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Subject: bug#32691: OpenMolcas
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for <bug-guix@HIDDEN>; Tue, 11 Sep 2018 00:23:43 -0400 (EDT)
From: Eric Brown <brown@HIDDEN>
Date: Mon, 10 Sep 2018 23:23:42 -0500
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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
--=-=-=
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From 784cb74747adcc513b75b16b9247bd3dc9a484a3 Mon Sep 17 00:00:00 2001
From: Eric Brown <brown@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 =C2=A9 2018 Konrad Hinsen <konrad.hinsen@HIDDEN>
;;; Copyright =C2=A9 2018 Kei Kebreau <kkebreau@HIDDEN>
+;;; Copyright =C2=A9 2018 Eric Brown <brown@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=3DOpenBLAS"
+ (string-append "-DOPENBLASROOT=3D"
+ (assoc-ref %build-inputs "blas"))
+ (string-append "-DLINALG_LIBRARIES=3D"
+ (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 devel=
oped
+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 =C2=A9 2018 Nadya Voronova <voronovank@HIDDEN>
;;; Copyright =C2=A9 2018 Adam Massmann <massmannak@HIDDEN>
;;; Copyright =C2=A9 2018 Marius Bakke <mbakke@HIDDEN>
+;;; Copyright =C2=A9 2018 Eric Brown <brown@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 versio=
n.")
(license license:bsd-3)))
=20
+(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 "/Ope=
nBLAS%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=3D" (assoc-ref %outputs "out"))
+ "SHELL=3Dbash"
+ ;; Build the library for all supported CPUs. This allows
+ ;; switching CPU targets at runtime with the environment vari=
able
+ ;; OPENBLAS_CORETYPE=3D<type>, where "type" is a supported CP=
U type.
+ ;; Unfortunately, this is not supported on non-x86 architectu=
res,
+ ;; 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=3D1" "INTERFACE64=3D1" "LIBNAMESUFFIX=
=3Dilp64"))
+ ;; On MIPS we force the "SICORTEX" TARGET, as for the ot=
her
+ ;; two available MIPS targets special extended instructi=
ons
+ ;; for Loongson cores are used.
+ ((string-prefix? "mips" system)
+ '("TARGET=3DSICORTEX" "INTERFACE64=3D1" "LIBNAMESUFFIX=
=3Dilp64"))
+ ;; On aarch64 force the generic 'armv8-a' target
+ ((string-prefix? "aarch64" system)
+ '("TARGET=3DARMV8" "INTERFACE64=3D1" "LIBNAMESUFFIX=3Di=
lp64"))
+ (else '("INTERFACE64=3D1" "LIBNAMESUFFIX=3Dilp64")))))
+ ;; 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 versio=
n. (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 ()
+=20
+ # 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 functiona=
lity
+- 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_LAPAC=
K)
+- if (NOT OPENBLAS_WITH_LAPACK)
+- unset (LIBOPENBLAS CACHE)
+- message (FATAL_ERROR
+- "LAPACK functionality missing from OpenBL=
AS library, "
+- "please build OpenBLAS with NO_LAPACK=3D0=
defined."
+- )
+- endif ()
+- # save the last location to check if it changed between c=
onfigurations
+- 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 function=
ality
++# 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_LAPA=
CK)
++# if (NOT OPENBLAS_WITH_LAPACK)
++# unset (LIBOPENBLAS CACHE)
++# message (FATAL_ERROR
++# "LAPACK functionality missing from OpenB=
LAS library, "
++# "please build OpenBLAS with NO_LAPACK=3D=
0 defined."
++# )
++# endif ()
++# # save the last location to check if it changed between =
configurations
++# set (LIBOPENBLAS_LAST ${LIBOPENBLAS} CACHE INTERNAL "las=
t 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
+ )
+=20
+- install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/ins=
tall_pymolcas.sh ${PYMOLCAS_TARGET})")
++# install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/in=
stall_pymolcas.sh ${PYMOLCAS_TARGET})")
+ endif ()
+=20
+ if (DEFINED EXTRA_DIR)
+@@ -3188,9 +3189,9 @@ if (DEFINED EXTRA_DIR)
+ DESTINATION ${CMAKE_INSTALL_PREFIX}/bin
+ )
+=20
+- install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/ins=
tall_driver.sh ${MOLCAS_DRIVER})")
++# install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/in=
stall_driver.sh ${MOLCAS_DRIVER})")
+ endif ()
+=20
+-if (IS_DIRECTORY "$ENV{HOME}/.Molcas")
+- install (CODE "execute_process(COMMAND sh \"-c\" \"cd ${CMAKE_INS=
TALL_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_IN=
STALL_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}
+ )
+=20
+- add_custom_command (TARGET pymolcas
+- POST_BUILD
+- COMMAND ${OPENMOLCAS_DIR}/sbin/install_pymolcas.s=
h ${PYMOLCAS_TARGET}
+- )
++# add_custom_command (TARGET pymolcas
++# POST_BUILD
++# COMMAND ${OPENMOLCAS_DIR}/sbin/install_pymolcas.=
sh ${PYMOLCAS_TARGET}
++# )
+=20
+ endif ()
+
--=20
2.18.0
--=-=-=
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filename=0001-gnu-Add-openmolcas-and-openblas-ilp64.patch
Content-Transfer-Encoding: quoted-printable
From 784cb74747adcc513b75b16b9247bd3dc9a484a3 Mon Sep 17 00:00:00 2001
From: Eric Brown <brown@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 =C2=A9 2018 Konrad Hinsen <konrad.hinsen@HIDDEN>
;;; Copyright =C2=A9 2018 Kei Kebreau <kkebreau@HIDDEN>
+;;; Copyright =C2=A9 2018 Eric Brown <brown@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=3DOpenBLAS"
+ (string-append "-DOPENBLASROOT=3D"
+ (assoc-ref %build-inputs "blas"))
+ (string-append "-DLINALG_LIBRARIES=3D"
+ (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 devel=
oped
+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 =C2=A9 2018 Nadya Voronova <voronovank@HIDDEN>
;;; Copyright =C2=A9 2018 Adam Massmann <massmannak@HIDDEN>
;;; Copyright =C2=A9 2018 Marius Bakke <mbakke@HIDDEN>
+;;; Copyright =C2=A9 2018 Eric Brown <brown@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 versio=
n.")
(license license:bsd-3)))
=20
+(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 "/Ope=
nBLAS%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=3D" (assoc-ref %outputs "out"))
+ "SHELL=3Dbash"
+ ;; Build the library for all supported CPUs. This allows
+ ;; switching CPU targets at runtime with the environment vari=
able
+ ;; OPENBLAS_CORETYPE=3D<type>, where "type" is a supported CP=
U type.
+ ;; Unfortunately, this is not supported on non-x86 architectu=
res,
+ ;; 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=3D1" "INTERFACE64=3D1" "LIBNAMESUFFIX=
=3Dilp64"))
+ ;; On MIPS we force the "SICORTEX" TARGET, as for the ot=
her
+ ;; two available MIPS targets special extended instructi=
ons
+ ;; for Loongson cores are used.
+ ((string-prefix? "mips" system)
+ '("TARGET=3DSICORTEX" "INTERFACE64=3D1" "LIBNAMESUFFIX=
=3Dilp64"))
+ ;; On aarch64 force the generic 'armv8-a' target
+ ((string-prefix? "aarch64" system)
+ '("TARGET=3DARMV8" "INTERFACE64=3D1" "LIBNAMESUFFIX=3Di=
lp64"))
+ (else '("INTERFACE64=3D1" "LIBNAMESUFFIX=3Dilp64")))))
+ ;; 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 versio=
n. (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 ()
+=20
+ # 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 functiona=
lity
+- 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_LAPAC=
K)
+- if (NOT OPENBLAS_WITH_LAPACK)
+- unset (LIBOPENBLAS CACHE)
+- message (FATAL_ERROR
+- "LAPACK functionality missing from OpenBL=
AS library, "
+- "please build OpenBLAS with NO_LAPACK=3D0=
defined."
+- )
+- endif ()
+- # save the last location to check if it changed between c=
onfigurations
+- 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 function=
ality
++# 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_LAPA=
CK)
++# if (NOT OPENBLAS_WITH_LAPACK)
++# unset (LIBOPENBLAS CACHE)
++# message (FATAL_ERROR
++# "LAPACK functionality missing from OpenB=
LAS library, "
++# "please build OpenBLAS with NO_LAPACK=3D=
0 defined."
++# )
++# endif ()
++# # save the last location to check if it changed between =
configurations
++# set (LIBOPENBLAS_LAST ${LIBOPENBLAS} CACHE INTERNAL "las=
t 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
+ )
+=20
+- install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/ins=
tall_pymolcas.sh ${PYMOLCAS_TARGET})")
++# install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/in=
stall_pymolcas.sh ${PYMOLCAS_TARGET})")
+ endif ()
+=20
+ if (DEFINED EXTRA_DIR)
+@@ -3188,9 +3189,9 @@ if (DEFINED EXTRA_DIR)
+ DESTINATION ${CMAKE_INSTALL_PREFIX}/bin
+ )
+=20
+- install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/ins=
tall_driver.sh ${MOLCAS_DRIVER})")
++# install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/in=
stall_driver.sh ${MOLCAS_DRIVER})")
+ endif ()
+=20
+-if (IS_DIRECTORY "$ENV{HOME}/.Molcas")
+- install (CODE "execute_process(COMMAND sh \"-c\" \"cd ${CMAKE_INS=
TALL_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_IN=
STALL_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}
+ )
+=20
+- add_custom_command (TARGET pymolcas
+- POST_BUILD
+- COMMAND ${OPENMOLCAS_DIR}/sbin/install_pymolcas.s=
h ${PYMOLCAS_TARGET}
+- )
++# add_custom_command (TARGET pymolcas
++# POST_BUILD
++# COMMAND ${OPENMOLCAS_DIR}/sbin/install_pymolcas.=
sh ${PYMOLCAS_TARGET}
++# )
+=20
+ endif ()
+
--=20
2.18.0
--=-=-=--
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Subject: bug#32691: OpenMolcas
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From: ludo@HIDDEN (Ludovic =?UTF-8?Q?Court=C3=A8s?=)
References: <87d0tkk6gh.fsf@HIDDEN>
Date: Fri, 14 Sep 2018 11:27:50 +0200
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Sep 2018 23:23:42 -0500")
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Hi Eric,
Eric Brown <brown@HIDDEN> skribis:
> 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.
Here=E2=80=99s a revision of the patch with several modifications: I added
comments in the patch (though they don=E2=80=99t explain the Python-related
changes for instance; could you add a line about these?), stripped
unnecessary additions from the patch, added it to gnu/local.mk, fixed
an issue reported by =E2=80=98guix lint=E2=80=99 in the description.
However, could you explain why we have #:tests? #f ? In general
disabling tests should be accompanied with a comment explaining the
reason (lack of a test suite, or =E2=80=9Cunsolvable=E2=80=9D test failures=
.) If there
are test failures, we=E2=80=99d rather investigate than disable the tests.
Could you send an updated patch?
Thanks in advance!
Ludo=E2=80=99.
--=-=-=
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Content-Description: the patch
From c001d557e1cb23042c092c23d7612ad6197fac3c Mon Sep 17 00:00:00 2001
From: Eric Brown <brown@HIDDEN>
Date: Mon, 10 Sep 2018 23:12:51 -0500
Subject: [PATCH] gnu: Add openmolcas.
MIME-Version: 1.0
Content-Type: text/plain; charset=3DUTF-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 Court=C3=A8s <ludo@HIDDEN>
---
gnu/local.mk | 1 +
gnu/packages/chemistry.scm | 52 +++++++++++
.../openmolcas-pymolcas-openblas.patch | 89 +++++++++++++++++++
3 files changed, 142 insertions(+)
create mode 100644 gnu/packages/patches/openmolcas-pymolcas-openblas.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index 7b230cb6f..0974ce068 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1006,6 +1006,7 @@ dist_patch_DATA =3D \
%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..58151afce 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright =C2=A9 2018 Konrad Hinsen <konrad.hinsen@HIDDEN>
;;; Copyright =C2=A9 2018 Kei Kebreau <kkebreau@HIDDEN>
+;;; Copyright =C2=A9 2018 Eric Brown <brown@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 +327,50 @@ 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"
+ #:configure-flags
+ (list "-DLINALG=3DOpenBLAS"
+ (string-append "-DOPENBLASROOT=3D"
+ (assoc-ref %build-inputs "blas"))
+ (string-append "-DLINALG_LIBRARIES=3D"
+ (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)))
+ (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 devel=
oped
+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..b18c62e05
--- /dev/null
+++ b/gnu/packages/patches/openmolcas-pymolcas-openblas.patch
@@ -0,0 +1,89 @@
+Allow bulds with openblas-ilp64.
+Remove assumptions about $HOME.
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index a4071fd..53d8df5 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -1338,42 +1338,8 @@ if (LINALG STREQUAL "OpenBLAS")
+ endif ()
+=20
+ # 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 functiona=
lity
+- 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_LAPAC=
K)
+- if (NOT OPENBLAS_WITH_LAPACK)
+- unset (LIBOPENBLAS CACHE)
+- message (FATAL_ERROR
+- "LAPACK functionality missing from OpenBL=
AS library, "
+- "please build OpenBLAS with NO_LAPACK=3D0=
defined."
+- )
+- endif ()
+- # save the last location to check if it changed between c=
onfigurations
+- 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
+ )
+=20
+- install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/ins=
tall_pymolcas.sh ${PYMOLCAS_TARGET})")
+ endif ()
+=20
+ if (DEFINED EXTRA_DIR)
+@@ -3188,9 +3189,5 @@ if (DEFINED EXTRA_DIR)
+ DESTINATION ${CMAKE_INSTALL_PREFIX}/bin
+ )
+=20
+- install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/ins=
tall_driver.sh ${MOLCAS_DRIVER})")
+ endif ()
+=20
+-if (IS_DIRECTORY "$ENV{HOME}/.Molcas")
+- install (CODE "execute_process(COMMAND sh \"-c\" \"cd ${CMAKE_INS=
TALL_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 +52,5 @@ if (PYTHONINTERP_FOUND)
+ DEPENDS ${PYMOLCAS_TARGET}
+ )
+=20
+- add_custom_command (TARGET pymolcas
+- POST_BUILD
+- COMMAND ${OPENMOLCAS_DIR}/sbin/install_pymolcas.s=
h ${PYMOLCAS_TARGET}
+- )
+=20
+ endif ()
+
--=20
2.18.0
--=-=-=--
X-Loop: help-debbugs@HIDDEN
Subject: bug#32691: OpenMolcas
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From: Eric Brown <brown@HIDDEN>
References: <87d0tkk6gh.fsf@HIDDEN> <87h8isjund.fsf@HIDDEN>
Date: Fri, 14 Sep 2018 09:55:50 -0500
In-Reply-To: <87h8isjund.fsf@HIDDEN> ("Ludovic =?UTF-8?Q?Court=C3=A8s?="'s message of "Fri, 14 Sep 2018 11:27:50 +0200")
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--=-=-=
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: quoted-printable
ludo@HIDDEN (Ludovic Court=C3=A8s) writes:
> Here=E2=80=99s a revision of the patch with several modifications: I added
> comments in the patch (though they don=E2=80=99t explain the Python-relat=
ed
> changes for instance; could you add a line about these?), stripped
> unnecessary additions from the patch, added it to gnu/local.mk, fixed
> an issue reported by =E2=80=98guix lint=E2=80=99 in the description.
>
> However, could you explain why we have #:tests? #f ? In general
> disabling tests should be accompanied with a comment explaining the
> reason (lack of a test suite, or =E2=80=9Cunsolvable=E2=80=9D test failur=
es.) If there
> are test failures, we=E2=80=99d rather investigate than disable the tests.
>
> Could you send an updated patch?
>
Hi Ludo':
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 have removed the out-of-source build statement and re-enabled tests,
simply by omitting those flags.
Best regards,
Eric
--=-=-=
Content-Type: text/x-diff; charset=utf-8
Content-Disposition: inline; filename=openmolcas-v2.patch
Content-Transfer-Encoding: quoted-printable
From 315c2a58310f2af32cdbd59c97a10911c390ddd3 Mon Sep 17 00:00:00 2001
From: Eric Brown <brown@HIDDEN>
Date: Fri, 14 Sep 2018 09:27:35 -0500
Subject: [PATCH] gnu: Add openmolcas and openblas-ilp64.
* gnu/packages/chemistry.scm (openmolcas): New variable.
---
gnu/local.mk | 1 +
gnu/packages/chemistry.scm | 56 ++++++++++++
.../openmolcas-pymolcas-openblas.patch | 89 +++++++++++++++++++
3 files changed, 146 insertions(+)
create mode 100644 gnu/packages/patches/openmolcas-pymolcas-openblas.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index 7b230cb6f..0974ce068 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1006,6 +1006,7 @@ dist_patch_DATA =3D \
%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..d5461b08f 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright =C2=A9 2018 Konrad Hinsen <konrad.hinsen@HIDDEN>
;;; Copyright =C2=A9 2018 Kei Kebreau <kkebreau@HIDDEN>
+;;; Copyright =C2=A9 2018 Eric Brown <brown@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 +327,54 @@ 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
+ ;; 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 path is supplied as an argument to CMake.
+ (search-patches "openmolcas-pymolcas-openblas.patch"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:build-type "Release"
+ #:configure-flags
+ (list "-DLINALG=3DOpenBLAS"
+ (string-append "-DOPENBLASROOT=3D"
+ (assoc-ref %build-inputs "blas"))
+ (string-append "-DLINALG_LIBRARIES=3D"
+ (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)))
+ (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 devel=
oped
+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..b18c62e05
--- /dev/null
+++ b/gnu/packages/patches/openmolcas-pymolcas-openblas.patch
@@ -0,1 +1,89 @@
+Allow bulds with openblas-ilp64.
+Remove assumptions about $HOME.
+
+diff --git OpenMolcas-v18.09/CMakeLists.txt OpenMolcas-v18.09/CMakeLists.t=
xt
+index a4071fd..53d8df5 100644
+--- OpenMolcas-v18.09/CMakeLists.txt
++++ OpenMolcas-v18.09/CMakeLists.txt
+@@ -1338,42 +1338,8 @@ if (LINALG STREQUAL "OpenBLAS")
+ endif ()
+=20
+ # 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 functiona=
lity
+- 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_LAPAC=
K)
+- if (NOT OPENBLAS_WITH_LAPACK)
+- unset (LIBOPENBLAS CACHE)
+- message (FATAL_ERROR
+- "LAPACK functionality missing from OpenBL=
AS library, "
+- "please build OpenBLAS with NO_LAPACK=3D0=
defined."
+- )
+- endif ()
+- # save the last location to check if it changed between c=
onfigurations
+- 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
+ )
+=20
+- install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/ins=
tall_pymolcas.sh ${PYMOLCAS_TARGET})")
+ endif ()
+=20
+ if (DEFINED EXTRA_DIR)
+@@ -3188,9 +3189,5 @@ if (DEFINED EXTRA_DIR)
+ DESTINATION ${CMAKE_INSTALL_PREFIX}/bin
+ )
+=20
+- install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/ins=
tall_driver.sh ${MOLCAS_DRIVER})")
+ endif ()
+=20
+-if (IS_DIRECTORY "$ENV{HOME}/.Molcas")
+- install (CODE "execute_process(COMMAND sh \"-c\" \"cd ${CMAKE_INS=
TALL_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}
+ )
+=20
+- add_custom_command (TARGET pymolcas
+- POST_BUILD
+- COMMAND ${OPENMOLCAS_DIR}/sbin/install_pymolcas.s=
h ${PYMOLCAS_TARGET}
+- )
+=20
+ endif ()
+
--=20
2.19.0
--=-=-=
Content-Type: text/x-diff; charset=utf-8
Content-Disposition: attachment; filename=openmolcas-v2.patch
Content-Transfer-Encoding: quoted-printable
From 315c2a58310f2af32cdbd59c97a10911c390ddd3 Mon Sep 17 00:00:00 2001
From: Eric Brown <brown@HIDDEN>
Date: Fri, 14 Sep 2018 09:27:35 -0500
Subject: [PATCH] gnu: Add openmolcas and openblas-ilp64.
* gnu/packages/chemistry.scm (openmolcas): New variable.
---
gnu/local.mk | 1 +
gnu/packages/chemistry.scm | 56 ++++++++++++
.../openmolcas-pymolcas-openblas.patch | 89 +++++++++++++++++++
3 files changed, 146 insertions(+)
create mode 100644 gnu/packages/patches/openmolcas-pymolcas-openblas.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index 7b230cb6f..0974ce068 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1006,6 +1006,7 @@ dist_patch_DATA =3D \
%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..d5461b08f 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright =C2=A9 2018 Konrad Hinsen <konrad.hinsen@HIDDEN>
;;; Copyright =C2=A9 2018 Kei Kebreau <kkebreau@HIDDEN>
+;;; Copyright =C2=A9 2018 Eric Brown <brown@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 +327,54 @@ 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
+ ;; 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 path is supplied as an argument to CMake.
+ (search-patches "openmolcas-pymolcas-openblas.patch"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:build-type "Release"
+ #:configure-flags
+ (list "-DLINALG=3DOpenBLAS"
+ (string-append "-DOPENBLASROOT=3D"
+ (assoc-ref %build-inputs "blas"))
+ (string-append "-DLINALG_LIBRARIES=3D"
+ (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)))
+ (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 devel=
oped
+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..b18c62e05
--- /dev/null
+++ b/gnu/packages/patches/openmolcas-pymolcas-openblas.patch
@@ -0,1 +1,89 @@
+Allow bulds with openblas-ilp64.
+Remove assumptions about $HOME.
+
+diff --git OpenMolcas-v18.09/CMakeLists.txt OpenMolcas-v18.09/CMakeLists.t=
xt
+index a4071fd..53d8df5 100644
+--- OpenMolcas-v18.09/CMakeLists.txt
++++ OpenMolcas-v18.09/CMakeLists.txt
+@@ -1338,42 +1338,8 @@ if (LINALG STREQUAL "OpenBLAS")
+ endif ()
+=20
+ # 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 functiona=
lity
+- 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_LAPAC=
K)
+- if (NOT OPENBLAS_WITH_LAPACK)
+- unset (LIBOPENBLAS CACHE)
+- message (FATAL_ERROR
+- "LAPACK functionality missing from OpenBL=
AS library, "
+- "please build OpenBLAS with NO_LAPACK=3D0=
defined."
+- )
+- endif ()
+- # save the last location to check if it changed between c=
onfigurations
+- 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
+ )
+=20
+- install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/ins=
tall_pymolcas.sh ${PYMOLCAS_TARGET})")
+ endif ()
+=20
+ if (DEFINED EXTRA_DIR)
+@@ -3188,9 +3189,5 @@ if (DEFINED EXTRA_DIR)
+ DESTINATION ${CMAKE_INSTALL_PREFIX}/bin
+ )
+=20
+- install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/ins=
tall_driver.sh ${MOLCAS_DRIVER})")
+ endif ()
+=20
+-if (IS_DIRECTORY "$ENV{HOME}/.Molcas")
+- install (CODE "execute_process(COMMAND sh \"-c\" \"cd ${CMAKE_INS=
TALL_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}
+ )
+=20
+- add_custom_command (TARGET pymolcas
+- POST_BUILD
+- COMMAND ${OPENMOLCAS_DIR}/sbin/install_pymolcas.s=
h ${PYMOLCAS_TARGET}
+- )
+=20
+ endif ()
+
--=20
2.19.0
--=-=-=--
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Subject: bug#32691: OpenMolcas
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From: ludo@HIDDEN (Ludovic =?UTF-8?Q?Court=C3=A8s?=)
References: <87d0tkk6gh.fsf@HIDDEN> <87h8isjund.fsf@HIDDEN>
<87bm90uo09.fsf@HIDDEN>
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--=-=-=
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Hi Eric,
We=E2=80=99re almost there! :-)
Eric Brown <brown@HIDDEN> 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 =E2=80=98texlive-union=E2=80=99, which is much smaller tha=
n =E2=80=98texlive=E2=80=99),
leading to the attached patch.
It=E2=80=99s all good, except that the file layout really doesn=E2=80=99t m=
atch 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.pr=
gm
/gnu/store/6cj9n2rwsxwk582xqz2hxzlk520ghvm9-openmolcas-18.09/data/rasscf.pr=
gm
/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 =E2=80=98.exe=E2=80=99 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=E2=80=99.
--=-=-=
Content-Type: text/x-patch; charset=utf-8
Content-Disposition: inline; filename=0001-gnu-Add-openmolcas.patch
Content-Transfer-Encoding: quoted-printable
Content-Description: the patch
From b4caef67aaae349e0aa77fc22517872ff8ca79cb Mon Sep 17 00:00:00 2001
From: Eric Brown <brown@HIDDEN>
Date: Fri, 14 Sep 2018 09:27:35 -0500
Subject: [PATCH] gnu: Add openmolcas.
MIME-Version: 1.0
Content-Type: text/plain; charset=3DUTF-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 Court=C3=A8s <ludo@HIDDEN>
---
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 =3D \
%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 =C2=A9 2018 Konrad Hinsen <konrad.hinsen@HIDDEN>
;;; Copyright =C2=A9 2018 Kei Kebreau <kkebreau@HIDDEN>
+;;; Copyright =C2=A9 2018 Eric Brown <brown@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 +327,49 @@ 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=3DOpenBLAS"
+ (string-append "-DOPENBLASROOT=3D"
+ (assoc-ref %build-inputs "blas"))
+ (string-append "-DLINALG_LIBRARIES=3D"
+ (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 devel=
oped
+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 oth=
er
+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.t=
xt
+index a4071fd..53d8df5 100644
+--- OpenMolcas-v18.09/CMakeLists.txt
++++ OpenMolcas-v18.09/CMakeLists.txt
+@@ -1338,42 +1338,8 @@ if (LINALG STREQUAL "OpenBLAS")
+ endif ()
+=20
+ # 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 functiona=
lity
+- 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_LAPAC=
K)
+- if (NOT OPENBLAS_WITH_LAPACK)
+- unset (LIBOPENBLAS CACHE)
+- message (FATAL_ERROR
+- "LAPACK functionality missing from OpenBL=
AS library, "
+- "please build OpenBLAS with NO_LAPACK=3D0=
defined."
+- )
+- endif ()
+- # save the last location to check if it changed between c=
onfigurations
+- 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
+ )
+=20
+- install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/ins=
tall_pymolcas.sh ${PYMOLCAS_TARGET})")
+ endif ()
+=20
+ if (DEFINED EXTRA_DIR)
+@@ -3188,9 +3189,5 @@ if (DEFINED EXTRA_DIR)
+ DESTINATION ${CMAKE_INSTALL_PREFIX}/bin
+ )
+=20
+- install (CODE "execute_process(COMMAND ${OPENMOLCAS_DIR}/sbin/ins=
tall_driver.sh ${MOLCAS_DRIVER})")
+ endif ()
+=20
+-if (IS_DIRECTORY "$ENV{HOME}/.Molcas")
+- install (CODE "execute_process(COMMAND sh \"-c\" \"cd ${CMAKE_INS=
TALL_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}
+ )
+=20
+- add_custom_command (TARGET pymolcas
+- POST_BUILD
+- COMMAND ${OPENMOLCAS_DIR}/sbin/install_pymolcas.s=
h ${PYMOLCAS_TARGET}
+- )
+=20
+ endif ()
--=20
2.18.0
--=-=-=--
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Subject: bug#32691: OpenMolcas
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From: Eric Brown <brown@HIDDEN>
References: <87d0tkk6gh.fsf@HIDDEN> <87h8isjund.fsf@HIDDEN>
<87bm90uo09.fsf@HIDDEN> <875zz36du9.fsf@HIDDEN>
Date: Wed, 19 Sep 2018 19:13:40 -0500
In-Reply-To: <875zz36du9.fsf@HIDDEN> ("Ludovic =?UTF-8?Q?Court=C3=A8s?="'s message of "Mon, 17 Sep 2018 22:58:22 +0200")
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ludo@HIDDEN (Ludovic Court=C3=A8s) writes:
> Hi Eric,
>
> We=E2=80=99re almost there! :-)
>
> I made small changes (moved comments about the patch at the top of the
> patch; switch to =E2=80=98texlive-union=E2=80=99, which is much smaller t=
han =E2=80=98texlive=E2=80=99),
> leading to the attached patch.
>
> It=E2=80=99s all good, except that the file layout really doesn=E2=80=99t=
match the
> usual conventions:
>
> [...]
>
> 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 =E2=80=98.exe=E2=80=99 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!
Hi Ludo',
Thank you again. Indeed, "/" gets littered with some files that out to
go into share. This has been noted in discussions upstream.
Though we've put a bunch of work into this, I think it would be good to
pause and see if we can make some of these changes upstream, as you
suggest.
(Also I need some time to brush up on CMake -- perhaps I can contribute
some of these changes myself.)
Warm regards,
Eric
X-Loop: help-debbugs@HIDDEN
Subject: bug#32691: OpenMolcas
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From: ludo@HIDDEN (Ludovic =?UTF-8?Q?Court=C3=A8s?=)
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Hi Eric,
Eric Brown <brown@HIDDEN> skribis:
> ludo@HIDDEN (Ludovic Court=C3=A8s) writes:
[...]
>> 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 =E2=80=98.exe=E2=80=99 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!
>
> Hi Ludo',
>
> Thank you again. Indeed, "/" gets littered with some files that out to
> go into share. This has been noted in discussions upstream.
>
> Though we've put a bunch of work into this, I think it would be good to
> pause and see if we can make some of these changes upstream, as you
> suggest.
Sounds good, let us know how it goes.
Thanks,
Ludo=E2=80=99.
X-Loop: help-debbugs@HIDDEN
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Hello Eric,
Eric Brown <brown@HIDDEN> writes:
> ludo@HIDDEN (Ludovic Court=C3=A8s) writes:
>
>> Hi Eric,
>>
>> We=E2=80=99re almost there! :-)
>>
>> I made small changes (moved comments about the patch at the top of the
>> patch; switch to =E2=80=98texlive-union=E2=80=99, which is much smaller =
than =E2=80=98texlive=E2=80=99),
>> leading to the attached patch.
>>
>> It=E2=80=99s all good, except that the file layout really doesn=E2=80=99=
t match the
>> usual conventions:
>>
>> [...]
>>
>> 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 =E2=80=98.exe=E2=80=99 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!
>
> Hi Ludo',
>
> Thank you again. Indeed, "/" gets littered with some files that out to
> go into share. This has been noted in discussions upstream.
>
> Though we've put a bunch of work into this, I think it would be good to
> pause and see if we can make some of these changes upstream, as you
> suggest.
>
> (Also I need some time to brush up on CMake -- perhaps I can contribute
> some of these changes myself.)
>
> Warm regards,
> Eric
Thanks for all your work on this package. Did you ever make further
progress on this? Are you still interested in working on getting
OpenMolcas in Guix?
--
Sarah
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997 nCipher Corporation Ltd,
1994-97 Ian Jackson.