Re: Re: FW: NAMD 2.6, AMD64, MVAPICH2 compile error

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Mar 24 2009 - 22:56:40 CDT

On Thu, 19 Mar 2009, Thomas C. Bishop wrote:

> Greetings namder's
>
> I am having trouble compiling NAMD2.6
> this is an AMD64 system with inifiniband and MVAPICH2
>
>  My build output is below:
>

Try setting CHARM_OPTS to -memory os -thread context in the .arch file.

-Jim

> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `malloc_usable_size':
> mvapich_malloc.c:(.text+0x280): multiple definition of `malloc_usable_size'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x1e9): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `malloc_usable_size' changed from 48
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 51 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `_int_free':
> mvapich_malloc.c:(.text+0x5e0): multiple definition of `_int_free'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x87a): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `_int_free' changed from 771
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 573 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `__malloc_check_init':
> mvapich_malloc.c:(.text+0x850): multiple definition of `__malloc_check_init'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x30b0): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `__malloc_check_init' changed from 120
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 113 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.data+0x0):
> multiple definition of `__malloc_hook'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
> (.data+0x0): first defined here
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.bss+0x8):
> multiple definition of `__free_hook'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
> (.bss+0x8): first defined here
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.data+0x8):
> multiple definition of `__realloc_hook'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
> (.data+0x8): first defined here
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.data+0x10):
> multiple definition of `__memalign_hook'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
> (.data+0x10): first defined here
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.bss+0x10):
> multiple definition of `__after_morecore_hook'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
> (.bss+0x10): first defined here
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `_int_malloc':
> mvapich_malloc.c:(.text+0xb70): multiple definition of `_int_malloc'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0xdc1): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `_int_malloc' changed from 2863
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 3045 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `_int_memalign':
> mvapich_malloc.c:(.text+0x1760): multiple definition of `_int_memalign'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x1ba7): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `_int_memalign' changed from 525
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 583 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `_int_valloc':
> mvapich_malloc.c:(.text+0x19b0): multiple definition of `_int_valloc'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x1db4): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `_int_valloc' changed from 63
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 62 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `_int_realloc':
> mvapich_malloc.c:(.text+0x1a30): multiple definition of `_int_realloc'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x1df3): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `_int_realloc' changed from 1365
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 858 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `_int_new_arena':
> mvapich_malloc.c:(.text+0x1e40): multiple definition of `_int_new_arena'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x2348): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `_int_new_arena' changed from 214
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 158 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `independent_comalloc':
> mvapich_malloc.c:(.text+0x2460): multiple definition of
> `independent_comalloc'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x24cf): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `independent_comalloc' changed from 137
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 142 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `independent_calloc':
> mvapich_malloc.c:(.text+0x24f0): multiple definition of `independent_calloc'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x2558): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `independent_calloc' changed from 146
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 167 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `mallopt':
> mvapich_malloc.c:(.text+0x2800): multiple definition of `mallopt'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x33bd): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `mallopt' changed from 14
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 5 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.bss+0x0):
> multiple definition of `__malloc_initialize_hook'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
> (.bss+0x0): first defined here
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `pvalloc':
> mvapich_malloc.c:(.text+0x2a20): multiple definition of `pvalloc'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x33cb): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `pvalloc' changed from 129
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 170 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `valloc':
> mvapich_malloc.c:(.text+0x2ad0): multiple definition of `valloc'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x3e91): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `valloc' changed from 78
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 135 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `mallinfo':
> mvapich_malloc.c:(.text+0x2cc0): multiple definition of `mallinfo'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x31b): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `mallinfo' changed from 39
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 139 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `malloc_trim':
> mvapich_malloc.c:(.text+0x2d50): multiple definition of `malloc_trim'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x788): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `malloc_trim' changed from 49
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 110 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `calloc':
> mvapich_malloc.c:(.text+0x2dc0): multiple definition of `calloc'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x3f41): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `calloc' changed from 84
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 800 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `free':
> mvapich_malloc.c:(.text+0x30e0): multiple definition of `free'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0xc22): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `free' changed from 34
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 236 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `cfree':
> mvapich_malloc.c:(.text+0x31d0): multiple definition of `cfree'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0xc60): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `cfree' changed from 34
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 5 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `malloc':
> mvapich_malloc.c:(.text+0x31e0): multiple definition of `malloc'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x3f95): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `malloc' changed from 78
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 364 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `memalign':
> mvapich_malloc.c:(.text+0x3350): multiple definition of `memalign'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x3edf): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `memalign' changed from 98
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 407 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `realloc':
> mvapich_malloc.c:(.text+0x35a0): multiple definition of `realloc'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x2d8f): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `realloc' changed from 72
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 488 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `malloc_set_state':
> mvapich_malloc.c:(.text+0x38d0): multiple definition of `malloc_set_state'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x34b4): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `malloc_set_state' changed from 887
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 1013 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
> `malloc_get_state':
> mvapich_malloc.c:(.text+0x3cd0): multiple definition of `malloc_get_state'
> /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
> (.text+0x2dd7): first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
> Warning: size of symbol `malloc_get_state' changed from 376
> in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> to 476 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
> /usr/local/src/NAMD_2.6_Source/tcl/linux-amd64/lib/libtcl8.3.a(tclUnixPipe.o):
> In function `TclpCreateTempFile':
> tclUnixPipe.c:(.text+0xe0): warning: the use of `tmpnam' is dangerous, better
> use `mkstemp'
> collect2: ld returned 1 exit status
> Fatal Error by charmc in
> directory /usr/local/src/NAMD_2.6_Source/Linux-amd64-MPI
>    Command
> mpicxx -rdynamic -L/usr/local/src/NAMD_2.6_Source/tcl/linux-amd64/lib -L/root/tcl/lib -L/usr/local/src/NAMD_2.6_Source/fftw/linux-amd64/lib -L/root/fftw/lib -I/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -m64 -fexpensive-optimizations -ffast-math -o
> namd2 -L/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib -I/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../include /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libldb-rand.o
> obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.o obj/fitrms.o obj/main.o
> obj/mainfunc.o obj/memusage.o obj/strlib.o obj/AlgSeven.o
> obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o
> obj/BroadcastMgr.o obj/BroadcastClient.o obj/CollectionMaster.o
> obj/CollectionMgr.o obj/Communicate.o obj/Compute.o obj/ComputeAngles.o
> obj/ComputeBonds.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o
> obj/ComputeCrossterms.o obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o
> obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o
> obj/ComputeEField.o obj/ComputeEwald.o obj/ComputeExt.o
> obj/ComputeFullDirect.o obj/ComputeHomePatch.o obj/ComputeHomePatches.o
> obj/ComputeImpropers.o obj/ComputeGlobal.o obj/ComputeGlobalMsgs.o
> obj/ComputeMap.o obj/ComputeMgr.o obj/ComputeNonbondedSelf.o
> obj/ComputeNonbondedPair.o obj/ComputeNonbondedUtil.o
> obj/ComputeNonbondedStd.o obj/ComputeNonbondedFEP.o obj/ComputeNonbondedLES.o
> obj/ComputeNonbondedPProf.o obj/ComputePatch.o obj/ComputePatchPair.o
> obj/ComputePme.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o
> obj/ComputeStir.o obj/ComputeTclBC.o obj/ConfigList.o obj/Controller.o
> obj/ccsinterface.o obj/DataStream.o obj/DumpBench.o obj/FreeEnergyAssert.o
> obj/FreeEnergyGroup.o obj/FreeEnergyLambda.o obj/FreeEnergyLambdMgr.o
> obj/FreeEnergyParse.o obj/FreeEnergyRestrain.o obj/FreeEnergyRMgr.o
> obj/FreeEnergyVector.o obj/GlobalMaster.o obj/GlobalMasterServer.o
> obj/GlobalMasterTest.o obj/GlobalMasterIMD.o obj/GlobalMasterTcl.o
> obj/GlobalMasterSMD.o obj/GlobalMasterTMD.o obj/GlobalMasterFreeEnergy.o
> obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/GromacsTopFile.o obj/heap.o
> obj/HomePatch.o obj/IMDOutput.o obj/InfoStream.o obj/LdbCoordinator.o
> obj/LJTable.o obj/Measure.o obj/MStream.o obj/MigrateAtomsMsg.o
> obj/Molecule.o obj/NamdCentLB.o obj/NamdNborLB.o obj/NamdState.o
> obj/NamdOneTools.o obj/Node.o obj/Output.o obj/Parameters.o
> obj/ParseOptions.o obj/Patch.o obj/PatchMgr.o obj/PatchMap.o obj/PDB.o
> obj/PDBData.o obj/PmeBase.o obj/PmeKSpace.o obj/PmeRealSpace.o
> obj/ProcessorPrivate.o obj/ProxyMgr.o obj/ProxyPatch.o obj/Rebalancer.o
> obj/RecBisection.o obj/ReductionMgr.o obj/RefineOnly.o obj/ScriptTcl.o
> obj/Sequencer.o obj/Set.o obj/Settle.o obj/SimParameters.o obj/Sync.o
> obj/TclCommands.o obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o
> obj/imd.o obj/dcdplugin.o
> moduleinit1529.o -lmoduleNeighborLB -lmodulecommlib /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -lmpich -ldl -ltcl8.3 -ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib -lmpich -lm
> returned error code 1
> charmc exiting...
> rm -f moduleinit1529.C moduleinit1529.o
> make: *** [namd2] Error 1

>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:39 CST