From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Fri Dec 05 2008 - 09:13:07 CST
Hi Hannes, from your e-mail it seems you nailed down all the necessary
steps and all went well. What exactly did go wrong?
Center for Molecular Modeling at
University of Pennsylvania
231 S 34th Street, Philadelphia, PA 19104-6323
On Fri, Dec 5, 2008 at 8:52 AM, Hannes Loeffler
> I'm trying to run namd on our HP Cluster Platform 4000 with AMD Opteron
> 254 processor. OS is Red Hat Enterprise Linux AS release 4 (Nahant
> Update 2).
> I thought that the pre-compiled binaries from Linux-amd64 or
> Linux-amd64-TCP would be the right ones but they obviously don't do
> parallel runs on our machine (at least the run times from 2 to 32
> processors are basically the same).
> Next, I tried to compile from source. I got an executable but processes
> started seem to hang in the queue without producing any output until I
> kill the job. The output gives me only information about step 0 and
> 'Charm++ Warning: Non Charm++ Message Received.'
> How I compiled my own binary:
> * downloaded the sources for NAMD 2.6, tcl 8.3 (tcl-linux.tar.gz from
> the NAMD site) and fftw 2.1.5 from their web site. Tcl and FFTW
> compiled and installed without any problems.
> * charm++ was build with ./build charm++ mpi-linux-amd64 --no-shared -O
> -DCMK_OPTIMIZE=1. Compiler was /opt/hpmpi/bin/mpiCC.
> I modified src/arch/mpi-linux-amd64/conv-mach.sh to use libmpi instead
> of libmpich. The cluster comes with MPI libraries in /opt/hpmpi which I
> assume are HPs own MPI libraries. (Other options may
> be /opt/hpmpi/MPICH1.2, something called Voltaire and another one might
> be called Elan, though I am not sure if any of them would be useful.
> For both AMBER and GROMACS I used hpmpi.)
> * NAMD was configured with ./config tcl fftw Linux-amd64-MPI and
> compiled. ldd on the binary gives
> libmpi.so.1 => /opt/hpmpi/lib/linux_amd64/libmpi.so.1
> libdl.so.2 => /lib64/libdl.so.2 (0x0000003730e00000)
> libtcl8.3.so => /home/hhl/usr/lib/libtcl8.3.so
> libm.so.6 => /lib64/tls/libm.so.6 (0x0000003731000000)
> libmpio.so.1 => /opt/hpmpi/lib/linux_amd64/libmpio.so.1
> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003733800000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003733c00000)
> libc.so.6 => /lib64/tls/libc.so.6 (0x0000003730b00000)
> /lib64/ld-linux-x86-64.so.2 (0x0000003730900000)
> libpthread.so.0 => /lib64/tls/libpthread.so.0
> Jobs are run with /opt/hpmpi/bin/mpirun -srun /path/to/namd2 md.in
> submitted via bsub (LSF 6.1).
> Any advise would be welcome,
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