Re: Will MPICH2 work for NAMD?

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Wed Nov 11 2009 - 07:07:47 CST

On Monday 09 November 2009 19:37:58 you wrote:
> Dear NAMD users,
>
> We plan to use the 8 processors in a single machine with two Quadro-core
> Nehalem CPUs to run NAMD in parallel. I assume we need to install MPI.
>
No, you don't.

> The user guide says " NAMD uses the system-provided MPI library (with a
> few exceptions) and standard system tools such as mpirun are used to
> launch jobs. Since MPI libraries are very often incompatible between
> versions, you will likely need to recompile NAMD and its underlying
> Charm++ libraries to use these machines in parallel (the provided non-MPI
> binaries should still work for serial runs.) The provided charmrun program
> for these platforms is only a script that attempts to translate charmrun
> options into mpirun options, but due to the diversity of MPI libraries it
> often fails to work."
>
> Is it ok we install MPICH2?
>
MPICH works very well! If you can, try MPICH1 (as far as I know charm++/namd
does not use any of the MPI2 specific calls, so MPI1 could perform better)
(Someone pleas correct me here if I am wrong)

> After we compile the source codes, do we use ++local flag in the charmrun
> or not?
>
Yes, you have to, if you compile it with MPI support (alternatively you could
specify a hostfile containing only the localhost, but that would be
irrational)
 
> Any suggest helps. thanks.
>
You do not need a specific MPI library!
Just compile CHARM++ as "single threaded multicore"

Something like:
"./build charm++ multicore-linux64 icc -j8 -O2"

This will yield the most performance for a single machine cause it lacks all
the unnecessary code for "interconnect/MPI"

Run the resulting binary as follows:
"namd2 +setcpuaffinity +p${nCPUs} namd2.conf"

(you might remove the "+setcpuaffinity" option)

Cheers
Bjoern

-- 
Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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