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

From: Rene Salmon (rsalmon_at_tulane.edu)
Date: Wed Aug 24 2005 - 15:01:26 CDT

Hi list,

Thanks for all the replies they where all very helpful.
Got it to work i was missing the options iccstatic and -i-static here is
the summary:

./build charm++ net-linux-amd64 clustermatic iccstatic --no-build-shared
-i-static

Thanks again
Rene

Jim Phillips wrote:
>
> 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
>>

-- 
-
--
	Rene Salmon
	Tulane University
	Center for Computational Science
	Richardson Building 310
	New Orleans, LA 70118
	http://www.ccs.tulane.edu
	Tel 504-862-8393
	Fax 504-862-8392

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