aboutsummaryrefslogtreecommitdiff
path: root/gnu/packages/maths.scm
blob: cda3af8d979339f8bc03d999bd6ece41015e81be (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2014 John Darrington <jmd@gnu.org>
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages maths)
  #:use-module (gnu packages)
  #:use-module ((guix licenses)
                #:renamer (symbol-prefix-proc 'license:))
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system gnu)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages elf)
  #:use-module (gnu packages flex)
  #:use-module (gnu packages fltk)
  #:use-module (gnu packages fontutils)
  #:use-module (gnu packages gettext)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages gd)
  #:use-module (gnu packages ghostscript)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages less)
  #:use-module (gnu packages xorg)
  #:use-module (gnu packages gl)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages readline)
  #:use-module (gnu packages tcsh)
  #:use-module (gnu packages texinfo)
  #:use-module (gnu packages texlive)
  #:use-module (gnu packages xml))

(define-public units
  (package
   (name "units")
   (version "2.11")
   (source (origin
            (method url-fetch)
            (uri (string-append "mirror://gnu/units/units-" version
                                ".tar.gz"))
            (sha256 (base32
                     "1gjs3wc212aaiq4r76hx9nl1h3fa39n0ljwl9420d6ixl3rdmdjk"))))
   (build-system gnu-build-system)
   (synopsis "Conversion between thousands of scales")
   (description
    "GNU Units converts numeric quantities between units of measure.  It
can handle scale changes through adaptive usage of standard scale prefixes
(micro-, kilo-, etc.).  It can also handle nonlinear conversions such as
Fahrenheit to Celsius.  Its interpreter is powerful enough to be used
effectively as a scientific calculator.")
   (license license:gpl3+)
   (home-page "http://www.gnu.org/software/units/")))

(define-public gsl
  (package
    (name "gsl")
    (version "1.16")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "mirror://gnu/gsl/gsl-"
                          version ".tar.gz"))
      (sha256
       (base32
        "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))))
    (build-system gnu-build-system)
    (arguments
     `(#:parallel-tests? #f
       #:phases
        (alist-replace
         'configure
         (lambda* (#:key target system outputs #:allow-other-keys #:rest args)
           (let ((configure (assoc-ref %standard-phases 'configure)))
             ;; disable numerically unstable test on i686, see thread at
             ;; http://lists.gnu.org/archive/html/bug-gsl/2011-11/msg00019.html
             (if (string=? (or target system) "i686-linux")
                 (substitute* "ode-initval2/Makefile.in"
                   (("TESTS = \\$\\(check_PROGRAMS\\)") "TESTS =")))
             (apply configure args)))
         %standard-phases)))
    (home-page "http://www.gnu.org/software/gsl/")
    (synopsis "Numerical library for C and C++")
    (description
     "The GNU Scientific Library is a library for numerical analysis in C
and C++.  It includes a wide range of mathematical routines, with over 1000
functions in total.  Subject areas covered by the library include:
differential equations, linear algebra, Fast Fourier Transforms and random
numbers.")
    (license license:gpl3+)))

(define-public glpk
  (package
    (name "glpk")
    (version "4.54")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "mirror://gnu/glpk/glpk-"
                          version ".tar.gz"))
      (sha256
       (base32
        "18gr2anv8gyps6j9f22k7li6w07glvww666sdqblvlq2hh3whwmb"))))
    (build-system gnu-build-system)
    (inputs
     `(("gmp" ,gmp)))
    (arguments
     `(#:configure-flags '("--with-gmp")))
    (home-page "http://www.gnu.org/software/glpk/")
    (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
    (description
     "GLPK is a C library for solving large-scale linear programming (LP),
mixed integer programming (MIP), and other related problems.  It supports the
GNU MathProg modeling language, a subset of the AMPL language, and features a
translator for the language.  In addition to the C library, a stand-alone
LP/MIP solver is included in the package.")
    (license license:gpl3+)))

(define-public pspp
  (package
    (name "pspp")
    (version "0.8.3")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "mirror://gnu/pspp/pspp-"
                          version ".tar.gz"))
      (sha256
       (base32
        "0vri2pzvmm38qaihfvwlry30f40lcnps4blg59ixic4q20ldxf5d"))))
    (build-system gnu-build-system)
    (inputs
     `(("cairo" ,cairo)
       ("fontconfig" ,fontconfig)
       ("gettext" ,gnu-gettext)
       ("gsl" ,gsl)
       ("libxml2" ,libxml2)
       ("pango" ,pango)
       ("readline" ,readline)
       ("gtk" ,gtk+-2)
       ("gtksourceview" ,gtksourceview)
       ("zlib" ,zlib)))
    (native-inputs
     `(("perl" ,perl)
       ("pkg-config" ,pkg-config)))
    (home-page "http://www.gnu.org/software/pspp/")
    (synopsis "Statistical analysis")
    (description
     "GNU PSPP is a statistical analysis program.  It can perform
descriptive statistics, T-tests, linear regression and non-parametric tests. 
It features both a graphical interface as well as command-line input. PSPP is
designed to interoperate with Gnumeric, LibreOffice and OpenOffice.  Data can
be imported from spreadsheets, text files and database sources and it can be
output in text, PostScript, PDF or HTML.")
    (license license:gpl3+)))

(define-public lapack
  (package
    (name "lapack")
    (version "3.5.0")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "http://www.netlib.org/lapack/lapack-"
                          version ".tgz"))
      (sha256
       (base32
        "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))
    (build-system cmake-build-system)
    (home-page "http://www.netlib.org/lapack/")
    (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath
    (inputs `(("fortran" ,gfortran-4.8)
              ("python" ,python-2)))
    (arguments
     `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES")
       #:phases (alist-cons-before
                 'check 'patch-python
                 (lambda* (#:key inputs #:allow-other-keys)
                   (let ((python (assoc-ref inputs "python")))
                     (substitute* "lapack_testing.py"
                       (("/usr/bin/env python") python))))
                  %standard-phases)))
    (synopsis "Library for numerical linear algebra")
    (description
     "LAPACK is a Fortran 90 library for solving the most commonly occurring
problems in numerical linear algebra.")
    (license (license:bsd-style "file://LICENSE"
                                "See LICENSE in the distribution."))))

(define-public gnuplot
  (package
    (name "gnuplot")
    (version "4.6.3")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
                                version "/gnuplot-" version ".tar.gz"))
      (sha256
       (base32
        "1xd7gqdhlk7k1p9yyqf9vkk811nadc7m4si0q3nb6cpv4pxglpyz"))))
    (build-system gnu-build-system)
    (inputs `(("readline" ,readline)
              ("cairo" ,cairo)
              ("pango" ,pango)
              ("gd" ,gd)))
    (native-inputs `(("texlive" ,texlive)
                     ("pkg-config" ,pkg-config)))
    (home-page "http://www.gnuplot.info")
    (synopsis "Command-line driven graphing utility")
    (description "Gnuplot is a portable command-line driven graphing
utility. It was originally created to allow scientists and students to
visualize mathematical functions and data interactively, but has grown to
support many non-interactive uses such as web scripting. It is also used as a
plotting engine by third-party applications like Octave.")
    ;;  X11 Style with the additional restriction that derived works may only be
    ;;  distributed as patches to the original.
    (license (license:fsf-free
	      "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))

(define-public hdf5
  (package
    (name "hdf5")
    (version "1.8.12")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-"
                          version ".tar.bz2"))
      (sha256
       (base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
        (alist-cons-before
         'configure 'patch-configure
         (lambda _
           (substitute* "configure"
             (("/bin/mv") "mv")))
         %standard-phases)))
    (outputs '("out" "bin" "lib" "include"))
    (home-page "http://www.hdfgroup.org")
    (synopsis "Management suite for  extremely large and complex data")
    (description "HDF5 is a suite that makes possible the management of
extremely large and complex data collections.")
    (license (license:x11-style
              "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))


;; For a fully featured Octave, users  are strongly recommended also to install
;; the following packages: texinfo, less, ghostscript, gnuplot.
(define-public octave
  (package
    (name "octave")
    (version "3.8.0")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "mirror://gnu/octave/octave-"
			  version ".tar.gz"))
      (sha256
       (base32
	"0ks9pr154syw0vb3jn6xsnrkkrbvf9y7i7gaxa28rz6ngxbxvq9l"))))
    (build-system gnu-build-system)
    (inputs
     `(("lapack" ,lapack)
       ("readline" ,readline)
       ("glpk" ,glpk)
       ("curl" ,curl)
       ("pcre" ,pcre)
       ("fltk" ,fltk)
       ("fontconfig" ,fontconfig)
       ("freetype" ,freetype)
       ("hdf5-lib" ,hdf5 "lib")
       ("hdf5-include" ,hdf5 "include")
       ("libxft" ,libxft)
       ("mesa" ,mesa)
       ("zlib" ,zlib)))
    (native-inputs
     `(("gfortran" ,gfortran-4.8)
       ("pkg-config" ,pkg-config)
       ("perl" ,perl)
       ;; The following inputs are not actually used in the build process.  However, the
       ;; ./configure gratuitously tests for their existence and assumes that programs not
       ;; present at build time are also not, and can never be, available at run time!
       ;; If these inputs are therefore not present, support for them will be built out.
       ;; However, Octave will still run without them, albeit without the features they
       ;; provide.
       ("less" ,less)
       ("texinfo" ,texinfo)
       ("ghostscript" ,ghostscript)
       ("gnuplot" ,gnuplot)))
    (arguments
     `(#:configure-flags (list (string-append "--with-shell="
			    (assoc-ref %build-inputs "bash")
			    "/bin/sh"))))
    (home-page "http://www.gnu.org/software/octave/")
    (synopsis "High-level language for numerical computation")
    (description "GNU Octave is a high-level interpreted language that is specialized
for numerical computations.  It can be used for both linear and non-linear
applications and it provides great support for visualizing results.  Work may
be performed both at the interactive command-line as well as via script
files.")
    (license license:gpl3+)))

(define-public gmsh
  (package
    (name "gmsh")
    (version "2.8.4")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-"
                          version "-source.tgz"))
      (sha256
       (base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr"))
      (modules '((guix build utils)))
      (snippet
       ;; Remove non-free METIS code
       '(delete-file-recursively "contrib/Metis"))))
    (build-system cmake-build-system)
    (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath
    (propagated-inputs
     `(("fltk" ,fltk)
       ("gfortran" ,gfortran-4.8)
       ("gmp" ,gmp)
       ("hdf5-lib" ,hdf5 "lib")
       ("hdf5-include" ,hdf5 "include")
       ("lapack" ,lapack)
       ("mesa" ,mesa)
       ("libx11" ,libx11)
       ("libxext" ,libxext)))
    (arguments
     `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
                           "-DENABLE_BUILD_SHARED:BOOL=ON"
                           "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
    (home-page "http://www.geuz.org/gmsh/")
    (synopsis "3D finite element grid generator")
    (description "Gmsh is a 3D finite element grid generator with a built-in
CAD engine and post-processor.  Its design goal is to provide a fast, light
and user-friendly meshing tool with parametric input and advanced
visualization capabilities.  Gmsh is built around four modules: geometry,
mesh, solver and post-processing.  The specification of any input to these
modules is done either interactively using the graphical user interface or in
ASCII text files using Gmsh's own scripting language.")
    (license license:gpl2+)))

(define-public petsc
  (package
    (name "petsc")
    (version "3.4.4")
    (source
     (origin
      (method url-fetch)
      ;; The *-lite-* tarball does not contain the *large* documentation
      (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
                          "petsc-lite-" version ".tar.gz"))
      (sha256
       (base32 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv"))
      (patches
       (list (search-patch "petsc-fix-threadcomm.patch")))))
    (build-system gnu-build-system)
    (native-inputs
     `(("python" ,python-2)
       ("perl" ,perl)))
    (inputs
     `(("gfortran" ,gfortran-4.8)
       ("lapack" ,lapack)
       ("superlu" ,superlu)
       ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
       ;; leaving out opengl, as configuration seems to only be for mac
       ))
    (arguments
     `(#:test-target "test"
       #:parallel-build? #f
       #:configure-flags
       `("--with-mpi=0"
         "--with-openmp=1"
         "--with-superlu=1"
         ,(string-append "--with-superlu-include="
                         (assoc-ref %build-inputs "superlu") "/include")
         ,(string-append "--with-superlu-lib="
                         (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
       #:phases
       (alist-replace
        'configure
        ;; PETSc's configure script is actually a python script, so we can't
        ;; run it with bash.
        (lambda* (#:key outputs (configure-flags '())
                  #:allow-other-keys)
          (let* ((prefix (assoc-ref outputs "out"))
                 (flags `(,(string-append "--prefix=" prefix)
                          ,@configure-flags)))
            (format #t "build directory: ~s~%" (getcwd))
            (format #t "configure flags: ~s~%" flags)
            (zero? (apply system* "./configure" flags))))
        (alist-cons-after
         'configure 'clean-local-references
         ;; Try to keep build directory names from leaking into compiled code
         (lambda* (#:key inputs outputs #:allow-other-keys)
           (let ((out (assoc-ref outputs "out")))
             (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
               (((getcwd)) out))))
         (alist-cons-after
          'install 'clean-install
          ;; Try to keep installed files from leaking build directory names.
          (lambda* (#:key inputs outputs #:allow-other-keys)
            (let ((out     (assoc-ref outputs "out"))
                  (fortran (assoc-ref inputs  "gfortran")))
              (substitute* (map (lambda (file)
                                  (string-append out "/" file))
                                '("conf/petscvariables"
                                  "conf/PETScConfig.cmake"))
                (((getcwd)) out))
              ;; Make compiler references point to the store
              (substitute* (string-append out "/conf/petscvariables")
                (("= g(cc|\\+\\+|fortran)" _ suffix)
                 (string-append "= " fortran "/bin/g" suffix)))
              ;; PETSc installs some build logs, which aren't necessary.
              (for-each (lambda (file)
                          (let ((f (string-append out "/" file)))
                            (when (file-exists? f)
                              (delete-file f))))
                        '("conf/configure.log"
                          "conf/make.log"
                          "conf/test.log"
                          "conf/error.log"
                          "conf/RDict.db"
                          ;; Once installed, should uninstall with Guix
                          "conf/uninstall.py"))))
          %standard-phases)))))
    (home-page "http://www.mcs.anl.gov/petsc")
    (synopsis "Library to solve ODEs and algebraic equations")
    (description "PETSc, pronounced PET-see (the S is silent), is a suite of
data structures and routines for the scalable (parallel) solution of
scientific applications modeled by partial differential equations.")
    (license (license:bsd-style
              "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))

(define-public petsc-complex
  (package (inherit petsc)
    (name "petsc-complex")
    (arguments
     (substitute-keyword-arguments (package-arguments petsc)
       ((#:configure-flags cf)
        `(cons "--with-scalar-type=complex" ,cf))))
    (description
     (string-append (package-description petsc)
                    "  Complex scalar type version."))))

(define-public petsc-openmpi
  (package (inherit petsc)
    (name "petsc-openmpi")
    (inputs
     `(("openmpi" ,openmpi)
       ,@(package-inputs petsc)))
    (arguments
     (substitute-keyword-arguments (package-arguments petsc)
       ((#:configure-flags cf)
        ``("--with-mpiexec=mpirun"
           ,(string-append "--with-mpi-dir="
                           (assoc-ref %build-inputs "openmpi"))
           ,@(delete "--with-mpi=0" ,cf)))))
    (description
     (string-append (package-description petsc)
                    "  With OpenMPI parallelism support."))))

(define-public petsc-complex-openmpi
  (package (inherit petsc-complex)
    (name "petsc-complex-openmpi")
    (inputs
     `(("openmpi" ,openmpi)
       ,@(package-inputs petsc-complex)))
    (arguments
     (substitute-keyword-arguments (package-arguments petsc-complex)
       ((#:configure-flags cf)
        ``("--with-mpiexec=mpirun"
           ,(string-append "--with-mpi-dir="
                           (assoc-ref %build-inputs "openmpi"))
           ,@(delete "--with-mpi=0" ,cf)))))
    (description
     (string-append (package-description petsc-complex)
                    "  With OpenMPI parallelism support."))))

(define-public superlu
  (package
    (name "superlu")
    (version "4.3")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
                           "superlu_" version ".tar.gz"))
       (sha256
        (base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("tcsh" ,tcsh)))
    (inputs
     `(("lapack" ,lapack)
       ("gfortran" ,gfortran-4.8)))
    (arguments
     `(#:parallel-build? #f
       #:tests? #f                      ;tests are run as part of `make all`
       #:phases
       (alist-replace
        'configure
        (lambda* (#:key inputs outputs #:allow-other-keys)
          (call-with-output-file "make.inc"
            (lambda (port)
              (format port "
PLAT        =
SuperLUroot = ~a
SUPERLULIB  = ~a/lib/libsuperlu.a
TMGLIB      = libtmglib.a
BLASDEF     = -DUSE_VENDOR_BLAS
BLASLIB     = -L~a/lib -lblas
LIBS        = $(SUPERLULIB) $(BLASLIB)
ARCH        = ar
ARCHFLAGS   = cr
RANLIB      = ranlib
CC          = gcc
PIC         = -fPIC
CFLAGS      = -O3 -DPRNTlevel=0 $(PIC)
NOOPTS      = -O0 $(PIC)
FORTRAN     = gfortran
FFLAGS      = -O2 $(PIC)
LOADER      = $(CC)
CDEFS       = -DAdd_"
                      (getcwd)
                      (assoc-ref outputs "out")
                      (assoc-ref inputs "lapack")))))
        (alist-cons-before
         'build 'create-install-directories
         (lambda* (#:key outputs #:allow-other-keys)
           (for-each
            (lambda (dir)
              (mkdir-p (string-append (assoc-ref outputs "out")
                                      "/" dir)))
            '("lib" "include")))
         (alist-replace
          'install
          (lambda* (#:key outputs #:allow-other-keys)
            ;; Library is placed in lib during the build phase.  Copy over
            ;; headers to include.
            (let* ((out    (assoc-ref outputs "out"))
                   (incdir (string-append out "/include")))
              (for-each (lambda (file)
                          (let ((base (basename file)))
                            (format #t "installing `~a' to `~a'~%"
                                    base incdir)
                            (copy-file file
                                       (string-append incdir "/" base))))
                        (find-files "SRC" ".*\\.h$"))))
          %standard-phases)))))
    (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
    (synopsis "Supernodal direct solver for sparse linear systems")
    (description
     "SuperLU is a general purpose library for the direct solution of large,
sparse, nonsymmetric systems of linear equations on high performance machines.
The library is written in C and is callable from either C or Fortran.  The
library routines perform an LU decomposition with partial pivoting and
triangular system solves through forward and back substitution.  The library
also provides threshold-based ILU factorization preconditioners.")
    (license license:bsd-3)))

(define-public superlu-dist
  (package
    (name "superlu-dist")
    (version "3.3")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
                           "superlu_dist_" version ".tar.gz"))
       (sha256
        (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
       (patches (list (search-patch "superlu-dist-scotchmetis.patch")))))
    (build-system gnu-build-system)
    (native-inputs
     `(("tcsh" ,tcsh)))
    (inputs
     `(("gfortran" ,gfortran-4.8)))
    (propagated-inputs
     `(("openmpi" ,openmpi)             ;headers include MPI heades
       ("lapack" ,lapack)               ;required to link with output library
       ("pt-scotch" ,pt-scotch)))       ;same
    (arguments
     `(#:parallel-build? #f             ;race conditions using ar
       #:phases
       (alist-replace
        'configure
        (lambda* (#:key inputs outputs #:allow-other-keys)
          (call-with-output-file "make.inc"
            (lambda (port)
              (format port "
PLAT        =
DSuperLUroot = ~a
DSUPERLULIB  = ~a/lib/libsuperlu_dist.a
BLASDEF     = -DUSE_VENDOR_BLAS
BLASLIB     = -L~a/lib -lblas
PARMETISLIB = -L~a/lib \
              -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
              -lscotch -lscotcherr -lscotcherrexit
METISLIB    = -L~:*~a/lib \
              -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
LIBS        = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
ARCH        = ar
ARCHFLAGS   = cr
RANLIB      = ranlib
CC          = mpicc
PIC         = -fPIC
CFLAGS      = -O3 -g -DPRNTlevel=0 $(PIC)
NOOPTS      = -O0 -g $(PIC)
FORTRAN     = mpifort
FFLAGS      = -O2 -g $(PIC)
LOADER      = $(CC)
CDEFS       = -DAdd_"
                      (getcwd)
                      (assoc-ref outputs "out")
                      (assoc-ref inputs "lapack")
                      (assoc-ref inputs "pt-scotch")))))
        (alist-cons-after
         'unpack 'remove-broken-symlinks
         (lambda _
           (for-each delete-file
                     (find-files "MAKE_INC" "\\.#make\\..*")))
         (alist-cons-before
          'build 'create-install-directories
          (lambda* (#:key outputs #:allow-other-keys)
            (for-each
             (lambda (dir)
               (mkdir-p (string-append (assoc-ref outputs "out")
                                       "/" dir)))
             '("lib" "include")))
          (alist-replace
           'check
           (lambda _
             (with-directory-excursion "EXAMPLE"
               (and
                (zero? (system* "mpirun" "-n" "2"
                                "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
                (zero? (system* "mpirun" "-n" "2"
                                "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
           (alist-replace
            'install
            (lambda* (#:key outputs #:allow-other-keys)
              ;; Library is placed in lib during the build phase.  Copy over
              ;; headers to include.
              (let* ((out    (assoc-ref outputs "out"))
                     (incdir (string-append out "/include")))
                (for-each (lambda (file)
                            (let ((base (basename file)))
                              (format #t "installing `~a' to `~a'~%"
                                      base incdir)
                              (copy-file file
                                         (string-append incdir "/" base))))
                          (find-files "SRC" ".*\\.h$"))))
            %standard-phases)))))))
    (home-page (package-home-page superlu))
    (synopsis "Parallel supernodal direct solver")
    (description
     "SuperLU_DIST is a parallel extension to the serial SuperLU library.
It is targeted for distributed memory parallel machines.  SuperLU_DIST is
implemented in ANSI C, and MPI for communications.")
    (license license:bsd-3)))

(define-public scotch
  (package
    (name "scotch")
    (version "6.0.0")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://gforge.inria.fr/frs/download.php/31831/"
                          "scotch_" version ".tar.gz"))
      (sha256
       (base32 "0yfqf9lk7chb3h42777x42x4adx0v3n0b41q0cdqrdmscp4iczp5"))
      (patches (list (search-patch "scotch-test-threading.patch")))))
    (build-system gnu-build-system)
    (inputs
     `(("zlib" ,zlib)
       ("flex" ,flex)
       ("bison" ,bison)))
    (arguments
     `(#:phases
       (alist-cons-after
        'unpack 'chdir-to-src
        (lambda _ (chdir "src"))
        (alist-replace
         'configure
         (lambda _
           (call-with-output-file "Makefile.inc"
             (lambda (port)
               (format port "
EXE =
LIB = .a
OBJ = .o
MAKE = make
AR = ar
ARFLAGS = -ruv
CCS = gcc
CCP = mpicc
CCD = gcc
CPPFLAGS =~{ -D~a~}
CFLAGS = -O2 -g $(CPPFLAGS)
LDFLAGS = -lz -lm -lrt -lpthread
CP = cp
LEX = flex -Pscotchyy -olex.yy.c
LN = ln
MKDIR = mkdir
MV = mv
RANLIB = ranlib
YACC = bison -pscotchyy -y -b y
"
                       '("COMMON_FILE_COMPRESS_GZ"
                         "COMMON_PTHREAD"
                         "COMMON_RANDOM_FIXED_SEED"
                         ;; TODO: Define once our MPI supports
                         ;; MPI_THREAD_MULTIPLE
                         ;; "SCOTCH_PTHREAD"
                         ;; "SCOTCH_PTHREAD_NUMBER=2"
                         "restrict=__restrict")))))
         (alist-replace
          'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((out (assoc-ref outputs "out")))
              (mkdir out)
              (zero? (system* "make"
                              (string-append "prefix=" out)
                              "install"))))
          %standard-phases)))))
    (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
    (synopsis "Programs and libraries for graph algorithms")
    (description "SCOTCH is a set of programs and libraries which implement
the static mapping and sparse matrix reordering algorithms developed within
the SCOTCH project.  Its purpose is to apply graph theory, with a divide and
conquer approach, to scientific computing problems such as graph and mesh
partitioning, static mapping, and sparse matrix ordering, in application
domains ranging from structural mechanics to operating systems or
bio-chemistry.")
    ;; See LICENSE_en.txt
    (license license:cecill-c)))

(define-public pt-scotch
  (package (inherit scotch)
    (name "pt-scotch")
    (propagated-inputs
     `(("openmpi" ,openmpi)))           ;Headers include MPI headers
    (arguments
     (substitute-keyword-arguments (package-arguments scotch)
       ((#:phases scotch-phases)
        `(alist-replace
          'build
          ;; TODO: Would like to add parallelism here
          (lambda _
            (and
             (zero? (system* "make" "ptscotch"))
             ;; Install the serial metis compatibility library
             (zero? (system* "make" "-C" "libscotchmetis" "install"))))
          (alist-replace
           'check
           (lambda _ (zero? (system* "make" "ptcheck")))
           (alist-replace
            'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out")))
                (mkdir out)
                (zero? (system* "make"
                                (string-append "prefix=" out)
                                "install"))))
            ,scotch-phases))))))
    (synopsis "Programs and libraries for graph algorithms (with MPI)")))