Re: Problem building NAMD (multiple definitions)

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon May 23 2011 - 17:12:21 CDT

jim,

On Mon, May 23, 2011 at 6:08 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
> Hi Miro,
>
> My first guess is that you're trying to build a 32-bit Charm++ with a 64-bit
> MPI and that you should be using mpi-linux-x86_64 instead.

.. or a consequence of enforced static linkage.

recent versions of the linker on linux refuse to link
the same object twice unless it is identical. this doesn't
apply to shared objects, since they are fully resolved only
at runtime. -Wl,--allow-multiple-definition might help.

       --allow-multiple-definition
       -z muldefs
           Normally when a symbol is defined multiple times, the
linker will report a
           fatal error. These options allow multiple definitions and
the first definition
           will be used.

cheers,
    axel.

> Were you able to build and run tests/charm++/megatest?
>
> -Jim
>
>
> On Mon, 23 May 2011, Miroslav Hodak wrote:
>
>> Dear All,
>>
>> I have been struggling getting to build NAMD. I know that binaries are
>> provided, but I want to try NAMD with Plumed, which requires building
>> from source.
>>
>> My compilation actually goes pretty well, I follow instructions from
>> notes.txt, and it makes it through the NAMD compilation, but I receive
>> the following errors at the linking step:
>>
>> /usr/lib/libc.a(malloc.o):(.data+0x10): multiple definition of
>> `__libc_malloc_initialized'
>>
>> .rootdir/charm-6.3.2/mpi-linux/bin/../lib/libmemory-default.o:(.data+0x10):
>> first defined here
>> /usr/lib/libc.a(malloc.o): In function `__malloc_check_init':
>> (.text+0x200): multiple definition of `__malloc_check_init'
>>
>> .rootdir/charm-6.3.2/mpi-linux/bin/../lib/libmemory-default.o:/home/miro/src/NAMD_2.8b3_Source/charm-6.3.2/mpi-linux/tmp/memory-gnu-hooks.c:393:
>> first defined here
>> /usr/lib/libc.a(malloc.o): In function `free':
>> (.text+0x4b50): multiple definition of `free'
>>
>> .rootdir/charm-6.3.2/mpi-linux/bin/../lib/libmemory-default.o:/home/miro/src/NAMD_2.8b3_Source/charm-6.3.2/mpi-linux/tmp/memory.c:601:
>> first defined here
>> /usr/lib/libc.a(malloc.o): In function `malloc':
>> (.text+0x4c10): multiple definition of `malloc'
>>
>> .rootdir/charm-6.3.2/mpi-linux/bin/../lib/libmemory-default.o:/home/miro/src/NAMD_2.8b3_Source/charm-6.3.2/mpi-linux/tmp/memory.c:594:
>> first defined here
>> /usr/lib/libc.a(malloc.o): In function `realloc':
>> (.text+0x59a0): multiple definition of `realloc'
>>
>> .rootdir/charm-6.3.2/mpi-linux/bin/../lib/libmemory-default.o:/home/miro/src/NAMD_2.8b3_Source/charm-6.3.2/mpi-linux/tmp/memory.c:620:
>> first defined here
>> collect2: ld returned 1 exit status
>>
>> I also get bunch of warning about static libraries (statically linked
>> applications requires at runtime the shared libraries from the glibc
>> version used for linking), but I assume that those are harmless and
>> error comes from multiple definitions anyways.
>>
>> The errors apparently come from CHARMM, it appears that these files have
>> statically compiled standard system memory management libraries in them.
>> I am not really sure how to solve this, I looked at charmm compile
>> option and I do not see anything relevant.
>>
>> Can somebody help?
>>
>> Thanks,
>> Miro
>>
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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