I never built the parallel version of pmemd.cuda so far. So I assume
this can't be an MPI issue as MPI is not used in this case. Am I wrong?
Thanks,
JP
On 08/22/2012 05:53 PM, Scott Le Grand wrote:
> OpenMPI's MPI 2.0 support is broken. It's not an AMBER issue. Try again
> with mvapich2 or mpich2...
>
>
> On Wed, Aug 22, 2012 at 8:00 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
>> wrote:
>
>> Hello,
>>
>> I have just built Amber 12 cuda on Ubuntu 12.04 with Intel 12.1.3 and
>> NVCC 4.2 V0.2.1221 and then invoked the test suite on a Tesla C2075.
>>
>> The test below did not produce output for about 40 minutes (I then
>> killed the pmemd.cuda process):
>>
>>> cd gb_ala3/ && ./Run.irest1_ntt2_igb1_ntc2 SPDP
>> /apps11/bioinfp/amber12_centos58_intel1213_openmpi16/amber12/include/netcdf.mod
>>>
>>> Killed
>>> ./Run.irest1_ntt2_igb1_ntc2: Program error
>>
>> With "did not produce output" I mean that it did not change the mdout
>> file anymore. These are the last lines in the mdout file before and
>> after killing the process:
>>
>>
>>> | Intermolecular bonds treatment:
>>> | no_intermolecular_bonds = 1
>>>
>>> | Energy averages sample interval:
>>> | ene_avg_sampling = 1
>>>
>>>
>> --------------------------------------------------------------------------------
>>> 3. ATOMIC COORDINATES AND VELOCITIES
>>>
>> --------------------------------------------------------------------------------
>>>
>>> ACE
>>> begin time read from input coords = 1050.000 ps
>>
>> The tests before this one (about 20 of them) PASSED. While I am writing
>> this email, the test suite proceeds. However, it currently hangs at
>>
>>> cd myoglobin/ && ./Run_md_myoglobin
>>
>> for already about 15 minutes which is suspicious, right?
>>
>> If I will have to kill this one, too, and maybe others, I will rerun the
>> tests and see if the same tests are hanging or if they are hanging
>> randomly. I'll then get back to you.
>>
>> Have you seen such behavior before?
>>
>> Any suggestion would be helpful.
>>
>> Thanks,
>>
>> Jan-Philip
>>
>>
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>>
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Received on Wed Aug 22 2012 - 09:00:05 PDT
