bug#32691: OpenMolcas

[Eric Brown]

Dear Guix:

I am pleased to submit a patch that adds OpenMolcas to Guix. Also
included in this submission is a new variable called `openblas-ilp64'
which OpenMolcas needs to compile and run.

I would like to point out that I have already submitted the
openblas-ilp64 patch to the list for approval, and I am aware that this
submission may need to be revised to include just the program of
immediate interest.

Best regards,
Eric

>From 784cb74747adcc513b75b16b9247bd3dc9a484a3 Mon Sep 17 00:00:00 2001
From: Eric Brown <address@hidden>
Date: Mon, 10 Sep 2018 23:12:51 -0500
Subject: [PATCH] gnu: Add openmolcas and openblas-ilp64.

* gnu/packages/chemistry.scm (openmolcas): New variable.
* gnu/packages/maths.scm (openblas-ilp64): New variable.
---
 gnu/packages/chemistry.scm                    |  55 ++++++++
 gnu/packages/maths.scm                        |  71 ++++++++++
 .../openmolcas-pymolcas-openblas.patch        | 131 ++++++++++++++++++
 3 files changed, 257 insertions(+)
 create mode 100644 gnu/packages/patches/openmolcas-pymolcas-openblas.patch

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 03120aaee..b4064ee8c 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Konrad Hinsen <address@hidden>
 ;;; Copyright © 2018 Kei Kebreau <address@hidden>
+;;; Copyright © 2018 Eric Brown <address@hidden>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26,12 +27,16 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages documentation)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages gv)
   #:use-module (gnu packages maths)
+  #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages qt)
+  #:use-module (gnu packages tex)
   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
@@ -322,3 +327,53 @@ chemical data.  It's a collaborative project allowing 
anyone to search, convert,
 analyze, or store data from molecular modeling, chemistry, solid-state
 materials, biochemistry, or related areas.")
     (license license:gpl2)))
+
+(define-public openmolcas
+  (package
+    (name "openmolcas")
+    (version "18.09")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://gitlab.com/Molcas/OpenMolcas";
+                                  "/-/archive/v" version "/OpenMolcas-v"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1krrkff5b4zp9ii1m9v3zzw8d99k72fcwwv3rif8cp10cpxi1wxl"))
+              (patches (search-patches "openmolcas-pymolcas-openblas.patch"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:out-of-source? #t
+       #:tests? #f
+       #:build-type "Release"
+       #:parallel-build? #t
+       #:configure-flags
+       (list "-DLINALG=OpenBLAS"
+             (string-append "-DOPENBLASROOT="
+                            (assoc-ref %build-inputs "blas"))
+             (string-append "-DLINALG_LIBRARIES="
+                            (assoc-ref %build-inputs "blas")
+                            "/lib/libopenblas_ilp64.so"))))
+    (native-inputs
+     `(("fortran" ,gfortran)
+       ("gcc" ,gcc)
+       ("ghostscript" ,ghostscript)
+       ("hdf5" ,hdf5)
+       ("blas" ,openblas-ilp64)
+       ("perl" ,perl)
+       ("pkg-config" ,pkg-config)
+       ("python" ,python)
+       ("python-pyparsing" ,python-pyparsing)
+       ("python-six" ,python-six)
+       ("texlive" ,texlive)))
+    (inputs
+     `())
+    (home-page "https://gitlab.com/Molcas/OpenMolcas";)
+    (synopsis "Multi-reference electronic structure theory program")
+    (description "OpenMolcas is a quantum chemistry software package developed
+by scientists and intended to be used by scientists. It includes programs to
+apply many different electronic structure methods to chemical systems, but its
+key feature is the multiconfigurational approach, with methods like CASSCF and
+CASPT2.")
+    (license license:lgpl2.1)))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 01bd03c60..5f1dfec8a 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -27,6 +27,7 @@
 ;;; Copyright © 2018 Nadya Voronova <address@hidden>
 ;;; Copyright © 2018 Adam Massmann <address@hidden>
 ;;; Copyright © 2018 Marius Bakke <address@hidden>
+;;; Copyright © 2018 Eric Brown <address@hidden>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2909,6 +2910,76 @@ parts of it.")
      "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
     (license license:bsd-3)))
 
+(define-public openblas-ilp64
+  (package
+    (name "openblas-ilp64")
+    (version "0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/openblas/v" version 
"/OpenBLAS%20"
+                           version "%20version.tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0b20km2jv7m6qiylrlvhq2vnmkmilb633mr8rhqmgbn1wqrp58jq"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:test-target "test"
+       ;; DYNAMIC_ARCH is only supported on x86.  When it is disabled and no
+       ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
+       ;; we need to disable substitutions.
+       #:substitutable?
+        ,(let ((system (or (%current-target-system) (%current-system))))
+           (or (string-prefix? "x86_64" system)
+               (string-prefix? "i686" system)
+               (string-prefix? "mips" system)
+               (string-prefix? "aarch64" system)))
+       #:make-flags
+       (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+             "SHELL=bash"
+             ;; Build the library for all supported CPUs.  This allows
+             ;; switching CPU targets at runtime with the environment variable
+             ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
+             ;; Unfortunately, this is not supported on non-x86 architectures,
+             ;; where it leads to failed builds.
+             ,@(let ((system (or (%current-target-system) (%current-system))))
+                 (cond
+                  ((or (string-prefix? "x86_64" system)
+                       (string-prefix? "i686" system))
+                   '("DYNAMIC_ARCH=1" "INTERFACE64=1" "LIBNAMESUFFIX=ilp64"))
+                  ;; On MIPS we force the "SICORTEX" TARGET, as for the other
+                  ;; two available MIPS targets special extended instructions
+                  ;; for Loongson cores are used.
+                  ((string-prefix? "mips" system)
+                   '("TARGET=SICORTEX" "INTERFACE64=1" "LIBNAMESUFFIX=ilp64"))
+                  ;; On aarch64 force the generic 'armv8-a' target
+                  ((string-prefix? "aarch64" system)
+                   '("TARGET=ARMV8" "INTERFACE64=1" "LIBNAMESUFFIX=ilp64"))
+                  (else '("INTERFACE64=1" "LIBNAMESUFFIX=ilp64")))))
+       ;; no configure script
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before 'build 'set-extralib
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Get libgfortran found when building in utest.
+             (setenv "FEXTRALIB"
+                     (string-append "-L" (assoc-ref inputs "fortran-lib")
+                                    "/lib"))
+             #t)))))
+    (inputs
+     `(("fortran-lib" ,gfortran "lib")))
+    (native-inputs
+     `(("cunit" ,cunit)
+       ("fortran" ,gfortran)
+       ("perl" ,perl)))
+    (home-page "http://www.openblas.net/";)
+    (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
+    (description
+     "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version. 
(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.)
diff --git a/gnu/packages/patches/openmolcas-pymolcas-openblas.patch 
b/gnu/packages/patches/openmolcas-pymolcas-openblas.patch
new file mode 100644
index 000000000..2c7feade6
--- /dev/null
+++ b/gnu/packages/patches/openmolcas-pymolcas-openblas.patch
@@ -0,0 +1,131 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index a4071fd..53d8df5 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -1338,42 +1338,43 @@ if (LINALG STREQUAL "OpenBLAS")
+         endif ()
+ 
+         # search for the OpenBLAS library
+-        find_library (LIBOPENBLAS
+-                NAMES openblas
+-                PATHS ${OPENBLASROOT}
+-                PATH_SUFFIXES lib
+-                NO_DEFAULT_PATH)
+-
+-        if (NOT LIBOPENBLAS)
+-                message (FATAL_ERROR
+-                        "OpenBLAS library not found, please check that "
+-                        "the OPENBLASROOT variable is set and points to "
+-                        "a valid OpenBLAS installation directory."
+-                        )
+-        endif ()
+-
+-        # here we check if LIBOPENBLAS has changed after it was processed
+-        # succesfully, if not we do not need to rerun anything here.
+-        if (NOT LIBOPENBLAS STREQUAL LIBOPENBLAS_LAST)
+-                # check if the OpenBLAS library contains LAPACK functionality
+-                message ("-- Checking OpenBLAS for LAPACK functionality...")
+-                include(CheckFortranFunctionExists)
+-                set (CMAKE_REQUIRED_LIBRARIES ${LIBOPENBLAS})
+-                unset (OPENBLAS_WITH_LAPACK CACHE)
+-                check_fortran_function_exists("dsyev" OPENBLAS_WITH_LAPACK)
+-                if (NOT OPENBLAS_WITH_LAPACK)
+-                        unset (LIBOPENBLAS CACHE)
+-                        message (FATAL_ERROR
+-                                "LAPACK functionality missing from OpenBLAS 
library, "
+-                                "please build OpenBLAS with NO_LAPACK=0 
defined."
+-                                )
+-                endif ()
+-                # save the last location to check if it changed between 
configurations
+-                set (LIBOPENBLAS_LAST ${LIBOPENBLAS} CACHE INTERNAL "last 
value." FORCE)
+-        endif ()
+-
+-        add_definitions (-D_OPENBLAS_)
+-        set (LINALG_LIBRARIES ${LIBOPENBLAS})
++#        find_library (LIBOPENBLAS
++#                NAMES openblas
++#                PATHS ${OPENBLASROOT}
++#                PATH_SUFFIXES lib
++#                NO_DEFAULT_PATH)
++#
++#        if (NOT LIBOPENBLAS)
++#                message (FATAL_ERROR
++#                        "OpenBLAS library not found, please check that "
++#                        "the OPENBLASROOT variable is set and points to "
++#                        "a valid OpenBLAS installation directory."
++#                        )
++#        endif ()
++#
++#        # here we check if LIBOPENBLAS has changed after it was processed
++#        # succesfully, if not we do not need to rerun anything here.
++#        if (NOT LIBOPENBLAS STREQUAL LIBOPENBLAS_LAST)
++#                # check if the OpenBLAS library contains LAPACK functionality
++#                message ("-- Checking OpenBLAS for LAPACK functionality...")
++#                include(CheckFortranFunctionExists)
++#                set (CMAKE_REQUIRED_LIBRARIES ${LIBOPENBLAS})
++#                unset (OPENBLAS_WITH_LAPACK CACHE)
++#                check_fortran_function_exists("dsyev" OPENBLAS_WITH_LAPACK)
++#                if (NOT OPENBLAS_WITH_LAPACK)
++#                        unset (LIBOPENBLAS CACHE)
++#                        message (FATAL_ERROR
++#                                "LAPACK functionality missing from OpenBLAS 
library, "
++#                                "please build OpenBLAS with NO_LAPACK=0 
defined."
++#                                )
++#                endif ()
++#                # save the last location to check if it changed between 
configurations
++#                set (LIBOPENBLAS_LAST ${LIBOPENBLAS} CACHE INTERNAL "last 
value." FORCE)
++#        endif ()
++#
++        add_definitions (-D_OPENBLAS_)
++#        set (LINALG_LIBRARIES ${LIBOPENBLAS})
++         set (LINALG_LIBRARIES ${LINALG_LIBRARIES})
+ else ()
+         mark_as_advanced(FORCE OPENBLASROOT)
+ endif ()
+@@ -3167,11 +3168,11 @@ install (PROGRAMS
+ if (DEFINED PYMOLCAS_TARGET)
+         install (PROGRAMS
+                 ${PYMOLCAS_TARGET}
+-                DESTINATION ${CMAKE_INSTALL_PREFIX}/sbin
++                DESTINATION ${CMAKE_INSTALL_PREFIX}/bin
+                 RENAME pymolcas
+                 )
+ 
+-        install (CODE "execute_process(COMMAND 
${OPENMOLCAS_DIR}/sbin/install_pymolcas.sh ${PYMOLCAS_TARGET})")
++#        install (CODE "execute_process(COMMAND 
${OPENMOLCAS_DIR}/sbin/install_pymolcas.sh ${PYMOLCAS_TARGET})")
+ endif ()
+ 
+ if (DEFINED EXTRA_DIR)
+@@ -3188,9 +3189,9 @@ if (DEFINED EXTRA_DIR)
+                 DESTINATION ${CMAKE_INSTALL_PREFIX}/bin
+                 )
+ 
+-        install (CODE "execute_process(COMMAND 
${OPENMOLCAS_DIR}/sbin/install_driver.sh ${MOLCAS_DRIVER})")
++#        install (CODE "execute_process(COMMAND 
${OPENMOLCAS_DIR}/sbin/install_driver.sh ${MOLCAS_DRIVER})")
+ endif ()
+ 
+-if (IS_DIRECTORY "$ENV{HOME}/.Molcas")
+-        install (CODE "execute_process(COMMAND sh \"-c\" \"cd 
${CMAKE_INSTALL_PREFIX}; echo `pwd` > $HOME/.Molcas/molcas 2> /dev/null\")")
+-endif ()
++#if (IS_DIRECTORY "$ENV{HOME}/.Molcas")
++#        install (CODE "execute_process(COMMAND sh \"-c\" \"cd 
${CMAKE_INSTALL_PREFIX}; echo `pwd` > $HOME/.Molcas/molcas 2> /dev/null\")")
++#endif ()
+diff --git a/Tools/pymolcas/CMakeLists.txt b/Tools/pymolcas/CMakeLists.txt
+index 0d576fa..f9ba6d7 100644
+--- a/Tools/pymolcas/CMakeLists.txt
++++ b/Tools/pymolcas/CMakeLists.txt
+@@ -52,9 +52,9 @@ if (PYTHONINTERP_FOUND)
+                         DEPENDS ${PYMOLCAS_TARGET}
+                         )
+ 
+-                add_custom_command (TARGET pymolcas
+-                        POST_BUILD
+-                        COMMAND ${OPENMOLCAS_DIR}/sbin/install_pymolcas.sh 
${PYMOLCAS_TARGET}
+-                )
++#                add_custom_command (TARGET pymolcas
++#                        POST_BUILD
++#                        COMMAND ${OPENMOLCAS_DIR}/sbin/install_pymolcas.sh 
${PYMOLCAS_TARGET}
++#                )
+ 
+         endif ()
+
-- 
2.18.0

0001-gnu-Add-openmolcas-and-openblas-ilp64.patch
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