[gmx-users] Split Trajectory file into parts

Peter Kroon p.c.kroon at rug.nl
Mon Aug 31 09:50:52 CEST 2015

On 29/08/15 16:22, Justin Lemkul wrote:
> On 8/29/15 9:10 AM, Johnny Lu wrote:
>> Dear Users,
>> Simulation writes to a Lustre file system (a distributed file system
>> made
>> of many hard drives).
>> About 100 Gb was written in 1 hrs. After a while, gromacs 5.1 says it
>> can't
>> write the trajectory file.
>> The file system still has lots of space. Not sure if that was because
>> one
>> of the many hard drives filled up.
Does your cluster implement filesystem quotas? Did you reach it? On our
cluster (which also uses Lustre) I use `lfs quota /home` to see my quota
and usage on the partition /home.

>> Is it possible to ask gromacs to automatically split the trajectory
>> files
>> into parts?
> No.
>> Or, I have to write a shell script to make gromacs restart the
>> simulation
>> every 15 minutes?
> Yes.  Or, heed what grompp tells you about how much data will be
> generated and simply construct a very trivial loop to execute mdrun
> for N steps, invoke convert-tpr, mdrun -cpi -noappend, etc.
> -Justin

More information about the gromacs.org_gmx-users mailing list