Paymon Pirzadeh wrote:
Hello all,
A follow up from my previous problems on running the gromacs on glacier
turned out that I had problems in installation. The guide in the manual
was not clear enough. So, I installed the code fine this time, so, I get
errors from 4.0.4 version.
I ran the code interactively on the master node and everything went
smooth and fine without any problems. But as soon as I started running
it in parallel through que line, job gets killed. Following are the
messages I received:
PBS Job Id: 4686006.teva.westgrid.ubc
Job Name: sixsite-test
Exec host: ice1_2/1+ice1_2/0+ice1_1/1+ice1_1/0
Aborted by PBS Server
Job cannot be executed
The error messages I receive in error file:
Killed by signal 2.^M
Killed by signal 2.^M
Killed by signal 2.^M
Running on 4 processors.
Starting run at: Mon May 25 20:29:34 PDT 2009
p2_11876: p4_error: Timeout in establishing connection to remote
process: 0
p0_4273: p4_error: net_recv read: probable EOF on socket: 1
Job finished at: Mon May 25 20:34:40 PDT 2009
All the clues show that the program had started working, initial
conditions were reviewed by the code, but suddenly everything crashed. I
So what was at the end of stderr and stdout from the job? There's no
GROMACS output given here, so we've got no evidence of a non-cluster
GROMACS problem.
really do not know where the error originates from!!! This is while my
friend has compiled the code in the same way as I did, and she is
running fine on another cluster.
Make sure you've followed the instructions for parallel compilation and
execution for your facility and for GROMACS. Make a shell script that
does the build so that you can do a build reproducibly, check it has the
same problems and then ask for advice on it from your sysadmins or from
this list.
Mark
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