[gmx-users] GROMACS on glacier.westgrid.ca

Paymon Pirzadeh ppirzade at ucalgary.ca
Thu May 28 18:35:45 CEST 2009

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
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.


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