restarting suspended namd jobs

From: J. Rui Rodrigues (
Date: Mon Nov 10 2003 - 13:56:54 CST


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

Any idea on how to solve this?

Here is my submission script:
#PBS -q centopeia_i_at_pata38.fisica
#PBS -l nodes=8
#PBS -l cput=100:00:00
#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

Rui Rodrigues

J. Rui Rodrigues
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra

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