Hello Jeff,
Thank you for replying. I ran it using PBS like this:
#!/bin/bash
#PBS -l nodes=2:ppn=32
#PBS -N cond_0_h3
#PBS -o cond_0_h3.o
#PBS -e cond_0_h3.e
PATH=$PATH:/usr/mpi/intel/openmpi-1.10.3/bin
LD_LIBRARY_PATH=/share/apps/composerxe-2011.2.137/lib/intel64:$LD_LIBRARY_PATH
cd $PBS_O_WORKDIR
mpirun -np 64 ./flash4
Besides that, my .bashrc has the following lines:
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
#irya.guido.intel
export PATH=$PATH:/home/guido/libraries/compiled_with_intel/hdf5-1.8.20/bin
export
INCLUDE=$INCLUDE:/home/guido/libraries/compiled_with_intel/hdf5-1.8.20/include
export
CPATH=$CPATH:/home/guido/libraries/compiled_with_intel/hdf5-1.8.20/include
export
LIBRARY_PATH=$LIBRARY_PATH:/home/guido/libraries/compiled_with_intel/hdf5-1.8.20/lib
export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/guido/libraries/compiled_with_intel/hdf5-1.8.20/lib
###intel open-mpi system###
export PATH=$PATH:/usr/mpi/intel/openmpi-1.10.3/bin
export INCLUDE=$INCLUDE:/usr/mpi/intel/openmpi-1.10.3/include
export CPATH=$CPATH:/usr/mpi/intel/openmpi-1.10.3/include
export LIBRARY_PATH=$LIBRARY_PATH:/usr/mpi/intel/openmpi-1.10.3/lib
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/mpi/intel/openmpi-1.10.3/lib
##anaconda 3 ##
export PATH="$PATH:/home/guido/anaconda3/bin" # commented out by conda
initialize
# Intel
export
PATH=$PATH:/share/apps/composerxe-2011.2.137/composerxe-2011.2.137/bin/intel64/
export
INCLUDE=$INCLUDE:/share/apps/composerxe-2011.2.137/composerxe-2011.2.137/bin/intel64/
export
CPATH=$CPATH:/share/apps/composerxe-2011.2.137/composerxe-2011.2.137/bin/intel64/
export
LIBRARY_PATH=$LIBRARY_PATH:/share/apps/composerxe-2011.2.137/composerxe-2011.2.137/bin/intel64/
export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/apps/composerxe-2011.2.137/composerxe-2011.2.137/bin/intel64/
How Can I check that what you suggested was the reason for this error?
Cheers,
El jue., 5 dic. 2019 a las 18:02, Jeff Squyres (jsquyres) (<
jsquy...@cisco.com>) escribió:
> How did you try to execute your application?
>
> An error message like this can mean that you accidentally mixed versions
> of Open MPI within your run (e.g., used Open MPI va.b.c on node A but used
> Open MPI vx.y.z on node B).
>
>
> > On Dec 5, 2019, at 5:28 PM, Guido granda muñoz via users <
> users@lists.open-mpi.org> wrote:
> >
> > Hello open-mpi users,
> > I'm getting some problem while using openmpi-1.10.3. The executable was
> compiled using : (ldd output)
> >
> > linux-vdso.so.1 => (0x00007fffd9e8b000)
> > libhdf5.so.10 =>
> /home/guido/libraries/compiled_with_intel/hdf5-1.8.20/lib/libhdf5.so.10
> (0x00002ac4313c4000)
> > libhdf5_fortran.so.10 =>
> /home/guido/libraries/compiled_with_intel/hdf5-1.8.20/lib/libhdf5_fortran.so.10
> (0x00002ac4319ca000)
> > libz.so.1 => /lib64/libz.so.1 (0x00002ac431c2d000)
> > libmpi_usempif08.so.11 =>
> /usr/mpi/intel/openmpi-1.10.3/lib/libmpi_usempif08.so.11
> (0x00002ac431e44000)
> > libmpi_usempi_ignore_tkr.so.6 =>
> /usr/mpi/intel/openmpi-1.10.3/lib/libmpi_usempi_ignore_tkr.so.6
> (0x00002ac432077000)
> > libmpi_mpifh.so.12 =>
> /usr/mpi/intel/openmpi-1.10.3/lib/libmpi_mpifh.so.12 (0x00002ac432280000)
> > libmpi.so.12 => /usr/mpi/intel/openmpi-1.10.3/lib/libmpi.so.12
> (0x00002ac4324df000)
> > libm.so.6 => /lib64/libm.so.6 (0x00002ac4327e7000)
> > libpthread.so.0 => /lib64/libpthread.so.0 (0x00002ac432a6b000)
> > libc.so.6 => /lib64/libc.so.6 (0x00002ac432c88000)
> > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002ac43301d000)
> > libdl.so.2 => /lib64/libdl.so.2 (0x00002ac433233000)
> > libimf.so =>
> /share/apps/composerxe-2011.2.137/composerxe-2011.2.137/compiler/lib/intel64/libimf.so
> (0x00002ac433437000)
> > libsvml.so =>
> /share/apps/composerxe-2011.2.137/composerxe-2011.2.137/compiler/lib/intel64/libsvml.so
> (0x00002ac43381b000)
> > libintlc.so.5 =>
> /share/apps/composerxe-2011.2.137/composerxe-2011.2.137/compiler/lib/intel64/libintlc.so.5
> (0x00002ac433ec3000)
> > libifport.so.5 =>
> /share/apps/composerxe-2011.2.137/composerxe-2011.2.137/compiler/lib/intel64/libifport.so.5
> (0x00002ac434013000)
> > libifcore.so.5 =>
> /share/apps/composerxe-2011.2.137/composerxe-2011.2.137/compiler/lib/intel64/libifcore.so.5
> (0x00002ac43414c000)
> > libopen-rte.so.12 => /usr/mpi/intel/openmpi-1.10.3/lib/libopen-rte.so.12
> (0x00002ac4343ad000)
> > libopen-pal.so.13 => /usr/mpi/intel/openmpi-1.10.3/lib/libopen-pal.so.13
> (0x00002ac43464e000)
> > librt.so.1 => /lib64/librt.so.1 (0x00002ac43496a000)
> > libutil.so.1 => /lib64/libutil.so.1 (0x00002ac434b72000)
> > libifcoremt.so.5 =>
> /share/apps/composerxe-2011.2.137/composerxe-2011.2.137/compiler/lib/intel64/libifcoremt.so.5
> (0x00002ac434d76000)
> > /lib64/ld-linux-x86-64.so.2 (0x00002ac4311a2000)
> >
> > When I run it, I get the following message:
> >
> > [compute-0-34.local:17553] [[5279,0],0] mca_oob_tcp_recv_handler:
> invalid message type: 15
> >
> --------------------------------------------------------------------------
> > mpirun noticed that the job aborted, but has no info as to the process
> > that caused that situation.
> >
> > The executable was also compiled using hdf5-1.8.20
> > I really don't know wht this error means, could please help me?
> > Cheers,
> > --
> > Guido
>
>
> --
> Jeff Squyres
> jsquy...@cisco.com
>
>
--
Guido
