Package: guix;
Reported by: Eric Brown <brown <at> fastmail.com>
Date: Tue, 11 Sep 2018 04:25:02 UTC
Severity: normal
View this message in rfc822 format
From: ludo <at> gnu.org (Ludovic Courtès) To: Eric Brown <brown <at> fastmail.com> Cc: 32691 <at> debbugs.gnu.org Subject: bug#32691: OpenMolcas Date: Mon, 17 Sep 2018 22:58:22 +0200
[Message part 1 (text/plain, inline)]
Hi Eric, We’re almost there! :-) Eric Brown <brown <at> fastmail.com> 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’.
[0001-gnu-Add-openmolcas.patch (text/x-patch, inline)]
From b4caef67aaae349e0aa77fc22517872ff8ca79cb Mon Sep 17 00:00:00 2001
From: Eric Brown <brown <at> fastmail.com>
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 <ludo <at> gnu.org>
---
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 <konrad.hinsen <at> fastmail.net>
;;; Copyright © 2018 Kei Kebreau <kkebreau <at> posteo.net>
+;;; Copyright © 2018 Eric Brown <brown <at> fastmail.com>
;;;
;;; 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 ()
--
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1994-97 Ian Jackson.