RE: Problems compiling NAMD

From: Jesper Soerensen (jes_at_chem.au.dk)
Date: Fri Oct 03 2008 - 15:50:37 CDT

Hi Alexander,

It's a AMD/Opteron cluster with gigabit infrastructure.
It's running CentOS 4.5 and I'm using OpenMPI 1.2.6

Any other details that I can/should provide?

Kind regards,

Jesper

-----Oprindelig meddelelse-----
Fra: Alexander A. Vakhrushev [mailto:makaveli.lcf_at_gmail.com]
Sendt: 3. oktober 2008 19:45
Til: Jesper Soerensen
Cc: namd-l_at_ks.uiuc.edu
Emne: Re: namd-l: Problems compiling NAMD

Hi Jesper!

What is platform of your cluster?

2008/10/3 Jesper Soerensen <jes_at_chem.au.dk>:
> Hi,
>
> I've just compiled NAMD on our cluster and this runs through fine, but
> when I start a job I get the following error in the log file:
>> Info: Entering startup phase 8 with 134856 kB of memory in use.
>> Info: Finished startup with 143120 kB of memory in use.
>> 1 additional process aborted (not shown)
>
> And the cluster job-error log says:
>> mpirun noticed that job rank 0 with PID 25232 on node s07n06 exited on
>> signal 11 (Segmentation fault).
>
> I am running a Linux-amd64-MPI-icc-ifort version if this helps. Also, let
> me know if there is more information I can give to help solve the
> problem. I'm just wondering if anybody has seen this type of error
> before.
>
> Kind regards,
>
> Jesper Soerensen
>
>
> --
> Jesper Sørensen, M.Sc.
> Ph.D.-student
> Biomodelling Group, inSPIN and iNANO centers
> Department of Chemistry
> University of Aarhus
> Langelandsgade 140
> 8000 Aarhus C
> Office: 1510-419
> Tlf. 89423385
> email: jes_at_chem.au.dk
> www: www.chem.au.dk/~biomodelling
>
>

-- 
Best regards,
Dr. Alexander Vakhrushev
Institute of Applied Mechanics
Dep. of Mech. and Phys.-Chem.
of heterogeneous media
UB of Russian Academy of Sciences
34 T. Baramzinoy St.
Izhevsk, Russia 426067
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