From: J. Rui Rodrigues (jrui_at_ci.uc.pt)
Date: Mon Nov 10 2003 - 13:56:54 CST
Hi,
I am not sure if this is a namd question...
I am using NAMD 2.5 for Linux-i686 in a Pentium cluster running PBS.
This cluster has 2 execution queues for short and long jobs, the "short"
queue having priority over the "long" queue. When a short job is submitted
and there are no availables nodes, a job on the long queue is suspended until
the short job is completed.
My problem is that my namd runs are sent to the long queue and, after being
suspended, the job restarts from the beginning and not at the point it was
suspended.
Any idea on how to solve this?
Here is my submission script:
#!/bin/bash
#PBS -q centopeia_i_at_pata38.fisica
#PBS -l nodes=8
#PBS -l cput=100:00:00
#PBS -N NAMD
#PBS -o NAMD_prod.out
#PBS -e NAMD_prod.err
cd /home/biomd/WT
echo "group main" > mynodes
awk '{print " host " $0}' < $PBS_NODEFILE >> mynodes
/home/biomd/bin/charmrun ++verbose ++p 8 ++nodelist
mynodes /home/biomd/bin/namd2 /home/biomd/WT/prod.namd
>> /home/biomd/WT/prod.log
Thanks,
Rui Rodrigues
-- J. Rui Rodrigues Departamento de Química Faculdade de Ciências e Tecnologia Universidade de Coimbra 3004-535 Coimbra Portugal
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