ZKM |
December 25, 2010 11:48 |
Hello all and thanks Gijs for your help
I am still in battle for installing it. I managed to find the source of the libPstream.so problem. For some reasons that I can't understand FOAM_MPI_LIBBIN is not set inside the switch ("$WM_MPLIB") in settings.csh. I set it manually again:
Code:
setenv FOAM_MPI_LIBBIN $FOAM_LIBBIN/hpmpi
It solves this problem but I still have this typical errors/warnings for all solvers:
Code:
+ cd applications
+ ./Allwmake
+ cd solvers
+ wmake all
make[2]: Nothing to be done for `application'.
make[2]: Nothing to be done for `application'.
make[3]: Nothing to be done for `application'.
make[2]: Nothing to be done for `application'.
make[3]: Nothing to be done for `application'.
make[3]: Nothing to be done for `application'.
make[3]: Nothing to be done for `application'.
make[4]: Nothing to be done for `application'.
make[3]: Nothing to be done for `application'.
make[4]: Nothing to be done for `application'.
make[3]: Nothing to be done for `application'.
make[4]: Nothing to be done for `application'.
make[3]: Nothing to be done for `application'.
make[3]: Nothing to be done for `application'.
make[3]: Nothing to be done for `application'.
make[4]: Nothing to be done for `application'.
make[4]: Nothing to be done for `application'.
make[4]: Nothing to be done for `application'.
Making dependency list for source file conjugateHeatFoam.C
Making dependency list for source file potentialFoam.C
SOURCE=potentialFoam.C ; g++ -m64 -Dlinux64 -DDP -DFOAM_DEV_REVISION_NUMBER=1861 -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast -O3 -DNoRepository -ftemplate-depth-40 -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/finiteVolume/lnInclude -IlnInclude -I. -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/OpenFOAM/lnInclude -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/OSspecific/Unix/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/potentialFoam.o
SOURCE=conjugateHeatFoam.C ; g++ -m64 -Dlinux64 -DDP -DFOAM_DEV_REVISION_NUMBER=1861 -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast -O3 -DNoRepository -ftemplate-depth-40 -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/coupledMatrix/lnInclude -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/finiteVolume/lnInclude -IlnInclude -I. -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/OpenFOAM/lnInclude -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/OSspecific/Unix/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/conjugateHeatFoam.o
g++ -m64 -Dlinux64 -DDP -DFOAM_DEV_REVISION_NUMBER=1861 -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast -O3 -DNoRepository -ftemplate-depth-40 -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/coupledMatrix/lnInclude -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/finiteVolume/lnInclude -IlnInclude -I. -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/OpenFOAM/lnInclude -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/OSspecific/Unix/lnInclude -fPIC Make/linux64GccDPOpt/conjugateHeatFoam.o -L/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt \
-lcoupledLduMatrix -lfiniteVolume -lOpenFOAM -liberty -ldl /sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so -lm -o /sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/applications/bin/linux64GccDPOpt/conjugateHeatFoam
g++ -m64 -Dlinux64 -DDP -DFOAM_DEV_REVISION_NUMBER=1861 -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast -O3 -DNoRepository -ftemplate-depth-40 -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/finiteVolume/lnInclude -IlnInclude -I. -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/OpenFOAM/lnInclude -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/OSspecific/Unix/lnInclude -fPIC Make/linux64GccDPOpt/potentialFoam.o -L/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt \
-lfiniteVolume -llduSolvers -lOpenFOAM -liberty -ldl /sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so -lm -o /sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/applications/bin/linux64GccDPOpt/potentialFoam
/usr/bin/ld: warning: libPstream.so, needed by /sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libmpi.so.1, needed by /sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so, not found (try using -rpath or -rpath-link)
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Finalize'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Buffer_detach'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_rwlockattr_setkind_np'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_create'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_rwlock_rdlock'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Bsend'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_rwlock_init'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Probe'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_mutexattr_destroy'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Send'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_rwlock_destroy'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_rwlock_unlock'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Test'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Allreduce'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Buffer_attach'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Comm_size'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Recv'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Isend'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Get_count'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Abort'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Waitall'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Get_processor_name'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_rwlock_wrlock'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_rwlockattr_init'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Init'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Comm_rank'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_mutexattr_settype'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `MPI_Irecv'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `hpmp_sum'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_rwlockattr_destroy'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_rwlock_trywrlock'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_rwlock_tryrdlock'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_mutexattr_init'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `hpmp_byte'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `hpmp_double'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_mutex_trylock'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `hpmp_packed'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so: undefined reference to `hpmp_comm_world'
/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so: undefined reference to `pthread_join'
collect2: ld returned 1 exit status
make[2]: *** [/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/applications/bin/linux64GccDPOpt/conjugateHeatFoam] Error 1
make[1]: *** [conjugateHeatFoam] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [conjugate] Error 2
/usr/bin/ld: warning: libPstream.so, needed by /sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/libOpenFOAM.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libmpi.so.1, needed by /sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so, not found (try using -rpath or -rpath-link)
I have no idea how to use -rpath or -rpath-link as suggested in the warning message.
I found out that libmpi.so.1 is located in two locations /opt/hpmpi/lib/linux_amd64 and /opt/hpmpi/lib/linux_amd64/nomalloc/
I am going to do something like this manually:
Code:
setenv LD_LIBRARY_PATH /opt/hpmpi/lib/linux_amd64:$LD_LIBRARY_PATH
but I am not sure which libmpi.so.1 is required.
As for the other warning, that I think ends in those errors, again I don't know which libPstream.so is needed (in lib/linux64GccDPOpt/dummy or in lib/linux64GccDPOpt/hpmpi) and how to tell it to use from that path.
Our admin advised me to add -lpthread after the "-ldl" in:
Code:
g++ -m64 -Dlinux64 -DDP -DFOAM_DEV_REVISION_NUMBER=1861 -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast -O3 -DNoRepository -ftemplate-depth-40 -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/finiteVolume/lnInclude -IlnInclude -I. -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/OpenFOAM/lnInclude -I/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/src/OSspecific/Unix/lnInclude -fPIC Make/linux64GccDPOpt/potentialFoam.o -L/sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt \
-lfiniteVolume -llduSolvers -lOpenFOAM -liberty -ldl /sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPOpt/hpmpi/libPstream.so -lm -o /sfs/nobackup/z/z_kesha/OpenFOAM/OpenFOAM-1.5-dev/applications/bin/linux64GccDPOpt/potentialFoam
because he thinks that the pthread library was not linked in, but again I don't know where this command is read from to edit it.
Any help and comments are appreciated.
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