Hi Ross,
I sent again the test and now it stops in:
cd myoglobin/ && ./Run_md_myoglobin SPDP
/opt/amber12//include/netcdf.mod
I attach the myoglobin_md.out. The details of the system are:
OS: 2.6.34.9-69.fc13.x86_64
gcc: gcc version 4.4.5 20101112 (Red Hat 4.4.5-2) (GCC)
nvcc: Cuda compilation tools, release 3.2, V0.2.1221
The gpu is a Tesla C2070. As you can see, I'm using CUDA 3.2. I don't
know if it would be better to install CUDA 4.0 or CUDA 4.2 (I'm not sure
if it is available for Fedora 13).
Thanks for your help
Fernando
On Wed, 16 May 2012 08:19:10 -0700, Ross Walker wrote:
> Hi Fernando,
>
>> I've been running the test for cuda version of Amber 12. First 28
>> test
>> passed without problems but in this one:
>>
>> cd myoglobin/ && ./Run_md_myoglobin_igb8 SPDP
>> /opt/amber12//include/netcdf.mod
>>
>> test has been running constantly. I have to force the exit after 2
>> days. Is this test a time consuming test and takes a long time to
>> pass
>> it or it could exist a problem in my configuration?
>
> This is very strange. This test should only take a few seconds at
> most so something is weird. Can you take a look at the output file:
> $AMBERHOME/test/cuda/myoglobin/myoglobin_md_igb8.out and attach it to
> an email so we can see where it got to.
>
> Could you also provide some details about your system. The GPUs
> installed, the compilers you used (gcc, gfortran, nvcc) and the
> versions. This will help debug what is going on.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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--
==============================================
Fernando Martín García
Molecular Modelling Group - Lab 312.1
Molecular Biology Center "Severo Ochoa"
C/ NICOLáS CABRERA, 5.
UAM University. Cantoblanco, 28049 Madrid. Spain.
TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
Web: http://fertoledo.wordpress.com/
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Received on Thu May 17 2012 - 00:00:03 PDT
