sunhwan

Compiling CHARMM on Mac OS X is supposed to be easy; The install script has identifier osx. However, I encountered numerous problems while I tried to compile it. So here I leave some comment how I worked around the problems. Probably, I suspect some of the problems are because of my group is using little modified version of CHARMM, so this may not same for everyone.

1. pre-requisites:

   • Intel Fortran for Mac OS (optional)
   • g77 or gfortran (if you have Intel Fortran, you only need g77)

2. ./install.com osx large ifort nolog

3. The first error message that I’ve encountered is:

   eutil.f: In subroutine ‘enerin’:
   eutil.f:2234:
   ceterm(XMAP) = ‘XMAP’
   ^
   Invalid declaration of or reference to symbol `xmap’ at (^) [initially seen at (^)]
   make: *** [/Users/sunhwan/Programs/c33a1/lib/osx/energy.a(eutil.o)] Error 1

   The workaround for this error is putting XRAYMAP to the file build/osx/pref.dat.

4. The second one is:

   /Users/sunhwan/Programs/c33a1/source/machdep/cstuff.c:30:23: error: bits/time.h: No such file or directory
   /Users/sunhwan/Programs/c33a1/source/machdep/cstuff.c: In function ‘fmalloc_’:
   /Users/sunhwan/Programs/c33a1/source/machdep/cstuff.c:104: warning: conflicting types for built-in function ‘malloc’
   /Users/sunhwan/Programs/c33a1/source/machdep/cstuff.c: In function ‘fsystem_’:
   /Users/sunhwan/Programs/c33a1/source/machdep/cstuff.c:145: warning: incompatible implicit declaration of built-in function ‘exit’
   /Users/sunhwan/Programs/c33a1/source/machdep/cstuff.c: In function ‘fputenv_’:
   /Users/sunhwan/Programs/c33a1/source/machdep/cstuff.c:278: warning: incompatible implicit declaration of built-in function ‘exit’

   The workaround: edit the file source/machdep/cstuff.c line 30, from bits/time.h to time.h

5. Lastly:

   /usr/bin/ld: Undefined symbols:
   xraymap0
   collect2: ld returned 1 exit status

   Workaround: replace build/osx/energy.mk to energy.txt.

Again: I am suspecting the first and the last errors are related with my source, others may not suffer from them.

This entry was posted on Wednesday, August 15th, 2007 at 6:57 am and is filed under Uncategorized. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.