Error compiling NAMD2.9 after patching with PLUMED2.1

From: Rubén Granero (ruben.granero_at_geo.uni-goettingen.de)
Date: Mon Dec 15 2014 - 06:47:27 CST

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.

Rubén

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