On Tue, Jul 23, 2013 at 8:58 AM, Changqing Yan <ycqchemical.gmail.com>wrote:
> *Dear Amber experts,*
> *
> *
> *Recently I want to run an entropy calculation. I always failed with the
> following error:*
>
> Line minimizer aborted: step at upper bound 0.0025465977
> Line minimizer aborted: step at upper bound 0.0010051508
> Line minimizer aborted: step at upper bound 0.0011997471
> Line minimizer aborted: step at upper bound 0.019940301
> Line minimizer aborted: step at upper bound 0.044056357
> FATAL: allocation failure in vector()
> CalcError: /opt/share/amber12/bin/mmpbsa_py_nabnmode failed with prmtop
> complex.prmtop!
> Error occured on rank 2.
> [snip]
>
>
> pbs_mpirun $AMBERHOME/bin/MMPBSA.py.MPI -O -i nmodeigb2e1.in -o
> nmodeigb2e1.dat -sp complex-sol.prmtop -cp complex.prmtop -rp
> protein.prmtop -lp ligand.prmtop -y
> /scratch/s1007018600/analysis/PBSA/salt/50/ligand-md1-3.binpos >
> progress.log
>
> date
>
>
> What is the problem? How can I fix it? Please advise!
>
There is typically only one reason the message "allocation failure in
vector()" arises in this case: you have run out of available RAM. Note
that normal mode calculations can consume incredibly large quantities of
RAM. Furthermore, you are trying to run 15 threads on the same node, which
means you must have enough RAM on your node to run 15 concurrent nmode
runs, which could be over 30 GB of required RAM.
Usual debugging advice: if something breaks in parallel, try it in serial
with a small number of frames to test it out. You will probably find that
when you do this, the error has something to do with running in parallel.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 23 2013 - 08:00:03 PDT
