[AMBER] : Can a Nudged elastic band (NEB) job run on a single GPU?

From: Li, Dailin <d.li.northeastern.edu>
Date: Fri, 7 Dec 2018 22:16:11 +0000

Hi,

I have tried running with pmemd.cuda.MPI by the following commands and everything is ok.

export CUDA_VISIBLE_DEVICES=0,1
mpirun -np 2 pmemd.cuda.MPI -O -i ....

For the NEB job, I tried the following commands and got the same error as before:

export CUDA_VISIBLE_DEVICES=0,1
mpirun -np 16 pmemd.cuda.MPI -ng 16 -groupfile groupfile

Anyway, thanks a lot for your reply.

Regards,
Dailin

-----ʼԭ-----
: Ghoreishi, Delaram <delaram.phys.ufl.edu>
ʱ: 2018127 16:10
ռ: AMBER Mailing List <amber.ambermd.org>
: Re: [AMBER] Can a Nudged elastic band (NEB) job run on a single GPU?

This seems like an Open MPI error, not an Amber one. Apparently, you are oversubscribing your processors. Look here for info:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.open-mpi.org%2Ffaq%2F%3Fcategory%3Drunning%23oversubscribing&amp;data=02%7C01%7Cd.li%40northeastern.edu%7Cabc50ddf04e54e890bc508d65c886fd1%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636798138453770686&amp;sdata=Xk0elhTK0IQP%2BkmZrsqFn90D1iNdxdSWKaYzfY1sZx0%3D&amp;reserved=0
Have you tried running your simulations with pmemd.MPI? If yes, do you receive the same error message?

I suggest trying the NEB simulation with a fewer number of replicas, maybe 16.

Best,
Delaram



________________________________________
From: Li, Dailin <d.li.northeastern.edu>
Sent: Friday, December 7, 2018 3:09 PM
To: AMBER Mailing List
Subject: [AMBER] : Can a Nudged elastic band (NEB) job run on a single GPU?

Hi Delaram,



Thanks a lot for your reply. I have issued mpirun -np 32 $AMBERHOME/bin/pmemd.cuda.MPI -ng 32 -groupfile groupfile on the 2-GPU platform and got the error as below:



There are not enough slots available in the system to satisfy the 32 slots that were requested by the application:

  pmemd.cuda.MPI

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



Is there any methods to let the command work? Thanks.



Regards,

Dailin



-----ʼԭ-----

: Ghoreishi, Delaram <delaram.phys.ufl.edu>

ʱ: 2018127 14:49

ռ: AMBER Mailing List <amber.ambermd.org>

: Re: [AMBER] Can a Nudged elastic band (NEB) job run on a single GPU?



Hi Dailin,



1) The MPI size (number of processors that you ask in the -np flag) should be a multiple of the number of replicas (that you state in the -ng flag). With 32 replicas your command should look like this:

mpirun -np 32 $AMBERHOME/bin/pmemd.cuda.MPI -ng 32 -groupfile groupfile For optimum Amber performance, you need to have 32 GPUs available when you execute this command, however, this command is still going to work if you have a fewer number of GPUs. But the computational performance is not going to be efficient. As you are overloading a single GPU with calculations that would otherwise be executed on other cards, you should see a drastic decrease in the performance. Thus, not a good idea.



2) NEB is an MPI job and is set to run with pmemd.MPI or pmemd.cuda.MPI only.



All the best,

Delaram



________________________________________

From: Li, Dailin <d.li.northeastern.edu>

Sent: Friday, December 7, 2018 2:11 PM

To: amber.ambermd.org

Subject: [AMBER] Can a Nudged elastic band (NEB) job run on a single GPU?



Hi,



I want to do NEB computations on GPUs. There are 32 images in the NEB job and only 2 GPUs could be used. When the job was submitted to the 2 GPUs, error concerning number of GPUs is not multiple will appear.



(1) Is it possible to do the NEB job on 2 GPUs? If yes, then how? Amber18 manual says "In case pmemd.cuda.MPI is used, it is best that the number of GPUs is equal to the number of images". Does "it is best" mean "it is required"?



(2) Is it possible to do the NEB job with pmemd.cuda, which means only 1GPU is used?



Thanks.



Regards,



Dailin

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Received on Fri Dec 07 2018 - 14:30:02 PST
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