Hi Amber experts,
We had pmemd.MPI (amber 14) installed correctly and running, but after a disk addition to our cluster it fails to run, we try to run pmemd.MPI with the following setup
> source /usr/local/amber14/setup.csh
which contains the following definitions
> more /usr/local/amber14/setup.csh
#!/bin/csh -f
#
# Setup for Amber 14
#
setenv AMBERHOME /usr/local/amber14
setenv PATH $AMBERHOME/bin:$PATH
setenv LD_LIBRARY_PATH $AMBERHOME/lib:$LD_LIBRARY_PATH
and sets the MPI path as follows:
> which mpirun
/usr/local/amber14/bin/mpirun
we get the following error message:
> mpirun -np 12 pmemd.MPI
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
it seems that the "numtasks" parameter is not passed to the pmemd.MPI executable.
We would quite appreciate any help, and are ready to provide any additional
information regarding the AMBER 14 installation and compilation on our system.
All the other non-MPI programs including pmemd or sander run fine.
Regards,
Yulia Halupovich,
Technion - CIS, TAMNUN Team
phone: 972-4-8292654, fax: 972-4-8236212
Reply-to: hpc.technion.ac.il
Thansk a lot,
Fabian
_______________________________
Fabian Glaser, PhD
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
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Received on Sun Dec 21 2014 - 06:30:03 PST
