* [PATCH] gnu: Add openfoam
@ 2017-07-23 20:11 Paul Garlick
2017-07-25 9:02 ` Ludovic Courtès
0 siblings, 1 reply; 4+ messages in thread
From: Paul Garlick @ 2017-07-23 20:11 UTC (permalink / raw)
To: guix-devel; +Cc: Paul Garlick
* gnu/packages/maths.scm(openfoam): Add it
* gnu/packages/patches/openfoam-cleanup.patch: New file
* gnu/local.mk(dist_patch_DATA): Add patch
---
gnu/local.mk | 1 +
gnu/packages/maths.scm | 195 ++++++++++++++++++++
gnu/packages/patches/openfoam-cleanup.patch | 267 ++++++++++++++++++++++++++++
3 files changed, 463 insertions(+)
create mode 100644 gnu/packages/patches/openfoam-cleanup.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index 4b2bdfe37..a7c456c1d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -866,6 +866,7 @@ 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/maths.scm b/gnu/packages/maths.scm
index 88a46f8e9..9eaa606a3 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -47,7 +47,9 @@
#:use-module (guix build-system gnu)
#:use-module (guix build-system ocaml)
#:use-module (guix build-system r)
+ #:use-module (guix build-system trivial)
#:use-module (gnu packages algebra)
+ #:use-module (gnu packages bash)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
@@ -64,10 +66,12 @@
#:use-module (gnu packages gcc)
#:use-module (gnu packages gd)
#:use-module (gnu packages ghostscript)
+ #:use-module (gnu packages graphics)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages gtk)
#:use-module (gnu packages image)
#:use-module (gnu packages less)
+ #:use-module (gnu packages linux)
#:use-module (gnu packages lisp)
#:use-module (gnu packages logging)
#:use-module (gnu packages lua)
@@ -79,6 +83,7 @@
#:use-module (gnu packages m4)
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
+ #:use-module (gnu packages ncurses)
#:use-module (gnu packages netpbm)
#:use-module (gnu packages ocaml)
#:use-module (gnu packages pcre)
@@ -94,9 +99,11 @@
#:use-module (gnu packages texinfo)
#:use-module (gnu packages tex)
#:use-module (gnu packages tls)
+ #:use-module (gnu packages version-control)
#:use-module (gnu packages wxwidgets)
#:use-module (gnu packages xml)
#:use-module (gnu packages zip)
+ #:use-module (ice-9 ftw)
#:use-module (srfi srfi-1))
(define-public aris
@@ -1174,6 +1181,194 @@ modules is done either interactively using the graphical user interface or in
ASCII text files using Gmsh's own scripting language.")
(license license:gpl2+)))
+(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 trivial-build-system)
+ (inputs
+ `(("coreutils" ,(@ (gnu packages base) coreutils))
+ ("diffutils" ,(@ (gnu packages base) diffutils))
+ ("findutils" ,(@ (gnu packages base) findutils))
+ ("git" ,git)
+ ("grep" ,(@ (gnu packages base) grep))
+ ("ld-wrapper" ,((@ (gnu packages base) make-ld-wrapper)
+ "ld-wrapper"
+ #:binutils (@ (gnu packages base) binutils)))
+ ("linux-libre-headers" ,linux-libre-headers)
+ ("locales" ,(@ (gnu packages base) glibc-utf8-locales))
+ ("patch" ,(@ (gnu packages base) patch))
+ ("sed" ,(@ (gnu packages base) sed))
+ ("tar" ,(@ (gnu packages base) tar))
+ ("xz" ,xz)))
+ (native-inputs
+ `(("bash" ,bash)
+ ("bison" ,bison)))
+ (propagated-inputs
+ `(("binutils" ,(@ (gnu packages base) binutils))
+ ("boost" ,boost)
+ ("cgal" ,cgal)
+ ("flex" ,flex)
+ ("gcc" ,gcc)
+ ("glibc" ,(@ (gnu packages base) glibc))
+ ("gmp" ,gmp)
+ ("gzip" ,gzip)
+ ("gnuplot" ,gnuplot)
+ ("libxt" ,libxt)
+ ("make" ,(@ (gnu packages base) gnu-make))
+ ("metis" ,metis)
+ ("mpfr" ,mpfr)
+ ("ncurses" ,ncurses)
+ ("openmpi" ,openmpi)
+ ("readline" ,readline)
+ ("pt-scotch" ,pt-scotch)
+ ("scotch" ,scotch)
+ ("zlib" ,zlib)))
+ (arguments
+ `(#:modules ((guix build utils)
+ (ice-9 ftw)
+ (ice-9 regex))
+ #:builder (begin
+ (use-modules (guix build utils))
+ (use-modules (ice-9 ftw))
+ (use-modules (ice-9 regex))
+ (let* ((input-path (lambda (binary path)
+ (string-append
+ (assoc-ref %build-inputs binary)
+ path ":")))
+ (binaries '("bash" "ld-wrapper" "binutils"
+ "coreutils" "findutils" "flex" "git"
+ "gcc" "grep" "make" "openmpi" "sed"
+ "tar" "xz"))
+ (binary-directories (string-concatenate
+ (map-in-order (lambda (binary)
+ (input-path binary "/bin"))
+ binaries))))
+ ;; set PATH environment variable for unpacking and building
+ (setenv "PATH" (string-drop-right binary-directories 1))
+ ;; unpack source code
+ (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
+ )
+ (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 top level directory
+ (rename-file unpack-dir build-dir)
+ ;; move to top level directory
+ (chdir (basename build-dir))
+ ;; replace interpreter paths in scripts
+ (patch-shebang "Allwmake")
+ (for-each patch-shebang
+ (find-files "applications"
+ (format #f "(~a|~a|~a|~a)$"
+ "Allwmake" "Allwclean" "Allrun"
+ "ensightFoamReaderTest")))
+ (for-each patch-shebang
+ (find-files "bin"))
+ (for-each patch-shebang
+ (find-files "doc"
+ "(Allwmake|find-its)$"))
+ (for-each patch-shebang
+ (find-files "etc"))
+ (for-each patch-shebang
+ (find-files "src"
+ "(Allwmake|Allwclean|AllwmakeLnInclude)$"))
+ (for-each patch-shebang
+ (find-files "tutorials"
+ (format #f "(~a|~a|~a|~a|~a|~a|~a|~a|~a|~a|~a)$"
+ "Allclean" "Allmesh" "Allrun.*" "Alltest"
+ "makeMesh" "createGraph.*" "extractHeightData"
+ "patchifyObstacles" "sampleCone"
+ "externalSolver" "surfaceProcess.sh")))
+ (for-each patch-shebang
+ (find-files "wmake"))
+ )
+ (let ((install-dir (string-append
+ %output "/OpenFOAM-" ,version))
+ (libraries '("boost" "cgal" "flex" "glibc" "gmp"
+ "linux-libre-headers" "metis" "mpfr"
+ "pt-scotch" "readline" "scotch" "zlib")))
+ ;; set environment variables to define library versions
+ (setenv "SCOTCHVERSION" ,(package-version scotch))
+ (setenv "METISVERSION" ,(package-version metis))
+ ;; set environment variables to define library paths
+ (map (lambda (library)
+ (setenv (string-append
+ (string-upcase library) "_ROOT")
+ (assoc-ref %build-inputs library))) libraries)
+ (setenv "LIBRARY_PATH" (string-append
+ (getenv "GLIBC_ROOT") "/lib" ":"
+ (getenv "ZLIB_ROOT") "/lib"))
+ ;; set environment variables to define header paths
+ (setenv "CPATH" (string-append
+ (getenv "LINUX-LIBRE-HEADERS_ROOT")
+ "/include"))
+ (setenv "CPLUS_INCLUDE_PATH" (string-append
+ (getenv "METIS_ROOT") "/include" ":"
+ (getenv "FLEX_ROOT") "/include" ":"
+ (getenv "ZLIB_ROOT") "/include"))
+ ;; compile OpenFOAM libraries and applications
+ (system (format #f "source ./etc/bashrc && ./Allwmake -j~a"
+ (parallel-job-count)))
+ ;; update configuration files
+ (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"
+ "$CGAL_ROOT" "etc/config.sh/CGAL"))
+ (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"
+ "$BOOST_ROOT" "etc/config.sh/CGAL"))
+ (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"
+ "$METIS_ROOT" "etc/config.sh/metis"))
+ (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"
+ "$METISVERSION" "etc/config.sh/metis"))
+ (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"
+ "$SCOTCH_ROOT" "etc/config.sh/scotch"))
+ (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"
+ "$SCOTCHVERSION" "etc/config.sh/scotch"))
+ (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"
+ "$GMP_ROOT" "etc/config.sh/settings"))
+ (system (format #f "sed -i 's|~a|'~:*~s'|' ~a"
+ "$MPFR_ROOT" "etc/config.sh/settings"))
+ ;; set write permission on tutorial files
+ (system (format #f "chmod -R u+w ~a" "tutorials"))
+ ;; create install directory
+ (mkdir-p install-dir)
+ ;; move contents of build directory to install directory
+ (copy-recursively "." install-dir)
+ )
+ )
+ )
+ )
+ (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++. Discrete versions of governing equations such as the Navier-Stokes
+equations can be solved in integral form. OpenFOAM implements the Finite
+Volume Method for discretizing the spacial dimensions. Grids are accepted that
+define complex geometries in two- and three-dimensional domains. Grids may be
+unstructured in layout and may contain any combination of polyhedral cells.
+Large problems can be split into connected smaller problems for efficient
+solution on parallel systems")
+ (license license:gpl3+)
+ (home-page "https://openfoam.org")))
+
(define-public maxflow
(package
(name "maxflow")
diff --git a/gnu/packages/patches/openfoam-cleanup.patch b/gnu/packages/patches/openfoam-cleanup.patch
new file mode 100644
index 000000000..e7760b7a5
--- /dev/null
+++ b/gnu/packages/patches/openfoam-cleanup.patch
@@ -0,0 +1,267 @@
+# 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 [ -f $READLINE_ROOT/include/readline/readline.h ]
+ then
+ echo "Found <readline/readline.h> -- enabling readline support."
+ export COMP_FLAGS="-DHAS_READLINE"
+diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Make/options OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Make/options
+--- OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Make/options
++++ OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Make/options
+@@ -1,7 +1,9 @@
+ EXE_INC = \
+ -I$(LIB_SRC)/meshTools/lnInclude \
++ -I$(READLINE_ROOT)/include \
+ $(COMP_FLAGS)
+
+ EXE_LIBS = \
++ -L$(READLINE_ROOT)/lib \
+ -lmeshTools \
+ $(LINK_FLAGS)
+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
+@@ -3,10 +3,9 @@
+
+ EXE_INC = \
+ $(PFLAGS) $(PINC) \
+- -I$(SCOTCH_ROOT)/include \
++ -I$(PT-SCOTCH_ROOT)/include \
+ -I$(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 ${LINK_FLAGS} -lrt
++ -L$(PT-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 \
--
2.13.0
^ permalink raw reply related [flat|nested] 4+ messages in thread* Re: [PATCH] gnu: Add openfoam
2017-07-23 20:11 [PATCH] gnu: Add openfoam Paul Garlick
@ 2017-07-25 9:02 ` Ludovic Courtès
2017-07-28 16:01 ` Paul Garlick
0 siblings, 1 reply; 4+ messages in thread
From: Ludovic Courtès @ 2017-07-25 9:02 UTC (permalink / raw)
To: Paul Garlick; +Cc: guix-devel
Hello Paul,
Thanks for this patch!
Paul Garlick <pgarlick@tourbillion-technology.com> skribis:
> * gnu/packages/maths.scm(openfoam): Add it
> * gnu/packages/patches/openfoam-cleanup.patch: New file
> * gnu/local.mk(dist_patch_DATA): Add patch
I think it might make sense to create a new “simulation” module, and
eventually move OpenCascade there as well, WDYT?
Some comments:
> + (build-system trivial-build-system)
Did you consider using ‘gnu-build-system’? I think this would save
quite a few lines corresponding to the initial setup (set-paths, unpack,
patch-shebang, etc.), and also ensure that the final phases (strip,
compress-documentation, etc.) are run. In addition you wouldn’t need to
list all the usual build inputs (GCC, Coreutils, Make, etc.). WDYT?
> + )
> + )
> + )
> + )
Please listen to what ‘guix lint’ has to say about these. :-)
> + (native-search-paths
> + ;; define the FOAM_INST_DIR variable
> + (list (search-path-specification
> + (variable "FOAM_INST_DIR")
> + (files '(".")))))
My guess is that ‘FOAM_INST_DIR’ is not a search path (in the sense of a
colon-separated list of directories like ‘PATH’.)
What about wrapping the resulting binaries so that they have
‘FOAM_INST_DIR’ set to %output?
> diff --git a/gnu/packages/patches/openfoam-cleanup.patch b/gnu/packages/patches/openfoam-cleanup.patch
> new file mode 100644
> index 000000000..e7760b7a5
> --- /dev/null
> +++ b/gnu/packages/patches/openfoam-cleanup.patch
> @@ -0,0 +1,267 @@
> +# This patch removes all need for the ThirdParty files of OpenFOAM
Nice!
> +# 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 [ -f $READLINE_ROOT/include/readline/readline.h ]
You could make it “if true”, thereby avoiding the need to define
$READLINE_ROOT.
> +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Make/options
> ++++ OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Make/options
> +@@ -1,7 +1,9 @@
> + EXE_INC = \
> + -I$(LIB_SRC)/meshTools/lnInclude \
> ++ -I$(READLINE_ROOT)/include \
Likewise, ‘gnu-build-system’ will set C_INCLUDE_PATH appropriately so
this -I flag won’t be needed.
Could you send an updated patch to guix-patches@gnu.org, where it will
be visible in the patch tracker?
Thank you!
Ludo’.
^ permalink raw reply [flat|nested] 4+ messages in thread* Re: [PATCH] gnu: Add openfoam
2017-07-25 9:02 ` Ludovic Courtès
@ 2017-07-28 16:01 ` Paul Garlick
2017-08-01 12:18 ` Ludovic Courtès
0 siblings, 1 reply; 4+ messages in thread
From: Paul Garlick @ 2017-07-28 16:01 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix-devel
[-- Attachment #1: Type: text/plain, Size: 2711 bytes --]
Hello Ludo,
> I think it might make sense to create a new “simulation” module, and
> eventually move OpenCascade there as well, WDYT?
>
Sure. I will create a new module and put the OpenFOAM package
definition in there as the first one.
> Some comments:
>
>
> >
> > + (build-system trivial-build-system)
> >
>
>
> Did you consider using ‘gnu-build-system’? I think this would save
> quite a few lines corresponding to the initial setup (set-paths, unpack,
> patch-shebang, etc.), and also ensure that the final phases (strip,
> compress-documentation, etc.) are run. In addition you wouldn’t need to
> list all the usual build inputs (GCC, Coreutils, Make, etc.). WDYT?
>
I did consider both options, removing and modifying stages in the gnu-
build-system or starting from scratch with the trivial-build-system. I
can give the gnu-build-system option a go, reverting to the trivial-
build-system if the new attempt proves too troublesome.
One aspect I will need to investigate in the gnu-build-system is using
the "./Allwmake" command to trigger the build process. In OpenFOAM,
wmake is short for "wrapped-make" and the package has its own
configuration step. In brief, it has its own sequence and does not
follow the standard "./configure && make && make install" steps.
Using the trivial-build-system the patch-shebang section is indeed a
little extended. I found this was necessary to avoid a failure of the
patch-shebang command using a simple 'find-files "."' from top-level
directory. There is a scenario where sub-directories named '0', in the
'tutorials' directory, identified by the find-files command, being
passed to 'patch-shebang', which should only receive files, not
directories. This causes 'patch-shebang' to stop and the build fails.
> >
> > + )
> > + )
> > + )
> > + )
> >
>
>
> Please listen to what ‘guix lint’ has to say about these. :-)
>
Interestingly, 'guix lint' let me get away with this without making
comment. However, I shall condense things accordingly in the new
patch.
> What about wrapping the resulting binaries so that they have
> ‘FOAM_INST_DIR’ set to %output?
>
>
In fact, FOAM_INST_DIR is used in multiple places to navigate around
the installed files (not just the binaries), so I think this variable
may need to remain available as is.
>
> You could make it “if true”, thereby avoiding the need to define
> $READLINE_ROOT.
>
>
Could you elaborate on this idea a little? At the moment the test is
"if file exists".
> Could you send an updated patch to guix-patches@gnu.org, where it will
> , where it will
> be visible in the patch tracker?
>
>
>
Aha, a new system!
Best,
Paul.
[-- Attachment #2: Type: text/html, Size: 3542 bytes --]
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] gnu: Add openfoam
2017-07-28 16:01 ` Paul Garlick
@ 2017-08-01 12:18 ` Ludovic Courtès
0 siblings, 0 replies; 4+ messages in thread
From: Ludovic Courtès @ 2017-08-01 12:18 UTC (permalink / raw)
To: Paul Garlick; +Cc: guix-devel
Hi Paul,
Paul Garlick <pgarlick@tourbillion-technology.com> skribis:
>> I think it might make sense to create a new “simulation” module, and
>> eventually move OpenCascade there as well, WDYT?
>>
> Sure. I will create a new module and put the OpenFOAM package
> definition in there as the first one.
Sounds good.
>> Some comments:
>>
>>
>> >
>> > + (build-system trivial-build-system)
>> >
>
>>
>>
>> Did you consider using ‘gnu-build-system’? I think this would save
>> quite a few lines corresponding to the initial setup (set-paths, unpack,
>> patch-shebang, etc.), and also ensure that the final phases (strip,
>> compress-documentation, etc.) are run. In addition you wouldn’t need to
>> list all the usual build inputs (GCC, Coreutils, Make, etc.). WDYT?
>>
>
> I did consider both options, removing and modifying stages in the gnu-
> build-system or starting from scratch with the trivial-build-system. I
> can give the gnu-build-system option a go, reverting to the trivial-
> build-system if the new attempt proves too troublesome.
With ‘gnu-build-system’ you’ll have to replace/remove some of the
phases, but hopefully it’ll be less troublesome nonetheless.
> One aspect I will need to investigate in the gnu-build-system is using
> the "./Allwmake" command to trigger the build process. In OpenFOAM,
> wmake is short for "wrapped-make" and the package has its own
> configuration step. In brief, it has its own sequence and does not
> follow the standard "./configure && make && make install" steps.
> Using the trivial-build-system the patch-shebang section is indeed a
> little extended. I found this was necessary to avoid a failure of the
> patch-shebang command using a simple 'find-files "."' from top-level
> directory. There is a scenario where sub-directories named '0', in the
> 'tutorials' directory, identified by the find-files command, being
> passed to 'patch-shebang', which should only receive files, not
> directories. This causes 'patch-shebang' to stop and the build fails.
‘find-files’ excludes directories by default, so it’s a little
surprising. Anyway, we can surely find a way to work around the
problem.
>> >
>> > + )
>> > + )
>> > + )
>> > + )
>> >
>
>>
>>
>> Please listen to what ‘guix lint’ has to say about these. :-)
>>
>
> Interestingly, 'guix lint' let me get away with this without making
> comment. However, I shall condense things accordingly in the new
> patch.
Oh indeed, until now it would only scan 60 lines from the start of the
definition. Fixed!
>> What about wrapping the resulting binaries so that they have
>> ‘FOAM_INST_DIR’ set to %output?
>>
>>
>
> In fact, FOAM_INST_DIR is used in multiple places to navigate around
> the installed files (not just the binaries), so I think this variable
> may need to remain available as is.
OK, though it would be good to make it work out-of-the-box when
FOAM_INST_DIR is undefined.
>> You could make it “if true”, thereby avoiding the need to define
>> $READLINE_ROOT.
>>
>>
>
> Could you elaborate on this idea a little? At the moment the test is
> "if file exists".
I was thinking about doing something like this:
-if [ -f /usr/include/readline/readline.h ]
+if true
and thus we wouldn’t need to define READLINE_ROOT, IIUC.
HTH,
Ludo’.
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2017-08-01 12:18 UTC | newest]
Thread overview: 4+ messages (download: mbox.gz follow: Atom feed
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2017-07-23 20:11 [PATCH] gnu: Add openfoam Paul Garlick
2017-07-25 9:02 ` Ludovic Courtès
2017-07-28 16:01 ` Paul Garlick
2017-08-01 12:18 ` Ludovic Courtès
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