Hi,
when doing `make install` (after `./configure -mpi gnu`) on our cluster
(LSF running on CentOS 6.2), I'm getting the following error (only the
lines for the last compilation block are shown):
amber-12 > make install
[...]
make[2]: Entering directory
`/g/software/linux/pack/amber-12/AmberTools/src/nab'
mpicc -DCC='"mpicc"' -DCPP='"ucpp -l"' -DFLIBS='"-lsff_mpi -lpbsa
-larpack -llapack -lblas -L/g/software/linux/pack/amber-12/lib -lnetcdf
-lgfortran -w "' \
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI \
-o /g/software/linux/pack/amber-12/bin/mpinab nab.c
/g/software/linux/pack/amber-12/bin/mpinab -c allatom_to_dna3.nab
/g/software/linux/pack/amber-12/bin/mpinab -c dna3.nab
/g/software/linux/pack/amber-12/bin/mpinab -c dna3_to_allatom.nab
/g/software/linux/pack/amber-12/bin/mpinab -c fd_helix.nab
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c
-o select_atoms.o select_atoms.c
In file included from select_atoms.c:5:
/usr/include/string.h:548: error: expected declaration specifiers or
'...' before '__locale_t'
/usr/include/string.h:549: error: nonnull argument with out-of-range
operand number (argument 1, operand 3)
/usr/include/string.h:552: error: expected declaration specifiers or
'...' before '__locale_t'
/usr/include/string.h:553: error: nonnull argument with out-of-range
operand number (argument 1, operand 4)
make[2]: *** [select_atoms.o] Error 1
make[2]: Leaving directory
`/g/software/linux/pack/amber-12/AmberTools/src/nab'
make[1]: *** [parallel] Error 2
make[1]: Leaving directory `/g/software/linux/pack/amber-12/AmberTools/src'
make: *** [install] Error 2
amber-12 >
The full output of `make install` is posted on
http://pastebin.com/QqT9d6pj.
This is on CentOS 6.2 (kernel 2.6.32-220.el6.x86_64) on an LSF 7.0.6
cluster using the MPI implementation which comes with LSF.
Any idea what's going wrong here? The compilation of the serial part
went fine w/o errors.
Cheers
frank
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Received on Thu Jun 13 2013 - 02:00:03 PDT
