From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jan 25 2016 - 01:06:05 CST
Ok, but the error you posted
Fatal error on Partition 0 PE 0> REPLICA 0 FATAL ERROR: Unknown command-line
option +devices
just tells you didn't use a cuda enabled namd.
So what error or problem comes up, when using the proper binary?
Norman Geist
Von: Abhishek TYAGI [mailto:atyagiaa_at_connect.ust.hk]
Gesendet: Samstag, 23. Januar 2016 20:05
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Cc: namd-l_at_ks.uiuc.edu
Betreff: Re: Enabling GPU for Replica exchange umbrella sampling
Hi Norman,
I had tried using CUDA enabled NAMD on gpu cluster. I can run normal
simulations, however when I am trying to use this version for Replica
exchange umbrella sampling, it got failed. I had even tried to install
source code on the cluster and observed the error. Previously I had
discussed this issue on mailing list and comeup with the recent version of
NAMD that I am using now.
The cluster node is 4 GPU k20 2 CPU 32 core.
I tried using other versions, but unable to execute the command.
Thanks
Abi
Abhishek Tyagi
PhD Student
Chemical and Biomolecular Engineering
Hong Kong University of Science and Technology
Clear Water Bay, Hong Kong
_____
From: Norman Geist < <mailto:norman.geist_at_uni-greifswald.de>
norman.geist_at_uni-greifswald.de>
Sent: Friday, January 22, 2016 5:09 PM
To: Abhishek TYAGI
Cc: <mailto:namd-l_at_ks.uiuc.edu> namd-l_at_ks.uiuc.edu
Subject: AW: Enabling GPU for Replica exchange umbrella sampling
BTW. you need to use a CUDA enabled built of NAMD.
Norman Geist
Von: Abhishek TYAGI [mailto:atyagiaa_at_connect.ust.hk]
Gesendet: Freitag, 22. Januar 2016 05:03
An: Namd Mailing List < <mailto:namd-l_at_ks.uiuc.edu> namd-l_at_ks.uiuc.edu>
Cc: <mailto:norman.geist_at_uni-greifswald.de> norman.geist_at_uni-greifswald.de;
<mailto:aliigleed16_at_gmail.com> aliigleed16_at_gmail.com
Betreff: 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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