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gnu: slepc: Update to 3.10.1.
[jackhill/guix/guix.git] / gnu / packages / maths.scm
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 42136f6..6053d76 100644 (file)
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -27,6 +27,8 @@
 ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
 ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
 ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
+;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -238,16 +240,60 @@ triangulations.")
     (license (license:non-copyleft "file://COPYING.txt"
                                    "See COPYING in the distribution."))))
 
     (license (license:non-copyleft "file://COPYING.txt"
                                    "See COPYING in the distribution."))))
 
+(define-public python-cvxopt
+  (package
+    (name "python-cvxopt")
+    (version "1.2.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/cvxopt/cvxopt.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "05mnjil9palaa48xafdfh4f5pr4z7aqjr995rwl08qfyxs8y0crf"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'find-libraries
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "CVXOPT_BLAS_LIB" "openblas")
+             (setenv "CVXOPT_BUILD_FFTW" "1")
+             (setenv "CVXOPT_BUILD_GLPK" "1")
+             (setenv "CVXOPT_BUILD_GSL" "1")
+             #t)))))
+    (inputs
+     `(("fftw" ,fftw)
+       ("glpk" ,glpk)
+       ("gsl" ,gsl)
+       ("lapack" ,lapack)
+       ("openblas" ,openblas)
+       ("suitesparse" ,suitesparse)))
+    (home-page "https://www.cvxopt.org")
+    (synopsis "Python library for convex optimization")
+    (description
+     "CVXOPT is a package for convex optimization based on the Python
+programming language.  Its main purpose is to make the development of software
+for convex optimization applications straightforward by building on Python’s
+extensive standard library and on the strengths of Python as a high-level
+programming language.")
+    (license license:gpl3+)))
+
+(define-public python2-cvxopt
+  (package-with-python2 python-cvxopt))
+
 (define-public units
   (package
    (name "units")
 (define-public units
   (package
    (name "units")
-   (version "2.17")
+   (version "2.18")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/units/units-" version
                                 ".tar.gz"))
             (sha256 (base32
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/units/units-" version
                                 ".tar.gz"))
             (sha256 (base32
-                     "1n2xzpnxfn475zkd8rzs5gg58xszjbr4bdbgvk6hryzimvwwj0qz"))))
+                     "0y26kj349i048y4z3xrk90bvciw2j6ds3rka7r7yn3183hirr5b4"))))
    (build-system gnu-build-system)
    (inputs
     `(("readline" ,readline)
    (build-system gnu-build-system)
    (inputs
     `(("readline" ,readline)
@@ -459,16 +505,15 @@ computing convex hulls.")
 (define-public arpack-ng
   (package
     (name "arpack-ng")
 (define-public arpack-ng
   (package
     (name "arpack-ng")
-    (version "3.6.2")
+    (version "3.6.3")
     (home-page "https://github.com/opencollab/arpack-ng")
     (home-page "https://github.com/opencollab/arpack-ng")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append home-page "/archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "16jrvdl0gh78rrfnvrcxwys4slwfh6qmwwjhfc9d6vwrvq184g37"))))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference (url home-page) (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -508,7 +553,11 @@ large scale eigenvalue problems.")
     (arguments
      (substitute-keyword-arguments (package-arguments arpack-ng)
        ((#:configure-flags _ '())
     (arguments
      (substitute-keyword-arguments (package-arguments arpack-ng)
        ((#:configure-flags _ '())
-        ''("--enable-mpi"))))
+        ''("--enable-mpi"))
+       ((#:phases phases '%standard-phases)
+        `(modify-phases ,phases
+           (add-before 'check 'mpi-setup
+             ,%openmpi-setup)))))
     (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
 
 (define-public lapack
     (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
 
 (define-public lapack
@@ -569,14 +618,8 @@ problems in numerical linear algebra.")
     (arguments
      `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
        #:phases (modify-phases %standard-phases
     (arguments
      `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
        #:phases (modify-phases %standard-phases
-                  (add-before 'check 'set-test-environment
-                    (lambda _
-                      ;; By default, running the test suite would fail because
-                      ;; 'ssh' could not be found in $PATH.  Define this
-                      ;; variable to placate Open MPI without adding a
-                      ;; dependency on OpenSSH (the agent isn't used anyway.)
-                      (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
-                      #t)))))
+                  (add-before 'check 'mpi-setup
+                   ,%openmpi-setup))))
     (home-page "http://www.netlib.org/scalapack/")
     (synopsis "Library for scalable numerical linear algebra")
     (description
     (home-page "http://www.netlib.org/scalapack/")
     (synopsis "Library for scalable numerical linear algebra")
     (description
@@ -816,8 +859,11 @@ incompatible with HDF5.")
                 (mkdir-p flib)
                 (mkdir-p finc)
                 (mkdir-p fex)
                 (mkdir-p flib)
                 (mkdir-p finc)
                 (mkdir-p fex)
-                (rename-file (string-append bin "/h5fc")
-                             (string-append fbin "/h5fc"))
+                ;; Note: When built with --enable-parallel, the 'h5fc' file
+                ;; doesn't exist, hence this condition.
+                (when (file-exists? (string-append bin "/h5fc"))
+                  (rename-file (string-append bin "/h5fc")
+                               (string-append fbin "/h5fc")))
                 (for-each (lambda (file)
                             (rename-file file
                                          (string-append flib "/" (basename file))))
                 (for-each (lambda (file)
                             (rename-file file
                                          (string-append flib "/" (basename file))))
@@ -839,6 +885,25 @@ extremely large and complex data collections.")
     (license (license:x11-style
               "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
 
     (license (license:x11-style
               "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
 
+(define-public hdf5-1.10
+  (package (inherit hdf5)
+    (version "1.10.4")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
+                                "hdf5-" (version-major+minor version)
+                                "/hdf5-" version "/src/hdf5-"
+                                version ".tar.bz2")
+                 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
+                                "current"
+                                (apply string-append
+                                       (take (string-split version #\.) 2))
+                                "/src/hdf5-" version ".tar.bz2")))
+      (sha256
+       (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
+      (patches (list (search-patch "hdf5-config-date.patch")))))))
+
 (define-public hdf-java
   (package
    (name "hdf-java")
 (define-public hdf-java
   (package
    (name "hdf-java")
@@ -1036,10 +1101,13 @@ Swath).")
      `(("mpi" ,openmpi)
        ,@(package-inputs hdf5)))
     (arguments
      `(("mpi" ,openmpi)
        ,@(package-inputs hdf5)))
     (arguments
-     (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
-                                     ,@(package-arguments hdf5))
+     (substitute-keyword-arguments (package-arguments hdf5)
+       ((#:configure-flags flags)
+        ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags)))
        ((#:phases phases)
         `(modify-phases ,phases
        ((#:phases phases)
         `(modify-phases ,phases
+           (add-after 'build 'mpi-setup
+             ,%openmpi-setup)
            (add-before 'check 'patch-tests
              (lambda _
                ;; OpenMPI's mpirun will exit with non-zero status if it
            (add-before 'check 'patch-tests
              (lambda _
                ;; OpenMPI's mpirun will exit with non-zero status if it
@@ -1398,6 +1466,13 @@ can solve two kinds of problems:
        ("less" ,less)
        ("ghostscript" ,ghostscript)
        ("gnuplot" ,gnuplot)))
        ("less" ,less)
        ("ghostscript" ,ghostscript)
        ("gnuplot" ,gnuplot)))
+    ;; Octave code uses this variable to detect directories holding multiple CA
+    ;; certificates to verify peers with.  This is required for the networking
+    ;; functions that require encryption to work properly.
+    (native-search-paths
+     (list (search-path-specification
+            (variable "CURLOPT_CAPATH")
+            (files '("etc/ssl/certs")))))
     (arguments
      `(#:configure-flags
        (list (string-append "--with-shell="
     (arguments
      `(#:configure-flags
        (list (string-append "--with-shell="
@@ -1580,7 +1655,7 @@ September 2004}")
 (define-public petsc
   (package
     (name "petsc")
 (define-public petsc
   (package
     (name "petsc")
-    (version "3.8.0")
+    (version "3.10.2")
     (source
      (origin
       (method url-fetch)
     (source
      (origin
       (method url-fetch)
@@ -1588,7 +1663,9 @@ September 2004}")
       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
                           "petsc-lite-" version ".tar.gz"))
       (sha256
       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
                           "petsc-lite-" version ".tar.gz"))
       (sha256
-       (base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s"))))
+       (base32 "0bl64pydak3rblnjffi482r8bin4xim9sb37ksl2jkcxf0i0irsi"))))
+    (outputs '("out"                    ;libraries and headers
+               "examples"))             ;~30MiB of examples
     (build-system gnu-build-system)
     (native-inputs
      `(("python" ,python-2)))
     (build-system gnu-build-system)
     (native-inputs
      `(("python" ,python-2)))
@@ -1605,11 +1682,7 @@ September 2004}")
        #:configure-flags
        `("--with-mpi=0"
          "--with-openmp=1"
        #: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"))
+         "--with-superlu=1")
        #:make-flags
        ;; Honor (parallel-job-count) for build.  Do not use --with-make-np,
        ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
        #:make-flags
        ;; Honor (parallel-job-count) for build.  Do not use --with-make-np,
        ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
@@ -1662,6 +1735,15 @@ September 2004}")
                           "PETScBuildInternal.cmake"
                           ;; Once installed, should uninstall with Guix
                           "uninstall.py"))
                           "PETScBuildInternal.cmake"
                           ;; Once installed, should uninstall with Guix
                           "uninstall.py"))
+              #t)))
+        (add-after 'install 'move-examples
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let* ((out (assoc-ref outputs "out"))
+                   (examples (assoc-ref outputs "examples"))
+                   (exdir (string-append out "/share/petsc/examples"))
+                   (exdir' (string-append examples "/share/petsc/examples")))
+              (copy-recursively exdir exdir')
+              (delete-file-recursively exdir)
               #t))))))
     (home-page "http://www.mcs.anl.gov/petsc")
     (synopsis "Library to solve PDEs")
               #t))))))
     (home-page "http://www.mcs.anl.gov/petsc")
     (synopsis "Library to solve PDEs")
@@ -1684,13 +1766,21 @@ scientific applications modeled by partial differential equations.")
   (package (inherit petsc)
     (name "petsc-openmpi")
     (inputs
   (package (inherit petsc)
     (name "petsc-openmpi")
     (inputs
-     `(("openmpi" ,openmpi)
-       ("hdf5" ,hdf5-parallel-openmpi)
+     `(("hdf5" ,hdf5-parallel-openmpi)
+       ("metis" ,metis)
+       ("mumps" ,mumps-openmpi)
+       ("openmpi" ,openmpi)
+       ("scalapack" ,scalapack)
+       ("scotch" ,pt-scotch)
        ,@(package-inputs petsc)))
     (arguments
      (substitute-keyword-arguments (package-arguments petsc)
        ((#:configure-flags cf)
         ``("--with-mpiexec=mpirun"
        ,@(package-inputs petsc)))
     (arguments
      (substitute-keyword-arguments (package-arguments petsc)
        ((#:configure-flags cf)
         ``("--with-mpiexec=mpirun"
+           "--with-metis=1"
+           "--with-mumps=1"
+           "--with-scalapack=1"
+           "--with-ptscotch=1"
            ,(string-append "--with-mpi-dir="
                            (assoc-ref %build-inputs "openmpi"))
            ,(string-append "--with-hdf5-include="
            ,(string-append "--with-mpi-dir="
                            (assoc-ref %build-inputs "openmpi"))
            ,(string-append "--with-hdf5-include="
@@ -1700,15 +1790,9 @@ scientific applications modeled by partial differential equations.")
            ,@(delete "--with-mpi=0" ,cf)))
        ((#:phases phases)
         `(modify-phases ,phases
            ,@(delete "--with-mpi=0" ,cf)))
        ((#:phases phases)
         `(modify-phases ,phases
-           (add-before 'check 'set-test-environment
-             (lambda _
-               ;; By default, running the test suite would fail because 'ssh'
-               ;; could not be found in $PATH.  Define this variable to
-               ;; placate Open MPI without adding a dependency on OpenSSH (the
-               ;; agent isn't used anyway.)
-               (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
-               #t))))))
-    (synopsis "Library to solve PDEs (with MPI support)")))
+           (add-before 'configure 'mpi-setup
+             ,%openmpi-setup)))))
+    (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
 
 (define-public petsc-complex-openmpi
   (package (inherit petsc-complex)
 
 (define-public petsc-complex-openmpi
   (package (inherit petsc-complex)
@@ -1725,6 +1809,40 @@ scientific applications modeled by partial differential equations.")
            ,@(delete "--with-mpi=0" ,cf)))))
     (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
 
            ,@(delete "--with-mpi=0" ,cf)))))
     (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
 
+(define-public python-petsc4py
+  (package
+    (name "python-petsc4py")
+    (version "3.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "petsc4py" version))
+        (sha256
+          (base32
+            "1f8zd1ac9irsgkyqmzq30d9kl10fy1nh6zk312dhs43g449fkkhc"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'pre-build
+           (lambda _
+             ;; Define path to PETSc installation.
+             (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
+             #t))
+         (add-before 'check 'mpi-setup
+           ,%openmpi-setup))))
+    (inputs
+     `(("petsc" ,petsc-openmpi)
+       ("python-numpy" ,python-numpy)))
+    (home-page "https://bitbucket.org/petsc/petsc4py/")
+    (synopsis "Python bindings for PETSc")
+    (description "PETSc, the Portable, Extensible Toolkit for
+Scientific Computation, is a suite of data structures and routines for
+the scalable (parallel) solution of scientific applications modeled by
+partial differential equations.  It employs the MPI standard for all
+message-passing communication.  @code{petsc4py} provides Python
+bindings to almost all functions of PETSc.")
+    (license license:bsd-3)))
 
 (define-public python-kiwisolver
   (package
 
 (define-public python-kiwisolver
   (package
@@ -1753,7 +1871,7 @@ savings are consistently > 5x.")
 (define-public slepc
   (package
     (name "slepc")
 (define-public slepc
   (package
     (name "slepc")
-    (version "3.8.2")
+    (version "3.10.1")
     (source
      (origin
        (method url-fetch)
     (source
      (origin
        (method url-fetch)
@@ -1761,7 +1879,7 @@ savings are consistently > 5x.")
                            version ".tar.gz"))
        (sha256
         (base32
                            version ".tar.gz"))
        (sha256
         (base32
-         "04zd48p43rnvg68p6cp28zll0px5whglc5v0sc3s6vdj1v920z8y"))))
+         "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("python" ,python-2)))
     (build-system gnu-build-system)
     (native-inputs
      `(("python" ,python-2)))
@@ -1838,14 +1956,8 @@ arising after the discretization of partial differential equations.")
      (substitute-keyword-arguments (package-arguments slepc)
        ((#:phases phases '%standard-phases)
         `(modify-phases ,phases
      (substitute-keyword-arguments (package-arguments slepc)
        ((#:phases phases '%standard-phases)
         `(modify-phases ,phases
-           (add-before 'check 'set-test-environment
-             (lambda _
-               ;; By default, running the test suite would fail because 'ssh'
-               ;; could not be found in $PATH.  Define this variable to
-               ;; placate Open MPI without adding a dependency on OpenSSH (the
-               ;; agent isn't used anyway.)
-               (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
-               #t))))))
+           (add-before 'check 'mpi-setup
+            ,%openmpi-setup)))))
     (inputs
      `(("mpi" ,openmpi)
        ("arpack" ,arpack-ng-openmpi)
     (inputs
      `(("mpi" ,openmpi)
        ("arpack" ,arpack-ng-openmpi)
@@ -1863,6 +1975,43 @@ arising after the discretization of partial differential equations.")
        ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
     (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
 
        ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
     (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
 
+(define-public python-slepc4py
+  (package
+    (name "python-slepc4py")
+    (version "3.9.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "slepc4py" version))
+        (sha256
+          (base32
+            "02xr0vndgibgkz3rgprqk05n3mk5mpgqw550sr4681vcsgz4zvb7"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'pre-build
+           (lambda _
+             ;; Define path to PETSc installation.
+             (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
+             ;; Define path to SLEPc installation.
+             (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
+             #t))
+         (add-before 'check 'mpi-setup
+           ,%openmpi-setup))))
+    (inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-petsc4py" ,python-petsc4py)
+       ("slepc" ,slepc-openmpi)))
+    (home-page "https://bitbucket.org/slepc/slepc4py/")
+    (synopsis "Python bindings for SLEPc")
+    (description "SLEPc, the Scalable Library for Eigenvalue Problem
+Computations, is based on PETSc, the Portable, Extensible Toolkit for
+Scientific Computation.  It employs the MPI standard for all
+message-passing communication.  @code{slepc4py} provides Python
+bindings to almost all functions of SLEPc.")
+    (license license:bsd-3)))
+
 (define-public mumps
   (package
     (name "mumps")
 (define-public mumps
   (package
     (name "mumps")
@@ -2015,14 +2164,8 @@ sparse system of linear equations A x = b using Guassian elimination.")
      (substitute-keyword-arguments (package-arguments mumps)
        ((#:phases phases)
         `(modify-phases ,phases
      (substitute-keyword-arguments (package-arguments mumps)
        ((#:phases phases)
         `(modify-phases ,phases
-           (add-before 'check 'set-test-environment
-             (lambda _
-               ;; By default, running the test suite would fail because 'ssh'
-               ;; could not be found in $PATH.  Define this variable to
-               ;; placate Open MPI without adding a dependency on OpenSSH (the
-               ;; agent isn't used anyway.)
-               (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
-               #t))
+           (add-before 'check 'mpi-setup
+            ,%openmpi-setup)
            (replace 'check
              (lambda _
                ((assoc-ref ,phases 'check)
            (replace 'check
              (lambda _
                ((assoc-ref ,phases 'check)
@@ -2059,16 +2202,14 @@ programming problems.")
 (define-public r-pracma
   (package
     (name "r-pracma")
 (define-public r-pracma
   (package
     (name "r-pracma")
-    (version "2.1.5")
+    (version "2.1.8")
     (source (origin
       (method url-fetch)
       (uri (cran-uri "pracma" version))
       (sha256
     (source (origin
       (method url-fetch)
       (uri (cran-uri "pracma" version))
       (sha256
-        (base32 "18cv7c2gvagbmggfbsy2xk9bpn47izd0qrmqnc3q7afvj6pr6nf9"))))
+        (base32 "0m8ladhrfyxwybblkcdgg4xv1mk5kibmwarpj2k0c2y34zzcix4z"))))
     (build-system r-build-system)
     (build-system r-build-system)
-    (propagated-inputs
-     `(("r-quadprog" ,r-quadprog)))
-    (home-page "https://cran.r-project.org/web/packages/pracma")
+    (home-page "https://cran.r-project.org/web/packages/pracma/")
     (synopsis "Practical numerical math functions")
     (description "This package provides functions for numerical analysis and
 linear algebra, numerical optimization, differential equations, plus some
     (synopsis "Practical numerical math functions")
     (description "This package provides functions for numerical analysis and
 linear algebra, numerical optimization, differential equations, plus some
@@ -2097,7 +2238,8 @@ porting.")
            (lambda _
              (substitute* "spec/parser_spec.rb"
                (("\\\\\"")
            (lambda _
              (substitute* "spec/parser_spec.rb"
                (("\\\\\"")
-                "\"")))))))
+                "\""))
+             #t)))))
     (native-inputs
      `(("bundler" ,bundler)
        ("ruby-rspec" ,ruby-rspec)))
     (native-inputs
      `(("bundler" ,bundler)
        ("ruby-rspec" ,ruby-rspec)))
@@ -2268,13 +2410,10 @@ CDEFS       = -DAdd_"
                                         "/" dir)))
               '("lib" "include"))
              #t))
                                         "/" dir)))
               '("lib" "include"))
              #t))
+        (add-before 'check 'mpi-setup
+          ,%openmpi-setup)
          (replace 'check
            (lambda _
          (replace 'check
            (lambda _
-             ;; By default, running the test suite would fail because 'ssh'
-             ;; could not be found in $PATH.  Define this variable to placate
-             ;; Open MPI without adding a dependency on OpenSSH (the agent
-             ;; isn't used anyway.)
-             (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
              (with-directory-excursion "EXAMPLE"
                (invoke "mpirun" "-n" "2"
                        "./pddrive" "-r" "1" "-c" "2" "g20.rua")
              (with-directory-excursion "EXAMPLE"
                (invoke "mpirun" "-n" "2"
                        "./pddrive" "-r" "1" "-c" "2" "g20.rua")
@@ -2367,15 +2506,8 @@ YACC = bison -pscotchyy -y -b y
                           ;; "SCOTCH_PTHREAD_NUMBER=2"
                           "restrict=__restrict"))))
             #t))
                           ;; "SCOTCH_PTHREAD_NUMBER=2"
                           "restrict=__restrict"))))
             #t))
-         (add-after
-          'build 'build-esmumps
+         (add-after 'build 'build-esmumps
           (lambda _
           (lambda _
-            ;; By default, running the test suite would fail because 'ssh'
-            ;; could not be found in $PATH.  Define this variable to placate
-            ;; Open MPI without adding a dependency on OpenSSH (the agent
-            ;; isn't used anyway.)
-            (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
-
             (invoke "make"
                     (format #f "-j~a" (parallel-job-count))
                     "esmumps")))
             (invoke "make"
                     (format #f "-j~a" (parallel-job-count))
                     "esmumps")))
@@ -2558,14 +2690,8 @@ schemes.")
                                            (assoc-ref %build-inputs "lapack")
                                            " -llapack"))
        #:phases (modify-phases %standard-phases
                                            (assoc-ref %build-inputs "lapack")
                                            " -llapack"))
        #:phases (modify-phases %standard-phases
-                  (add-before 'check 'set-test-environment
-                    (lambda _
-                      ;; By default, running the test suite would fail because
-                      ;; 'ssh' could not be found in $PATH.  Define this
-                      ;; variable to placate Open MPI without adding a
-                      ;; dependency on OpenSSH (the agent isn't used anyway.)
-                      (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
-                      #t)))))
+                  (add-before 'check 'mpi-setup
+                   ,%openmpi-setup))))
     (home-page "http://www.p4est.org")
     (synopsis "Adaptive mesh refinement on forests of octrees")
     (description
     (home-page "http://www.p4est.org")
     (synopsis "Adaptive mesh refinement on forests of octrees")
     (description
@@ -2623,7 +2749,7 @@ to BMP, JPEG or PNG image formats.")
 (define-public maxima
   (package
     (name "maxima")
 (define-public maxima
   (package
     (name "maxima")
-    (version "5.41.0")
+    (version "5.42.0")
     (source
      (origin
        (method url-fetch)
     (source
      (origin
        (method url-fetch)
@@ -2631,7 +2757,7 @@ to BMP, JPEG or PNG image formats.")
                            version "-source/" name "-" version ".tar.gz"))
        (sha256
         (base32
                            version "-source/" name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s"))
+         "0d5pdihvcbwb7r4i4qs5qqgsz46hxlq33qj8is053llrgn9ylpyn"))
        (patches (search-patches "maxima-defsystem-mkdir.patch"))))
     (build-system gnu-build-system)
     (inputs
        (patches (search-patches "maxima-defsystem-mkdir.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -2663,6 +2789,18 @@ to BMP, JPEG or PNG image formats.")
            (lambda _
              (chmod "src/maxima" #o555)
              #t))
            (lambda _
              (chmod "src/maxima" #o555)
              #t))
+         (replace 'check
+           (lambda _
+             ;; This is derived from the testing code in the "debian/rules" file
+             ;; of Debian's Maxima package.
+             ;; If Maxima can successfully run this, the binary to be installed
+             ;; should be fine.
+             (zero?
+              (system
+               (string-append "./maxima-local "
+                              "--lisp=gcl "
+                              "--batch-string=\"run_testsuite();\" "
+                              "| grep -q \"No unexpected errors found\"")))))
          ;; Make sure the doc and emacs files are found in the
          ;; standard location.  Also configure maxima to find gnuplot
          ;; without having it on the PATH.
          ;; Make sure the doc and emacs files are found in the
          ;; standard location.  Also configure maxima to find gnuplot
          ;; without having it on the PATH.
@@ -2710,18 +2848,16 @@ point numbers.")
 (define-public wxmaxima
   (package
     (name "wxmaxima")
 (define-public wxmaxima
   (package
     (name "wxmaxima")
-    (version "18.02.0")
+    (version "18.10.1")
     (source
      (origin
        (method url-fetch)
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://github.com/andrejv/" name "/archive"
-                           "/Version-" version ".tar.gz"))
+       (uri (string-append "https://github.com/wxMaxima-developers/" name
+                           "/archive/Version-" version ".tar.gz"))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj"))
-       (patches
-        (search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch"))))
+         "0c2blq65r0am509p3rjqpwqk6vl5r2yg1p9nh2jczf80vhi3ldas"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)))
     (build-system cmake-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)))
@@ -2839,8 +2975,8 @@ parts of it.")
     (source
      (origin
        (method url-fetch)
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
-                           version))
+       (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
+                           version "%20version.tar.gz"))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
@@ -2902,6 +3038,18 @@ parts of it.")
      "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
     (license license:bsd-3)))
 
      "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
     (license license:bsd-3)))
 
+(define-public openblas-ilp64
+  (package (inherit openblas)
+    (name "openblas-ilp64")
+    (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
+    (arguments
+     (substitute-keyword-arguments (package-arguments openblas)
+       ((#:make-flags flags '())
+        `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
+                 ,flags))))
+    (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
+    (license license:bsd-3)))
+
 (define* (make-blis implementation #:optional substitutable?)
   "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
 source tree for a list of implementations.)
 (define* (make-blis implementation #:optional substitutable?)
   "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
 source tree for a list of implementations.)
@@ -3246,7 +3394,7 @@ Failure to do so will result in a library with poor performance.")
 (define-public glm
   (package
     (name "glm")
 (define-public glm
   (package
     (name "glm")
-    (version "0.9.9.0")
+    (version "0.9.9.3")
     (source
      (origin
        (method url-fetch)
     (source
      (origin
        (method url-fetch)
@@ -3254,7 +3402,7 @@ Failure to do so will result in a library with poor performance.")
                            version  "/glm-" version ".zip"))
        (sha256
         (base32
                            version  "/glm-" version ".zip"))
        (sha256
         (base32
-         "0ihjadp2sb8w312a276skfjsljm3y41bjscbxf79wn23gi00giz1"))))
+         "0yqk5r3qh60d4r2iab5q7wq0fryn8p3pz6s28y1i7amqj1aqavj9"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("unzip" ,unzip)))
     (build-system cmake-build-system)
     (native-inputs
      `(("unzip" ,unzip)))
@@ -3632,14 +3780,8 @@ problems.")
            ,@(delete "--without-MPI" ,flags)))
        ((#:phases phases)
         `(modify-phases ,phases
            ,@(delete "--without-MPI" ,flags)))
        ((#:phases phases)
         `(modify-phases ,phases
-           (add-before 'check 'set-test-environment
-             (lambda _
-               ;; By default, running the test suite would fail because 'ssh'
-               ;; could not be found in $PATH.  Define this variable to
-               ;; placate Open MPI without adding a dependency on OpenSSH (the
-               ;; agent isn't used anyway.)
-               (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
-               #t))))))
+           (add-before 'check 'mpi-setup
+            ,%openmpi-setup)))))
     (synopsis "Parallel solvers and preconditioners for linear equations")
     (description
      "HYPRE is a software library of high performance preconditioners and
     (synopsis "Parallel solvers and preconditioners for linear equations")
     (description
      "HYPRE is a software library of high performance preconditioners and
@@ -3804,15 +3946,15 @@ as equations, scalars, vectors, and matrices.")
 (define-public z3
   (package
     (name "z3")
 (define-public z3
   (package
     (name "z3")
-    (version "4.5.0")
+    (version "4.8.1")
+    (home-page "https://github.com/Z3Prover/z3")
     (source (origin
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/Z3Prover/z3/archive/z3-"
-                    version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference (url home-page)
+                                  (commit (string-append "z3-" version))))
               (sha256
                (base32
               (sha256
                (base32
-                "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf"))))
+                "1vr57bwx40sd5riijyrhy70i2wnv9xrdihf6y5zdz56yq88rl48f"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
@@ -3841,43 +3983,57 @@ as equations, scalars, vectors, and matrices.")
     (synopsis "Theorem prover")
     (description "Z3 is a theorem prover and @dfn{satisfiability modulo
 theories} (SMT) solver.  It provides a C/C++ API, as well as Python bindings.")
     (synopsis "Theorem prover")
     (description "Z3 is a theorem prover and @dfn{satisfiability modulo
 theories} (SMT) solver.  It provides a C/C++ API, as well as Python bindings.")
-    (home-page "https://github.com/Z3Prover/z3")
     (license license:expat)))
 
 (define-public cubicle
   (package
     (name "cubicle")
     (license license:expat)))
 
 (define-public cubicle
   (package
     (name "cubicle")
-    (version "1.1.1")
+    (version "1.1.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://cubicle.lri.fr/cubicle-"
                                   version ".tar.gz"))
               (sha256
                (base32
     (source (origin
               (method url-fetch)
               (uri (string-append "http://cubicle.lri.fr/cubicle-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h"))))
+                "10kk80jdmpdvql88sdjsh7vqzlpaphd8vip2lp47aarxjkwjlz1q"))))
     (build-system gnu-build-system)
     (native-inputs
     (build-system gnu-build-system)
     (native-inputs
-     `(("ocaml" ,ocaml)
+     `(("automake" ,automake)
+       ("ocaml" ,ocaml)
        ("which" ,(@@ (gnu packages base) which))))
     (propagated-inputs
        ("which" ,(@@ (gnu packages base) which))))
     (propagated-inputs
-     `(("z3" ,z3)))
+     `(("ocaml-num" ,ocaml-num)
+       ("z3" ,z3)))
     (arguments
      `(#:configure-flags (list "--with-z3")
     (arguments
      `(#:configure-flags (list "--with-z3")
+       #:make-flags (list "QUIET=")
        #:tests? #f
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'configure-for-release
            (lambda _
              (substitute* "Makefile.in"
        #:tests? #f
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'configure-for-release
            (lambda _
              (substitute* "Makefile.in"
-               (("SVNREV=") "#SVNREV="))))
+               (("SVNREV=") "#SVNREV="))
+             #t))
          (add-before 'configure 'fix-/bin/sh
            (lambda _
              (substitute* "configure"
          (add-before 'configure 'fix-/bin/sh
            (lambda _
              (substitute* "configure"
-               (("/bin/sh") (which "sh")))))
+               (("-/bin/sh") (string-append "-" (which "sh"))))
+             #t))
          (add-before 'configure 'fix-smt-z3wrapper.ml
            (lambda _
              (substitute* "Makefile.in"
          (add-before 'configure 'fix-smt-z3wrapper.ml
            (lambda _
              (substitute* "Makefile.in"
-               (("\\\\n") "")))))))
+               (("\\\\n") ""))
+             #t))
+         (add-before 'configure 'fix-ocaml-num
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "Makefile.in"
+               (("= \\$\\(FUNCTORYLIB\\)")
+                (string-append "= -I "
+                               (assoc-ref inputs "ocaml-num")
+                               "/lib/ocaml/site-lib"
+                               " $(FUNCTORYLIB)")))
+             #t)))))
     (home-page "http://cubicle.lri.fr/")
     (synopsis "Model checker for array-based systems")
     (description "Cubicle is a model checker for verifying safety properties
     (home-page "http://cubicle.lri.fr/")
     (synopsis "Model checker for array-based systems")
     (description "Cubicle is a model checker for verifying safety properties
@@ -3922,6 +4078,8 @@ exclusion algorithms are typical examples of such systems.")
                            "-DCMAKE_INSTALL_LIBDIR=lib"
                            "-DGFORTRAN_LIB=gfortran")
        #:phases (modify-phases %standard-phases
                            "-DCMAKE_INSTALL_LIBDIR=lib"
                            "-DGFORTRAN_LIB=gfortran")
        #:phases (modify-phases %standard-phases
+                 (add-before 'check 'mpi-setup
+                   ,%openmpi-setup)
                   (add-before 'check 'setup-tests
                     (lambda _
                       ;; Parallelism is done at the MPI layer.
                   (add-before 'check 'setup-tests
                     (lambda _
                       ;; Parallelism is done at the MPI layer.
@@ -3968,7 +4126,7 @@ toolset supports analysis and automatic verification, linearisation, simulation,
 state-space exploration and generation, and tools to optimise and analyse
 specifications.  Also, state spaces can be manipulated, visualised and
 analysed.")
 state-space exploration and generation, and tools to optimise and analyse
 specifications.  Also, state spaces can be manipulated, visualised and
 analysed.")
-    (home-page "http://mcrl2.org")
+    (home-page "https://mcrl2.org")
     (license license:boost1.0)))
 
 (define-public r-subplex
     (license license:boost1.0)))
 
 (define-public r-subplex
@@ -4042,3 +4200,70 @@ terminal do calculations simply and quickly.  The formula to be calculated can
 be fed to @command{tcalc} through the command line.")
   (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
   (license license:gpl3+)))
 be fed to @command{tcalc} through the command line.")
   (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
   (license license:gpl3+)))
+
+(define-public sundials
+  (package
+    (name "sundials")
+    (version "3.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
+                           "sundials-" version ".tar.gz"))
+       (sha256
+        (base32
+         "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("python" ,python-2)))    ;for tests; syntax incompatible with python 3
+    (inputs
+     `(("fortran" ,gfortran)            ;for fcmix
+       ("blas" ,openblas)
+       ("suitesparse" ,suitesparse)))   ;TODO: Add hypre
+    (arguments
+     `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
+                           "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
+                           "-DEXAMPLES_ENABLE_F77:BOOL=ON"
+                           "-DEXAMPLES_ENABLE_F90:BOOL=ON"
+                           "-DEXAMPLES_INSTALL:BOOL=OFF"
+
+                           "-DFCMIX_ENABLE:BOOL=ON"
+
+                           "-DKLU_ENABLE:BOOL=ON"
+                           ,(string-append "-DKLU_INCLUDE_DIR="
+                                           (assoc-ref %build-inputs "suitesparse")
+                                           "/include")
+                           ,(string-append "-DKLU_LIBRARY_DIR="
+                                           (assoc-ref %build-inputs "suitesparse")
+                                           "/lib"))))
+    (home-page "https://computation.llnl.gov/projects/sundials")
+    (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
+    (description "SUNDIALS is a family of software packages implemented with
+the goal of providing robust time integrators and nonlinear solvers that can
+easily be incorporated into existing simulation codes.")
+    (license license:bsd-3)))
+
+(define-public sundials-openmpi
+  (package (inherit sundials)
+    (name "sundials-openmpi")
+    (inputs
+     `(("mpi" ,openmpi)
+       ("petsc" ,petsc-openmpi)         ;support in SUNDIALS requires MPI
+       ,@(package-inputs sundials)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments sundials)
+       ((#:configure-flags flags '())
+        `(cons* "-DMPI_ENABLE:BOOL=ON"
+                "-DPETSC_ENABLE:BOOL=ON"
+                (string-append "-DPETSC_INCLUDE_DIR="
+                               (assoc-ref %build-inputs "petsc")
+                               "/include")
+                (string-append "-DPETSC_LIBRARY_DIR="
+                               (assoc-ref %build-inputs "petsc")
+                               "/lib")
+                ,flags))
+       ((#:phases phases '%standard-phases)
+        `(modify-phases ,phases
+           (add-before 'check 'mpi-setup
+            ,%openmpi-setup)))))
+    (synopsis "SUNDIALS with OpenMPI support")))
jackhill's copy of GNU Guix: https://guix.gnu.org/