[gmx-users] Error when for gmx tune_pme on Cray
Viveca Lindahl
vivecalindahl at gmail.com
Tue Apr 10 15:10:20 CEST 2018
Hi users,
I never used gmx tune_pme before and thought I'd try. On a Cray machine,
using aprun instead of mpirun, I did
args="/cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx
mdrun -pin on -quiet -stepout 5000 -ntomp 2 -noconfout"
export MPIRUN=aprun; aprun -n 1 $gmx tune_pme -npstring n -s topol.tpr -np
32 -mdrun "$args"
It hangs (no output) for some minutes, then I get the error
Program: gmx tune_pme, version 2018.1-dev-20180315-3dfa11852
Source file: src/gromacs/gmxana/gmx_tune_pme.cpp (line 740)
Fatal error:
Cannot execute mdrun. Please check benchtest.log for problems!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Making sure that mdrun can be executed. Trying 'aprun -n 32
/cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx mdrun -pin
on -quiet -stepout 5000 -ntomp 2 -noconfout -version -maxh 0.001 1>
benchtest.log 2>&1' ... Rank 0 [Tue Apr 10 14:58:12 2018] [c1-0c0s4n0]
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
the suggested log file to look in has
craylog: WARNING: log tmp dir /var/spool/cray/llm is not writable
aprun: Unable to contact apsys
aprun: Exiting due to errors. Application aborted
Am I doing something wrong or is this a bug/limitation of the system I am
trying to run on?
Thanks,
--
Viveca
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