RE: AMBER7 on linux cluster

From: Yong Duan <>
Date: Fri, 20 Jun 2003 21:35:04 -0400

Dear Venkata,

It may be a good idea to run a 10-step simulation to see if the problem
is related to compatibility of two version or something else. It is a
little difficult to wait for three days and get nothing. You can reduce
it to 2 steps if you are like me who is not terribly patient.
It would be relatively simple to fix the problem if it indeed is a
compatibility problem. What you can do, in that case and if you want to
preserve the coordinates, is to generate a PDB file on your SGI machine,
ship it to your cluster, read it through leap, addbox, save it, you will
be able generate a topology file for AMBER7 with identical system. You
may even be able to use the restart file.
Having said that, however, I am a little skeptical about the
compatibility problem.


-----Original Message-----
From: Venkata S Koppuravuri []
Sent: Friday, June 20, 2003 10:53 AM
To: Carlos Simmerling
Subject: Re: AMBER7 on linux cluster

Hi Dr.Simmerling,

The cluster works fine when i tried smaller structures. When I tried
to run the job interactively the error message was

mpiexec: Warning: main: task 2 died with signal 15
mpiexec: Warning: main: task 3 died with signal 15
=>> PBS: job killed: walltime # exceeded limit #

I did the same run on an sgi with 2 processors it took me about 3 days.
Then to check it on the cluster I reran it on the cluster(4nodes and
2ppn/node) giving the same walltime (3days) but still i get the same
error(as above) that walltime not sufficient.

2. When the job crashes because it exceeded the runtime limit I wonder
what happens to job directory and all the output files. It should have
atleast some of the calculations done. When i run the job in the current
directory rather in the TEMPDIR. I still have all the output files empty
nothing is written to them.

3. I have done the minimization of the structure on SGI using Amber5
i transfered the required files to the cluster(cluster has Amber7) to
equilibrate it. Is it possible that the cluster is NOT doing any
calculations because the files were generated on a different Amber

Can you please help me solve the problem


On Tue, 17 Jun 2003, Carlos Simmerling wrote:

> can you run a non-MPI job on the cluster?
> if so, does it work ok or also dies?
> are you using a batch scheduler? if so, sometimes
> the error messages may go into an output file
> created by the scheduler. run it interactively and
> you get errors messages and also you can be sure
> your working directory is correct, with schedulers
> you need to set it.
> ----- Original Message -----
> From: "Venkata S Koppuravuri" <>
> To: <>
> Sent: Tuesday, June 17, 2003 12:49 PM
> Subject: AMBER7 on linux cluster
> > Hi,
> >
> > I am a new user of AMBER7 on a LINUX cluster. When I tried to give a
> > simple equilibrating job to the cluster using 4 nodes and 2 pps on
> > node I got the following error message
> >
> > ------------------------------------
> > mpiexec: Warning: main: task 4 died with signal 15.
> > mpiexec: Warning: main: task 5 died with signal 15.
> > ------------------------------------
> >
> > All the output files are empty.
> >
> > Can anyone help me what the problem could be.
> >
> > (I did the minimization on an SGI machine using Amber5. i then
> > the output files to the cluster and tried to do equilibration.
> > uses AMBER7 . Hope this does not create a problem).
> >
> >
> > Regards
> > -Venkat
> >
> >
Received on Sat Jun 21 2003 - 02:53:01 PDT
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