[PATCH] gnu: Add openfoam

> * gnu/packages/simulation.scm: New file

> * gnu/packages/patches/openfoam-cleanup.patch: New file

> * gnu/local.mk(GNU_SYSTEM_MODULES): Add module

> (dist_patch_DATA): Add patch

> +diff -ur OpenFOAM-4.x-version-4.1.org/wmake/src/Makefile OpenFOAM-4.x-version-4.1/wmake/src/Makefile

> +--- OpenFOAM-4.x-version-4.1.org/wmake/src/Makefile

> ++++ OpenFOAM-4.x-version-4.1/wmake/src/Makefile

> +@@ -33,7 +33,7 @@

> + # The Makefile use a POSIX shell

> + #------------------------------------------------------------------------------

> +

> +-SHELL = /bin/sh

> ++# SHELL = /bin/sh

> +diff -ur OpenFOAM-4.x-version-4.1.org/wmake/makefiles/general OpenFOAM-4.x-version-4.1/wmake/makefiles/general

> +--- OpenFOAM-4.x-version-4.1.org/wmake/makefiles/general

> ++++ OpenFOAM-4.x-version-4.1/wmake/makefiles/general

> +@@ -33,7 +33,7 @@

> + # The Makefile uses a POSIX shell

> + #------------------------------------------------------------------------------

> +

> +-SHELL = /bin/sh

> ++# SHELL = /bin/sh

> + #------------------------------------------------------------------------------

> +diff -ur OpenFOAM-4.x-version-4.1.org/wmake/wmake OpenFOAM-4.x-version-4.1/wmake/wmake

> +--- OpenFOAM-4.x-version-4.1.org/wmake/wmake

> ++++ OpenFOAM-4.x-version-4.1/wmake/wmake

> +@@ -163,7 +163,7 @@

> + then

> + if [ "$WM_NCOMPPROCS" -gt 1 -a ! "$MAKEFLAGS" ]

> + then

> +- lockDir=$HOME/.$WM_PROJECT/.wmake

> ++ lockDir=$(cd $(dirname $BASH_SOURCE)/../.. && pwd -P)/.$WM_PROJECT/.wmake

> +

> + if [ -d $lockDir ]

> + then

> +diff -ur OpenFOAM-4.x-version-4.1.org/wmake/wmakeScheduler OpenFOAM-4.x-version-4.1/wmake/wmakeScheduler

> +--- OpenFOAM-4.x-version-4.1.org/wmake/wmakeScheduler

> ++++ OpenFOAM-4.x-version-4.1/wmake/wmakeScheduler

> +@@ -53,7 +53,7 @@

> + # csh sets HOST, bash sets HOSTNAME

> + : ${HOST:=$HOSTNAME}

> +

> +-lockDir=$HOME/.$WM_PROJECT/.wmake

> ++lockDir=$(cd $(dirname $BASH_SOURCE)/../.. && pwd -P)/.$WM_PROJECT/.wmake

> +

> + # Fallback - 1 core on current host

> + : ${WM_HOSTS:=$HOST:1}

> +diff -ur OpenFOAM-4.x-version-4.1.org/wmake/wmakeSchedulerUptime OpenFOAM-4.x-version-4.1/wmake/wmakeSchedulerUptime

> +--- OpenFOAM-4.x-version-4.1.org/wmake/wmakeSchedulerUptime

> ++++ OpenFOAM-4.x-version-4.1/wmake/wmakeSchedulerUptime

> +@@ -53,7 +53,7 @@

> + # csh sets HOST, bash sets HOSTNAME

> + : ${HOST:=$HOSTNAME}

> +

> +-lockDir=$HOME/.$WM_PROJECT/.wmake

> ++lockDir=$(cd $(dirname $BASH_SOURCE)/../.. && pwd -P)/.$WM_PROJECT/.wmake

> + # Fallback - 1 core on current host

> + : ${WM_HOSTS:=$HOST:1}

> +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/metisDecomp/metisDecomp.C OpenFOAM-4.x-version-4.1/src/parallel/decompose/metisDecomp/metisDecomp.C

> +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/metisDecomp/metisDecomp.C

> ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/metisDecomp/metisDecomp.C

> +@@ -67,7 +67,7 @@

> +

> + // Processor weights initialised with no size, only used if specified in

> + // a file

> +- Field<scalar> processorWeights;

> ++ Field<floatScalar> processorWeights;

> diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm

> new file mode 100644

> index 000000000..5aa5f8f03

> --- /dev/null

> +++ b/gnu/packages/simulation.scm

> @@ -0,0 +1,197 @@

> +;;; GNU Guix --- Functional package management for GNU

> +;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>

> +;;;

> +;;; This file is part of GNU Guix.

> +;;;

> +;;; GNU Guix is free software; you can redistribute it and/or modify it

> +;;; under the terms of the GNU General Public License as published by

> +;;; the Free Software Foundation; either version 3 of the License, or (at

> +;;; your option) any later version.

> +;;;

> +;;; GNU Guix is distributed in the hope that it will be useful, but

> +;;; WITHOUT ANY WARRANTY; without even the implied warranty of

> +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

> +;;; GNU General Public License for more details.

> +;;;

> +;;; You should have received a copy of the GNU General Public License

> +;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.

> +

> +(define-module (gnu packages simulation)

> + #:use-module (gnu packages)

> + #:use-module (gnu packages base)

> + #:use-module (gnu packages bash)

> + #:use-module (gnu packages bison)

> + #:use-module (gnu packages boost)

> + #:use-module (gnu packages compression)

> + #:use-module (gnu packages flex)

> + #:use-module (gnu packages gettext)

> + #:use-module (gnu packages gcc)

> + #:use-module (gnu packages gl)

> + #:use-module (gnu packages graphics)

> + #:use-module (gnu packages gtk)

> + #:use-module (gnu packages linux)

> + #:use-module (gnu packages m4)

> + #:use-module (gnu packages maths)

> + #:use-module (gnu packages mpi)

> + #:use-module (gnu packages multiprecision)

> + #:use-module (gnu packages ncurses)

> + #:use-module (gnu packages readline)

> + #:use-module (gnu packages tls)

> + #:use-module (gnu packages version-control)

> + #:use-module (gnu packages xml)

> + #:use-module (gnu packages xorg)

> + #:use-module (guix download)

> + #:use-module (guix build utils)

> + #:use-module (guix build-system gnu)

> + #:use-module ((guix licenses) #:prefix license:)

> + #:use-module (guix packages)

> + #:use-module (guix utils)

> + #:use-module (ice-9 ftw)

> + #:use-module (ice-9 regex)

> + #:use-module (srfi srfi-1))

> +

> +(define-public openfoam

> + (package

> + (name "openfoam")

> + (version "4.1")

> + (source

> + (origin

> + (method url-fetch)

> + (uri (string-append

> + "http://dl.openfoam.org/source/"

> + (string-replace-substring version "." "-")))

> + (file-name (string-append name "-" version ".tar.gz"))

> + (sha256

> + (base32 "1hgh2kw7fqv4bfachhbjhw16v8j35jbv6s576fmz4ka2q4ks4wg3"))

> + (patches (search-patches "openfoam-cleanup.patch"))

> + (modules '((guix build utils)))))

> + (build-system gnu-build-system)

> + (native-inputs

> + `(("bison" ,bison)))

> + (propagated-inputs

> + `(("boost" ,boost)

> + ("cgal" ,cgal)

> + ("flex" ,flex)

> + ("git" ,git)

> + ("gmp" ,gmp)

> + ("gzip" ,gzip)

> + ("gnuplot" ,gnuplot)

> + ("libxt" ,libxt)

> + ("metis" ,metis)

> + ("mpfr" ,mpfr)

> + ("ncurses" ,ncurses)

> + ("openmpi" ,openmpi)

> + ("readline" ,readline)

> + ("scotch" ,pt-scotch)

> + ("zlib" ,zlib)))

> + (arguments

> + `(;; executable files and shared libraries are located in the 'platforms'

> + ;; subdirectory

> + #:strip-directories (list (string-append

> + "OpenFOAM-" ,version

> + "/platforms/linux64GccDPInt32Opt/bin")

> + (string-append

> + "OpenFOAM-" ,version

> + "/platforms/linux64GccDPInt32Opt/lib"))

> + ;; '#:elf-directories' is not recognised here so skip validation phase

> + #:validate-runpath? #f

> + #:phases (modify-phases %standard-phases

> + (add-after 'unpack 'rename-build-directory

> + (lambda _

> + (use-modules (ice-9 ftw))

> + (use-modules (ice-9 regex))

> + (chdir "..")

> + ;; use 'OpenFOAM-version' convention to match path name

> + ;; expectations in the build phase

> + (let ((unpack-dir (string-append

> + (getcwd) "/"

> + (list-ref (scandir (getcwd) (lambda (name)

> + (string-match "^OpenFOAM" name))) 0)))

> + (build-dir (string-append

> + (getcwd) "/OpenFOAM-" ,version)))

> + ;; re-name build directory

> + (rename-file unpack-dir build-dir)

> + ;; move to build directory

> + (chdir (basename build-dir)))))

> + (add-after 'patch-source-shebangs 'set-environment-variables

> + (lambda _

> + (let ((libraries '("boost" "cgal" "gmp" "metis" "mpfr" "scotch")))

> + ;; set variables to define store paths

> + (for-each (lambda (library)

> + (setenv (string-append

> + (string-upcase library) "_ROOT")

> + (assoc-ref %build-inputs library))) libraries))

> + ;; set variables to define package versions

> + (setenv "SCOTCHVERSION" ,(package-version scotch))

> + (setenv "METISVERSION" ,(package-version metis))))

> + (delete 'configure) ; no configure phase

> + (delete 'patch-generated-file-shebangs) ; no generated files

> + (replace 'build

> + (lambda _

> + ;; compile OpenFOAM libraries and applications

> + (zero? (system (format #f

> + "source ./etc/bashrc && ./Allwmake -j~a"

> + (parallel-job-count))))))

> + (add-after 'build 'update-configuration-files

> + (lambda _

> + ;; record store paths and package versions in configuration files

> + (zero? (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"

> + "$CGAL_ROOT" "etc/config.sh/CGAL")))

> + (zero? (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"

> + "$BOOST_ROOT" "etc/config.sh/CGAL")))

> + (zero? (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"

> + "$METIS_ROOT" "etc/config.sh/metis")))

> + (zero? (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"

> + "$METISVERSION" "etc/config.sh/metis")))

> + (zero? (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"

> + "$SCOTCH_ROOT" "etc/config.sh/scotch")))

> + (zero? (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"

> + "$SCOTCHVERSION" "etc/config.sh/scotch")))

> + (zero? (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"

> + "$GMP_ROOT" "etc/config.sh/settings")))

> + (zero? (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"

> + "$MPFR_ROOT" "etc/config.sh/settings")))))

> + (delete 'check) ; no tests to run

> + (replace 'install

> + (lambda _

> + ;; use 'OpenFOAM-version' convention

> + (let ((install-dir (string-append

> + %output "/OpenFOAM-" ,version)))

> + ;; create install directory

> + (mkdir-p install-dir)

> + ;; move contents of build directory to install directory

> + (copy-recursively "." install-dir)))))))

> + ;; Note: tutorial files are installed read-only in /gnu/store.

> + ;; To allow write permissions on files copied from the store a

> + ;; 'chmod' step is needed before running the applications. For

> + ;; example, from a user's login:

> + ;; $ source $GUIX_PROFILE/OpenFOAM-4.1/etc/bashrc

> + ;; $ mkdir -p $FOAM_RUN

> + ;; $ cd $FOAM_RUN

> + ;; $ cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzdaily .

> + ;; $ cd pitzdaily

> + ;; $ chmod -R u+w .

> + ;; $ blockMesh

> + (native-search-paths

> + ;; define the FOAM_INST_DIR variable

> + (list (search-path-specification

> + (variable "FOAM_INST_DIR")

> + (files '(".")))))

> + (synopsis "Framework for numerical simulation of fluid flow")

> + (description "OpenFOAM provides a set of solvers and methods for tackling

> +problems in the field of Computational Fluid Dynamics (CFD). It is written in

> +C++. Complex governing equations such as the Navier-Stokes equations can be

> +solved in integral form. Physical processes such as phase change, droplet

> +transport and chemical reaction can be modelled. Numerical methods are

> +included to deal with sharp gradients, such as those encountered in flows with

> +shock waves and flows with gas/liquid interfaces.

> +

> +OpenFOAM implements the Finite Volume Method for discretizing the spacial

> +dimensions. Computational grids defining geometries in two- and

> +three-dimensional domains may be generated by the included blockMesh and

> +snappyHexMesh routines or imported from external grid-generation packages.

> +Grids may be unstructured in layout and may contain any combination of

> +polyhedral cells. Large problems may be split into smaller, connected

> +problems for efficient solution on parallel systems")

> * gnu/packages/simulation.scm: New file

> * gnu/packages/patches/openfoam-cleanup.patch: New file

> * gnu/local.mk(GNU_SYSTEM_MODULES): Add module

> (dist_patch_DATA): Add patch

> ---

> gnu/local.mk | 2 +

> gnu/packages/patches/openfoam-cleanup.patch | 251 ++++++++++++++++++++++++++++

> gnu/packages/simulation.scm | 197 ++++++++++++++++++++++

> 3 files changed, 450 insertions(+)

> create mode 100644 gnu/packages/patches/openfoam-cleanup.patch

> create mode 100644 gnu/packages/simulation.scm

>

> diff --git a/gnu/local.mk b/gnu/local.mk

> index 4b2bdfe37..b00ec1ac7 100644

> --- a/gnu/local.mk

> +++ b/gnu/local.mk

> @@ -357,6 +357,7 @@ GNU_SYSTEM_MODULES = \

> %D%/packages/shells.scm \

> %D%/packages/shellutils.scm \

> %D%/packages/simh.scm \

> + %D%/packages/simulation.scm \

> %D%/packages/skarnet.scm \

> %D%/packages/skribilo.scm \

> %D%/packages/slang.scm \

> @@ -866,6 +867,7 @@ dist_patch_DATA = \

> %D%/packages/patches/ola-readdir-r.patch \

> %D%/packages/patches/openscenegraph-ffmpeg3.patch \

> %D%/packages/patches/openexr-missing-samples.patch \

> + %D%/packages/patches/openfoam-cleanup.patch \

> %D%/packages/patches/openjpeg-CVE-2016-9850-CVE-2016-9851.patch \

> %D%/packages/patches/openjpeg-CVE-2016-9572-CVE-2016-9573.patch \

> %D%/packages/patches/openldap-CVE-2017-9287.patch \

> diff --git a/gnu/packages/patches/openfoam-cleanup.patch b/gnu/packages/patches/openfoam-cleanup.patch

> new file mode 100644

> index 000000000..b2c0ddcd1

> --- /dev/null

> +++ b/gnu/packages/patches/openfoam-cleanup.patch

> @@ -0,0 +1,251 @@

> +# This patch removes all need for the ThirdParty files of OpenFOAM

> +

> +# Derived from easybuild patch: Ward Poelmans <wpoely86@gmail.com>

> +# Modified for GNU Guix: Paul Garlick <pgarlick@tourbillion-technology.com>

> +

> +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Allwmake

> +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Allwmake

> ++++ OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Allwmake

> +@@ -9,7 +9,7 @@

> + #

> + # use readline if available

> + #

> +-if [ -f /usr/include/readline/readline.h ]

> ++if true

> + then

> + echo "Found <readline/readline.h> -- enabling readline support."

> + export COMP_FLAGS="-DHAS_READLINE"

> +diff -ur OpenFOAM-4.x-version-4.1.org/etc/bashrc OpenFOAM-4.x-version-4.1/etc/bashrc

> +--- OpenFOAM-4.x-version-4.1.org/etc/bashrc

> ++++ OpenFOAM-4.x-version-4.1/etc/bashrc

> +@@ -43,8 +43,10 @@

> + # Please set to the appropriate path if the default is not correct.

> + #

> + [ $BASH_SOURCE ] && \

> +-export FOAM_INST_DIR=$(cd ${BASH_SOURCE%/*/*/*} && pwd -P) || \

> ++export FOAM_INST_DIR=$(cd $(dirname $BASH_SOURCE)/../.. && pwd -P) || \

> + export FOAM_INST_DIR=$HOME/$WM_PROJECT

> ++# For GNU Guix: set initially for build then re-set at runtime

> ++#

> + # export FOAM_INST_DIR=~$WM_PROJECT

> + # export FOAM_INST_DIR=/opt/$WM_PROJECT

> + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT

> +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL

> +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL

> ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL

> +@@ -36,37 +36,7 @@

> + #

> + #------------------------------------------------------------------------------

> +

> +-boost_version=boost-system

> +-cgal_version=cgal-system

> +-#cgal_version=CGAL-4.8

> +-

> +-if [ -z "$SOURCE_CGAL_VERSIONS_ONLY" ]

> +-then

> +-

> +- common_path=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER

> +-

> +- export BOOST_ARCH_PATH=$common_path/$boost_version

> +- export CGAL_ARCH_PATH=$common_path/$cgal_version

> +-

> +- if [ "$FOAM_VERBOSE" -a "$PS1" ]

> +- then

> +- echo "Using CGAL and boost" 1>&2

> +- echo " $cgal_version at $CGAL_ARCH_PATH" 1>&2

> +- echo " $boost_version at $BOOST_ARCH_PATH" 1>&2

> +- fi

> +-

> +- if [ -d "$CGAL_ARCH_PATH" -a "$cgal_version" != "cgal-system" ]

> +- then

> +- _foamAddLib $CGAL_ARCH_PATH/lib

> +- fi

> +-

> +- if [ -d "$BOOST_ARCH_PATH" -a "$boost_version" != "boost-system" ]

> +- then

> +- _foamAddLib $BOOST_ARCH_PATH/lib

> +- fi

> +-

> +- unset boost_version cgal_version common_path

> +-

> +-fi

> ++export CGAL_ARCH_PATH=$CGAL_ROOT

> ++export BOOST_ARCH_PATH=$BOOST_ROOT

> +

> + #------------------------------------------------------------------------------

> +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools OpenFOAM-4.x-version-4.1/etc/config.sh/gperftools

> +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools 2016-10-16 16:11:45.000000000 +0200

> ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/gperftools 2017-04-10 14:51:01.473221230 +0200

> +@@ -29,13 +29,13 @@

> + #

> + #------------------------------------------------------------------------------

> +

> +-version=svn

> +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER

> +-

> +-GPERFTOOLS_VERSION=gperftools-$version

> +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION

> +-

> +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH

> +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH

> ++# version=svn

> ++# gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER

> ++#

> ++# GPERFTOOLS_VERSION=gperftools-$version

> ++# GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION

> ++#

> ++# export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH

> ++# export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH

> +

> + #------------------------------------------------------------------------------

> +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis OpenFOAM-4.x-version-4.1/etc/config.sh/metis

> +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis

> ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/metis

> +@@ -34,7 +34,7 @@

> + #

> + #------------------------------------------------------------------------------

> +

> +-export METIS_VERSION=metis-5.1.0

> +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION

> ++export METIS_VERSION=metis-$METISVERSION

> ++export METIS_ARCH_PATH=$METIS_ROOT

> +

> + #------------------------------------------------------------------------------

> +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch OpenFOAM-4.x-version-4.1/etc/config.sh/scotch

> +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch

> ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/scotch

> +@@ -37,7 +37,7 @@

> + #

> + #------------------------------------------------------------------------------

> +

> +-export SCOTCH_VERSION=scotch_6.0.3

> +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION

> ++export SCOTCH_VERSION=scotch_$SCOTCHVERSION

> ++export SCOTCH_ARCH_PATH=$SCOTCH_ROOT

> +

> + #------------------------------------------------------------------------------

> +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings OpenFOAM-4.x-version-4.1/etc/config.sh/settings

> +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings

> ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/settings

> +@@ -279,6 +279,9 @@

> + ;;

> + system)

> + # Use system compiler

> ++ # Use system GMP and MPFR packages

> ++ export GMP_ARCH_PATH=$GMP_ROOT

> ++ export MPFR_ARCH_PATH=$MPFR_ROOT

> + ;;

> + *)

> + echo "Warn: WM_COMPILER_TYPE='$WM_COMPILER_TYPE' is unsupported" 1>&2

> +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options

> +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options

> ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options

> +@@ -5,8 +5,7 @@

> + $(PFLAGS) $(PINC) \

> + -I$(SCOTCH_ROOT)/include \

> + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \

> +- -I/usr/include/scotch \

> + -I../decompositionMethods/lnInclude

> +

> + LIB_LIBS = \

> +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt

> ++ -L$(SCOTCH_ROOT)/lib -L$(MPI_ARCH_PATH)/lib -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt

> +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options

> +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options

> ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options

> +@@ -9,8 +9,7 @@

> + $(PFLAGS) $(PINC) \

> + -I$(SCOTCH_ROOT)/include \

> + -I$(SCOTCH_ARCH_PATH)/include \

> +- -I/usr/include/scotch \

> + -I../decompositionMethods/lnInclude

> +

> + LIB_LIBS = \

> +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt

> ++ -L$(SCOTCH_ROOT)/lib -lscotch -lscotcherrexit -lrt

> +diff -ur OpenFOAM-4.x-version-4.1.org/wmake/src/Makefile OpenFOAM-4.x-version-4.1/wmake/src/Makefile

> +--- OpenFOAM-4.x-version-4.1.org/wmake/src/Makefile

> ++++ OpenFOAM-4.x-version-4.1/wmake/src/Makefile

> +@@ -33,7 +33,7 @@

> + # The Makefile use a POSIX shell

> + #------------------------------------------------------------------------------

> +

> +-SHELL = /bin/sh

> ++# SHELL = /bin/sh

> +

> + #------------------------------------------------------------------------------

> + # Unset suffices list (suffix rules are not used)

> +diff -ur OpenFOAM-4.x-version-4.1.org/wmake/makefiles/general OpenFOAM-4.x-version-4.1/wmake/makefiles/general

> +--- OpenFOAM-4.x-version-4.1.org/wmake/makefiles/general

> ++++ OpenFOAM-4.x-version-4.1/wmake/makefiles/general

> +@@ -33,7 +33,7 @@

> + # The Makefile uses a POSIX shell

> + #------------------------------------------------------------------------------

> +

> +-SHELL = /bin/sh

> ++# SHELL = /bin/sh

> +

> +

> + #------------------------------------------------------------------------------

> +diff -ur OpenFOAM-4.x-version-4.1.org/wmake/wmake OpenFOAM-4.x-version-4.1/wmake/wmake

> +--- OpenFOAM-4.x-version-4.1.org/wmake/wmake

> ++++ OpenFOAM-4.x-version-4.1/wmake/wmake

> +@@ -163,7 +163,7 @@

> + then

> + if [ "$WM_NCOMPPROCS" -gt 1 -a ! "$MAKEFLAGS" ]

> + then

> +- lockDir=$HOME/.$WM_PROJECT/.wmake

> ++ lockDir=$(cd $(dirname $BASH_SOURCE)/../.. && pwd -P)/.$WM_PROJECT/.wmake

> +

> + if [ -d $lockDir ]

> + then

> +diff -ur OpenFOAM-4.x-version-4.1.org/wmake/wmakeScheduler OpenFOAM-4.x-version-4.1/wmake/wmakeScheduler

> +--- OpenFOAM-4.x-version-4.1.org/wmake/wmakeScheduler

> ++++ OpenFOAM-4.x-version-4.1/wmake/wmakeScheduler

> +@@ -53,7 +53,7 @@

> + # csh sets HOST, bash sets HOSTNAME

> + : ${HOST:=$HOSTNAME}

> +

> +-lockDir=$HOME/.$WM_PROJECT/.wmake

> ++lockDir=$(cd $(dirname $BASH_SOURCE)/../.. && pwd -P)/.$WM_PROJECT/.wmake

> +

> + # Fallback - 1 core on current host

> + : ${WM_HOSTS:=$HOST:1}

> +diff -ur OpenFOAM-4.x-version-4.1.org/wmake/wmakeSchedulerUptime OpenFOAM-4.x-version-4.1/wmake/wmakeSchedulerUptime

> +--- OpenFOAM-4.x-version-4.1.org/wmake/wmakeSchedulerUptime

> ++++ OpenFOAM-4.x-version-4.1/wmake/wmakeSchedulerUptime

> +@@ -53,7 +53,7 @@

> + # csh sets HOST, bash sets HOSTNAME

> + : ${HOST:=$HOSTNAME}

> +

> +-lockDir=$HOME/.$WM_PROJECT/.wmake

> ++lockDir=$(cd $(dirname $BASH_SOURCE)/../.. && pwd -P)/.$WM_PROJECT/.wmake

> + # Fallback - 1 core on current host

> + : ${WM_HOSTS:=$HOST:1}

> +

> +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/metisDecomp/metisDecomp.C OpenFOAM-4.x-version-4.1/src/parallel/decompose/metisDecomp/metisDecomp.C

> +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/metisDecomp/metisDecomp.C

> ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/metisDecomp/metisDecomp.C

> +@@ -67,7 +67,7 @@

> +

> + // Processor weights initialised with no size, only used if specified in

> + // a file

> +- Field<scalar> processorWeights;

> ++ Field<floatScalar> processorWeights;

> +

> + // Cell weights (so on the vertices of the dual)

> + List<label> cellWeights;

> +diff -ur OpenFOAM-4.x-version-4.1.org/wmake/rules/General/CGAL OpenFOAM-4.x-version-4.1/wmake/rules/General/CGAL

> +--- OpenFOAM-4.x-version-4.1.org/wmake/rules/General/CGAL

> ++++ OpenFOAM-4.x-version-4.1/wmake/rules/General/CGAL

> +@@ -6,8 +6,8 @@

> + -I/usr/include

> +

> + CGAL_LIBS = \

> +- -L$(MPFR_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \

> +- -L$(GMP_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \

> ++ -L$(MPFR_ARCH_PATH)/lib \

> ++ -L$(GMP_ARCH_PATH)/lib \

> + -L$(BOOST_ARCH_PATH)/lib \

> + -L$(CGAL_ARCH_PATH)/lib \

> + -lCGAL \

> diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm

> new file mode 100644

> index 000000000..5aa5f8f03

> --- /dev/null

> +++ b/gnu/packages/simulation.scm

> @@ -0,0 +1,197 @@

> +;;; GNU Guix --- Functional package management for GNU

> +;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>

> +;;;

> +;;; This file is part of GNU Guix.

> +;;;

> +;;; GNU Guix is free software; you can redistribute it and/or modify it

> +;;; under the terms of the GNU General Public License as published by

> +;;; the Free Software Foundation; either version 3 of the License, or (at

> +;;; your option) any later version.

> +;;;

> +;;; GNU Guix is distributed in the hope that it will be useful, but

> +;;; WITHOUT ANY WARRANTY; without even the implied warranty of

> +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

> +;;; GNU General Public License for more details.

> +;;;

> +;;; You should have received a copy of the GNU General Public License

> +;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.

> +

> +(define-module (gnu packages simulation)

> + #:use-module (gnu packages)

> + #:use-module (gnu packages base)

> + #:use-module (gnu packages bash)

> + #:use-module (gnu packages bison)

> + #:use-module (gnu packages boost)

> + #:use-module (gnu packages compression)

> + #:use-module (gnu packages flex)

> + #:use-module (gnu packages gettext)

> + #:use-module (gnu packages gcc)

> + #:use-module (gnu packages gl)

> + #:use-module (gnu packages graphics)

> + #:use-module (gnu packages gtk)

> + #:use-module (gnu packages linux)

> + #:use-module (gnu packages m4)

> + #:use-module (gnu packages maths)

> + #:use-module (gnu packages mpi)

> + #:use-module (gnu packages multiprecision)

> + #:use-module (gnu packages ncurses)

> + #:use-module (gnu packages readline)

> + #:use-module (gnu packages tls)

> + #:use-module (gnu packages version-control)

> + #:use-module (gnu packages xml)

> + #:use-module (gnu packages xorg)

> + #:use-module (guix download)

> + #:use-module (guix build utils)

> + #:use-module (guix build-system gnu)

> + #:use-module ((guix licenses) #:prefix license:)

> + #:use-module (guix packages)

> + #:use-module (guix utils)

> + #:use-module (ice-9 ftw)

> + #:use-module (ice-9 regex)

> + #:use-module (srfi srfi-1))

> +

> +(define-public openfoam

> + (package

> + (name "openfoam")

> + (version "4.1")

> + (source

> + (origin

> + (method url-fetch)

> + (uri (string-append

> + "http://dl.openfoam.org/source/"

> + (string-replace-substring version "." "-")))

> + (file-name (string-append name "-" version ".tar.gz"))

> + (sha256

> + (base32 "1hgh2kw7fqv4bfachhbjhw16v8j35jbv6s576fmz4ka2q4ks4wg3"))

> + (patches (search-patches "openfoam-cleanup.patch"))

> + (modules '((guix build utils)))))

> + (build-system gnu-build-system)

> + (native-inputs

> + `(("bison" ,bison)))

> + (propagated-inputs

> + `(("boost" ,boost)

> + ("cgal" ,cgal)

> + ("flex" ,flex)

> + ("git" ,git)

> + ("gmp" ,gmp)

> + ("gzip" ,gzip)

> + ("gnuplot" ,gnuplot)

> + ("libxt" ,libxt)

> + ("metis" ,metis)

> + ("mpfr" ,mpfr)

> + ("ncurses" ,ncurses)

> + ("openmpi" ,openmpi)

> + ("readline" ,readline)

> + ("scotch" ,pt-scotch)

> + ("zlib" ,zlib)))

> + (arguments

> + `(;; executable files and shared libraries are located in the 'platforms'

> + ;; subdirectory

> + #:strip-directories (list (string-append

> + "OpenFOAM-" ,version

> + "/platforms/linux64GccDPInt32Opt/bin")

> + (string-append

> + "OpenFOAM-" ,version

> + "/platforms/linux64GccDPInt32Opt/lib"))

> + ;; '#:elf-directories' is not recognised here so skip validation phase

> + #:validate-runpath? #f

> + #:phases (modify-phases %standard-phases

> + (add-after 'unpack 'rename-build-directory

> + (lambda _

> + (use-modules (ice-9 ftw))

> + (use-modules (ice-9 regex))

> + (chdir "..")

> + ;; use 'OpenFOAM-version' convention to match path name

> + ;; expectations in the build phase

> + (let ((unpack-dir (string-append

> + (getcwd) "/"

> + (list-ref (scandir (getcwd) (lambda (name)

> + (string-match "^OpenFOAM" name))) 0)))

> + (build-dir (string-append

> + (getcwd) "/OpenFOAM-" ,version)))

> + ;; re-name build directory

> + (rename-file unpack-dir build-dir)

> + ;; move to build directory

> + (chdir (basename build-dir)))))

> + (add-after 'patch-source-shebangs 'set-environment-variables

> + (lambda _

> + (let ((libraries '("boost" "cgal" "gmp" "metis" "mpfr" "scotch")))

> + ;; set variables to define store paths

> + (for-each (lambda (library)

> + (setenv (string-append

> + (string-upcase library) "_ROOT")

> + (assoc-ref %build-inputs library))) libraries))

> + ;; set variables to define package versions

> + (setenv "SCOTCHVERSION" ,(package-version scotch))

> + (setenv "METISVERSION" ,(package-version metis))))

> + (delete 'configure) ; no configure phase

> + (delete 'patch-generated-file-shebangs) ; no generated files

> + (replace 'build

> + (lambda _

> + ;; compile OpenFOAM libraries and applications

> + (zero? (system (format #f

> + "source ./etc/bas

> Hello Paul,

>

> Thank you for the patch!

>

>

>Hello Guix,

>Thank you Marius and Eric for your reviews and comments.

>I have been working through the changes and updating the patch.

> However, in the process of rebasing I have noticed a change in Guix

>that impacts on the OpenFOAM definition.  Specifically, a recent commit

>(26599d6) has changed the definition of the scotch package so that it

>now uses 64bit integers.  In a nutshell, this causes a build failure in

>OpenFOAM.

>In OpenFOAM, there is a variable to specify the size of the integer

>values (32bit or 64bit).  This single variable is used by both metis

>and scotch, meaning that they both have to use 32bit integers or both

>use 64bit integers.  At present, Guix offers a 64bit scotch and a 32bit

>metis.

>A straightforward solution would be to add the extra packages, a 32bit

>scotch and/or a 64bit metis.  For scotch, that would be the same

>definition, except for the 'INTSIZE64' line.  For metis, that would

>involve an edit of 'metis.h', setting IDXTYPEWIDTH and REALTYPEWIDTH to

>64.

>Would you prefer this to be the subject of a separate patch, or

>included in the OpenFOAM patch?  There is also a question about how to

>name the packages; scotch and scotch32, for example, or scotch and

>scotch-64int etc.

>Best regards,

>Paul

>On Mon, 2017-08-14 at 21:49 -0500, Eric Bavier wrote:

>> Hello Paul,

>>

>> Thank you for the patch!

>>

>>

> For metis this might mean a build phase that patches metis.h's

> IDXTYPEWIDTH macro appropriately for the target system. 

> To stick with the OpenFOAM default a 32bit version of scotch/pt-scotch

> would be needed.  This would mean either reverting commit 26599d6, or

> introducing a new scotch32 package, the same as the previous

> definition, guaranteed to use 32bit integers.

> I think we should introduce a “scotch32” variant (with a clear

> explanation of what the “32” means).

> A method of implementing this would be for 'scotch32' to inherit the

> 'scotch' definition, replacing the configure phase with a similar

> section specifying INTSIZE32 instead of INTSIZE64.  This would be

> similar to the Debian approach, in which a different Makefile.inc is

> used for 32-bit and 64-bit integers.

>

> A new package 'pt-scotch32' would then be the same as 'pt-scotch' but

> inherit from 'scotch32' instead of 'scotch'.

>

> Any comments?

> This sounds like the right approach to me (you could even omit

> ‘pt-scotch32’ as a first stab if you don’t need it for Openfoam.)

>> +- Field<scalar> processorWeights;

>> ++ Field<floatScalar> processorWeights;

>

>This seems unrelated to unbundling :) Is this a known issue?

>> + #:validate-runpath? #f

>

>I don't suppose it's easy to move everything up to the top store level,

>which is already in a versioned directory and would allow these phases

>to proceed normally?

>> + ;; define the FOAM_INST_DIR variable

>> + (list (search-path-specification

>> + (variable "FOAM_INST_DIR")

>> + (files '(".")))))

>

>...maybe by utilizing this variable? It would also be better to wrap

>the binaries with it, instead of depending on it being in a profile.

>> * gnu/packages/simulation.scm: New file

>

>Would this package not fit nicely in gnu/packages/engineering.scm?

>

> Would it be possible to follow a layout closer to what we usually do:

>

> Or perhaps there’s a middle ground we could find?  

>> Would it be possible to follow a layout closer to what we usually do:

>

> There are some advantages of keeping the standard OpenFOAM layout,

> different though it is.  Firstly, if it the layout remains upstream's

> responsibility it makes the Guix maintenance task simpler.  Secondly,

> OpenFOAM users will immediately recognise the standard structure.

>> Or perhaps there’s a middle ground we could find?  

>

> Possibly but we would need to think of a way to avoid version clashes.

>  

>

> One objective in packaging OpenFOAM for Guix is to allow users to have

> multiple versions of OpenFOAM installed at once.  This is a common

> Could we achieve this versatility using a Guix-like layout?  A possible

> problem might be executable files in version B clashing with executable

> files of the same name in version A, if they both share the

> $GUIX_PROFILE/bin directory.

> Does it address the use case you have in mind?

> Hi Ludo,

>

>

> > Does it address the use case you have in mind?

>

> Yes, I think that both the multiple-profile solution and the 'ad-hoc'

> environment will work for Guix/OpenFOAM.

>

> The traditional method of installing multiple OpenFOAM versions is to

> install to a common $FOAM_INST_DIR directory.  However, as you point

> out, this is not strictly necessary and does not provide any

> advantage

> in the Guix system.

>

> So, continuing the 'middle road' line of thought, the 'install-dir'

> variable would be modified to add a '/lib' element:

>

> -                                %output "/OpenFOAM-" ,version)))

> +                                %output "/OpenFOAM-" ,version

> "/lib")))

>

> You suggest adding a link between bin and lib/OpenFOAM-

> 4.1/platforms/linux64GccDPInt32Opt/bin.  What would be the best way

> to

> add this to the package definition?

>

> There could also be a link between lib and lib/OpenFOAM-

> 4.1/platforms/linux64GccDPInt32Opt/lib.

>

> The links would allow the runpaths to be validated.  So;

>

> -       #:validate-runpath? #f ; '#:elf-directories' is not

> recognised

> here

>

> The FOAM_INST_DIR variable would need to be updated:

>

> -            (files '(".")))))

>  +          (files '("./lib")))))

>

> WDYT?>

>> Does it address the use case you have in mind?

>

> Yes, I think that both the multiple-profile solution and the 'ad-hoc'

> environment will work for Guix/OpenFOAM.  

> So, continuing the 'middle road' line of thought, the 'install-dir'

> variable would be modified to add a '/lib' element:

>

> -                                %output "/OpenFOAM-" ,version)))

> +                                %output "/OpenFOAM-" ,version

> "/lib")))

> You suggest adding a link between bin and lib/OpenFOAM-

> 4.1/platforms/linux64GccDPInt32Opt/bin.  What would be the best way to

> add this to the package definition?  

> There could also be a link between lib and lib/OpenFOAM-

> 4.1/platforms/linux64GccDPInt32Opt/lib.

> The links would allow the runpaths to be validated.  So; 

>

> -       #:validate-runpath? #f ; '#:elf-directories' is not recognised

> here

> The FOAM_INST_DIR variable would need to be updated:

>

> -            (files '(".")))))

>  +          (files '("./lib")))))

> It seems to me that if using Guix's profiles and environments, we could entirely do without OpenFOAM's installation directories and simply install into a standard bin/lib structure. Just install libraries into (string-append %output "/lib") and the binaries into (string-append %output "/bin").

> Hi Eric,

>

> Eric Bavier <ericbavier@centurylink.net> skribis:

>

> >

> > It seems to me that if using Guix's profiles and environments, we

> > could entirely do without OpenFOAM's installation directories and

> > simply install into a standard bin/lib structure.  Just install

> > libraries into (string-append %output "/lib") and the binaries into

> > (string-append %output "/bin").

> Fair enough.  I guess the question is more whether (1) this would

> work

> :-), and (2) whether seasoned OpenFOAM users would be happy with

> this.

>

> WDYT, Paul?

>

> Ludo’.

> I think it is helpful to consider this question in two ways; thinking about the short term and the longer term. I think in the short term it is best to stick with the OpenFOAM-standard layout, modified in the 'middle-road' way suggested

> earlier. On top of the previous points made, there is an additional advantage to this approach in that the OpenFOAM-standard layout has been thoroughly tested in production use over many years.

>

> In the longer term I think it would be possible to develop a Guix-standard layout. I cannot see any reason why this would not work. However, with a large system such as OpenFOAM, this may not necessarily be an easy task. I see this

> as principally an upstream job, since they are the most knowledgeable people on the current layout and are best placed to deal with any subleties involved. With a working Guix package in place it will be a good time to contact

> upstream and discuss the merits of a new layout.

> Today I hope to finish the package definition. I have placed the tree under the 'lib' directory and this allows the 'validate-runpath' phase to run. The phase currently fails as ld-wrapper does not add the runpaths of the shared objects in

> the build tree. I plan to use patchelf to fix this.

> I would refrain from using PatchELF, if possible, by just passing

> -Wl,-rpath=DIR at link time, where DIR is the final library directory.

> I really dislike this FOAM_INST_DIR variable

> *gnu/packages/patches/openfoam-4.1-cleanup.patch: New file

> *gnu/packages/simulation.scm: New file

> *gnu/local.mk (GNU_SYSTEM_MODULES): Add module

> (dist_patch_DATA): Add patch