Category Archives: Elmer

Elmer is a FEM program: http://www.csc.fi/english/pages/elmer

Elmer tetgen plugin and more

tetgen plugin in
module load tetgen/1.4.3 qt/4.8.6
export ELMER_HOME=/opt/elmer/7
qmake
make -j4
make install

elmer solvers
#build elmer solvers
export FC=gfortran
export F77=gfortran

#Optimization:
export CFLAGS=”-O3″
export FCFLAGS=”-O3″
export FFLAGS=”-O3″
export CXXFLAGS=”-O3″

export NPROCS=4
#export USE_OWN_MATHLIBS=”yes”
export LIBS=-lpthread
buildtools/compile.sh

mathlibs
export LIBS=-lpthread
./configure –prefix=/opt/elmer/7 –exec-prefix=/opt/elmer/7 –oldincludedir=/opt/elmer/7 –with-mpi=yes –with-mpi-inc-dir=/usr/include/openmpi-x86_64 –with-mpi-lib-dir=/usr/lib64/openmpi/lib/openmpi/

compile elmerfem/fem
module load openfoam/2.3.x
cd fem
./configure –prefix=/opt/elmer/7 –exec-prefix=/opt/elmer/7
compile post
change in configure file: acx_tcltk_tcl_h_locs=”$acx_tcltk_tcl_h_locs /opt/tcltk/8.5.13/include /usr/include /usr/local/include /include /usr/swf/include /sw/include /sw/usr/include /really/weird/place /ok/I/quit”
./configure –prefix=/opt/elmer/7 –exec-prefix=/opt/elmer/7
make -j4;make install

ElmerGUI standalone installation on CentOS

elmergui dir from elmerfem trunk (http://www.csc.fi/english/pages/elmer)
edit ElmerGUI.pri
module load qt/4.8.6 vtk/5.10.1 tbb/3.0-018
qmake
make
make install

module file /etc/modulefiles/elmer/7

#%Module1.0#########################################
##
## Discretizer AB modulefile
##
##
setenv ELMER_HOME /opt/elmer/7
setenv ELMERGUI_HOME /opt/elmer/7/bin
setenv ELMER_POST_HOME /opt/elmer/7/share/elmerpost
prepend-path PATH /opt/elmer/7/bin
prepend-path LD_LIBRARY_PATH /opt/elmer/7/lib

module load qwt/6.0.2 vtk/5.10.1 occ/6.5.4 tbb/3.0-018 openfoam/2.3.x

Elmergui.pri file: ElmerGUI.pri

PythonQT 2.1 standalone install on CentOS

Download PythonQt2.1_Qt4.8.zip from http://sourceforge.net/projects/pythonqt
module load cmake/2.8.12.2 qt/4.8.6  # check cmake and qt installations (also python should be loaded?)
cmake . -DCMAKE_INSTALL_PREFIX=/opt/pyqt/2.1
make -j4
make install

module file /etc/modulefiles/pyqt/2.1

#%Module1.0#########################################
##
##  Discretizer AB modulefile
##
##
## Set environment variables
setenv          PYQT4_ROOT_DIR     “/opt/pyqt/2.1”
prepend-path    LD_LIBRARY_PATH    /opt/pyqt/2.1/lib

VTK 5.10.1 standalone install on CentOS

Download vtk-5.10.1.tar.gz from http://www.vtk.org
module load cmake/2.8.12.2  # (cmake installation)
module load qt/4.8.6   # (qt installation)

cmake -DVTK_USE_QT:BOOL=ON -DVTK_USE_GUISUPPORT:BOOL=ON -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_INSTALL_PREFIX=/opt/vtk/5.10.1 .
make -j4
make install

module file /etc/modulefiles/vtk/5.10.1

#%Module1.0##########################################
##
##  Discretizer AB modulefile
##
##
## Add directory to the path
prepend-path    PATH    /opt/vtk/5.10.1/bin
prepend-path    LD_LIBRARY_PATH  /opt/vtk/5.10.1/lib/vtk-5.10

Standalone cmake 2.8 on CentOS

Download cmake-2.8.12.2.tar.gz from http://www.cmake.org

Probably load qt module: module load qt/4.8.6
./bootstrap –prefix=/opt/cmake/2.8.12.2 –qt-gui
make -j4
make install

module file /etc/modulefiles/cmake/2.8.12.2

#%Module1.0##########################################
##
##  Discretizer AB modulefile
##
##
prepend-path    PATH    /opt/cmake/2.8.12.2/bin

## Set environment variables
setenv          CMAKE_ROOT_DIR      “/opt/cmake/2.8.12.2”

Standalone Opencascade 6.5.4 installation on CentOS

Download OpenCASCADE654.tar.gz from http://www.opencascade.org you have to register
You have to complete compilation of tcltk, freetype, ftgl, gl2ps, freeimage and qt.
export MMGT_REENTRANT=1
# this variable only needed for DRAWEXE
export CASROOT=/opt/occ/6.5.4
module load tbb/3.0-018

./build_configure
./configure –prefix=/opt/occ/6.5.4 –exec-prefix=/opt/occ/6.5.4 –oldincludedir=/opt/occ/6.5.4/include –with-tcl=/opt/tcltk/8.5.13/lib –with-tk=/opt/tcltk/8.5.13/lib –with-java-include=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.55.x86_64/include –with-freetype=/opt/freetype/2.4.10 –with-ftgl=/opt/ftgl/2.1.3rc5 –with-gl2ps=/opt/gl2ps/1.3.5 –with-freeimage=/opt/freeimage/3.14.1 –with-tbb-include=/opt/tbb/3.0-018/include –with-tbb-library=/opt/tbb/3.0-018/lib/intel64/cc4.1.0_libc2.4_kernel2.6.16.21 –with-qt=/opt/qt/4.8.6
make -j4
make install

Note: the tbb 3.0-018 was found in the salome-platform installation…

module file /etc/modulefiles/occ/6.5.4

#%Module1.0###########################################
##
## Discretizer AB modulefile
##
##
prepend-path PATH /opt/occ/6.5.4/bin
prepend-path LD_LIBRARY_PATH /opt/occ/6.5.4/lib

FreeImage standalone install on CentOS

Download FreeImage3141.zip from http://en.sourceforge.jp/projects/sfnet_freeimage
In Makefile.fip:
# General configuration variables:
DESTDIR ?= /opt/freeimage/3.14.1
INCDIR ?= $(DESTDIR)/include
INSTALLDIR ?= $(DESTDIR)/lib

make -f Makefile.fip
make -f Makefile.fip install

Note: replaced OpenEXR dir with 3.15.0 version’s

module file /etc/modulefiles/freeimage/3.14.1

#%Module1.0##############################################
##
## Discretizer AB modulefile
##
##
prepend-path LD_LIBRARY_PATH /opt/freeimage/3.14.1/lib

Standalone gl2ps installation on CentOS

Download gl2ps-1.3.5.tgz from http://geuz.org/gl2ps
mkdir build; cd build; cmake ../
make -j4
in cmake_install.cmake: SET(CMAKE_INSTALL_PREFIX “/opt/gl2ps/1.3.5”)
make install

module file /etc/modulefiles/gl2ps/1.3.5

#%Module1.0############################################
##
##  Discretizer AB modulefile
##
##
prepend-path    LD_LIBRARY_PATH    /opt/gl2ps/1.3.5/lib