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

haadah haadah at gmail.com
Wed Apr 11 17:42:53 CEST 2012

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.

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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