AW: Re: Enabling GPU for Replica exchange umbrella sampling

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Jan 22 2016 - 03:07:59 CST

Please give some info on:

 

How many nodes do you have?

How many cores and gpus does one node have?

 

Norman Geist

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Abhishek TYAGI
Gesendet: Freitag, 22. Januar 2016 05:03
An: Namd Mailing List <namd-l_at_ks.uiuc.edu>
Cc: norman.geist_at_uni-greifswald.de; aliigleed16_at_gmail.com
Betreff: namd-l: Re: Enabling GPU for Replica exchange umbrella sampling

 

Hi,

 

I am working on the tutorial "One-dimensional replica-exchange umbrella
sampling".

 

I tried to follow the following script mentioned
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/2522.html
, still not able to combine GPU with CPU on cluster.

export cores=16
export coresPerReplica=1
export replicas=`echo "$cores / $coresPerReplica" | bc`
for (( i = 0; i < $replicas; i++ )); do mkdir -p output/$i; done

Any help appreciated.

Thanks

Abhi

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

 

 

  _____

From: <mailto:owner-namd-l_at_ks.uiuc.edu> owner-namd-l_at_ks.uiuc.edu <
<mailto:owner-namd-l_at_ks.uiuc.edu> owner-namd-l_at_ks.uiuc.edu> on behalf of
Abhishek TYAGI < <mailto:atyagiaa_at_connect.ust.hk> atyagiaa_at_connect.ust.hk>
Sent: Thursday, January 21, 2016 11:12 AM
To: Namd Mailing List
Subject: namd-l: Enabling GPU for REUS

 

Hi,

 

I am using REUS for the system of 42 k atoms. I have a problem in increasing
benchmark time for the MD. I have cluster resource in which I have access to
1 node (4 GPU (K20) and 32 cores CPU), therefore, I can run REUS for 16
windows (2 cores 1 window).

I had checked the previously discussed link
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/2522.html
, it is helpful to some extent but I am not using mpi, the command I am
following is:

NAMD_2.11_Linux-x86_64-netlrts/charmrun NAMD_2.11_Linux-x86_64-netlrts/namd2
++ppn 2 +p32 +replicas 16 job0.conf +stdout output/%d/job0.%d.log

 

After executing above command the REUS implicated on 32 cores, not on GPU.
The system right now on 32 core CPU. The benchmark time right now is 10
day/ns.

 

Than, I had modified the command and added +devices 0,1,2,3 :

 

NAMD_2.11_Linux-x86_64-netlrts/charmrun NAMD_2.11_Linux-x86_64-netlrts/namd2
+devices 0,1,2,3 ++ppn 2 +p32 +replicas 16 job0.conf +stdout
output/%d/job0.%d.log

 

It produces error :

Charmrun> scalable start enabled.
Charmrun> started all node programs in 5.236 seconds.
Charm++> Running in non-SMP mode: numPes 32
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Charm++> TORUS A SIZE 32 USING 0 1 2 3 4 5 6 7 8 9...
Charm++> TORUS B SIZE 1 USING 0
Charm++> TORUS C SIZE 1 USING 0
Charm++> TORUS MINIMAL MESH SIZE IS 32 BY 1 BY 1
Redirecting stdout to files output/0/job0.0.log through 15
------- Partition 0 Processor 0 Exiting: Called CmiAbort ------
Reason: REPLICA 0 FATAL ERROR: Unknown command-line option +devices

Fatal error on Partition 0 PE 0> REPLICA 0 FATAL ERROR: Unknown command-line
option +devices

I want to utilize the GPU with CPU, however I am not able to do it. Can
anyone suggest to solve this problem.

Thanks in advance
Abhi

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

 

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