[gmx-users] Re: any chance to write avoid writing out trr but only xtc file ?

Jörn-Benjamin Lenz joern.lenz at screeningport.com
Wed Dec 2 14:37:05 CET 2009


here is what the is written out if I remove on eof the trr files during the REMD simulation although the xtc files should still be written out.
just for your information: I am not out of quota. that I can promise !!!
Any ideas why the program behaves like this ? 
Is there anything that was changed in gromacs which could explain this ?
Another additional info on the problem: 
I used the older gromacs versions with lam mpi. now i compiled it against mpich2. Could that be the problem ? 
If so, does anyone have an idea how to circumvent it, i.e. still being able to write out xtc files while the trr files are deletetd and the job does not crash ?
Cheers and many thanks,

step 5600, will finish Thu Dec 10 09:43:05 2009
step 5700, will finish Thu Dec 10 09:41:10 2009
step 5800, will finish Thu Dec 10 09:39:19 2009
step 5900, will finish Thu Dec 10 07:51:36 2009
step 6000, will finish Thu Dec 10 07:51:39 2009

Program mdrun_mpi, VERSION 4.0.5
Source code file: trnio.c, line: 252

File input/output error:
Cannot write trajectory frame; maybe you are out of quota?

"Make the Floor Burn" (2 Unlimited)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 5

gcq#181: "Make the Floor Burn" (2 Unlimited)

[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
mdrun07 REMD finished
ln: accessing `traj0.trr': No such file or directory
ln: accessing `traj1.trr': No such file or directory
ln: accessing `traj2.trr': No such file or directory
ln: accessing `traj3.trr': No such file or directory
ln: accessing `traj4.trr': No such file or directory

Jörn-Benjamin Lenz wrote:
> thanks you xavier and justin for your answers on my problem, however, i still
> wonder why i could completely delete the e.g. five trr files (from an REMD
> simulation on our cluster) named trajX.trr (with X = 0..4) and the
> corresponding xtc files (trajX.xtc) were still written out in one of the
> former gromacs versions. now this is not possible any more, i.e. as soon as i
> delete one of the trajX.trr files, the whole simulation breaks. does anyone

Do you get any sort of error?  I would think mdrun would at least report the I/O 
problem.  I don't know what the difference would be in this regard between the 
older and newer versions, but perhaps some changes were made such that mdrun 
expects all files standard output files to be present (perhaps to allow for the 
use of checkpointing?).  Just a guess, but certainly Xavier's solution is much 
more elegant.  My approach is usually to save very few frames (nstxout, etc = 
large # of steps), but certainly setting these parameters to zero is even better!


More information about the gromacs.org_gmx-users mailing list