[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

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?


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