From: Alexander Tzanov (Alexander.Tzanov_at_csi.cuny.edu)
Date: Wed Jun 24 2015 - 13:37:01 CDT
HI Josh
Thanks for reply. I did not use charmrun in my scripts. However I downloaded and recompiled the newest version (06-2015) from your site with the same options as
before. Now the problem seems to me disapper and NAMD works fine on single node.
#!/bin/bash
#PBS -q production
#PBS -N apoa_job_nsf
#PBS -l select=1:ncpus=4:ngpus=2:mpiprocs=4
#PBS -l place=free
#PBS -V
cd $PBS_O_WORKDIR
NN=`cat $PBS_NODEFILE | wc -l`
echo "Processors received = "$NN >> myout
MM=`cat $PBS_NODEFILE`
echo "MM = "$MM >> myout
# Use 'mpirun' and point to the MPI parallel executable to run echo ">>>> Begin NAMD MPI Parallel Run ..."
mpirun -np 4 -machinefile $PBS_NODEFILE namd2 +idlepoll +devices 0,1 ./apoa1.namd > apoa1.out
====
Thanks. $PBS_NODEFILE reports correctly now:
Processors received = 4
MM = compute-0-21.ib compute-0-21.ib compute-0-21.ib compute-0-21.ib
Alex
On Jun 24, 2015, at 12:14 PM, Josh Vermaas <vermaas2_at_illinois.edu<mailto:vermaas2_at_illinois.edu>> wrote:
What does your submit script look like? The error message looks like one from mpirun, not NAMD, so there may be something obvious going on if we were to see what options were given.
-Josh Vermaas
On 6/24/15 11:03 AM, Alexander Tzanov wrote:
Just to clarify a bit more:
NAMD cannot use more than one core on a node. If I run with one core per node,
the NAMD runs. If I ask for more than one core i.e. 4 cores, I got the error:
--------------------------------------------------------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 4 slots
that were requested by the application:
namd2
Either request fewer slots for your application, or make more slots available
for use.
--------------------------------------------------------------------------
Thank you for your help.
Alex
On Jun 24, 2015, at 10:56 AM, Alexander Tzanov <Alexander.Tzanov_at_csi.cuny.edu<mailto:Alexander.Tzanov_at_csi.cuny.edu>> wrote:
Dear all,
I am trying to run NAMD 2.10 with CUDA support on single virtual node. My CUDA is 6.5.14. I am running
on IB cluster which runs PBS pro ver. 12.1.0.131281. I want to run on a single virtual node with
4 CPU cores and 2 GPU (the CPU itself has 16 cores). I compiled NAMD with cuda support
(mpi, smp CHARMM++ underneath). However when the NAMD cannot address more than one core.
As a result I get error “ Not enough slots”. Does anyone see the problem and if so to share his/her experience.
Thank you
Alex
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