[AMBER] GAMD not running in CPU cluster

From: Midhun K Madhu <midhunk16.iiserb.ac.in>
Date: Mon, 15 Oct 2018 16:49:18 +0530

Hi all,

I was trying to run Gaussian accelerated MD in pmemd.MPI using the
following command:

mpirun -machinefile $PBS_NODEFILE -np $NPROCS $AMBERHOME/bin/pmemd.MPI -O
-i protein.mdin -o protein.out -p protein.prmtop -c protein-prev.rst -r
protein.rst -x protein.nc -inf protein.mdinfo -e protein.e -gamd gamd.log

but I am getting the following error:

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
/var/spool/PBS/mom_priv/epilogue: line 30: kill: (26340) - No such process

It also says:

  unknown flag: gamd.log

  usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
              [-ref refc -x mdcrd -v mdvel -frc mdfrc -e mden -inf mdinfo
-l logfile]
              [-ng numgroups -groupfile groupfile -rem remd_method]
              [-amd amdlog_name -gamd gamdlog_name -scaledMD
scaledMDlog_name -suffix output_files_suffix]

The same command was working fine with pmemd.cuda.MPI, in a GPU machine.
How can I fix this?

Ph.D Student
Dept. of Biological Sciences
IISER Bhopal
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Received on Mon Oct 15 2018 - 04:30:02 PDT
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