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

[Mark Abraham]

On 16/04/2011 7:06 PM, delara aghaie wrote:
> 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.
>

Anything could cause that - including some problem with the hardware - 
and we can see no diagnostic information. Look at the .log file also. 
Try to run the .tpr in serial.

Mark

> Thanks
> 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.
>
>     -Justin
>
>     > 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
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
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