From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Jun 24 2015 - 11:14:16 CDT
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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