NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers

From: Rene Salmon (rsalmon_at_tulane.edu)
Date: Fri Aug 19 2005 - 10:38:20 CDT

Hi list,

We are trying to test drive the new version of NAMD 2.6b1 on our AMD64
Clustermatic/Bproc cluster.
Also we are trying to compile using the intel compilers which seem to
give us better performance than gcc.

Both Charm and NAMD compile fine and we are able to get executables.
They both compile with this option so the libcxa intel lib gets
statically linked.

-static-libcxa link Intel libcxa C++ library statically

If a do an ldd on the charmrun and NAMD executables i get this:

charm
-------
         libsvml.so => /opt/intel_fce_80/lib/libsvml.so (0x0000002a95772000)
         libimf.so => /opt/intel_fce_80/lib/libimf.so (0x0000002a958b3000)
         libirc.so => /opt/intel_fce_80/lib/libirc.so (0x0000002a95c64000)

namd2
------
         libsvml.so => /opt/intel_fce_80/lib/libsvml.so (0x0000002a959ce000)
         libimf.so => /opt/intel_fce_80/lib/libimf.so (0x0000002a95b0f000)
         libirc.so => /opt/intel_fce_80/lib/libirc.so (0x0000002a95f43000)

So I make sure and copy these intel libs to the /opt/intel_fce_80/lib
directory on the cluster nodes where I want to run.

The problem is that NAMD can't seem to find the libs. Here is the
output i get from NAMD:

tcsh> ./charmrun ++skipmaster ++verbose ++debug ++nodelist nodelitxt ++p
2 ./namd2 run_dum_1.conf
Charmrun> charmrun started...
Charmrun> using nodelist.txt as nodesfile
Charmrun> adding client 0: "9", IP:10.0.0.109
Charmrun> adding client 1: "9", IP:10.0.0.109
Charmrun> Charmrun = 10.0.0.10, port = 41186
Charmrun> start node program on slave node: 9.
Charmrun> start node program on slave node: 9.
Charmrun> node programs all started
Charmrun> Waiting for 0-th client to connect.
./namd2: error while loading shared libraries: libsvml.so: cannot open
shared
ject file: No such file or directory
./namd2: error while loading shared libraries: libsvml.so: cannot open
shared
ject file: No such file or directory

The libs are there any clues as to why Namd can't find them?
Thanks in advance for any help on this.

Rene

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