From: Damon Smith (damon_at_vpac.org)
Date: Thu Dec 30 2004 - 22:23:09 CST
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
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