[gmx-users] Re: GROMACS (w. OpenMPI) fails to run with -np larger than 10

[Szilárd Páll]

On Wed, Apr 11, 2012 at 6:16 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 12/04/2012 1:42 AM, haadah wrote:
>>
>> Could you clarify what you mean by "Sounds like an MPI configuration
>> program.
>> I'd get a test program running on 18 cores before worrying about anything
>> else."? My problem is that i can't get anything to work with -np set to
>> more
>> than 10.
>
>
> Only you can configure your hardware to use your MPI software correctly. You
> should use some simple non-GROMACS test program to probe whether it is
> working correctly. Only then is testing GROMACS a reasonable thing to do,
> given your existing observations.

That's a good point, test a (few) simple, but not "hello world"
trivial, program(s) first. If that works, it might be a GROMACS issue.

Above >10 processes separate PME nodes are used. Try the -npme 0
option to see if the error occurs without separate PME nodes on >10
processes.

Cheers,
--
Szilárd


> Mark
>
>
>>
>>
>> The “Cannot rename checkpoint file; maybe you are out of quota?” problem
>> is
>> fixed, i needed to set the NFS to sync instead of async.
>>
>>
>>
>> Mark Abraham wrote
>>>
>>> On 11/04/2012 11:03 PM, Seyyed Mohtadin Hashemi wrote:
>>>>
>>>> Hello,
>>>>
>>>> I have a very peculiar problem: I have a micro cluster with three
>>>> nodes (18 cores total); the nodes are clones of each other and
>>>> connected to a frontend via Ethernet. I am using Debian squeeze as the
>>>> OS for all nodes.
>>>>
>>>> I have compiled a GROMACS v.4.5.5 environment with FFTW v.3.3.1 and
>>>> OpenMPI v.1.4.2 (OpenMPI version that is standard for Debian). On the
>>>> nodes, individually, I can do simulations of any size and complexity;
>>>> however, as soon as I want to do a parallel job the whole thing crashes.
>>>> Since my own simulations can be non-ideal for a parallel situation I
>>>> have used the gmxbench d.dppc files, this is the result I get:
>>>>
>>>> For a simple parallel job I use: path/mpirun --hostfile
>>>> path/machinefile --np XX path/mdrun_mpi --p tcp --s path/topol.tpr --o
>>>> path/output.trr
>>>> For --np XX being smaller than or 10 it works, however as soon as I
>>>> make use of 11 or larger the whole thing crashes and I get:
>>>> [host:xxxx] Signal: Bus error (7)
>>>> [host:xxxx] Signal code: Non-existant physical address (2)
>>>> [host]xxxx] Lots of lines with libmpi.so.0
>>>>
>>>> I have tried using different versions of OpenMPI, v.1.4.5 and all the
>>>> way to beta v.1.5.5, they all behave exactly the same. This is making
>>>> no sense.
>>>
>>> Sounds like an MPI configuration program. I'd get a test program running
>>> on 18 cores before worrying about anything else.
>>>
>>>> When I use threads over the OpenMPI interface I can get all cores
>>>> engaged and the simulation works until 5-7 minutes in then it gives an
>>>> error "Cannot rename checkpoint file; maybe you are out of quota?"
>>>> even though I have more than 500gb left on each node.
>>>
>>> Sounds like a filesystem availability problem. Checkpoint files are
>>> written in the working directory, so the available local disk space is
>>> not strictly relevant.
>>>
>>> Mark
>>>
>>>> I hope somebody can help me figure out what is wrong and maybe a
>>>> possible solution.
>>>>
>>>> regards,
>>>> Mohtadin
>>>>
>>>>
>>>
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>>
>> --
>> View this message in context:
>> http://gromacs.5086.n6.nabble.com/GROMACS-w-OpenMPI-fails-to-run-with-np-larger-than-10-tp4832034p4832579.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
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