Re: run on sungle node

From: Alexander Tzanov (
Date: Wed Jun 24 2015 - 11:03:24 CDT

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:

Either request fewer slots for your application, or make more slots available
for use.

Thank you for your help.


On Jun 24, 2015, at 10:56 AM, Alexander Tzanov <<>> 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. 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


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