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Commit 74e040be authored by Ondrej Vysocky's avatar Ondrej Vysocky
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Modules for clear GCC version of OpenFoam

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FOAMMODULES-GCC-Taurus.sh 0 → 100644
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#!/bin/sh
# SELECT MACHINE ##############################################################
MERIC_LIBS_COMMON="-L$HOME/OpenFOAM/meric/lib/ -lmericmpi "
MERIC_LIBS_TAURUS="-lhdeem -lfreeipmi -lcpufreq -lx86_adapt -L/sw/taurus/libraries/papi/5.4.1/lib/ -lpapi"
MERIC_LIBS_SALOMON="-L$HOME/readex/MERIC/x86adaptGCC/x86_adapt/build/ -lx86_adapt"
export READEX_INCLUDE="-I/scratch/p_readex/OPENFOAM/meric/include "
export READEX_DEFINE=" " # -DUSE_SCOREP #-DENDKILL"
#export READEX_LIBS=$MERIC_LIBS_COMMON$MERIC_LIBS_TAURUS
#FM_DIR=~/OpenFOAM
FM_DIR=/scratch/p_readex/OPENFOAM/OpenFOAM-clear
# SELECT GCC #################################################################
# GCC compiler
#cp ~/OpenFOAM/OpenFOAM-v1612+/etc/bashrc-GCC6 ~/OpenFOAM/OpenFOAM-v1612+/etc/bashrc
cp $FM_DIR/OpenFOAM-v1612+/etc/bashrc-GCC6 $FM_DIR/OpenFOAM-v1612+/etc/bashrc
# SCOREP flags
# #0 clear OpenFOAM
cp $FM_DIR/OpenFOAM-v1612+/wmake/rules/linux64Gcc/c++ORIGIN $FM_DIR/OpenFOAM-v1612+/wmake/rules/linux64Gcc/c++
# #1 autofilter
# --mpp=mpi
#cp ~/OpenFOAM/OpenFOAM-v1612+/wmake/rules/linux64Gcc/c++SCOREP ~/OpenFOAM/OpenFOAM-v1612+/wmake/rules/linux64Gcc/c++
# #2 dyndetect
# --online-access --user --thread=none --mpp=mpi
#cp $FM_DIR/OpenFOAM-v1612+/wmake/rules/linux64Gcc/c++SCOREPuser $FM_DIR/OpenFOAM-v1612+/wmake/rules/linux64Gcc/c++
# compilation with a filter file - according Andreas script
# --noopenmp --instrument-filter=$(HOME)/OpenFOAM/exp/scorep.filt --online-access --user
#cp ~/OpenFOAM/OpenFOAM-v1612+/wmake/rules/linux64Gcc/c++AUTOFILTER ~/OpenFOAM/OpenFOAM-v1612+/wmake/rules/linux64Gcc/c++
# LOAD MODULES and SET ENV ####################################################
module purge
module use /projects/p_readex/modules
module load readex/ci_readex_bullxmpi1.2.8.4_gcc6.3.0
# OpenFoam modules
#module load intel/2016.2.181
#module load intel/2016.1.150
#module load boost/1.61.0-intel2017.0.020-intelmpi2017
#module load mpirt/5.1.2.150
module load zlib
module load flex
module load cmake
source $FM_DIR/OpenFOAM-v1612+/etc/bashrc
export WM_NCOMPPROCS=24
export BOOST_ARCH_PATH=$BOOST_ROOT
# Meric modules
#module load hdeem
#module load papi/5.4.1
export LD_LIBRARY_PATH+=:$HOME/OpenFOAM/meric/lib # meric without openMP !
export LD_LIBRARY_PATH+=:/usr/local/lib #x86adapt
export MERIC_NUM_THREADS=0
export MERIC_FREQUENCY=25
export MERIC_UNCORE_FREQUENCY=30
return # << << << <<
# vim /ThirdParty-v1612+/scotch_6.0.3/src/Makefile.inc
# "-shared-intel" to LDFLAGS
BOOST_INC=/sw/taurus/libraries/boost/1.61.0-intel2017.0.020-intelmpi2017/include
BOOST_ARCH_PATH=/home/h6/vysocky/OpenFOAM/ThirdParty-v1612+/platforms/linux64Icc/boost_1_62_0
BOOST_LIB=/sw/taurus/libraries/boost/1.61.0-intel2017.0.020-intelmpi2017/lib
BOOST_ROOT=/sw/taurus/libraries/boost/1.61.0-intel2017.0.020-intelmpi2017
bash-4.1$ export BOOST_ARCH_PATH=/sw/taurus/libraries/boost/1.61.0-intel2017.0.020-intelmpi2017
################################################################################
# OpenFOAM + Intel
# 1
module load intel/2016.2.181
module load mpirt/5.1.2.150
module load zlib
module load flex
module load cmake
module load boost/1.62.0-intel2016.2.181
# 2
# module load intel/2015.3.187
# module load zlib
# module load flex
# module load cmake
# module load boost/1.61.0-intel2015.3.187-python2.7
# 3
# module load intel/2017.0.020
# module load zlib
# module load flex
# module load cmake
# module load boost/1.61.0-intel2017.0.020-intelmpi2017
#source ~/OpenFOAM/OpenFOAM-4.1/etc/bashrc
export MPI_ARCH_FLAGS="-DOMPI_SKIP_MPICXX"
export MPI_ARCH_INC="-isystem $MPI_ROOT/include"
export MPI_ARCH_LIBS="-L$MPI_ROOT/lib -lmpi"
source ~/OpenFOAM/OpenFOAM-v1612+/etc/bashrc
export WM_CXX=mpiicpc
exit 0
#################################################################### instalace #
srun -N 1 --tasks-per-node=1 --cpus-per-task=24 --exclusive -p haswell --x11 --pty bash
source ~/OpenFOAM/OpenFOAM-v1612+/etc/bashrc
export WM_NCOMPPROCS=22
printenv | grep icpc # kdyz nevis, tak vsude nastav mpiicpc
export WM_CXX=mpiicpc
# export MPICXX_CXX=mpiicpc
# export MPI_ROOT=$I_MPI_ROOT
# vim $WM_PROJECT_DIR/etc/config/settings.sh
foam
vim etc/bashrc
# export WM_COMPILER=Icc
# export WM_MPLIB=SYSTEMMPI
vim wmake/rules/linux64Icc/c++
# CC = mpiicpc -std=c++11 -fp-trap=common -fp-model precise
./Allwmake
################################################################################
# post-compilation test
foamInstallationTest
mkdir -p $FOAM_RUN
run
cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily ./
cd pitzDaily
blockMesh
simpleFoam
# paraFoam
################################################################################
# run example:
/home/vysocky/OpenFOAM/OpenFOAM-v1612+/tutorials/incompressible/icoFoam/cavity/cavity
mpirun -n 4 icoFoam -parallel
system/blockMeshDict - velikost problemu
system/decomposeParDict - dekompozice problemu
mpirun -n 4 --bind-to-none icoFoam -parallel
################################################################################
# zdrojaky
# icoFoam
vim applications/solvers/incompressible/icoFoam/icoFoam.C
vim tutorials/incompressible/icoFoam/cavity/cavity/system/fvSolution
# solvers
vim src/OpenFOAM/matrices/lduMatrix/solvers/PCG/PCG.C
vim src/OpenFOAM/matrices/lduMatrix/solvers/PBiCG/PBiCG.C
# matrix
vim src/OpenFOAM/matrices/lduMatrix/lduMatrix/lduMatrix.C
vim src/OpenFOAM/matrices/lduMatrix/lduMatrix/lduMatrixATmul.C
# simpleFoam
vim applications/solvers/incompressible/simpleFoam/UEqn.H
vim applications/solvers/incompressible/simpleFoam/pEqn.H
vim applications/solvers/incompressible/simpleFoam/simpleFoam.C
vim applications/solvers/incompressible/simpleFoam/Make/options # nastaveni prekladu
# pitzDaily
vim tutorials/incompressible/simpleFoam/pitzDaily/system/fvSolution
vim tutorials/incompressible/simpleFoam/pitzDaily/system/controlDict
vim tutorials/incompressible/simpleFoam/pitzDaily/system/blockMeshDict
# motorBike
vim tutorials/incompressible/simpleFoam/motorBike/system/fvSolution
################################## motorBike
- GAMG
- PBiCG + DILU
mpiicpc -std=c++11 -fp-trap=common -fp-model precise -DOPENFOAM_PLUS=1612 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -diag-disable 327,654,1125,2289,2304,11062,11074,11076 -O3 -DNoRepository -I/home/h6/vysocky/OpenFOAM/OpenFOAM-v1612+/src/TurbulenceModels/turbulenceModels/lnInclude -I/home/h6/vysocky/OpenFOAM/OpenFOAM-v1612+/src/TurbulenceModels/incompressible/lnInclude -I/home/h6/vysocky/OpenFOAM/OpenFOAM-v1612+/src/transportModels -I/home/h6/vysocky/OpenFOAM/OpenFOAM-v1612+/src/transportModels/incompressible/singlePhaseTransportModel -I/home/h6/vysocky/OpenFOAM/OpenFOAM-v1612+/src/finiteVolume/lnInclude -I/home/h6/vysocky/OpenFOAM/OpenFOAM-v1612+/src/meshTools/lnInclude -I/home/h6/vysocky/OpenFOAM/OpenFOAM-v1612+/src/sampling/lnInclude -I/home/vysocky/meric/include -IlnInclude -I. -I/home/h6/vysocky/OpenFOAM/OpenFOAM-v1612+/src/OpenFOAM/lnInclude -I/home/h6/vysocky/OpenFOAM/OpenFOAM-v1612+/src/OSspecific/POSIX/lnInclude -fPIC -c simpleFoam.C -o /home/h6/vysocky/OpenFOAM/OpenFOAM-v1612+/platforms/linux64IccDPInt32Opt/applications/solvers/incompressible/simpleFoam/simpleFoam.o
################################################################################
# OpenFOAM + gcc
module load gcc/6.2.0
module load zlib
module load flex
module load cmake
module load boost/1.62.0-gnu6.2
export WM_NCOMPPROCS=22
source ~/OpenFOAM/OpenFOAM-v1612+/etc/bashrc
module load boost/1.62.0-gnu6.2
# gcc/6.2.0
# boost/1.62.0-gnu6.2
# bullxmpi/1.2.8.4
module load zlib
module load flex
module load cmake
module load hdeem
################################################################################
openfoam/2.2.2
1) intel/2016.1.150 2) bullxmpi/1.2.8.4 3) gcc/5.3.0 4) openfoam/2.2.2
openfoam/2.3.0(default)
1) intel/2013 2) bullxmpi/1.2.8.4 3) openfoam/2.3.0
openfoam/2.4.0
1) intel/2013 2) bullxmpi/1.2.8.4 3) openfoam/2.4.0
openfoam/4.0
1) intel/2017.0.020 2) intelmpi/2017.0.098 3) openfoam/4.0
# MPI ERROR ####################################################################
bash-4.1$ mpirun -n 4 icoFoam -parallel
--------------------------------------------------------------------------
Not enough processors were found on the local host to meet the requested
binding action:
Local host: taurusi5217
Action requested: bind-to-core
Application name: /home/h6/vysocky/OpenFOAM/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/bin/icoFoam
Please revise the request and try again.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun was unable to start the specified application as it encountered an error
on node taurusi5217. More information may be available above.
--------------------------------------------------------------------------
4 total processes failed to start
################################################################################
bash-4.1$ srun icoFoam -parallel
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
PMI2_Job_GetId failed failed
--> Returned value (null) (14) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
PMI2_Job_GetId failed failed
--> Returned value (null) (14) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
PMI2_Job_GetId failed failed
--> Returned value (null) (14) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
PMI2_Job_GetId failed failed
--> Returned value (null) (14) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_ess_init failed
--> Returned value (null) (14) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_ess_init failed
--> Returned value (null) (14) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_ess_init failed
--> Returned value (null) (14) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_ess_init failed
--> Returned value (null) (14) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: ompi_rte_init failed
--> Returned "(null)" (14) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: ompi_rte_init failed
--> Returned "(null)" (14) instead of "Success" (0)
--------------------------------------------------------------------------
[taurusi4160:10295] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: ompi_rte_init failed
--> Returned "(null)" (14) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[taurusi4160:10298] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[taurusi4160:10296] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: ompi_rte_init failed
--> Returned "(null)" (14) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[taurusi4160:10297] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
srun: error: taurusi4160: tasks 0-3: Exited with exit code 1
boost/1.49
boost/1.54.0-gnu4.6(default)
boost/1.54.0-gnu4.6.2
boost/1.54.0-intel12.1
boost/1.54.0-pgi13.6
boost/1.55.0-gnu4.8
boost/1.55.0-pgi14.1
boost/1.56.0-gnu4.9.1
boost/1.56.0-intel2015.3.187-python2.7
boost/1.57.0-intel2013-sp1
boost/1.58.0-gnu5.1
boost/1.59.0-intel2015.3.187
boost/1.60.0
boost/1.60.0-gnu5.3
boost/1.60.0-gnu5.3-intelmpi5.1
boost/1.60.0-intel2016.1.150
boost/1.60.0-intel2016.2.181-intelmpi5.1-knc
boost/1.61.0-intel2015.3.187-python2.7
boost/1.61.0-intel2017.0.020-intelmpi2017
boost/1.62.0-gnu6.2
boost/1.62.0-intel2016.2.181
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