Subject: bug#32691: OpenMolcas

From: Eric Brown <[email-masked]>
Date: Fri, 14 Sep 2018 09:55:50 -0500

[email-masked] (Ludovic Courtès) writes:

> Here’s a revision of the patch with several modifications: I added
> comments in the patch (though they don’t 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 ‘guix lint’ 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 “unsolvable” test failures.)  If there
> are test failures, we’d 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

>From 315c2a58310f2af32cdbd59c97a10911c390ddd3 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 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 =						\
   %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 © 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 +327,54 @@ 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=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)))
+    (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..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.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 ()
+
-- 
2.19.0

>From 315c2a58310f2af32cdbd59c97a10911c390ddd3 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 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 =						\
   %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 © 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 +327,54 @@ 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=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)))
+    (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..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.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 ()
+
-- 
2.19.0