[gmx-users] error in running jobs in parallel !!!

delara aghaie d_aghaie at yahoo.com
Sat Apr 16 11:06:27 CEST 2011

Dear Justin
thanks for your previous explanations.
We are running job with gromacs in parallel. after having the outpus of the first run, when submitting the jobs for the next 10ns we encounter with this error. can you help me to fix that. Pleas let me know the possible reasons to see this kind of error.
Best wishes
D. Aghaie

tarting mdrun '3840 water (TIP4P-2005) molecules'
5000000 steps,  10000.0 ps.
NOTE: Turning on dynamic load balancing
[HPC-0-12.local:26592] *** An error occurred in MPI_Waitall
[HPC-0-12.local:26592] *** on communicator MPI_COMM_WORLD
[HPC-0-12.local:26592] *** MPI_ERR_TRUNCATE: message truncated
[HPC-0-12.local:26592] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
mpirun has exited due to process rank 2 with PID 26592 on
node HPC-0-12 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--- On Sat, 4/16/11, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] the ligand have more than one molecules
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Saturday, April 16, 2011, 3:38 AM

ahmet yıldırım wrote:
> Dear users,
> Is there anyone has a tutorial of the ligand have more than one molecules?

Perhaps you can describe in more detail what it is you hope to accomplish.  The procedure for dealing with multiple ligands is, in principle, no different from a single ligand.  There are not tutorials available for every variation of a procedure.


> For example:
> *_topol.top:_*
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> *ligandname  *         3
> Thanks in advance
> -- Ahmet YILDIRIM

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

-- gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110416/d617bb16/attachment.html>

More information about the gromacs.org_gmx-users mailing list