Re: Problem building NAMD (multiple definitions)

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon May 23 2011 - 17:41:37 CDT

On Mon, May 23, 2011 at 6:38 PM, Miroslav Hodak <hodak_at_chips.ncsu.edu> wrote:
> Guys:
>
> I was careful to specify 32 bit version for both charm++ and NAMD, so I do
> not think that would be a problem.
>
> Axel's suggestion appears to be correct, it indeed appears to be a linker
> problem. But where can I specify options for the linker in NAMD?

i would suspect that something went astray in your charm++ compile.

as jim suggested, i would try the charm++ tests first. if they have the
same problem, you'll have to check out the charm++ build and wrapper
scripts. only if this goes smoothly, you'll have to check your arch files
for NAMD.

cheers,
    axel.
>
> Thanks,
> Miro
>
> On 05/23/2011 06:12 PM, Axel Kohlmeyer wrote:
>>
>> 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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