Changes between Initial Version and Version 1 of Software/OpenFOAM

Timestamp:

02/14/17 00:07:39 (7 years ago)

Author:

Jens Henrik Goebbert

Comment:

--

Software/OpenFOAM

@@ +1 @@
+'''NOTE: THIS IS A WORK IN PROGRESS'''
+
+= OpenFOAM - Build Instructions
+[[PageOutline]]
+
+
+'''OpenFOAM''' is free, open-source software for computational fluid dynamics.
+* [http://www.openfoam.org OpenFOAM Foundation]
+* [http://www.openfoam.com OpenCFD Ltd] - owner of the trademark OpenFOAM
+
+OpenFOAM releases are scheduled every six months in June and December.
+Releases designated OpenFOAM+ contain client-sponsored developments of which much has been transferred to, but not released in the OpenFOAM Foundation branch.
+
+== Preliminaries ==
+* Follow build instructions from here:
+  * http://www.openfoam.com/code/build-guide.php
+  * http://www.openfoam.org/download/git.php
+
+* There are, roughly, two components to OpenFOAM:
+  * the actual CFD code FOAM -- definitely to be compiled with ICC
+  * the GUI analysis tools, based on !ParaView (using the Qt GUI toolkit)
+
+* All OpenFOAM applications do parallel communication through the Pstream library only.\\ So using any underlying message passing library (MPI, etc.) is just a matter of replacing Pstream. [https://openfoamwiki.net/index.php/Installation/HowTo_Pstream more...]
+
+* Some of the !ThirdParty packages need to be built first. These third party sources are required, but are not bundled. The source tarballs could be expanded in the !ThirdParty-${VERSION} directory, but we use installed modules instead.
+  * Boost - 1.61.0 works
+  * CGAL
+    * GMP - 6.1.1 works
+    * MPFR - 3.1.3 works
+  * METIS - 5.1.0 is expected [http://glaros.dtc.umn.edu/gkhome/metis/metis/download METIS Official Website]
+
+{{{ #!sh
+### set env. variables we will use
+
+VERSION=3.0.1
+INST_DIR=/homeb/zam/${USER}/my_OpenFOAM
+
+mkdir $INST_DIR
+cd $INST_DIR
+}}}
+
+== Download & Extract ==
+Source packages are available from the download section of the OpenFOAM website:
+     * http://www.openfoam.org/download/source.php
+     * https://github.com/OpenFOAM
+
+The source code must be unpacked into the top-level directory of the final installation.
+
+{{{ #!sh
+### download OpenFOAM
+
+wget https://downloads.sourceforge.net/project/foam/foam/${VERSION}/OpenFOAM-${VERSION}.tgz
+wget https://downloads.sourceforge.net/project/foam/foam/${VERSION}/ThirdParty-${VERSION}.tgz
+
+# extract OpenFOAM
+tar -xzf OpenFOAM-${VERSION}.tgz -C $INST_DIR
+tar -xzf ThirdParty-${VERSION}.tgz -C $INST_DIR
+}}}
+
+== Setup OpenFOAM ==
+
+=== Patch ===
+
+Patch $INST_DIR/OpenFOAM-${VERSION}/etc/bashrc
+{{{ #!sh
+### bashrc
+
++ foamInstall=${INST_DIR}
++ : ${WM_COMPILER:=Gcc}; export WM_COMPILER
++ : ${WM_MPLIB:=SYSTEMOPENMPI}; export WM_MPLIB
+}}}
+* Instead of setting variable in bashrc, they can be set via environment variables before you call bashrc later.
+  * {{{export FOAM_INST_DIR=...}}} overwrites foamInstall
+  * {{{export WM_COMPILER=...}}}, default is Gcc, should be set to **Icc**
+  * {{{export WM_MPLIB=...}}}, default is SYSTEMOPENMPI, should be set to **EASYBUILDMPI**
+
+Patch $INST_DIR/OpenFOAM-${VERSION}/etc/config/settings.sh
+{{{ #!sh
+### settings.sh
+Linux)
+...
+    x86_64)
+...
+        64)
+            WM_ARCH=linux64
+            export WM_COMPILER_LIB_ARCH=64
++           export WM_CC=${CC}
++           export WM_CXX=${CXX}
++           export WM_CFLAGS="${CFLAGS} -fPIC"
++           export WM_CXXFLAGS="${CXXFLAGS} -fPIC"
++           export WM_LDFLAGS=
+
+}}}
+{{{ #!sh
+### settings.sh
+
++ #unset MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN
+
++ EASYBUILDMPI)
++    export FOAM_MPI=mpi
++    ;;
+}}}
+
+Patch $INST_DIR/OpenFOAM-${VERSION}/wmake/rules
+{{{ #!sh
+### linux64Gcc/c, linux64Icc/c
++ cc        = ${MPICC}
+
+### linux64Gcc/c++, linux64Icc/c++
++ CC        = ${MPICXX} -std=c++0x -fp-trap=common -fp-model precise
+
+### linux64Gcc/cOpt, linux64Icc/cOpt
++ cOPT      = ${CFLAGS}
+                                 
+### linux64Gcc/c++Opt, linux64Icc/c++Opt
++ cOPT      = ${CXXFLAGS}
+}}}
+
+=== Set Environment ===
+
+The environment must be set up according to where the source code directories are located.
+{{{ #!sh
+VERSION=3.0.1
+INST_DIR=/homeb/zam/${USER}/my_OpenFOAM # must not end with a '/'
+cd $INST_DIR
+
+# load modules
+module --force purge
+module load Stages/Devel
+module load Intel/2017.0.098-GCC-5.4.0
+module load IntelMPI/2017.0.098
+module load flex/2.5.39 # flex 2.6.0 causes errors
+module load Boost/1.61.0-Intel-2017.0.098
+module load MPFR/3.1.5-Intel-2017.0.098
+module load GMP/6.1.2-Intel-2017.0.098
+module load CGAL/4.8.2-Intel-2017.0.098
+module load METIS/5.1.0-Intel-2017.0.098
+
+# configure environment
+export FOAM_INST_DIR=$INST_DIR
+export WM_COMPILER=Icc
+export WM_MPLIB=EASYBUILDMPI
+export MPICC=mpicc
+export MPICXX=mpiicpc
+export CC=icc
+export CXX=icpc
+export CFLAGS="-no-prec-div -O3 -xHost -fp-model precise -diag-disable 654 -diag-disable 1125"
+export CXXFLAGS="-O3 -xHost -fp-model precise -diag-disable 654 -diag-disable 1125 -DMPICH_SKIP_MPICXX"
+
+export WM_NCOMPPROCS=8  # parallel build
+export WM_LABEL_SIZE=32 # 32bit for labels/indices - relevant for METIS (if 64 needed patch METIS first)
+
+# load environment
+source OpenFOAM-${VERSION}/etc/bashrc
+foam
+foamSystemCheck
+}}}
+
+* build with Intel 2017.1.138: [[OpenFOAM/config_Intel-2017.1.138]]
+* build with Stage/2016a [[OpenFOAM/config_2016a]]
+* build with Stage/2016a + Score-P [[OpenFOAM/config_2016a_ScoreP]]
+
+== Setup !ThirdParty ==
+
+OpenFOAM has configs which set where it expects to find its "third party" packages.
+There are in {{{$FOAM_ETC/config/}}} as various shell scripts.
+
+The top-level ./Allwmake will build Scotch, but not CGAL, Boost, GMP, and MPFR.\\Those packages need to be built separately, and installed into the appropriate directory.
+
+=== CGAL ===
+Patch $INST_DIR/OpenFOAM-${VERSION}/etc/config/CGAL.sh
+{{{ #!sh
+### CGAL.sh
+
++ boost_version=$EBVERSIONBOOST
++ cgal_version=$EBVERSIONCGAL
+
++ export BOOST_ARCH_PATH=$EBROOTBOOST
++ export CGAL_ARCH_PATH=$EBROOTCGAL
+}}}
+* Boost -installed as module Boost/1.61.0-Intel-2017.0.098
+* GMP - installed as module GMP/6.1.2-Intel-2017.0.098
+* MPFR - installed as module MPFR/3.1.5-Intel-2017.0.098
+
+=== METIS ===
+Patch $INST_DIR/OpenFOAM-${VERSION}/etc/config/metis.sh
+{{{ #!sh
+# metis.sh
+
++ export METIS_ARCH_PATH=$EBROOTMETIS
+}}}
+{{{ #!sh
+# $WM_THIRD_PARTY_DIR/Allwmake
+
++ if [ -d "$METIS_ARCH_PATH" ] # if [ -d "$METIS_VERSION" ]
++ then
++    if [ -f $METIS_ARCH_PATH/include/metis.h \
++      -a -r $METIS_ARCH_PATH/lib/libmetis.so ]
++    then
++        cp $METIS_ARCH_PATH/lib/libmetis.so $FOAM_EXT_LIBBIN
++        echo "    metis header in $METIS_ARCH_PATH/include"
++        echo "    metis libs   in $FOAM_EXT_LIBBIN"
+}}}
+* ATTENTION: metis.h
+  * METIS library's IDXTYPEWIDTH  must fit to $WM_LABEL_SIZE       (for METIS/5.1.0-Intel-2017.0.098: IDXTYPEWIDTH=32)
+  * METIS library's REALTYPEWIDTH must fit to $WM_PRECISION_OPTION (for METIS/5.1.0-Intel-2017.0.098: REALTYPEWIDTH=64)
+
+
+=== Scotch ===
+Scotch decomposition which requires no geometric input from the user and attempts to minimise the number of processor boundaries.
+
+Patch $WM_THIRD_PARTY_DIR/etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM-64Int32
+{{{ #!sh
+# scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM-64Int32
++ AR             = ${CC}
++ CCS            = ${CC}
++ CCP            = ${MPICC}
++ CCD            = ${MPICC}
++ CFLAGS         = -O3 -xHost -fp-model precise -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict
+}}}
+
+Copy source to required location.
+{{{ #!sh
+
+source $INST_DIR/OpenFOAM-${VERSION}/etc/config/scotch.sh 
+
+mkdir -p $SCOTCH_ARCH_PATH
+cp -a $WM_THIRD_PARTY_DIR/scotch_6.0.3/* $SCOTCH_ARCH_PATH
+}}}
+
+
+== Build OpenFOAM ==
+{{{ #!sh
+
+# cd $WM_PROJECT_DIR
+foam
+
+# clean if this is a rebuild
+wclean all
+
+# build wmake
+./wmake/makeWmake
+
+# build OpenFOAM (except Qt & ParaView) 
+./Allwmake
+}}}
+
+== Build Tools ==
+
+=== Qt ===
+The '''<tt>makeQt</tt>''' script seems to fail. Run it once till it fails. Then, cd to the qt build directory and modify <tt>config.status</tt> so that gcc and g++ are used. Also add CFLAGS and CXXFLAGS as needed.
+
+Build and install:
+     ./config.status
+     make -j 8
+     make install
+
+=== ParaView ===
+* Must be built from source because OpenFOAM has !ParaView modules that need to be built, requiring !ParaView headers. 
+* Read https://github.com/OpenFOAM/ThirdParty-dev/blob/master/README.org
+** In particular: <blockquote>The ParaView-4.3.1/4.4.0 source-pack provided by KitWare will not build and install correctly without a minor correction: lines 653-656 must be removed or commented from file ThirdParty-dev/ParaView-4.?.?/Qt/Components/CMakeLists.txt after unpacking and renaming the ParaView-4.?.? directory. This is because the file ui_pqExportStateWizard.h referred to in the lines 653-656 … does not exist and cannot be installed causing the build and installation to fail.</blockquote>
+** And the fix to <tt>VTK/IO/Geometry/vtkSTLReader.cxx</tt>
+
+== References ==
+* flex 2.6.0
+  * 2.6.0 causes errors: undefined reference to `yyFlexLexer::yywrap()'
+  * https://www.cfd-online.com/Forums/openfoam-installation/163986-building-openfoam-3-0-archlinux.html
+* -fp-model precise
+  * Disables optimizations that are not value-safe on floating-point data.
+  * https://www.nccs.nasa.gov/images/FloatingPoint_consistency.pdf
+* -DMPICH_SKIP_MPICXX
+  * https://www.cfd-online.com/Forums/openfoam/90965-errors-building-openfoam-2-0-0-icc-sgi-mpt-2-03-a.html#post317630 
+  * https://sourceforge.net/p/openfoam-extend/foam-extend-3.1/ci/90bbdada8b322e227528311326783a80a1e26b35/#diff-4
+* -diag-disable 654
+  * hide warning !#654: 
+* -diag-disable 1125
+  * hide warning !#1125: function "..." is hidden by "..." -- virtual function override intended?