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

From: Jerry Ebalunode (jebalunode_at_UH.EDU)
Date: Fri Aug 19 2005 - 13:33:42 CDT

if u use bash shell, as default, add the following lines to your ~/.bashrc
file

export LD_LIBRARY_PATH=/opt/intel_fce_80/lib:$LD_LIBRARY_PATH

then run
source ~/.bashrc
before running your charmrun + namd

On Friday 19 August 2005 10:38 am, 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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