AMBER Archive (2009)

Subject: RE: [AMBER] Problems with running two separate jobs in the same time

From: Antonija Tomić (Antonija.Tomic_at_irb.hr)
Date: Thu Apr 09 2009 - 05:33:03 CDT

Hi Ross

to answer your questions:

  1) I am running these jobs in separate directories
  2) I have enough free disc space because I have just bought this
computer (I have over 700GB of free disc space).
  3) I am not using MVAPICH
  4) I have AMBER 10 installed on my computer. I have no experience
with PMEMD but I could try that in future.

But before that I would like to understand what is going wrong i.e.
why can't I do two separate steered molecular dynamics in sender on my
computer because I think that it should be capable of doing that. I
have computer with 2 processors each having 4 core (Intel Xeon
Quad-Core E5420 processor (2.50 GHz, 2 x 6 MB L2 cache, 1333 MHz FSB),
memory: 3.0GiB).

For example, I am running two same steered molecular dynamics for two
different molecules and they look like:

#input for steered dynamics_pulling two atoms

  &cntrl

    imin=0, scnb=2.0,

    nstlim=100000, cut=11.0, igb=0,

    ntpr=10000, ntwr=10000, ntt=3, gamma_ln=1.0,

    ntx=1, ntwx=10000, ig = 99931,

    ntc=2, ntf=2, tol=0.000001,

    dt=0.001, ntb=2, ntp=1, tempi=0., temp0=100.,

    jar=1,

  /

  &wt type='DUMPFREQ', istep1=1 /

  &wt type='END' /

DISANG=distP1_1.RST

DUMPAVE=dist_vs_t

LISTIN=POUT

LISTOUT=POUT

where distP1_1.RST is:

# Change distance between two group of atoms from 2.57 A to 2.1 A

  &rst iat=-1,-1, igr1=11365, igr2=11394,11397, r2=2.57, rk2 = 500., r2a=2.1 /

I would be very grateful if you could help me. I don't understand why
at least I don't get any error messages.

Antonija

Citiram Ross Walker <ross_at_rosswalker.co.uk>:

> Hi Antonija,
>
> It would be helpful to understand exactly how you are running these
> jobs, what your computer environment looks like etc.
>
> A few things to check.
>
> 1) Are you running these jobs in separate directories? There can
> often be problems running in the same directory since the two codes
> will compete to overwrite certain files such as mdinfo and
> profile_mpi. Depending on your filesystem and whether it is local or
> network mounted this can cause all sorts of problems from minor to
> major performance degredation to complete lock up.
>
> 2) Do you have enough disk space free? Are you certain the two jobs
> running together are not filling the disk?
>
> 3) Do you have enough memory. It is possible that the two jobs
> running together are running out of memory since they have to share
> it. Often when something is killed because you ran out of memory you
> see no error message other than perhaps the word 'Killed'. Note if
> you are using MVAPICH there are numerous memory leaks in it,
> especially in v0.9.9. This means that the memory usage, for MPI
> buffers I believe, can increase linearly over time. With just one
> job running you may have enough memory + swap that you don't see any
> problems within the length of the run. With two jobs running you may
> be pushing things over the edge.
>
> 4) You don't mention the version of AMBER. You could try running the
> calculation in AMBER 10 PMEMD in place of sander. This, in parallel,
> will use less memory and so you may not encounter the same problems.
>
> Good luck,
> Ross
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org]
> On Behalf Of Antonija Tomic
> Sent: Tuesday, April 07, 2009 1:09 AM
> To: amber_at_ambermd.org
> Subject: [AMBER] Problems with running two separate jobs in the same time
>
> Hi
>
> for example, if I try to run two separate molecular dynamics or
> steered molecular dynamics (nstlim=100000) on my computer in the same
> time the processes stop after some time without any warnings or error
> messages, but when I start to run that same jobs one after another all
> processes finish successfully. I don't know what is going on because I
> don't get any warning messages. On the other hand I can do few
> separate optimization processes simultaneously without any trouble. I
> would be very grateful if someone could help me. I don't think that
> the problem is in my computer because I have a new computer.
>
> Antonija
>
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