Hello,
I've had fun (?) today battling AmberTools on athena. Unfortunately I lost,
hitting a number of compilation failures. The ones that I could fix with
trivial changes I've done so. The ones that I couldn't involved cpptraj and
mdgx (which was recently enabled on 12/20 in configure).
The first cpptraj issue is that Makefile_at had hard-coded -Wall into the
compiler line, which PGI doesn't recognize (should this be removed to CFLAGS
or something?). However, after I took that out, I got the following error:
CC -c -I/nics/d/home/swails/amber/include -O2 -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -o PtrajFile.o
PtrajFile.cpp
/opt/cray/xt-asyncpe/4.0/bin/CC: INFO: linux target is being used
"/usr/include/glob.h", line 175: error: more than one instance of overloaded
function "glob64" has "C" linkage
extern int glob64 (__const char *__restrict __pattern, int __flags,
^
"/usr/include/glob.h", line 179: error: more than one instance of overloaded
function "globfree64" has "C" linkage
extern void globfree64 (glob64_t *__pglob) __THROW;
^
"PtrajFile.cpp", line 308: warning: statement is unreachable
break;
^
2 errors detected in the compilation of "PtrajFile.cpp".
make[1]: *** [PtrajFile.o] Error 2
make[1]: Leaving directory
`/nics/d/home/swails/amber/AmberTools/src/cpptraj/src'
make: *** [yes] Error 2
I would not be surprised if this was an athena issue, but I didn't want to
take on this one. Instead, I just added -nocpptraj to configure and set
cpptraj='no' when -crayxt5 was set.
With MDGX (what exactly is this? an MD engine for nab?), I got the following
errors:
./Bonded.c:456: undefined reference to `OrthoReim'
./Bonded.c:461: undefined reference to `NonOrthoReim'
./Bonded.c:461: undefined reference to `NonOrthoReim'
./Bonded.c:461: undefined reference to `NonOrthoReim'
./Bonded.c:549: undefined reference to `OrthoReim'
./Bonded.c:552: undefined reference to `NonOrthoReim'
Constraints.o: In function `ReimageConstraintGroup':
./Constraints.c:443: undefined reference to `OrthoReim'
./Constraints.c:446: undefined reference to `NonOrthoReim'
/usr/bin/ld: link errors found, deleting executable `mdgx'
make: *** [mdgx] Error 2
There were many more undefined references that I truncated. This seems more
likely to be a PGI incompatibility. In any case, I've set mdgx='no' for
-crayxt5, although this may have to become default for PGI compilers in
general (I have no way of testing this).
I hope everyone had a good holiday,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jan 10 2011 - 14:00:01 PST
