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[OpenFOAM.org] Compilation Error with OpenFOAM-5.x using Intel Compilers |
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April 17, 2019, 23:54 |
Compilation Error with OpenFOAM-5.x using Intel Compilers
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#1 |
Member
Andrew O. Winter
Join Date: Aug 2015
Location: Seattle, WA, USA
Posts: 78
Rep Power: 11 |
Hello CFD Online,
I've been trying to setup my own installation of OpenFOAM-5.x in an HPC cluster using Intel compiler and mpi modules provided in the cluster, particularly icc 18.0.2 and impi 18.0.2. To begin with, I modified some of the environment variables in $WORK/OpenFOAM-5.x/etc/bashrc as follows, where $WORK is the directory containing the OpenFOAM-5.x and ThirdParty-5.x directories. Code:
export FOAM_INST_DIR=$WORK export WM_COMPILER=Icc export WM_MPLIB=INTELMPI Code:
INTELMPI) # Stampede2 location of Intel MPI 18.0.2 export MPI_ROOT=/opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64 # No trailing slash [ "${MPI_ROOT%/}" = "${MPI_ROOT}" ] || MPI_ROOT="${MPI_ROOT%/}" export FOAM_MPI="${MPI_ROOT##*/}" export MPI_ARCH_PATH=$MPI_ROOT _foamAddPath $MPI_ARCH_PATH/bin _foamAddPath $MPI_ARCH_PATH/include _foamAddPath $MPI_ARCH_PATH/lib Code:
#!/bin/bash #SBATCH --job-name=compileOF5 # job name ##SBATCH --output=compileOF5.o$j # standard output file name ##SBATCH --error=compileOF5.e$j # standard error file name #SBATCH --account=DesignSafe-Motley-UW # project allocation name (required if you have >1) #SBATCH --partition=skx-dev # queue name #SBATCH --time=2:00:00 # run time (D-HH:MM:SS) #SBATCH --nodes=1 # total number of nodes #SBATCH --ntasks=48 # total number of MPI tasks ##SBATCH --chdir=$WORK # path to job work directory ##SBATCH --mail-type=all # send emails when the job begins, ends, or fails ##SBATCH --mail-user=andrew25@uw.edu # job alert emails are sent to this address # Remove old log files for object in 'log.'*; do if [ -f $object ]; then rm $object fi done # Remove old slurm output files for object in 'slurm-'*; do if [ -f $object ]; then rm $object fi done # COMPILER: # -------- # According to https://openfoam.org/download/source/software-for-compilation/ gcc version # 4.8 or higher and icc version 17.0.4 or higher are required for OpenFOAM-5.x to compile. module load intel/18.0.2 # options: intel/16.0.3, intel/17.0.4, intel/18.0.0, intel/18.0.2 # PARALLEL PROCESSING: # ------------------- # To find the Intel MPI root, enter "module load impi/18.0.2" and then "echo $TACC_IMPI_DIR". # Based on https://linuxcluster.wordpress.com/2018/06/04/compiling-openfoam-5-with-intel-mpi/ # I added "/intel64" to the end of the path printed to the command line and exported this path # within the script $WORK/OpenFOAM-5.x/etc/config.sh/mpi using the command... # export MPI_ROOT=/opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64 # ..., which I only added to the INTELMPI section of the script. I also modified mplibINTELMPI # in the linux64Icc and linuxIA64Icc sub-directories of $WORK/OpenFOAM-5.x/wmake/rules so that # PINC and PLIBS did not have "64" at the end of "include" and "lib". module load impi/18.0.2 # options: impi/17.0.3, impi/18.0.0, impi/18.0.2 # SET ENVIRONMENT VARIABLES: # ------------------------- cd $WORK source OpenFOAM-5.x/etc/bashrc export WM_SCHEDULER=wmakeScheduler export WM_NCOMPROCS=48 # make sure this is identical to ntasks in the SBATCH commands export WM_HOSTS=`hostname`:$WM_NCOMPROCS # COMPILE ThirdParty-5.x: # ---------------------- cd ThirdParty-5.x ./Allclean >> ../log.makeThirdParty 2>&1 # make sure nothing is left behind from a previous compilation attempt that shouldn't be here ./Allwmake -j >> ../log.makeThirdParty 2>&1 # -j runs the command in parallel #./makeParaView >> ../log.makeThirdParty 2>&1 cd .. # COMPILE OpenFOAM-5.0: # -------------------- cd OpenFOAM-5.x wmRefresh >> ../log.makeOpenFOAM 2>&1 # reset environment variables based on newly created directories after compiling ThirdParty-5.x wcleanPlatform >> ../log.makeOpenFOAM 2>&1 # make sure nothing is left behind from a previous compilation attempt that shouldn't be here ./Allwmake -j >> ../log.makeOpenFOAM 2>&1 Code:
EXE = LIB = .so OBJ = .o MAKE = make AR = icc ARFLAGS = $(WM_CFLAGS) -shared -o CAT = cat CCS = icc CCP = mpiicc CCD = mpiicc CFLAGS = $(WM_CFLAGS) -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict ifeq ($(WM_LABEL_OPTION),Int64) CFLAGS += -DINTSIZE64 endif CLIBFLAGS = -shared LDFLAGS = -Xlinker --no-as-needed $(WM_LDFLAGS) -lz -lm -lrt CP = cp LEX = flex -Pscotchyy -olex.yy.c LN = ln MKDIR = mkdir MV = mv RANLIB = echo YACC = bison -pscotchyy -y -b y Code:
# building scotch is still a bit of a pain echo ======================================== echo "Build Scotch decomposition library $SCOTCH_VERSION" echo " $SCOTCH_ARCH_PATH" # this needs generalizing for any compiler, since it's hard-coded to GCC #scotchMakefile=../../etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM scotchMakefile=../../etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM-Icc Code:
export PATH=$WORK/procmail-3.22/bin:$PATH Finally, I reached the point I'm stuck at now, where I'm getting two odd results in my log file for running $WORK/OpenFOAM-5.x/Allwmake. Code:
LINE 1: /work/04697/winter89/stampede2/OpenFOAM-5.x/etc/config.sh/aliases: line 84: wmUnset: command not found LINES 39 - 53: Allwmake src version changed from previous build removing .o files corresponding to OpenFOAM/global/global.o ... Allwmake src/Pstream wmake dummy Making dependency list for source file UOPwrite.C Making dependency list for source file UIPread.C Making dependency list for source file UPstream.C wmakeScheduler icpc -std=c++11 -fp-trap=common -fp-model precise -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 -IlnInclude -I. -I/work/04697/winter89/stampede2/OpenFOAM-5.x/src/OpenFOAM/lnInclude -I/work/04697/winter89/stampede2/OpenFOAM-5.x/src/OSspecific/POSIX/lnInclude -fPIC -c UPstream.C -o /work/04697/winter89/stampede2/OpenFOAM-5.x/platforms/linux64IccDPInt32Opt/src/Pstream/dummy/UPstream.o wmakeScheduler icpc -std=c++11 -fp-trap=common -fp-model precise -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 -IlnInclude -I. -I/work/04697/winter89/stampede2/OpenFOAM-5.x/src/OpenFOAM/lnInclude -I/work/04697/winter89/stampede2/OpenFOAM-5.x/src/OSspecific/POSIX/lnInclude -fPIC -c UIPread.C -o /work/04697/winter89/stampede2/OpenFOAM-5.x/platforms/linux64IccDPInt32Opt/src/Pstream/dummy/UIPread.o wmakeScheduler icpc -std=c++11 -fp-trap=common -fp-model precise -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 -IlnInclude -I. -I/work/04697/winter89/stampede2/OpenFOAM-5.x/src/OpenFOAM/lnInclude -I/work/04697/winter89/stampede2/OpenFOAM-5.x/src/OSspecific/POSIX/lnInclude -fPIC -c UOPwrite.C -o /work/04697/winter89/stampede2/OpenFOAM-5.x/platforms/linux64IccDPInt32Opt/src/Pstream/dummy/UOPwrite.o Warning: Permanently added 'c506-101.stampede2.tacc.utexas.edu' (ECDSA) to the list of known hosts. bash: icpc: command not found bash: icpc: command not found bash: icpc: command not found Code:
icpc --version icpc (ICC) 18.0.2 20180210 Copyright (C) 1985-2018 Intel Corporation. All rights reserved. Does anyone have any ideas about where to go from here and/or experience compiling OpenFOAM-5.x using Intel software? In case they prove helpful, I've attached the two log files created during running Allwmake in the ThirdParty-5.x and OpenFOAM-5.x directories. |
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April 18, 2019, 00:09 |
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#2 |
Member
Andrew O. Winter
Join Date: Aug 2015
Location: Seattle, WA, USA
Posts: 78
Rep Power: 11 |
I just realized I forgot to mention that I also edited two files in the $WORK/OpenFOAM-5.x/wmake/rules directories. Specifically, in ../rules/linux64Icc/mplibINTELMPI and ../rules/linuxIA64Icc/mplibINTELMPI, I modified both files to read as follows.
Code:
PFLAGS = -DMPICH_SKIP_MPICXX PINC = -isystem $(MPI_ARCH_PATH)/include PLIBS = -L$(MPI_ARCH_PATH)/lib -lmpi |
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April 18, 2019, 18:09 |
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#3 | |
Member
Fatih Ertinaz
Join Date: Feb 2011
Location: Istanbul
Posts: 64
Rep Power: 15 |
Hello Andrew
First error: Quote:
Code:
set +u In fact, you can completely avoid using wmUnset and wmRefresh and instead apply them manually when needed. For the compiler error, you might want to have a look at the Intel's environment variable ${I_MPI_ROOT}. I guess it'd be easier using it before setting up env-vars used by OF such as ${MPI_ROOT} and ${MPI_ARCH_PATH}. In general the error you get indicates a problem with the way those modules are loaded, but your Slurm script looks correct. Therefore if you can use those compilation nodes interactively, I'd highly suggest you doing that. To me it looks like, after you source OF your entire path gets cleaned and as a result system cannot find the compiler you loaded. For scotch, I'd use the file called Makefile.inc.x86-64_pc_linux2.shlib but that depends on the platform you're using. I doubt that the cluster you're working on has 32bit hardware architecture though... However if you were able to compile successfully, it shouldn't hurt. Anyway, hope this helps Fatih Last edited by fertinaz; April 18, 2019 at 23:28. Reason: Wording |
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April 25, 2019, 16:54 |
Compilation Error with OpenFOAM-5.x using Intel Compilers
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#4 |
Member
Andrew O. Winter
Join Date: Aug 2015
Location: Seattle, WA, USA
Posts: 78
Rep Power: 11 |
Hey Fatih,
Thanks for your reply! I was able to successfully compile OpenFOAM-5.x as well as OlaFlow last week on Friday, when I had some time to dig into the matter. Concerning the "First Error", I still don't totally understand why this was an issue, but I ended up just pasting the commands directly instead of using the command aliases. Concerning the "Second Error", I was able to resolve it by going through the following steps, some of which are the same as I mentioned in my first post. First, I made sure to install all of the third party software besides scotch that I would need, some of which I think might have been missing during my initial compilation efforts. Note that in all code below $WORK refers to the directory in which I compiled ThirdParty-5.x and OpenFOAM-5.x in the TACC HPC cluster. The following list of software was installed... Pre-installed in HPC cluster: cmake 3.10.2 flex 2.5.37 gcc 6.3.0 ---> not used, I used icc instead icc 18.0.2 impi 18.0.2 qt 4.8.7 ---> not used, ParaView 5.6.0 is already installed in the cluster Installed by me in $WORK: gmp 6.1.2 mpfr 4.0.2 mpc 1.1.0 procmail 3.22 After I installed these, I added the following lines to my .bashrc file in my $HOME directory. Code:
export PATH=$WORK/bin:$PATH export CPATH=$WORK/include:$CPATH export LD_LIBRARY_PATH=$WORK/lib:$LD_LIBRARY_PATH export LD_RUN_PATH=$WORK/lib:$LD_RUN_PATH Code:
export FOAM_INST_DIR=$WORK export WM_COMPILER_TYPE=system export WM_COMPILER=Icc export WM_MPLIB=INTELMPI Code:
case "$WM_COMPILER_TYPE" in OpenFOAM | ThirdParty) # Default versions of GMP, MPFR and MPC, override as necessary #gmp_version=gmp-5.1.2 #mpfr_version=mpfr-3.1.2 #mpc_version=mpc-1.0.1 gmp_version=gmp-6.1.2 mpfr_version=mpfr-4.0.2 mpc_version=mpc-1.1.0 case "$WM_COMPILER" in Icc) # Using Icc - not gcc export WM_CC='mpicc' export WM_CXX='mpicxx' ;; Gcc | Gcc48) gcc_version=gcc-4.8.5 ;; Gcc49) gcc_version=gcc-4.9.3 ;; Gcc51) gcc_version=gcc-5.1.0 ;; Gcc52) gcc_version=gcc-5.2.0 ;; Gcc53) gcc_version=gcc-5.3.0 ;; Gcc61) gcc_version=gcc-6.1.0 ;; Gcc81) gcc_version=gcc-8.1.0 ;; Clang) # Using clang - not gcc export WM_CC='clang' export WM_CXX='clang++' clang_version=llvm-3.7.0 ;; *) echo 1>&2 echo "Warning in $WM_PROJECT_DIR/etc/config.sh/compiler:" 1>&2 echo " Unknown OpenFOAM compiler type '$WM_COMPILER'" 1>&2 echo " Please check your settings" 1>&2 echo 1>&2 ;; esac ;; esac Code:
INTELMPI) ## Stampede2 location of Intel MPI 18.0.2 #export MPI_ROOT=/opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64 # No trailing slash [ "${MPI_ROOT%/}" = "${MPI_ROOT}" ] || MPI_ROOT="${MPI_ROOT%/}" export FOAM_MPI="${MPI_ROOT##*/}" export MPI_ARCH_PATH=$MPI_ROOT #_foamAddPath $MPI_ARCH_PATH/bin #_foamAddPath $MPI_ARCH_PATH/include #_foamAddPath $MPI_ARCH_PATH/lib if [ ! -d "$MPI_ROOT" -o -z "$MPI_ARCH_PATH" ] then echo "Warning in $WM_PROJECT_DIR/etc/config.sh/settings:" 1>&2 echo " MPI_ROOT not a valid mpt installation directory or ending" \ " in a '/'." 1>&2 echo " Please set MPI_ROOT to the mpt installation directory." 1>&2 echo " MPI_ROOT currently set to '$MPI_ROOT'" 1>&2 fi if [ "$FOAM_VERBOSE" -a "$PS1" ] then echo "Using INTEL MPI:" 1>&2 echo " MPI_ROOT : $MPI_ROOT" 1>&2 echo " FOAM_MPI : $FOAM_MPI" 1>&2 fi _foamAddPath $MPI_ARCH_PATH/bin64 _foamAddLib $MPI_ARCH_PATH/lib64 #_foamAddPath $MPI_ARCH_PATH/include64 ;; Code:
export MPI_ROOT=$I_MPI_ROOT Code:
cc = mpicc Code:
CC = mpicxx -std=c++11 -fp-trap=common -fp-model precise Code:
PFLAGS = -DMPICH_SKIP_MPICXX PINC = -isystem $(MPI_ARCH_PATH)/include64 PLIBS = -L$(MPI_ARCH_PATH)/lib64 -lmpi Code:
AR= icc CCS= icc CCP= mpiicc CCD= mpiicc Code:
# this needs generalizing for any compiler, since it's hard-coded to GCC #scotchMakefile=../../etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM scotchMakefile=../../etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM-Icc Code:
export LD_PRELOAD="libmpi.so" Code:
export LD_PRELOAD=$I_MPI_ROOT/lib64/libmpi.so Code:
#!/bin/bash #SBATCH --job-name=compileOF5x # job name ##SBATCH --output=compileOF5x.o$j # standard output file name ##SBATCH --error=compileOF5x.e$j # standard error file name #SBATCH --account=DesignSafe-Motley-UW # project allocation name (required if you have >1) #SBATCH --partition=skx-dev # queue name #SBATCH --time=2:00:00 # run time (D-HH:MM:SS) #SBATCH --nodes=1 # total number of nodes #SBATCH --ntasks=48 # total number of MPI tasks ##SBATCH --chdir=$WORK # path to job work directory ##SBATCH --mail-type=all # send emails when the job begins, ends, or fails ##SBATCH --mail-user=andrew25@uw.edu # job alert emails are sent to this address # Remove old log files for object in 'log.'*; do if [ -f $object ]; then rm $object fi done # Remove old slurm output files for object in 'slurm-'*; do if [ -f $object ]; then rm $object fi done # COMPILER: # -------- # According to https://openfoam.org/download/source/software-for-compilation/ gcc version # 4.8 or higher and icc version 17.0.4 or higher are required for OpenFOAM-5.x to compile. module load intel/18.0.2 # options: intel/16.0.3, intel/17.0.4, intel/18.0.0, intel/18.0.2 # PARALLEL PROCESSING: # ------------------- # To find the Intel MPI root, enter "module load impi/18.0.2" and then "echo $TACC_IMPI_DIR" # or "echo $I_MPI_ROOT". module load impi/18.0.2 # options: impi/17.0.3, impi/18.0.0, impi/18.0.2 # SET ENVIRONMENT VARIABLES: # ------------------------- export MPI_ROOT=$I_MPI_ROOT # should be identical to $TACC_IMPI_DIR export LD_PRELOAD=$MPI_ROOT/lib64/libmpi.so # see the "Using IntelMPI" discussion at https://www.openfoam.com/documentation/system-requirements.php source $WORK/OpenFOAM-5.x/etc/bashrc cd $WORK/ThirdParty-5.x ./Allclean >> ../log.compileOF5x # make sure nothing is left behind from a previous compilation attempt that shouldn't be here cd $WORK/OpenFOAM-5.x ./wcleanPlatform >> ../log.compileOF5x # make sure nothing is left behind from a previous compilation attempt that shouldn't be here export WM_COMPILE_OPTION=Debug export WM_SCHEDULER=wmakeScheduler export WM_NCOMPROCS=48 # make sure this is identical to ntasks in the SBATCH commands export WM_HOSTS=`hostname`:$WM_NCOMPROCS # COMPILE ThirdParty-5.x: # ---------------------- cd $WORK/ThirdParty-5.x ./Allwmake -j >> ../log.compileOF5x 2>&1 # -j runs the command in parallel #./makeParaView >> ../log.compileOF5x 2>&1 # RESET ENVIRONMENT VARIABLES: needs to be done to account for newly created directories after compiling ThirdParty-5.x # --------------------------- #wmRefresh >> ../log.compileOF5x 2>&1 # alias for the four command lines below (doesn't work in this script running on skx-dev) wmProjectDir=$WM_PROJECT_DIR foamSettings=$FOAM_SETTINGS #wmUnset # alias for the command line below (doesn't work in this script running on skx-dev) . $WM_PROJECT_DIR/etc/config.sh/unset . $wmProjectDir/etc/bashrc $foamSettings # COMPILE OpenFOAM-5.0: # -------------------- cd $WORK/OpenFOAM-5.x ./Allwmake -j >> ../log.compileOF5x 2>&1 Code:
#!/bin/bash #SBATCH --job-name=compileOlaFlow # job name ##SBATCH --output=compileOlaFlow.o$j # standard output file name ##SBATCH --error=compileOlaFlow.e$j # standard error file name #SBATCH --account=DesignSafe-Motley-UW # project allocation name (required if you have >1) #SBATCH --partition=skx-dev # queue name #SBATCH --time=2:00:00 # run time (D-HH:MM:SS) #SBATCH --nodes=1 # total number of nodes #SBATCH --ntasks=48 # total number of MPI tasks # Remove old slurm output files for object in 'slurm-'*; do if [ -f $object ]; then rm $object fi done # COMPILER: # -------- # According to https://openfoam.org/download/source/software-for-compilation/ gcc version # 4.8 or higher and icc version 17.0.4 or higher are required for OpenFOAM-5.x to compile. module load intel/18.0.2 # options: intel/16.0.3, intel/17.0.4, intel/18.0.0, intel/18.0.2 # PARALLEL PROCESSING: # ------------------- # To find the Intel MPI root, enter "module load impi/18.0.2" and then "echo $TACC_IMPI_DIR" # or "echo $I_MPI_ROOT". module load impi/18.0.2 # options: impi/17.0.3, impi/18.0.0, impi/18.0.2 # SET ENVIRONMENT VARIABLES: # ------------------------- export MPI_ROOT=$I_MPI_ROOT # should be identical to $TACC_IMPI_DIR export LD_PRELOAD=$MPI_ROOT/lib64/libmpi.so # see the "Using IntelMPI" discussion at https://www.openfoam.com/documentation/system-requirements.php source $WORK/OpenFOAM-5.x/etc/bashrc # CLEANUP POSSIBLE PRIOR INSTALLATION: # ----------------------------------- if [ -f $WORK/OpenFOAM-5.x/platforms/linux64IccDPInt32Opt/lib/libwaveGeneration.so ]; then rm -f $WORK/OpenFOAM-5.x/platforms/linux64IccDPInt32Opt/lib/libwaveGeneration.so fi if [ -f $WORK/OpenFOAM-5.x/platforms/linux64IccDPInt32Opt/lib/libwaveAbsorption.so ]; then rm -f $WORK/OpenFOAM-5.x/platforms/linux64IccDPInt32Opt/lib/libwaveAbsorption.so fi if [ -f $WORK/OpenFOAM-5.x/platforms/linux64IccDPInt32Opt/bin/olaDyMFlow ]; then rm -f $WORK/OpenFOAM-5.x/platforms/linux64IccDPInt32Opt/bin/olaDyMFlow fi if [ -f $WORK/OpenFOAM-5.x/platforms/linux64IccDPInt32Opt/bin/olaFlow ]; then rm -f $WORK/OpenFOAM-5.x/platforms/linux64IccDPInt32Opt/bin/olaFlow fi if [ -d $WORK/olaFlow ]; then rm -rf $WORK/olaFlow fi git clone git://github.com/phicau/olaFlow.git # REDIRECT COMPILATION OUTPUT: install in $WORK/OpenFOAM-5.x/platforms/linux64IccDPInt32Opt instead of in $HOME/OpenFOAM/winter89-5.x/platforms/linux64IccDPInt32Opt # --------------------------- sed -i "s/FOAM_USER_LIBBIN/FOAM_LIBBIN/g" $WORK/olaFlow/genAbs/waveAbsorption/Make/files sed -i "s/FOAM_USER_LIBBIN/FOAM_LIBBIN/g" $WORK/olaFlow/genAbs/waveGeneration/Make/files sed -i "s/FOAM_USER_APPBIN/FOAM_APPBIN/g" $WORK/olaFlow/solvers/olaFlowOF500/Make/files sed -i "s/FOAM_USER_APPBIN/FOAM_APPBIN/g" $WORK/olaFlow/solvers/olaFlowOF500/olaDyMFlow/Make/files strA=$(grep "ln -s" $WORK/olaFlow/allMake) strB ='echo Not creating symbolic link to HOME/OpenFOAM/winter89-5.x/platforms/linux64IccDPInt32Opt/bin/olaDyMFlow' sed -i "s/$strA/$strB/g" $WORK/olaFlow/allMake # prevent unnecessary attempt to create symbolic link # SOURCE CODE TYPO FIXES: needed for now to avoid a warning/error message until Pablo fixes it (I tried to do it properly, but failed) # ---------------------- strA='PointPatchFieldMapper' strB='pointPatchFieldMapper' sed -i "s/$strA/$strB/g" $WORK/olaFlow/genAbs/waveGeneration/wavemakerMovement/wavemakerMovement.H sed -i "s/$strA/$strB/g" $WORK/olaFlow/genAbs/waveGeneration/wavemakerMovement/wavemakerMovement.C # COMPILE olaFlow: # --------------- cd $WORK/olaFlow ./allMake > ../log.compileOlaFlow 2>&1 I hope this might be helpful to anyone else trying to work in a similar situation where you need to use Intel compiler and mpi software in an HPC cluster. Last edited by aow; April 30, 2019 at 18:28. |
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April 25, 2019, 17:17 |
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#5 |
Member
Andrew O. Winter
Join Date: Aug 2015
Location: Seattle, WA, USA
Posts: 78
Rep Power: 11 |
I had one more thing I forgot to mention...
Fatih, you mentioned that I was using a 32-bit Makefile.inc for compiling scotch 6.0.3, which I did not realize at first since I was not familiar with the i686 notation as opposed to x86-64; however, the file I modified is the one selected by the openfoam.org developers and is setup to be used by default when you run ./Allwmake in the ThirdParty-5.x directory. I'm wondering if it's intentionally 32-bit for some reason or if it's a mistake in the naming of the file and in fact it's actually set to be 64-bit instead. I'm not a pro enough at this sort of thing to be able to tell immediately by looking at the contents of the file so I cannot really say anything for sure other than my compiled OpenFOAM version has successfully run all of the tutorials and models of my own that I've tried out so far. Maybe Bruno (i.e. wyldckat) has something to say about this...? |
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