From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Dec 16 2014 - 09:22:04 CST
It looks like you modified the files in the NAMD src directory but not
plugins/include/libmolfile_plugin.h or plugins/molfile_plugin/src/...
Jim
On Tue, 16 Dec 2014, Rubén Granero wrote:
> Hi Jim,
>
> Thanks for your help. I've tried your suggestion and renamed all affected
> functions (added PLUMED to their names) but this creates undefined
> references when I try to compile (see output below). I thought I would need
> to change the name of the functions where they are defined, but didn't find
> where that is.
>
> obj/ScriptTcl.o: In function `ScriptTcl::ScriptTcl()':
> ScriptTcl.C:(.text+0x49f9): undefined reference to
> `molfile_PLUMED_dcdplugin_init'
> ScriptTcl.C:(.text+0x4a05): undefined reference to
> `molfile_PLUMED_dcdplugin_register'
> obj/ScriptTcl.o: In function `ScriptTcl::~ScriptTcl()':
> ScriptTcl.C:(.text+0x50b6): undefined reference to
> `molfile_PLUMED_dcdplugin_fini'
> obj/PluginIOMgr.o: In function `PluginIOMgr::PluginIOMgr()':
> PluginIOMgr.C:(.text+0x15): undefined reference to
> `molfile_PLUMED_jsplugin_init'
> PluginIOMgr.C:(.text+0x23): undefined reference to
> `molfile_PLUMED_jsplugin_register'
> obj/PluginIOMgr.o: In function `PluginIOMgr::~PluginIOMgr()':
> PluginIOMgr.C:(.text+0x31): undefined reference to
> `molfile_PLUMED_jsplugin_fini'
> collect2: error: ld returned 1 exit status
> Fatal Error by charmc in directory
> /home/rubengpu/bin/NAMD_2.9_Source/Linux-x86_64-g++
>
> As it seems that the problem comes from PLUMED rather than NAMD, I'll
> contact the PLUMED users group to see if I can install PLUMED without the
> conflictive plugins.
>
> Rubén
>
>
> 2014-12-15 15:37 GMT+01:00 Jim Phillips <jim_at_ks.uiuc.edu>:
>>
>>
>> It appears that PLUMED and NAMD both include the VMD molfile plugins.
>> Since they have the same function names and neither is a library this is a
>> conflict. Renaming the affected molfile_XXXplugin_[init|register|fini]
>> functions everywhere in the NAMD src and plugins directories would work if
>> there is no way to build PLUMED without the plugins.
>>
>> Jim
>>
>>
>> On Mon, 15 Dec 2014, Rub?(c)n Granero wrote:
>>
>> Hi there,
>>>
>>> I've successfully compiled NAMD2.9 (multicore and CUDA) and installed
>>> PLUMED2.1 in CentOS7. I followed the exact compilation instructions from
>>> their respective user guides and both of them are working fine. I've also
>>> patched NAMD with PLUMED, which seems to go without problems; however,
>>> when
>>> I try to recompile NAMD after the patching, it won't do it. It gives a
>>> fatal error in charmc:
>>>
>>> obj/dcdplugin.o: In function `molfile_dcdplugin_init':
>>> dcdplugin.c:(.text+0x2350): multiple definition of
>>> `molfile_dcdplugin_init'
>>> /usr/local/lib/lib/plumed///src/molfile/dcdplugin.o:
>>> dcdplugin.cpp:(.text+0x208d):
>>> first defined here
>>> obj/dcdplugin.o: In function `molfile_dcdplugin_register':
>>> dcdplugin.c:(.text+0x2410): multiple definition of
>>> `molfile_dcdplugin_register'
>>> /usr/local/lib/lib/plumed///src/molfile/dcdplugin.o:
>>> dcdplugin.cpp:(.text+0x2165):
>>> first defined here
>>> obj/dcdplugin.o: In function `molfile_dcdplugin_fini':
>>> dcdplugin.c:(.text+0x2430): multiple definition of
>>> `molfile_dcdplugin_fini'
>>> /usr/local/lib/lib/plumed///src/molfile/dcdplugin.o:
>>> dcdplugin.cpp:(.text+0x217f):
>>> first defined here
>>> obj/pdbplugin.o: In function `molfile_pdbplugin_init':
>>> pdbplugin.c:(.text+0x1b70): multiple definition of
>>> `molfile_pdbplugin_init'
>>> /usr/local/lib/lib/plumed///src/molfile/pdbplugin.o:
>>> pdbplugin.cpp:(.text+0x16b5):
>>> first defined here
>>> obj/pdbplugin.o: In function `molfile_pdbplugin_register':
>>> pdbplugin.c:(.text+0x1c50): multiple definition of
>>> `molfile_pdbplugin_register'
>>> /usr/local/lib/lib/plumed///src/molfile/pdbplugin.o:
>>> pdbplugin.cpp:(.text+0x17cc):
>>> first defined here
>>> obj/pdbplugin.o: In function `molfile_pdbplugin_fini':
>>> pdbplugin.c:(.text+0x1c70): multiple definition of
>>> `molfile_pdbplugin_fini'
>>> /usr/local/lib/lib/plumed///src/molfile/pdbplugin.o:
>>> pdbplugin.cpp:(.text+0x17e6):
>>> first defined here
>>> collect2: error: ld returned 1 exit status
>>> Fatal Error by charmc in directory
>>> /home/rubengpu/bin/NAMD_2.9_Source/Linux-x86_64-g++
>>>
>>> And then exits the compilation with this message:
>>>
>>> obj/pdbplugin.o obj/psfplugin.o moduleinit4119.o -lmoduleNeighborLB
>>> -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB
>>> .rootdir/charm-6.4.0/multicore-linux64/bin/../lib/libmemory-default.o
>>> .rootdir/charm-6.4.0/multicore-linux64/bin/../lib/libthreads-default.o
>>> -lck
>>> -lconv-cplus-y -lconv-core -lconv-util -lpthread -lckqt -ldl -lcudart
>>> -ltcl8.5 -lpthread -lstdc++ -ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB
>>> -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lm returned error
>>> code 1
>>> charmc exiting...
>>> rm -f moduleinit4119.C moduleinit4119.o
>>> make: *** [namd2] Error 1
>>>
>>> I've created a log file of the compilation with the entire output:
>>> https://drive.google.com/file/d/0B_Lt9Zsl1_ASRk9KZjl2NTZGMW8/view?usp=
>>> sharing
>>>
>>> I would appreciate if somebody can point out what's failing here.
>>>
>>> Rub?(c)n
>>>
>>
>
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