Re: Installing NAMD

Date: Tue Nov 20 2007 - 13:02:42 CST

Hi Jason,

Thanks for your response. I had originally thought to use the binaries,
however the cluster uses MPI, and I read this in the installation guide:

"For workstation clusters and other massively parallel machines with
special high-performance networking, 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."

I don't know how I would find out if the particular MPI version (listed
below) is compatible, besides just trying it. This is the first time I've
used a cluster and I wouldn't know how to tell if it was the MPI libraries
or something else that was causing a problem.


> Hi Brittany, If you didn't get a response, you can find binaries for
> your situation on the NAMD website:
> You'll likely want the Linux-amd64-TCP version assuming the cluster's on
> gigabit Ethernet.
> -Jason
> wrote:
>> Hi,
>> I've been running NAMD on my local machine, but now I need to install it
>> on a cluster. From what I've read, I"ll need to compile it from the
>> source
>> code. However, I don't know which options to use or what I'll need to
>> change.
>> Here are the cluster specs:
>> 174 node compute farm, each node has dual AMD Opteron 240 processors
>> SuSE Linux 9.1 (kernel: 2.4.21-102-defaultx86_64 SMP)
>> gcc version 3.3.3
>> MPICH 1.2.6 parallel libraries
>> PBSpro version 5.4 job scheduling
>> I'd appreciate any help I can get.
>> Thanks,
>> Brittany

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