[gmx-users] Can not open file; traj.trr

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 13 18:28:08 CET 2009



Yi Peng wrote:
> Hi, everyone,
>  
> I was using Gromacs-4.0.3 to run my MD calculations parallell on our 
> High performance clusters for a large system which was crashed because I 
> run out the time limits. So I tried to resume my calculations by the 
> script as follows:
>  
> #PBS -N gromacs
> #PBS -l walltime=250:00:00
> #PBS -l nodes=8:ppn=2:quad
> #PBS -j oe
> echo Using nodes
> cat $PBS_NODEFILE
> module load mpich
> module load intel-f
> module load gromacs-4.0.3
> cd $PBS_O_WORKDIR
> cd /home/yxp17/impd/impd1/wt_wo
> /usr/local/bin/mpiexec mdrun -multi 16 -s md.tpr -cpi state.cpt -append
>  
>  
> But it will stop and show the message as follows
>  
> "Whatever Happened to Pong ?" (F. Black)
> Halting program mdrun
> gcq#180: "Whatever Happened to Pong ?" (F. Black)
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> p0_12952:  p4_error: : -1
>     p4_error: latest msg from perror: No such file or directory
> -------------------------------------------------------
> Program mdrun, VERSION 4.0.3
> Source code file: gmxfio.c, line: 736
> Can not open file:
> traj.trr
> -------------------------------------------------------
> How can I solve the problem? Thanks a lot
>  

"No such file or directory" and "Can not open file" seem to clearly indicate to 
me that traj.trr does not exist, and thus cannot be appended, as you have 
requested with mdrun -append.

-Justin

> Yi
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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