[gmx-developers] Problem with PME in CVS

[Justin MacCallum]

Hi,

I've noticed a problem when running simulations using PME with the  
CVS version of gromacs. I can run simulations with 1,2,3, and 4  
processors, but when I try to run on 8 or 16 processors things aren't  
working correctly. Gromacs seems to start correctly, but hangs before  
the output line for step 0 is printed.  Mpich prints out the  
following error: "Timeout in establishing connection to remote  
process: 0". Strangely the logfile for nodes 0-3 end with:

Iniitalizing LINear Constraint Solver
....
..


While nodes 4-7 end with:

Started mdrun on node X DATE
Grid: ...
Configuring non-bonded kernels
Testing AMD 3DNow support... not present
Testing ia32 SSE support... present


So it appears that some of the nodes aren't initializing properly.  
This is run on a cluster of dual xeons running ROCKS. I should  
mention that all of these jobs run fine with 3.2.1, although the  
performance is obviously quite poor for more than two processors.

Justin

--------------------------
Justin MacCallum
PhD Student
Departement of Biological Sciences
University of Calgary

email: jlmaccal at ucalgary.ca
web: moose.bio.ucalgary.ca

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