Compiling software on the user profile
This section aims at helping the users compile the software they need. They are mere guidelines!
Incompact3d
Following instructions from https://github.com/xcompact3d/Incompact3d
salloc
git clone https://github.com/xcompact3d/Incompact3d
cd Incompact3d/
git checkout v3.0
module load mpi/openmpi-x86_64
make
# once compiled
cd examples/Cylinder
pwd
/homes/<user>/Incompact3d/examples/Cylinder
mpirun -n 1 ~/Incompact3d/xcompact3d
Xcompact3d is run with the default file -->input.i3d
===========================================================
======================Xcompact3D===========================
===Copyright (c) 2018 Eric Lamballais and Sylvain Laizet===
===Modified by Felipe Schuch and Ricardo Frantz============
===Modified by Paul Bartholomew, Georgios Deskos and=======
===Sylvain Laizet -- 2018- ================================
===========================================================
Git version : v3.0-0-g9015765
Simulating cylinder
(lx,ly,lz)= 20.000000000000000 12.000000000000000 6.0000000000000000
(nx,ny,nz)= 257 128 64
(dx,dy,dz)= 7.8125000000000000E-002 9.3750000000000000E-002 9.3750000000000000E-002
(nx*ny*nz)= 2105344
(p_row,p_col)= 0 0
Numerical precision: Double
Boundary condition : (nclx1 ,nclxn )=(2,2)
(ncly1 ,nclyn )=(0,0)
(nclz1 ,nclzn )=(0,0)
High and low speed : u1= 1.00 and u2= 1.00
Reynolds number Re : 300.00000000
Gravity vector : (gx, gy, gz)=( 0.00000000, 0.00000000, 0.00000000)
Time step dt : 0.00250000
Spatial scheme : 0.69477383
Temporal scheme : Adams-bashforth 3
Scalar : off
Immersed boundary : on with Lagrangian Poly
In auto-tuning mode......
factors: 1
processor grid 1 by 1 time= 8.6869291961193085E-002
the best processor grid is probably 1 by 1
Initializing variables...
Using the hyperviscous operator with (nu_0/nu,c_nu) = ( 4.0000000000000000 , 0.44000000000000000 )
Using the hyperviscous operator with (nu_0/nu,c_nu) = ( 4.0000000000000000 , 0.44000000000000000 )
Using the hyperviscous operator with (nu_0/nu,c_nu) = ( 4.0000000000000000 , 0.44000000000000000 )
Generating the geometry!
step 1
step 2
step 3
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 16346 on node ava01 exited on signal 9 (Killed).
--------------------------------------------------------------------------
OpenFoam7
A Distro “Scientific Linux 7” não faz parte dos SO's suportados, pelo openfoam, pelo que não podemos garantir que funcione corretamente sendo tambem por isso que a aplicação terá de ser compilada na conta de cada um, para evitar a introdução de instabilidade no sistema important box
# infos https://openfoam.org/download/7-source/
salloc -n 16 -p big
mkdir OpenFOAM
cd OpenFOAM/
wget -O - http://dl.openfoam.org/source/7 | tar xvz
wget -O - http://dl.openfoam.org/third-party/7 | tar xvz
mv OpenFOAM-7-version-7 OpenFOAM-7
mv ThirdParty-7-version-7 ThirdParty-7
# https://openfoam.org/download/source/software-for-compilation/
source $HOME/OpenFOAM/OpenFOAM-7/etc/bashrc WM_LABEL_SIZE=64 WM_MPLIB=OPENMPI FOAMY_HEX_MESH=yes
cd ThirdParty-7
mkdir download
wget -P download https://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.1.tar.bz2
tar -xjf download/openmpi-2.1.1.tar.bz2
# https://openfoam.org/download/source/third-party-software/
./Allwmake -j 16
# https://www.paraview.org/download/
wget 'https://www.paraview.org/paraview-downloads/download.php?submit=Download&version=v5.6&type=binary&os=Linux&downloadFile=ParaView-5.6.0-MPI-Linux-64bit.tar.gz' -O ParaView.tar.gz
gunzip ParaView.tar.gz
tar -xf ParaView.tar
rm ParaView.tar
wmRefresh
cd ..
cd OpenFOAM-7
module load gcc/9.3.1
./Allwmake -j 16
# Getting started
mkdir -p $FOAM_RUN
cd $FOAM_RUN
cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily .
cd pitzDaily
blockMesh
simpleFoam
# more at http://cfd.direct/openfoam/user-guide
OpenFoam6
# A different approach! Just do:
salloc -n 6
source /soft/no_support/OpenFOAM/OpenFOAM-6/etc/bashrc WM_LABEL_SIZE=64 WM_MPLIB=OPENMPI FOAMY_HEX_MESH=yes
# Then You can run OpenFoam cmds like:
icoFoam -help
# Next, the compilation of this software and sources # NOTE: You do not need to compile if You use the method "source /soft/no_support/..." explained before! https://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-6/CentOS_SL_RHEL 2.3 CentOS 7.5 (1804) cd ~ mkdir OpenFOAM cd OpenFOAM git clone https://github.com/OpenFOAM/OpenFOAM-6.git git clone https://github.com/OpenFOAM/ThirdParty-6.git cd ThirdParty-6 mkdir download wget -P download https://www.cmake.org/files/v3.9/cmake-3.9.0.tar.gz wget -P download https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-4.10/CGAL-4.10.tar.xz wget -P download https://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.bz2 wget -P download https://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.1.tar.bz2 wget -P download http://www.paraview.org/files/v5.4/ParaView-v5.4.0.tar.gz tar -xzf download/cmake-3.9.0.tar.gz tar -xJf download/CGAL-4.10.tar.xz tar -xjf download/boost_1_55_0.tar.bz2 tar -xjf download/openmpi-2.1.1.tar.bz2 tar -xzf download/ParaView-v5.4.0.tar.gz --transform='s/ParaView-v5.4.0/ParaView-5.4.0/' cd .. sed -i -e 's/\(boost_version=\)boost-system/\1boost_1_55_0/' OpenFOAM-6/etc/config.sh/CGAL sed -i -e 's/\(cgal_version=\)cgal-system/\1CGAL-4.10/' OpenFOAM-6/etc/config.sh/CGAL source $HOME/OpenFOAM/OpenFOAM-6/etc/bashrc WM_LABEL_SIZE=64 WM_MPLIB=OPENMPI FOAMY_HEX_MESH=yes cd $WM_THIRD_PARTY_DIR ./makeCmake > log.makeCmake 2>&1 wmRefresh cd $WM_THIRD_PARTY_DIR ./Allwmake > log.make 2>&1 wmRefresh cd $WM_THIRD_PARTY_DIR ./makeParaView -mpi -python -qmake $(which qmake-qt4) > log.makePV 2>&1 wmRefresh cd $WM_PROJECT_DIR ./Allwmake -j 8 > log.make 2>&1 # Check if icoFoam is working, by running this command: icoFoam -help # https://openfoamwiki.net/index.php/FAQ/Installation_and_Running # manual # https://cfd.direct/openfoam/user-guide/ ls -A1 $WM_PROJECT_DIR/doc/Guides*/*UserGuide*.pdf