[gmx-users] error in running jobs in parallel !!!
Mark.Abraham at anu.edu.au
Sat Apr 16 11:12:01 CEST 2011
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.
> 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
> 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
> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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