Re: mpi opteron myrinet

From: Damon Smith (damon_at_vpac.org)
Date: Thu Dec 30 2004 - 23:51:01 CST

All the charm and namd object files are compiled:
ELF 64-bit LSB relocatable, AMD x86-64, version 1 (SYSV), not stripped

I suppose I should try the opteron arch for the new version of namd.
Charm++ doesn't have a myrinet gm option for mpi-linux-amd64 though, so
I don't think it's going to work properly until that happens.

Thanks again

On Thu, 2004-12-30 at 22:50 -0600, Gengbin Zheng wrote:
> Hi,
>
> Most of these gcc problem with templates and gcc3.4 have been fixed in
> the latest version. For build on opteron, you will have to use "opteron"
> option because it sets up several configurations for compiling on
> opteron, NAMD won't run even you can compile the binary.
>
> I am wondering if there is any additional error messages before the
> messages you patesed below, I mean the error message given by the actual
> gcc compiler? Could it because of not compiling object file in 64 bits,
> use command 'file foo.o' to verify. If this is the reason, use -m64
> compiler flag to generate 64 bit obj files.
>
> New version of NAMD has Linux-amd64-MPI.arch for compiling with
> Opteron and MPI.
> The content of this file is:
>
> NAMD_ARCH = Linux-amd64
> CHARMARCH = mpi-linux-opteron
>
> CXX = g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
> CXXOPTS = -O3 -m64 -fexpensive-optimizations -ffast-math
> CC = gcc
> COPTS = -O3 -m64 -fexpensive-optimizations -ffast-math
>
> You need to change CHARMARCH to your charm version compiled.
>
> Gengbin
>
> Damon Smith wrote:
>
> >Hi all,
> >
> >Sorry for this really long email, but as the subject suggests, I had a
> >go at compiling namd 2.5 on opteron with mpich 1.2.6 and myrinet, using
> >gcc 3.4. I haven't found good docs on this, I've only seen docs for
> >net-linux with amd64 and mpi, but no myrinet.
> >
> >A lot of the C++ code in charm++ and namd won't compile because of
> >gcc3.4's changes to the way templates work, but it's a simple fix, I can
> >post a patch if anyone is interested. The details on the gcc problem
> >are here:
> >http://www.dis.com/gnu/gcc/Name-lookup.html
> >(it won't break the code for old compilers either)
> >
> >
> >Once I got past that, and a lot more mucking around, it's hard to work
> >out what to do. Charm++ won't compile with:
> >mpi-linux opteron gm
> >
> >It gets the following error:
> >Fatal Error by charmc in
> >directory /home/san02/damon/tmp/charm-5.8/mpi-linux-gm-opteron/tmp
> > Command mpicc -rdynamic -o ../lib_so/libconv-core.so -shared
> >-L/home/san02/damon/tmp/charm-5.8/mpi-linux-gm-opteron/lib_so
> >convcore.o conv-conds.o queueing.o msgmgr.o cpm.o cpthreads.o futures.o
> >cldb.o topology.o random.o debug-conv.o generate.o edgelist.o conv-ccs.o
> >ccs-builtins.o traceCore.o traceCoreCommon.o converseProjections.o
> >machineProjections.o quiescence.o isomalloc.o global-nop.o returned
> >error code 1
> >charmc exiting...
> >make[2]: *** [../lib/libconv-core.a] Error 1
> >
> >but it will compile with just
> >mpi-linux gm
> >
> >and then namd doesn't appear to have an option for amd64 or opteron with
> >mpi and myrinet. So I modified the i686-gm-mpi to use -march=opteron,
> >and it compiles ok, but gets a linker error:
> >
> >collect2: ld returned 1 exit status
> >Fatal Error by charmc in
> >directory /home/san02/damon/tmp/NAMD_2.5_Source/Linux-i686-MPI
> > Command mpiCC -rdynamic -O3 -march=opteron -ffast-math -static
> >-L/home/san02/damon/tmp/fftw-3.0.1/lib
> >-L/home/san02/damon/fftw-linux/lib
> >-L/home/san02/damon/tmp/plugins//LINUXAMD64
> >-L/home/san02/damon/tmp/plugins//LINUXAMD64/molfile
> >-L/home/san02/damon/tmp/plugins/compile/LINUXAMD64
> >-L/home/san02/damon/tmp/plugins/compile/LINUXAMD64/molfile
> >-I/home/san02/damon/tmp/charm-5.8/mpi-linux-gm/include -o namd2
> >-L/home/san02/damon/tmp/charm-5.8/mpi-linux-gm/bin/../lib
> >-I/home/san02/damon/tmp/charm-5.8/mpi-linux-gm/bin/../include /home/san02/damon/tmp/charm-5.8/mpi-linux-gm/bin/../lib/libldb-rand.o obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.o obj/main.o
> >[..snip..]
> >obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o moduleinit.o
> >-lmoduleNeighborLB
> >-lmodulecommlib /home/san02/damon/tmp/charm-5.8/mpi-linux-gm/bin/../lib/libmemory-default.o /home/san02/damon/tmp/charm-5.8/mpi-linux-gm/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -lpmpich -lgm -lpthread -ldl -lz -lsrfftw -lsfftw -lmolfile_plugin -lm -lmoduleNeighborLB -lmodulecommlib returned error code 1
> >charmc exiting...
> >
> >So that's where I give up. Those linker errors tell me nothing useful.
> >Has anyone, anywhere got namd to compile with gcc, on opteron, using mpi
> >and myrinet? If so how??
> >
> >I maybe should try getting the latest version of charm from CVS, as it
> >appears to have changes to the amd64 code as of 6 days ago.
> >
> >Thanks,
> >
> >Damon
> >
> >

-- 
Damon Smith <damon_at_vpac.org>

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