Re: clustermatic 4 and 5 Namd/charm

From: John Saeger (list_at_whimsey.com)
Date: Sun Jan 02 2005 - 14:18:31 CST

It's a wonderful world. Almost magical at times. This is exactly what
I'm looking for. Would it be possible for somebody to put a binary of
this somewhere so I could try it out?

BTW, now that I know about CVS and Wiki, I may give compiling another
chance, but in the meantime, binaries are very helpful. Maybe you
should have some *bleeding edge* binaries to go along with CVS?

Thanks!

John

Gengbin Zheng wrote:
>
> Hi Rene,
>
> Good to hear Charm++ and NAMD runs on opteron with clustermatic 5.
>
> For fftw support, you need to download fftw version 2 instead of version
> 3 in order to compile NAMD.
> And you need to compile tcl in its static form (.a) instead of shared
> lib for NAMD.
> For detailed instruction on how to configure and compile it, please see
> my NAMD wiki at
> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdCompile
>
> Alternatively, I think there are binaries on NAMD website you can
> download for the fftw and tcl precompiled for opteron.
>
> Gengbin
>
> Rene Salmon wrote:
>
>>
>>
>> Hi,
>>
>> The problem with charm was indeed the missing libs on the slave nodes.
>> After I added the missing libs the charm tests worked fine.
>>
>> Next I moved to compile NAMD. I just followed your instructions and
>> copied the "Linux-i686-Clustermatic.arch" to
>> "Linux-amd64-Clustermatic.arch" here is what the file looks like:
>>
>> NAMD_2.5_Source/arch# cat Linux-amd64-Clustermatic.arch
>> include .rootdir/arch/Linux-amd64-g++.arch
>>
>> CHARMARCH = net-linux-amd64-clustermatic
>>
>>
>> --------
>> here is what Linux-amd64-g++.arch looks like:
>>
>> NAMD_2.5_Source/arch# cat Linux-amd64-g++.arch
>> NAMD_ARCH = Linux-amd64
>> CHARMARCH = net-linux-amd64-clustermatic
>>
>> CXX = g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
>> CXXOPTS = -O3 -fexpensive-optimizations -ffast-math
>> CC = gcc
>> COPTS = -O3 -fexpensive-optimizations -ffast-math
>>
>>
>>
>> -----------------------
>>
>> Next I tried to configure and compile:
>>
>> NAMD_2.5_Source/arch# ./config Linux-amd64-Clustermatic
>>
>> this worked and generated the NAMD executables with out any errors.
>> I ran this test on NAMD:
>>
>> ./charmrun ++skipmaster ++verbose ++startpe 0 +p2 ./namd2 /tmp/alanin
>>
>> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 9
>> WRITING COORDINATES TO OUTPUT FILE AT STEP 9
>> WRITING VELOCITIES TO OUTPUT FILE AT STEP 9
>> ==========================================
>> WallClock: 1.611247 CPUTime: 1.201816 Memory: 8895 kB
>> Charmrun> Graceful exit.
>>
>>
>> It seems to be working fine. Thank you very much for getting me this
>> far.
>>
>>
>>
>>
>> ----------------------
>> I would like to have the fftw libs with NAMD so I tried this:
>>
>> NAMD_2.5_Source/arch# ./config tcl fftw Linux-amd64-Clustermatic
>>
>> If I add the fftw or tcl or both I get error messages and I do not get
>> a NAMD binary.
>>
>> I installed fftw-3.0.1 from the fftw website with out any problems and
>> just pointed the Linux-amd64.fftw to the fftw install.
>>
>> I also have tcl-8.4 installed on the system and I edited the
>> Linux-amd64.tcl file to reflect the location of the libs and include
>> files for tcl.
>>
>>
>> Is there anything special I need to do to get NAMD to compile with
>> fftw support? I checked the NAMD www site for precompiled libraries
>> for both tcl and fftw for amd64 but found nothing. Anyone have these
>> libs precompiled to work with NAMD?
>>
>> Thank you very much for all the help
>>
>> Rene
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>

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