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easyconfigs-it4i/o/OpenFOAM/OpenFOAM-7-cleanup.patch
Lukáš Krupčík d4acbfbf7c new file: a/ASE/ASE-3.18.1-Py-3.6.eb 
new file:   a/Arrow/Arrow-0.15.0-intel-2018a-Py-3.6.eb
	new file:   b/BoltzTraP2/BoltzTraP2-19.7.3-Py-3.6.eb
	new file:   b/Boost/Boost-1.70.0-intel-2017c.eb
	new file:   b/Boost/Boost-1.70.0-intel-2018a-Py-3.6.eb
	new file:   b/Boost/Boost-1.70.0-intel-2018a.eb
	new file:   c/CIF2Cell/CIF2Cell-2.0.0a1-Py-3.6.eb
	new file:   c/click/click-7.0-Py-3.6.eb
	new file:   n/natsort/natsort-6.0.0-Py-3.6.eb
	new file:   o/OpenFOAM/OpenFOAM-7-cleanup.patch
	new file:   o/OpenFOAM/OpenFOAM-7-foss-2018a.eb
	new file:   o/OpenFOAM/OpenFOAM-7-intel-2017a.eb
	new file:   o/osm2pgsql/osm2pgsql-1.0.0-intel-2017c.eb
	new file:   p/PyCifRW/PyCifRW-4.4-Py-3.6.eb
	new file:   s/spglib/spglib-1.14.1-Py-3.6.eb
	deleted:    s/spglib-python/spglib-python-1.10.2.4-Py-3.6.eb
2019-10-23 12:02:58 +02:00

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# This patch removes all need for the ThirdParty files of OpenFOAM:
# we use EB dependencies for everything. It adjusts the paths, variables, etc
# We also let the install dir, compiler, etc be set by EB.
# Lastly, we also fix a small compile issue in 'ptscotchDecomp.C'
# by Jiri Furst <jiri.furst@gmail.com>, based on patch for OpenFOAM 5.0 and 4.1 by
# Kennet Hoste (HPC-UGent) and Ward Poelmans <wpoely86@gmail.com>
diff -ru OpenFOAM-6-version-6.orig/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-6-version-6/applications/utilities/mesh/manipulation/setSet/Allwmake
--- OpenFOAM-6-version-6.orig/applications/utilities/mesh/manipulation/setSet/Allwmake 2018-07-09 18:01:02.000000000 +0200
+++ OpenFOAM-6-version-6/applications/utilities/mesh/manipulation/setSet/Allwmake 2018-08-14 11:18:48.188975085 +0200
@@ -7,19 +7,12 @@
unset COMP_FLAGS LINK_FLAGS
# Use readline if available
-if [ -f /usr/include/readline/readline.h ]
+if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ]
then
echo " found <readline/readline.h> -- enabling readline support."
export COMP_FLAGS="-DHAS_READLINE"
- # readline may require ncurses
- if [ -f /usr/include/ncurses/ncurses.h ]
- then
- echo " found <ncurses/ncurses.h> -- maybe required by readline."
- export LINK_FLAGS="-lreadline -lncurses"
- else
- export LINK_FLAGS="-lreadline"
- fi
+ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses"
fi
wmake $targetType
diff -ru OpenFOAM-6-version-6.orig/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-6-version-6/applications/utilities/postProcessing/graphics/PVReaders/Allwmake
--- OpenFOAM-6-version-6.orig/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2018-07-09 18:01:02.000000000 +0200
+++ OpenFOAM-6-version-6/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2018-08-14 11:21:25.280419729 +0200
@@ -14,8 +14,8 @@
}
# ensure CMake gets the correct C/C++ compilers
- [ -n "$WM_CC" ] && export CC="$WM_CC"
- [ -n "$WM_CXX" ] && export CXX="$WM_CXX"
+# [ -n "$WM_CC" ] && export CC="$WM_CC"
+# [ -n "$WM_CXX" ] && export CXX="$WM_CXX"
wmake $targetType vtkPVblockMesh
wmake $targetType vtkPVFoam
diff -ru OpenFOAM-6-version-6.orig/etc/bashrc OpenFOAM-6-version-6/etc/bashrc
--- OpenFOAM-6-version-6.orig/etc/bashrc 2018-07-09 18:01:02.000000000 +0200
+++ OpenFOAM-6-version-6/etc/bashrc 2018-08-14 11:29:14.168761602 +0200
@@ -43,8 +43,9 @@
# Please set to the appropriate path if the default is not correct.
#
[ "$BASH" -o "$ZSH_NAME" ] && \
-export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \
-export FOAM_INST_DIR=$HOME/$WM_PROJECT
+#export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \
+#export FOAM_INST_DIR=$HOME/$WM_PROJECT
+# For Easybuild: set by the module
# export FOAM_INST_DIR=~$WM_PROJECT
# export FOAM_INST_DIR=/opt/$WM_PROJECT
# export FOAM_INST_DIR=/usr/local/$WM_PROJECT
diff -ru OpenFOAM-6-version-6.orig/etc/config.sh/CGAL OpenFOAM-6-version-6/etc/config.sh/CGAL
--- OpenFOAM-6-version-6.orig/etc/config.sh/CGAL 2018-07-09 18:01:02.000000000 +0200
+++ OpenFOAM-6-version-6/etc/config.sh/CGAL 2018-08-14 11:35:21.214457132 +0200
@@ -35,33 +35,8 @@
#
#------------------------------------------------------------------------------
-boost_version=boost-system
-cgal_version=cgal-system
-#cgal_version=CGAL-4.10
-
-thirdPartyPath=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER
-
-if [ "$boost_version" != "boost-system" ]
-then
- export BOOST_ARCH_PATH=$thirdPartyPath/$boost_version
- if [ -d "$BOOST_ARCH_PATH" ]
- then
- _foamAddLib $BOOST_ARCH_PATH/lib
- fi
-else
- unset BOOST_ARCH_PATH
-fi
-
-if [ "$cgal_version" != "cgal-system" ]
-then
- export CGAL_ARCH_PATH=$thirdPartyPath/$cgal_version
- if [ -d "$CGAL_ARCH_PATH" ]
- then
- _foamAddLib $CGAL_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH
- fi
-else
- unset CGAL_ARCH_PATH
-fi
+export CGAL_ARCH_PATH=$EBROOTCGAL
+export BOOST_ARCH_PATH=$EBROOTBOOST
if [ "$FOAM_VERBOSE" -a "$PS1" ]
then
@@ -70,6 +45,4 @@
echo " $cgal_version at $CGAL_ARCH_PATH" 1>&2
fi
-unset thirdPartyPath
-
#------------------------------------------------------------------------------
diff -ru OpenFOAM-6-version-6.orig/etc/config.sh/gperftools OpenFOAM-6-version-6/etc/config.sh/gperftools
--- OpenFOAM-6-version-6.orig/etc/config.sh/gperftools 2018-07-09 18:01:02.000000000 +0200
+++ OpenFOAM-6-version-6/etc/config.sh/gperftools 2018-08-14 11:37:07.582078984 +0200
@@ -29,13 +29,7 @@
#
#------------------------------------------------------------------------------
-version=svn
-gperftools_install=$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:$LD_LIBRARY_PATH
+GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS
+GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS
#------------------------------------------------------------------------------
diff -ru OpenFOAM-6-version-6.orig/etc/config.sh/metis OpenFOAM-6-version-6/etc/config.sh/metis
--- OpenFOAM-6-version-6.orig/etc/config.sh/metis 2018-07-09 18:01:02.000000000 +0200
+++ OpenFOAM-6-version-6/etc/config.sh/metis 2018-08-14 11:39:06.204657280 +0200
@@ -34,7 +34,7 @@
#
#------------------------------------------------------------------------------
-export METIS_VERSION=metis-5.1.0
-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION
+export METIS_VERSION=metis-$EBVERSIONMETIS
+export METIS_ARCH_PATH=$EBROOTMETIS
#------------------------------------------------------------------------------
diff -ru OpenFOAM-6-version-6.orig/etc/config.sh/mpi OpenFOAM-6-version-6/etc/config.sh/mpi
--- OpenFOAM-6-version-6.orig/etc/config.sh/mpi 2018-07-09 18:01:02.000000000 +0200
+++ OpenFOAM-6-version-6/etc/config.sh/mpi 2018-08-14 11:45:15.876343167 +0200
@@ -257,6 +257,9 @@
_foamAddPath $MPI_ARCH_PATH/bin64
_foamAddLib $MPI_ARCH_PATH/lib64
;;
+EASYBUILDMPI)
+ export FOAM_MPI=mpi
+ ;;
*)
export FOAM_MPI=dummy
;;
diff -ru OpenFOAM-6-version-6.orig/etc/config.sh/settings OpenFOAM-6-version-6/etc/config.sh/settings
--- OpenFOAM-6-version-6.orig/etc/config.sh/settings 2018-07-09 18:01:02.000000000 +0200
+++ OpenFOAM-6-version-6/etc/config.sh/settings 2018-08-14 11:53:15.092639797 +0200
@@ -61,11 +61,11 @@
64)
WM_ARCH=linux64
export WM_COMPILER_LIB_ARCH=64
- export WM_CC='gcc'
- export WM_CXX='g++'
- export WM_CFLAGS='-m64 -fPIC'
- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x'
- export WM_LDFLAGS='-m64'
+ export WM_CC=$CC
+ export WM_CXX=$CXX
+ export WM_CFLAGS=$CFLAGS
+ export WM_CXXFLAGS=$CXXFLAGS
+ export WM_LDFLAGS=$LDFLAGS
;;
*)
echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\
diff -ru OpenFOAM-6-version-6.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-6-version-6/src/parallel/decompose/ptscotchDecomp/Make/options
--- OpenFOAM-6-version-6.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2018-07-09 18:01:02.000000000 +0200
+++ OpenFOAM-6-version-6/src/parallel/decompose/ptscotchDecomp/Make/options 2018-08-14 11:55:27.323169812 +0200
@@ -5,14 +5,7 @@
$(PFLAGS) $(PINC) \
-I$(FOAM_SRC)/Pstream/mpi/lnInclude \
-I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \
- -I$(SCOTCH_ARCH_PATH)/include \
- -I/usr/include/scotch \
-I../decompositionMethods/lnInclude
LIB_LIBS = \
- -L$(SCOTCH_ARCH_PATH)/lib \
- -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \
- -lptscotch \
- -lptscotcherrexit \
- -lscotch \
- -lrt
+ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt
diff -ru OpenFOAM-6-version-6.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-6-version-6/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C
--- OpenFOAM-6-version-6.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2018-07-09 18:01:02.000000000 +0200
+++ OpenFOAM-6-version-6/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2018-08-14 11:57:24.057754914 +0200
@@ -31,10 +31,11 @@
#include "SubField.H"
#include "PstreamGlobals.H"
+#include <mpi.h>
+
extern "C"
{
#include <stdio.h>
- #include <mpi.h>
#include "ptscotch.h"
}
diff -ru OpenFOAM-6-version-6.orig/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-6-version-6/src/parallel/decompose/scotchDecomp/Make/options
--- OpenFOAM-6-version-6.orig/src/parallel/decompose/scotchDecomp/Make/options 2018-07-09 18:01:02.000000000 +0200
+++ OpenFOAM-6-version-6/src/parallel/decompose/scotchDecomp/Make/options 2018-08-14 11:58:42.345476668 +0200
@@ -8,7 +8,6 @@
EXE_INC = \
$(PFLAGS) $(PINC) \
-I$(SCOTCH_ARCH_PATH)/include \
- -I/usr/include/scotch \
-I../decompositionMethods/lnInclude
LIB_LIBS = \
--- OpenFOAM-7-version-7/etc/config.sh/paraview.orig 2019-07-05 15:06:58.000000000 +0200
+++ OpenFOAM-7-version-7/etc/config.sh/paraview 2019-10-21 10:05:22.064411589 +0200
@@ -41,21 +41,6 @@
) \
&& PATH="$cleaned"
-# Determine the cmake to be used
-unset CMAKE_HOME
-for cmake in cmake-3.2.1 cmake-2.8.12.1 cmake-2.8.8 cmake-2.8.4 cmake-2.8.3 \
- cmake-2.8.1 cmake-3.9.0
-do
- cmake=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cmake
- if [ -r $cmake ]
- then
- export CMAKE_HOME=$cmake
- export CMAKE_ROOT=$cmake
- export PATH=$CMAKE_HOME/bin:$PATH
- break
- fi
-done
-
#- ParaView version, automatically determine major version
#export ParaView_VERSION=3.12.0
@@ -67,7 +52,8 @@
#export ParaView_VERSION=5.0.1
#export ParaView_VERSION=5.4.0
#export ParaView_VERSION=5.5.0
-export ParaView_VERSION=5.6.0
+#export ParaView_VERSION=5.6.0
+export ParaView_VERSION=$EBVERSIONPARAVIEW
export ParaView_MAJOR=detect
#export ParaView_GL=system
@@ -110,21 +96,15 @@
paraviewInstDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION
paraviewArchName=ParaView-$ParaView_VERSION
-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName
+export ParaView_DIR=$EBROOTPARAVIEW
# Set paths if binaries or source are present
if [ -r $ParaView_DIR -o -r $paraviewInstDir ]
then
export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR
- if [ ! -d $ParaView_INCLUDE_DIR -a -d $ParaView_DIR/include/paraview-3.0 ]
- then
- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-3.0
- fi
ParaView_LIB_DIR=$ParaView_DIR/lib/paraview-$ParaView_MAJOR
- export PATH=$ParaView_DIR/bin:$PATH
- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH
export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR
if [ "$FOAM_VERBOSE" -a "$PS1" ]
@@ -137,16 +117,16 @@
fi
# Add in python libraries if required
- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping
- if [ -r $paraviewPython ]
- then
- if [ "$PYTHONPATH" ]
- then
- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR
- else
- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR
- fi
- fi
+# paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping
+# if [ -r $paraviewPython ]
+# then
+# if [ "$PYTHONPATH" ]
+# then
+# export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR
+# else
+# export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR
+# fi
+# fi
[ "$ParaView_GL" = mesa ] && alias paraview="paraview --mesa"
else
--- OpenFOAM-7-version-7/etc/config.sh/scotch.orig 2019-10-21 10:09:47.397150088 +0200
+++ OpenFOAM-7-version-7/etc/config.sh/scotch 2019-10-21 10:11:22.047494052 +0200
@@ -37,7 +37,7 @@
#
#------------------------------------------------------------------------------
-export SCOTCH_VERSION=scotch_6.0.6
-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_$EBVERSIONSCOTCH
+export SCOTCH_ARCH_PATH=$EBROOTSCOTCH
#------------------------------------------------------------------------------
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