RE: namd2 GPU error

From: Miraj Naik (Miraj.Naik_at_locuz.com)
Date: Tue Feb 20 2018 - 05:22:16 CST

Hello all,

Can anyone update on this error we are still enable to run application on GPU..

Thanks and Regards,
Miraj Naik
+91 9727264267

-----Original Message-----
From: Vermaas, Joshua [mailto:Joshua.Vermaas_at_nrel.gov]
Sent: 14 February 2018 23:44
To: namd-l_at_ks.uiuc.edu; Miraj Naik
Subject: Re: namd-l: namd2 GPU error

I recall a similar error message when I had a broken symlink, since otherwise the file should open just fine.
-Josh

On 02/14/2018 07:39 AM, Giacomo Fiorin wrote:
Please read the error message.

FATAL ERROR: Unable to open text file step4_equilibration.restart.xsc: File exists

On Tue, Feb 13, 2018 at 11:43 PM, Miraj Naik <Miraj.Naik_at_locuz.com<mailto:Miraj.Naik_at_locuz.com>> wrote:
Hello NAMD team,

I am trying to execute input file using NAMD 2.12 prebuild executable using following link.
https://apac01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FDevelopment%2FDownload%2Fdownload.cgi%3FUserID%3D%26AccessCode%3D%26ArchiveID%3D1499&data=02%7C01%7Cmiraj.naik%40mailone.locuz.com%7Cb8b8c2e525544db1349408d573d6ce42%7Cd47525bf602d4ed78c603db0ec37e266%7C0%7C0%7C636542288850851264&sdata=%2B%2Be0C9gw6nFj7PwEqZ7lgqgS2dSkln6FvXBkcWLp2ss%3D&reserved=0<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FDevelopment%2FDownload%2Fdownload.cgi%3FUserID%3D%26AccessCode%3D%26ArchiveID%3D1499&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Ccf69adbce31c4da206a208d573b8ac90%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636542159374983107&sdata=MnmR6b7bacCrG8hJiUuxioO6dRIwjpRuY81Vtu3yA74%3D&reserved=0>

Input file is woking fine with CPU version but with GPU it is sowing error, I also try to build from source and tested with after also getting same error.

command used to execute namd job.
#mpirun -np 2 namd2 step4_equilibration_NVT.inp > step4_equilibration_NVT.out

namd GPU version has showing following error.

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unable to open text file step4_equilibration.restart.xsc: File exists

Charm++ fatal error:
FATAL ERROR: Unable to open text file step4_equilibration.restart.xsc: File exists

I have attested job submission script and input file for your reference.

Thanks and Regards,
Miraj Naik
+91 9727264267<tel:+91%2097272%2064267> 

--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD https://apac01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7Cmiraj.naik%40mailone.locuz.com%7Cb8b8c2e525544db1349408d573d6ce42%7Cd47525bf602d4ed78c603db0ec37e266%7C0%7C0%7C636542288850851264&sdata=NRb46UWzHVbRC9jFc62zKFFmFdA3bCNMh3qm65uIzsA%3D&reserved=0<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Ccf69adbce31c4da206a208d573b8ac90%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636542159374983107&sdata=n7OA73MMXi%2FSdHwQFpnZCwM4bY%2FS3ex5fd%2BFnGmt8y0%3D&reserved=0>
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