View Issue Details
| ID | Project | Category | View Status | Date Submitted | Last Update |
|---|---|---|---|---|---|
| 0001052 | OpenFOAM | Bug | public | 2013-10-17 19:53 | 2015-01-01 14:29 |
| Reporter | Assigned To | henry | |||
| Priority | urgent | Severity | block | Reproducibility | always |
| Status | closed | Resolution | unable to reproduce | ||
| Platform | Linux | OS | Ubuntu | OS Version | 12.04 LTS x64 |
| Summary | 0001052: The compilation of OpenFOAM 2.2.x is not possible with SYSTEMOPENMPI | ||||
| Description | When I switch the mpi library to system in bashrc, the compilation crashes with If the export WM_MPLIB=SYSTEMOPENMPI is chosen, the source etc/bashrc leads in make[3]: Entering directory `/srv/groot/novakm/OpenFOAM/OpenFOAM-2.2.2/applications/utilities/mesh/advanced/PDRMesh' g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-100 -I/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/src/meshTools/lnInclude -I/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/src/dynamicMesh/lnInclude -I/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/src/finiteVolume/lnInclude -IlnInclude -I. -I/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/src/OpenFOAM/lnInclude -I/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/src/OSspecific/POSIX/lnInclude -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPOpt/PDRMesh.o -L/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib \ -lmeshTools -ldynamicMesh -lfiniteVolume -lcompressibleRASModels -lOpenFOAM -ldl -lm -o /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/bin/PDRMesh /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Waitall' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Abort' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_double' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Get_count' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Init' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Probe' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Send' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Allreduce' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_packed' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_op_min' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Buffer_detach' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Bsend' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_byte' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Irecv' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Recv' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_comm_world' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Wait' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Get_processor_name' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Test' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Isend' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Finalize' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_op_sum' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Buffer_attach' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_size' /usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_rank' collect2: ld returned 1 exit status make[3]: *** [/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64GccDPOpt/bin/PDRMesh] Error 1 make[3]: Leaving directory `/srv/groot/novakm/OpenFOAM/OpenFOAM-2.2.2/applications/utilities/mesh/advanced/PDRMesh' make[2]: *** [PDRMesh] Error 2 and this error repeated. | ||||
| Steps To Reproduce | export WM_MPLIB=SYSTEMOPENMPI && foam && ./Allwmake | ||||
| Tags | No tags attached. | ||||
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I've finished up a test just now, building OpenFOAM 2.2.2 on Ubuntu 12.04 x86_64, with the SYSTEMOPENMPI option and I had absolutely no problems! For reference, I followed these instructions: http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-2.2.2/Ubuntu#Ubuntu_12.04 Allow me to do a few questions: What do these commands give you? mpicc --showme:link | sed -e 's/.*-L\([^ ]*\).*/\1/' echo $MPI_ARCH_PATH In my system, they give me this: /usr/lib/openmpi/lib /usr/lib/openmpi In addition, did you start a new terminal window for using the modified WM_MPLIB? By the way, this will not work as expected: export WM_MPLIB=SYSTEMOPENMPI && foam && ./Allwmake But this should: wmSET WM_MPLIB=SYSTEMOPENMPI && foam && ./Allwmake |
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Thanks Bruno for quick response. I ve followed one of your posts and checked the outpouts of --showme:link. Moreover, I ve tried to insert the libDir link by hand. The problem was in badly loaded module. In fact, the compilation runs fine now. In the future, I will at first post the problems on cfd-online, on the thread http://www.cfd-online.com/Forums/openfoam/125058-openfoam-cluster-ubuntu-12-04-lts-x64.html#post457573 because it seems inappropriate to title not-knowing as a Bug. Could you be so kind an subscribe to the thread for further development? Best regards Martin |
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Hi Martin: done, I'm subscribed to the thread. By the way, a quick question: "badly loaded module" on Ubuntu? I usually only see that on Fedora... |
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Thanks Bruno. I really appreciate your help. I did not mentioned it, but the compilation were provided on cluster, where the software is added with module add <soft> and since it is an University cluster, there is plenty of issues with almost everything :) M |
| Date Modified | Username | Field | Change |
|---|---|---|---|
| 2013-10-17 19:53 |
|
New Issue | |
| 2013-10-17 21:49 | wyldckat | Note Added: 0002562 | |
| 2013-10-18 08:45 |
|
Note Added: 0002563 | |
| 2013-10-18 08:51 | wyldckat | Note Added: 0002564 | |
| 2013-10-18 08:54 |
|
Note Added: 0002565 | |
| 2015-01-01 14:28 | henry | Status | new => closed |
| 2015-01-01 14:29 | henry | Assigned To | => henry |
| 2015-01-01 14:29 | henry | Resolution | open => unable to reproduce |
