From: Rubén Granero (ruben.granero_at_geo.uni-goettingen.de)
Date: Tue Dec 16 2014 - 07:39:02 CST
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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