Hello all,
I am trying to install ET with OpenMPI 2.1.0 but it seems to be causing issues.
I have done it successfully once with OpenMPI-x86_64 in our cluster, but it turns out this MPI is only available in the login node and not available on computing nodes, hence, I am not able to use it once a job is submitted in the queue.
I could find OpenMPI 2.1.0 being available on computing nodes, so I was trying to compile with this version. I created a module file to load this module before installation. I could see the following in the terminal, which I guess, ET could recognise OpenMPI 2.1.0:
Running configuration script for thorn MPI: MPI selected, but MPI_DIR is not set. Computing settings... Found MPI compiler wrapper at /opt/mpi/openmpi/2.1.0/bin/mpic++! Successfully configured MPI. Finished running configuration script for thorn MPI.
Later, the progress stops with the following error:
/home2/mallick/ET3/Cactus/configs/sim/lib/libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o): In function `MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)': /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/op_inln.h:121: undefined reference to `ompi_mpi_cxx_op_intercept' /home2/mallick/ET3/Cactus/configs/sim/lib/libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o): In function `Intracomm': /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/intracomm_inln.h:23: undefined reference to `MPI::Comm::Comm()' /home2/mallick/ET3/Cactus/configs/sim/lib/libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o): In function `Intracomm': /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/intracomm.h:25: undefined reference to `MPI::Comm::Comm()' /home2/mallick/ET3/Cactus/configs/sim/lib/libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o): In function `Cartcomm': /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/intracomm.h:25: undefined reference to `MPI::Comm::Comm()' /home2/mallick/ET3/Cactus/configs/sim/lib/libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o): In function `Graphcomm': /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/intracomm.h:25: undefined reference to `MPI::Comm::Comm()' /home2/mallick/ET3/Cactus/configs/sim/lib/libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o): In function `Intracomm': /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/intracomm.h:25: undefined reference to `MPI::Comm::Comm()' /home2/mallick/ET3/Cactus/configs/sim/lib/libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o):/usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/intracomm.h:25: more undefined references to `MPI::Comm::Comm()' follow /home2/mallick/ET3/Cactus/configs/sim/lib/libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o):(.rodata._ZTVN3MPI8DatatypeE[_ZTVN3MPI8DatatypeE]+0x78): undefined reference to `MPI::Datatype::Free()' /home2/mallick/ET3/Cactus/configs/sim/lib/libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o):(.rodata._ZTVN3MPI3WinE[_ZTVN3MPI3WinE]+0x48): undefined reference to `MPI::Win::Free()' /home2/mallick/ET3/Cactus/configs/sim/lib/libthorn_CarpetLib.a(backtrace.cc.o): In function `MPI::Intracomm::Intracomm()': /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/intracomm.h:25: undefined reference to `MPI::Comm::Comm()' /home2/mallick/ET3/Cactus/configs/sim/lib/libthorn_CarpetLib.a(backtrace.cc.o): In function `MPI::Intracomm::Intracomm(ompi_communicator_t*)': /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/intracomm_inln.h:23: undefined reference to `MPI::Comm::Comm()' collect2: error: ld returned 1 exit status make[1]: *** [/home2/mallick/ET3/Cactus/exe/cactus_sim] Error 1 make: *** [sim] Error 2
I could not figure out the issue here. It seems */usr/include/openmpi-x86_64/openmpi/ompi/mpi *is being taken by ET from somewhere and it is not taking OpenMPI 2.1.0.
Some suggestions would be very helpful. Thank you.
Regards Shamim Haque Senior Research Fellow (SRF) Department of Physics IISER Bhopal