gmxcoco workflow on Bluewaters

[Ardita Shkurti]

Can anyone give a try to the gmxcoco on Bluewaters workflow?

Or if not, if anyone could have a look at: rp.session.moriarty.pharm.nottingham.ac.uk.ardita.016877.0003-pilot.0000/unit.000008/

This is the CU having to do with the coco analysis, and this CU fails. If one tries to execute the coco command as in rp.session.moriarty.pharm.nottingham.ac.uk.ardita.016877.0003-pilot.0000/unit.000008/radical_pilot_cu_launch_script.sh (that is pyCoCo "--grid" "30" "--dims" "3" "--frontpoints" "2" "--topfile" "md-0_0.gro" "--mdfile" "*.xtc" "--output" "coco_out_0.gro" "--logfile" "coco.log" "--selection" "protein") that will execute correctly.

Looking at rp.session.moriarty.pharm.nottingham.ac.uk.ardita.016877.0003-pilot.0000/unit.000008/STDERR we can notice the following:

MPI functionality is now available through bwpy-mpi.
To enable MPI packages `module load bwpy-mpi` after bwpy
assertion !pthread_create(&thr->thrH, &attr, rout, arg) failed, line 111 of file /u/sciteam/shkurti/atlas/ATLAS/intel/..//src/threads/ATL_thread_start.c

Any comments/suggestions?

[Vivek Balasubramanian]

I can't cd into your working directory.

 cd shkurti/
-bash: cd: shkurti/: Permission denied

Just to confirm, coco was compiled with the openmpi stack in /projects/sciteam/gkd/modules right ?

[Ardita Shkurti]

Can you try now for the access?

And yes, coco was compiled with the openmpi stack in /projects/sciteam/gkd/modules ...

[Vivek Balasubramanian]

cd scratch/
-bash: cd: scratch/: Permission denied

Also the specific pilot folder. Please try a recursive permission change with chmod -R

[Ardita Shkurti]

Does it work now?

[Vivek Balasubramanian]

Hmmm.. this seems to be an atlas specific error perhaps. thinks look fine in the shell script. I'm giving it a try too, but if the coco stage in coam example worked fine I wouldn't expect this to fail unless there is some change in data (?).

[Vivek Balasubramanian]

Update: I can reproduce this.

[Vivek Balasubramanian]

Old. This is probably fixed given our experiments in BW.