From: Chris Share (cpsmusic_at_yahoo.com)
Date: Sat Mar 07 2009 - 21:02:39 CST
Thanks for the response.
I tried a build using:
mpi-linux-amd64-mpicxx
as the build configuration. This built OK, however if I try make pgm (for megatest as suggested in the NAMD build notes) I get the following:
make pgm
./../../bin/charmc -c megatest.ci
./../../bin/charmc -o megatest.o megatest.C
"megatest.C", line 185: warning: variable "numtests" was declared but never
referenced
int numtests, i;
^
./../../bin/charmc -c groupring.ci
./../../bin/charmc -o groupring.o groupring.C
./../../bin/charmc -c nodering.ci
./../../bin/charmc -o nodering.o nodering.C
./../../bin/charmc -c varsizetest.ci
./../../bin/charmc -o varsizetest.o varsizetest.C
./../../bin/charmc -c varraystest.ci
./../../bin/charmc -o varraystest.o varraystest.C
./../../bin/charmc -c groupcast.ci
./../../bin/charmc -o groupcast.o groupcast.C
./../../bin/charmc -c nodecast.ci
./../../bin/charmc -o nodecast.o nodecast.C
./../../bin/charmc -c synctest.ci
./../../bin/charmc -o synctest.o synctest.C
./../../bin/charmc -c fib.ci
./../../bin/charmc -o fib.o fib.C
./../../bin/charmc -c arrayring.ci
./../../bin/charmc -o arrayring.o arrayring.C
./../../bin/charmc -c tempotest.ci
./../../bin/charmc -o tempotest.o tempotest.C
./../../bin/charmc -c packtest.ci
./../../bin/charmc -o packtest.o packtest.C
./../../bin/charmc -c queens.ci
./../../bin/charmc -o queens.o queens.C
./../../bin/charmc -c migration.ci
./../../bin/charmc -o migration.o migration.C
./../../bin/charmc -c marshall.ci
./../../bin/charmc -o marshall.o marshall.C
./../../bin/charmc -c priomsg.ci
./../../bin/charmc -o priomsg.o priomsg.C
./../../bin/charmc -c priotest.ci
./../../bin/charmc -o priotest.o priotest.C
./../../bin/charmc -c rotest.ci
./../../bin/charmc -o rotest.o rotest.C
./../../bin/charmc -o statistics.o statistics.C
./../../bin/charmc -c templates.ci
./../../bin/charmc -o templates.o templates.C
./../../bin/charmc -c inherit.ci
./../../bin/charmc -o inherit.o inherit.C
./../../bin/charmc -c reduction.ci
./../../bin/charmc -o reduction.o reduction.C
./../../bin/charmc -c bitvector.ci
./../../bin/charmc -o bitvector.o bitvector.C
./../../bin/charmc -c immediatering.ci
./../../bin/charmc -o immediatering.o immediatering.C
./../../bin/charmc -c callback.ci
./../../bin/charmc -o callback.o callback.C
./../../bin/charmc -o pgm megatest.o groupring.o nodering.o varsizetest.o varraystest.o groupcast.o nodecast.o synctest.o fib.o arrayring.o tempotest.o packtest.o queens.o migration.o marshall.o priomsg.o priotest.o rotest.o statistics.o templates.o inherit.o reduction.o bitvector.o immediatering.o callback.o -language charm++
megatest.o: In function `_registermegatest(void)':
/nfs/user2/cpsmusic/NAMD_INTEL/namd2/charm-6.0/mpi-linux-amd64-mpicxx/tests/charm++/megatest/megatest.C:152: undefined reference to `_registerInitCall(void (*)(void), int)'
megatest.o: In function `__register__12CkIndex_mainSFPCcUl':
/nfs/user2/cpsmusic/NAMD_INTEL/namd2/charm-6.0/mpi-linux-amd64-mpicxx/tests/charm++/megatest/megatest.C:130: undefined reference to `CkIndex_Chare::__idx(void)'
/nfs/user2/cpsmusic/NAMD_INTEL/namd2/charm-6.0/mpi-linux-amd64-mpicxx/tests/charm++/megatest/megatest.C:130: undefined reference to `CMessage_CkArgMsg::__idx(void)'
..
Fatal Error by charmc in directory /home/cpsmusic/NAMD_INTEL/namd2/charm-6.0/mpi-linux-amd64-mpicxx/tests/charm++/megatest
Command mpicxx -o pgm -L../../../bin/../lib -I../../../bin/../include ../../../bin/../lib/libldb-rand.o megatest.o groupring.o nodering.o varsizetest.o varraystest.o groupcast.o nodecast.o synctest.o fib.o arrayring.o tempotest.o packtest.o queens.o migration.o marshall.o priomsg.o priotest.o rotest.o statistics.o templates.o inherit.o reduction.o bitvector.o immediatering.o callback.o moduleinit11730.o ../../../bin/../lib/libmemory-default.o ../../../bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl -lm returned error code 2
charmc exiting...
make: *** [pgm] Error 1
Is the Charm++ build correct for the system I'm running on? Any idea why the test isn't building?
Cheers,
Chris
----- Original Message ----
From: Peter Freddolino <petefred_at_ks.uiuc.edu>
To: Chris Share <cpsmusic_at_yahoo.com>
Cc: namd-l_at_ks.uiuc.edu
Sent: Saturday, 7 March, 2009 4:18:12 PM
Subject: Re: namd-l: Building NAMD for Opteron Cluster with ICC
You'll actually want to build with mpicxx as the compiler (or whatever
the appropriate mpi wrapper for your compiler is), not icc. Also, don't
select SMP unless (as noted in the charm++ docs and by the build script)
you want to run on a *single, SMP node*.
Best,
Peter
Chris Share wrote:
> Hi,
>
> I'd like to build NAMD on an AMD Opteron Cluster using Infiniband and running 64-bit CentOS 5. I've managed to successfully build NAMD on my local machine (not the cluster) using several different configurations (GCC, PGI, CUDA). However, I'm unclear as to how to proceed in the case of the cluster build. I'd like to use the Intel compilers as these give the best performance. I'd also like to use MPI.
>
> Firstly, how should I build Charm++?
>
> Am I right in thinking that the Charm++ build configuration should be:
>
> ./build charm++ mpi-linux-amd64 icc smp
>
> When I run this I get the following error:
>
> Selected Compiler: icc
> Selected Options: smp
> Copying src/scripts/Makefile to mpi-linux-amd64-smp-icc/tmp
> Soft-linking over bin
> Soft-linking over lib
> Soft-linking over lib_so
> Soft-linking over include
> Soft-linking over tmp
> Generating mpi-linux-amd64-smp-icc/tmp/conv-mach-pre.sh
> Performing '/usr/bin/gmake charm++ OPTS=' in mpi-linux-amd64-smp-icc/tmp
> /usr/bin/gmake headerlinks
> gmake[1]: Entering directory `/nfs/user2/cpsmusic/NAMD_INTEL/namd2/charm-6.0/mpi-linux-amd64-smp-icc/tmp'
> ./configure
> checking machine name... mpi-linux-amd64-smp-icc
> checking "C++ compiler as"... "icpc -fpic -cxxlib-icc -D_REENTRANT "
> checking "whether C++ compiler works"... "no"
> Cannot compile C++ programs with icpc -fpic -cxxlib-icc -D_REENTRANT
> (check your charm++ version)
> gmake[1]: *** [conv-autoconfig.h] Error 1
> gmake[1]: Leaving directory `/nfs/user2/cpsmusic/NAMD_INTEL/namd2/charm-6.0/mpi-linux-amd64-smp-icc/tmp'
> gmake: *** [headers] Error 2
> -------------------------------------------------
> Charm++ NOT BUILT. Either cd into mpi-linux-amd64-smp-icc/tmp and try
> to resolve the problems yourself, visit
> http://charm.cs.uiuc.edu/
> for more information. Otherwise, email the developers at ppl_at_cs.uiuc.edu
>
> Am I on the right track here?
>
> Any help would be appreciated.
>
> Cheers,
>
> Chris
>
>
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