From 784cb74747adcc513b75b16b9247bd3dc9a484a3 Mon Sep 17 00:00:00 2001 From: Eric Brown 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 ;;; Copyright © 2018 Kei Kebreau +;;; Copyright © 2018 Eric Brown ;;; ;;; 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 ;;; Copyright © 2018 Adam Massmann ;;; Copyright © 2018 Marius Bakke +;;; Copyright © 2018 Eric Brown ;;; ;;; 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=, 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