On Sun, Apr 20, 2014 at 12:55 AM, Arunima Shilpi <writetoash28.gmail.com>wrote:
> Dear Sir
>
> While running the following command for entropy the following error is seen
>
> #!/bin/sh
> #PBS -N SAH1
> #PBS -l select=1:ncpus=8
> #PBS -j oe
> #PBS -q small
>
> cd $PBS_O_WORKDIR > pwd
> cat $PBS_NODEFILE > pbsnodes
>
>
> /opt/intel/impi/4.1.0.024/intel64/bin/mpirun -machinefile $PBS_NODEFILE
> -np
> 8 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa_nm.in -o
> FINAL_RESULTS_MMPBSA3.dat -sp 3pta_SAH_solvated.prmtop -cp 3pta_SAH.prmtop
> -rp 3pta.prmtop -lp SAH.prmtop -y *.mdcrd > progress.log 2>&1
>
> The error is as follows
>
> CalcError: /opt/apps/AMBER/ROOT/amber12/bin/mmpbsa_py_nabnmode failed with
> prmtop 3pta_SAH.prmtop!
> Error occured on rank 4.
> Exiting. All files have been retained.
>
> FATAL: allocation failure in vector()
> FATAL: allocation failure in vector()
> FATAL: allocation failure in vector()
> FATAL: allocation failure in vector()
> FATAL: allocation failure in vector()
>
> I request you to kindly guide me in debugging the error.
>
It looks like you don't have enough memory. If all 8 threads are running
on a single node, it will require about 8 times the amount of memory
required using only 1 processor.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Apr 19 2014 - 23:30:03 PDT
