc) | |
491 | ("petsc" ,petsc-openmpi) | |
492 | ("slepc" ,slepc-openmpi))) | |
493 | (arguments | |
494 | `(#:configure-flags | |
495 | `("-DDOLFIN_ENABLE_DOCS:BOOL=OFF" | |
496 | "-DDOLFIN_ENABLE_HDF5:BOOL=ON" | |
497 | "-DDOLFIN_ENABLE_MPI:BOOL=ON" | |
498 | "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF" | |
499 | "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON" | |
500 | "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON" | |
501 | "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF") | |
502 | #:phases | |
503 | (modify-phases %standard-phases | |
504 | (add-after 'patch-usr-bin-file 'mpi-setup | |
505 | ,%openmpi-setup) | |
506 | (add-after 'patch-source-shebangs 'set-paths | |
507 | (lambda _ | |
508 | ;; Define paths to store locations. | |
509 | (setenv "BLAS_DIR" (assoc-ref %build-inputs "blas")) | |
510 | (setenv "CATCH_DIR" (assoc-ref %build-inputs "catch")) | |
511 | (setenv "LAPACK_DIR" (assoc-ref %build-inputs "lapack")) | |
512 | (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) | |
513 | (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc")) | |
514 | (setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch")) | |
515 | (setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials")) | |
516 | (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse")) | |
517 | #t)) | |
518 | (add-before 'check 'pre-check | |
519 | (lambda _ | |
520 | ;; The Dolfin repository uses git-lfs, whereby web links are | |
521 | ;; substituted for large files. Guix does not currently support | |
522 | ;; git-lfs, so only the links are downloaded. The tests that | |
523 | ;; require the absent meshes cannot run and are skipped. | |
524 | ;; | |
525 | ;; Two other serial tests fail and are skipped. | |
526 | ;; i) demo_stokes-iterative_serial, | |
527 | ;; The MPI_Comm_rank() function was called before MPI_INIT was | |
528 | ;; invoked | |
529 | ;; ii) demo_multimesh-stokes_serial: | |
530 | ;; Warning: Found no facets matching domain for boundary | |
531 | ;; condition. | |
532 | ;; | |
533 | ;; One mpi test fails and is skipped. | |
534 | ;; i) demo_stokes-iterative_mpi: | |
535 | ;; The MPI_Comm_rank() function was called before MPI_INIT was | |
536 | ;; invoked | |
537 | (call-with-output-file "CTestCustom.cmake" | |
538 | (lambda (port) | |
539 | (display | |
540 | (string-append | |
541 | "set(CTEST_CUSTOM_TESTS_IGNORE " | |
542 | "demo_bcs_serial " | |
543 | "demo_bcs_mpi " | |
544 | "demo_eigenvalue_serial " | |
545 | "demo_eigenvalue_mpi " | |
546 | "demo_navier-stokes_serial " | |
547 | "demo_navier-stokes_mpi " | |
548 | "demo_stokes-taylor-hood_serial " | |
549 | "demo_stokes-taylor-hood_mpi " | |
550 | "demo_subdomains_serial " | |
551 | "demo_advection-diffusion_serial " | |
552 | "demo_advection-diffusion_mpi " | |
553 | "demo_auto-adaptive-navier-stokes_serial " | |
554 | "demo_contact-vi-snes_serial " | |
555 | "demo_contact-vi-snes_mpi " | |
556 | "demo_contact-vi-tao_serial " | |
557 | "demo_contact-vi-tao_mpi " | |
558 | "demo_curl-curl_serial " | |
559 | "demo_curl-curl_mpi " | |
560 | "demo_dg-advection-diffusion_serial " | |
561 | "demo_dg-advection-diffusion_mpi " | |
562 | "demo_elasticity_serial " | |
563 | "demo_elasticity_mpi " | |
564 | "demo_elastodynamics_serial " | |
565 | "demo_elastodynamics_mpi " | |
566 | "demo_lift-drag_serial " | |
567 | "demo_lift-drag_mpi " | |
568 | "demo_mesh-quality_serial " | |
569 | "demo_mesh-quality_mpi " | |
570 | "demo_multimesh-stokes_serial " | |
571 | "demo_stokes-iterative_serial " | |
572 | "demo_stokes-iterative_mpi " | |
573 | ")\n") port))) | |
574 | #t)) | |
575 | (replace 'check | |
576 | (lambda _ | |
577 | (and (invoke "make" "unittests") | |
578 | (invoke "make" "demos") | |
579 | (invoke "ctest" "-R" "unittests") | |
580 | (invoke "ctest" "-R" "demo" "-R" "serial") | |
581 | (invoke "ctest" "-R" "demo" "-R" "mpi"))))))) | |
582 | (home-page "https://bitbucket.org/fenics-project/dolfin/") | |
583 | (synopsis "Problem solving environment for differential equations") | |
584 | (description | |
585 | "DOLFIN is a computational framework for finding numerical | |
586 | solutions to problems described by differential equations. Numerical | |
587 | models in DOLFIN are constructed using general families of finite | |
588 | elements. Data structures are provided for discretizing the governing | |
589 | system on a computational mesh. A compact syntax, similar to | |
590 | mathematical notation, is made available for defining function spaces | |
591 | and expressing variational forms. Interfaces to specialized matrix | |
592 | solvers are provided for solving the resultant linear systems. | |
593 | ||
594 | @code{fenics-dolfin} is part of the FEniCS project. It is the C++ | |
595 | user interface to the FEniCS core components and external libraries.") | |
596 | ;; The source code for the DOLFIN C++ library is licensed under the | |
597 | ;; GNU Lesser General Public License, version 3 or later, with the | |
598 | ;; following exceptions: | |
599 | ;; | |
600 | ;; public-domain: dolfin/geometry/predicates.cpp | |
601 | ;; dolfin/geometry/predicates.h | |
602 | ;; | |
603 | ;; zlib: dolfin/io/base64.cpp | |
604 | ;; dolfin/io/base64.h | |
605 | ;; | |
606 | ;; expat: dolfin/io/pugiconfig.hpp | |
607 | ;; dolfin/io/pugixml.cpp | |
608 | ;; dolfin/io/pugixml.hpp | |
609 | (license (list license:public-domain | |
610 | license:zlib | |
611 | license:expat | |
612 | license:lgpl3+)))) | |
ae0f1dd1 PG |
613 | |
614 | (define-public fenics | |
615 | (package (inherit fenics-dolfin) | |
616 | (name "fenics") | |
617 | (build-system python-build-system) | |
618 | (inputs | |
619 | `(("pybind11" ,pybind11) | |
620 | ("python-matplotlib" ,python-matplotlib) | |
621 | ,@(alist-delete "python" (package-inputs fenics-dolfin)))) | |
622 | (native-inputs | |
623 | `(("cmake" ,cmake) | |
624 | ("ply" ,python-ply) | |
625 | ("pytest" ,python-pytest) | |
626 | ("python-decorator" ,python-decorator) | |
627 | ("python-pkgconfig" ,python-pkgconfig) | |
628 | ,@(package-native-inputs fenics-dolfin))) | |
629 | (propagated-inputs | |
630 | `(("dolfin" ,fenics-dolfin) | |
631 | ("petsc4py" ,python-petsc4py) | |
632 | ("slepc4py" ,python-slepc4py))) | |
633 | (arguments | |
634 | `(#:phases | |
635 | (modify-phases %standard-phases | |
636 | (add-after 'patch-source-shebangs 'set-paths | |
637 | (lambda _ | |
638 | ;; Define paths to store locations. | |
639 | (setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11")) | |
640 | ;; Move to python sub-directory. | |
641 | (chdir "python") | |
642 | #t)) | |
643 | (add-after 'build 'mpi-setup | |
644 | ,%openmpi-setup) | |
645 | (add-before 'check 'pre-check | |
646 | (lambda _ | |
647 | ;; Exclude tests that require meshes supplied by git-lfs. | |
648 | (substitute* "demo/test.py" | |
649 | (("(.*stem !.*)" line) | |
650 | (string-append | |
651 | line "\n" | |
652 | "excludeList = [\n" | |
653 | "'multimesh-quadrature', \n" | |
654 | "'multimesh-marking', \n" | |
655 | "'mixed-poisson-sphere', \n" | |
656 | "'mesh-quality', \n" | |
657 | "'lift-drag', \n" | |
658 | "'elastodynamics', \n" | |
659 | "'dg-advection-diffusion', \n" | |
dd6cb4a0 | 660 | "'curl-curl', \n" |
ae0f1dd1 PG |
661 | "'contact-vi-tao', \n" |
662 | "'contact-vi-snes', \n" | |
663 | "'collision-detection', \n" | |
664 | "'buckling-tao', \n" | |
665 | "'auto-adaptive-navier-stokes', \n" | |
666 | "'advection-diffusion', \n" | |
667 | "'subdomains', \n" | |
668 | "'stokes-taylor-hood', \n" | |
669 | "'stokes-mini', \n" | |
670 | "'navier-stokes', \n" | |
671 | "'eigenvalue']\n" | |
672 | "demos = [" | |
673 | "d for d in demos if d[0].stem not in " | |
674 | "excludeList]\n"))) | |
675 | (setenv "HOME" (getcwd)) | |
676 | (setenv "PYTHONPATH" | |
677 | (string-append | |
678 | (getcwd) "/build/lib.linux-x86_64-" | |
679 | ,(version-major+minor (package-version python)) ":" | |
680 | (getenv "PYTHONPATH"))) | |
681 | ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP. | |
682 | (setenv "OPENBLAS_NUM_THREADS" "1") | |
683 | #t)) | |
684 | (replace 'check | |
685 | (lambda _ | |
686 | (with-directory-excursion "test" | |
687 | ;; Note: The test test_snes_set_from_options() in the file | |
688 | ;; unit/nls/test_PETScSNES_solver.py fails and is ignored. | |
689 | (and (invoke "py.test" "unit" "--ignore" | |
690 | "unit/nls/test_PETScSNES_solver.py") | |
691 | (invoke "mpirun" "-np" "3" "python" "-B" "-m" | |
692 | "pytest" "unit" "--ignore" | |
693 | "unit/nls/test_PETScSNES_solver.py"))) | |
694 | (with-directory-excursion "demo" | |
695 | ;; Check demos. | |
696 | (invoke "python" "generate-demo-files.py") | |
697 | (and (invoke "python" "-m" "pytest" "-v" "test.py") | |
698 | (invoke "python" "-m" "pytest" "-v" "test.py" | |
699 | "--mpiexec=mpiexec" "--num-proc=3"))) | |
700 | #t)) | |
701 | (add-after 'install 'install-demo-files | |
702 | (lambda* (#:key outputs #:allow-other-keys) | |
703 | (let* ((demos (string-append | |
704 | (assoc-ref outputs "out") | |
705 | "/share/python-dolfin/demo"))) | |
706 | (mkdir-p demos) | |
707 | (with-directory-excursion "demo" | |
708 | (for-each (lambda (file) | |
709 | (let* ((dir (dirname file)) | |
710 | (tgt-dir (string-append demos "/" dir))) | |
711 | (unless (equal? "." dir) | |
712 | (mkdir-p tgt-dir) | |
713 | (install-file file tgt-dir)))) | |
714 | (find-files "." ".*\\.(py|gz|xdmf)$")))) | |
715 | #t))))) | |
716 | (home-page "https://fenicsproject.org/") | |
717 | (synopsis "High-level environment for solving differential equations") | |
718 | (description | |
719 | "@code{fenics} is a computing platform for solving general classes of | |
720 | problems that involve differential equations. @code{fenics} facilitates | |
721 | access to efficient methods for dealing with ordinary differential | |
722 | equations (ODEs) and partial differential equations (PDEs). Systems of | |
723 | equations such as these are commonly encountered in areas of engineering, | |
724 | mathematics and the physical sciences. It is particularly well-suited to | |
725 | problems that can be solved using the Finite Element Method (FEM). | |
726 | ||
727 | @code{fenics} is the top level of the set of packages that are developed | |
728 | within the FEniCS project. It provides the python user interface to the | |
729 | FEniCS core components and external libraries.") | |
730 | (license license:lgpl3+))) |