Subject: bug#32691: OpenMolcas

From: [email-masked] (Ludovic Courtès)
Date: Mon, 17 Sep 2018 22:58:22 +0200

Hi Eric,

We’re almost there!  :-)

Eric Brown <[email-masked]> skribis:

> Thank you for your fixes! I've attached a revised patch. I'm well beyond
> my comfort zone, so I hope it applies cleanly and works.
>
> The default location of pymolcas is a little sketchy, being placed in
> the first writable location in PATH, and I believe will not be fixed
> upstream:
>
> https://gitlab.com/Molcas/OpenMolcas/issues/70
>
> I have added comments to the chemistry.scm file.

I made small changes (moved comments about the patch at the top of the
patch; switch to ‘texlive-union’, which is much smaller than ‘texlive’),
leading to the attached patch.

It’s all good, except that the file layout really doesn’t match the
usual conventions:

--8<---------------cut here---------------start------------->8---
$ find /gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/basis_library
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/basis_library/TZ
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/basis_library/AUG-PC-4

[...]

/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/sbin
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/sbin/help_basis
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/sbin/help_doc
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/lib
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/lib/libmolcas.a
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/bin
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/bin/ffpt.exe
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/bin/loprop.exe

[...]

/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/data/quater.prgm
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/data/rasscf.prgm
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/.molcasversion
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/molcas.rte
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/CONTRIBUTORS.md
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/LICENSE
--8<---------------cut here---------------end--------------->8---

Ideally basis_library/ and data/ would go under share/openmolcas, while
CONTRIBUTORS.md and LICENSE would go to share/doc/openmolcas.  Also, it
would be nice to remove the ‘.exe’ extension.

Do you think you could easily fiddle with CMake to fix these and/or
report it upstream?  I could apply the patch as is but I think users may
not be pleased by this.  WDYT?

Thank you for your time, and sorry for the extra round trip!

Ludo’.

>From b4caef67aaae349e0aa77fc22517872ff8ca79cb Mon Sep 17 00:00:00 2001
From: Eric Brown <[email-masked]>
Date: Fri, 14 Sep 2018 09:27:35 -0500
Subject: [PATCH] gnu: Add openmolcas.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/chemistry.scm (openmolcas): New variable.
* gnu/packages/patches/openmolcas-pymolcas-openblas.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Ludovic Courtès <[email-masked]>
---
 gnu/local.mk                                  |  1 +
 gnu/packages/chemistry.scm                    | 51 ++++++++++
 .../openmolcas-pymolcas-openblas.patch        | 92 +++++++++++++++++++
 3 files changed, 144 insertions(+)
 create mode 100644 gnu/packages/patches/openmolcas-pymolcas-openblas.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index d37a193ad..4c5a1fbd4 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1006,6 +1006,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/opencascade-oce-glibc-2.26.patch		\
   %D%/packages/patches/openfoam-4.1-cleanup.patch			\
   %D%/packages/patches/openldap-CVE-2017-9287.patch		\
+  %D%/packages/patches/openmolcas-pymolcas-openblas.patch	\
   %D%/packages/patches/openocd-nrf52.patch			\
   %D%/packages/patches/opensmtpd-fix-crash.patch		\
   %D%/packages/patches/openssl-runpath.patch			\
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 03120aaee..bdb17c30d 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 <[email-masked]>
 ;;; Copyright © 2018 Kei Kebreau <[email-masked]>
+;;; Copyright © 2018 Eric Brown <[email-masked]>
 ;;;
 ;;; 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 +327,49 @@ 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
+     `(#:build-type "Release"
+       #: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)
+       ("ghostscript" ,ghostscript)
+       ("perl" ,perl)
+       ("pkg-config" ,pkg-config)
+       ("python" ,python)
+       ("python-pyparsing" ,python-pyparsing)
+       ("python-six" ,python-six)
+       ("texlive" ,(texlive-union))))
+    (inputs
+     `(("hdf5" ,hdf5)
+       ("blas" ,openblas-ilp64)))
+    (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/patches/openmolcas-pymolcas-openblas.patch b/gnu/packages/patches/openmolcas-pymolcas-openblas.patch
new file mode 100644
index 000000000..84f348721
--- /dev/null
+++ b/gnu/packages/patches/openmolcas-pymolcas-openblas.patch
@@ -0,0 +1,92 @@
+By default, pymolcas is installed in the first writable directory in the
+user's PATH.  This patch places it in the bin/ directory alongside the other
+OpenMolcas binaries.
+
+The default search for the OpenBLAS library is obviated and the directory name
+is supplied as an argument to CMake.
+
+diff --git OpenMolcas-v18.09/CMakeLists.txt OpenMolcas-v18.09/CMakeLists.txt
+index a4071fd..53d8df5 100644
+--- OpenMolcas-v18.09/CMakeLists.txt
++++ OpenMolcas-v18.09/CMakeLists.txt
+@@ -1338,42 +1338,8 @@ 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})
++        set (LINALG_LIBRARIES ${LINALG_LIBRARIES})
+ else ()
+         mark_as_advanced(FORCE OPENBLASROOT)
+ endif ()
+@@ -3167,11 +3168,10 @@ 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})")
+ endif ()
+ 
+ if (DEFINED EXTRA_DIR)
+@@ -3188,9 +3189,5 @@ if (DEFINED EXTRA_DIR)
+                 DESTINATION ${CMAKE_INSTALL_PREFIX}/bin
+                 )
+ 
+-        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 ()
+diff --git OpenMolcas-v18.09/Tools/pymolcas/CMakeLists.txt OpenMolcas-v18.09/Tools/pymolcas/CMakeLists.txt
+index 0d576fa..f9ba6d7 100644
+--- OpenMolcas-v18.09/Tools/pymolcas/CMakeLists.txt
++++ OpenMolcas-v18.09/Tools/pymolcas/CMakeLists.txt
+@@ -52,9 +52,5 @@ if (PYTHONINTERP_FOUND)
+                         DEPENDS ${PYMOLCAS_TARGET}
+                         )
+ 
+-                add_custom_command (TARGET pymolcas
+-                        POST_BUILD
+-                        COMMAND ${OPENMOLCAS_DIR}/sbin/install_pymolcas.sh ${PYMOLCAS_TARGET}
+-                )
+ 
+         endif ()
-- 
2.18.0