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

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Aug 22 2005 - 18:23:48 CDT

That's strange. I don't know where those would be coming from. Are you
using the iccstatic option for charm, not just icc?

I'm not sure how well manually copying libraries works on Clustermatic.
You might have better luck adding those libraries to
/etc/clustermatic/config, restarting beoserv, and rebooting the nodes.

Or, you could try -i-static to link all Intel libraries statically.

-Jim

On Fri, 19 Aug 2005, Rene Salmon wrote:

> 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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