Can you send me off-list your topology file? I will see if I can find out
what's wrong with it.
On Thu, Sep 24, 2015 at 6:55 AM, Damiano Spadoni <enxds6.nottingham.ac.uk>
wrote:
> Dear Ambers,
>
> try running enzymes simulations an hpc ARCHER, I often receive the same
> error text whatever I change in my input file:
>
> | ERROR: PMEMD does not support intermolecular PRFs!
>
> As you suggested, I checked my topology file with checkValidity (this kind
> of errors may due to something wrong in the .prmtop file) and it detected
> two CYS residues being within 3A distance and it suggested to change the
> name of the residues and build a disulfide bond, without specifying which
> cysteines it is referring about.
> But the only cysteines that might be so close, are actually involved in
> binding a 4Fe-4S cluster (already double checked on VMD).
>
> So the questions are:
> - might it be a bug justifying its panicking error texts?
- how to manually edit such residues to avoid this close contact (if you
> suggest so)?
>
> Many thanks
> Damiano
>
> ________________________________________
> From: David A Case [david.case.rutgers.edu]
> Sent: 18 August 2015 15:12
> To: AMBER Mailing List
> Subject: Re: [AMBER] hpc error
>
> On Tue, Aug 18, 2015, Damiano Spadoni wrote:
> >
> > I am trying to run the following script, involving a production step of
> > my simulation, on an hpc facility:
> >
> > #!/bin/bash --login
> >
> > #PBS -N S4F4_md
> > #PBS -l walltime=24:00:00
> > #PBS -l select=4
> > #PBS -j oe
> > #PBS -A e280-Croft
> >
> > module load amber
> >
> > cd /work/e280/e280/enxds6/SF4
> >
> > aprun -n 96 sander.MPI -O -i S4F4_md.in -o S4F4_md1.out -p SF4.prmtop -c
> > S4F4_heat.rst -r S4F4_md1.rst -x S4F4_md1.mdcrd
> > aprun -n 96 sander.MPI -O -i S4F4_md.in -o S4F4_md2.out -p SF4.prmtop -c
> > S4F4_md1.rst -r S4F4_md2.rst -x S4F4_md2.mdcrd
> ....
>
> Oh my goodness....
>
> (1) When things are not working, start simple (a single sander run, not 6
> of then in sequence).
> (2) sander will almost certainly perform very badly (if at all)
> on 96 processors. Try running on 2 or 4 to start. Then you can test the
> timing of larger numbers.
>
>
> > partition error in shake on processor 2
> > this processor has atoms 13055 through 19568
> > atom 19568 is within this range
> > atom 19569 is not within this range !
>
> You should look at the output file from the part of the run that failed.
> Is it really running on 96 processors? How many atoms are in your system?
> (Message above suggests that you have some 13000 atoms per processor....)
> If you have a million atoms or more, try running your script a much smaller
> system, then gradually build up. Consider whether or not you can use pmemd
> instead of sander.
>
> > It is the first time I am trying tu run this simulation on a cluster, I
> > previously ran (just the first sander.MPI command) it on my machine and
> > it worked, but I want to repeat this simulation on a cluster.
> > Any suggestions about something I'm probably missing?
>
> Was your local run also with the same number of processors? The "partition
> error" means that the system is trying to SHAKE (constrain) the bond
> between
> atoms 19568 and 19569. Check these atoms: is atom 19569 a hydrogen that is
> bonded to atom 19568? Are those two atoms in different residues?
>
> It is possible that partition errors can arise, depending on how complex
> your
> system is. Since this depends on the number of processors you are using,
> it
> could well show up on a cluster but not on a "local machine" (which, I'm
> guessing, has fewer than 96 cores.)
>
> Using the "checkValidity" command in parmed may help you localize the
> problem.
>
> ...good luck...dac
>
>
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 24 2015 - 05:30:04 PDT
