[gmx-users] Split Trajectory file into parts
johnny.lu128 at gmail.com
Wed Sep 2 05:11:36 CEST 2015
The file system seemed to have no quota, after checking with that command.
The problem seems to be that the simulation I set up save too quickly for
the file system.
Splitting the trajectory into parts only alleviated but not solved the
in the end I ran the simulation at another place.
On Mon, Aug 31, 2015 at 3:50 AM, Peter Kroon <p.c.kroon at rug.nl> wrote:
> 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
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