[AMBER-Developers] missing symbols in netcdf/sander compile (mac osx)?

From: case <case.biomaps.rutgers.edu>
Date: Mon, 16 Nov 2009 10:52:08 -0500

Hi everyone:

My sander compile on MacOSX (10.5) has suddenly stopped working, with this

Undefined symbols:
  "_nf_put_var1_int_", referenced from:
      ___netcdf_MOD_nf90_put_var_fourbyteint in libnetcdf.a(netcdf.o)
      ___netcdf_MOD_nf90_put_var_eightbyteint in libnetcdf.a(netcdf.o)

....many more such problems.

If I revert to CVS version 1.29 of the configure script, things work again.
It looks like the main difference is that the "new" configure updates add
"-mtune=generic -msse -mfpmath=sse" to the options send to netcdf configure,
and to load commands.

OR, it may be related to this comment (from revision 1.30):

"Finally, netCDF should, if on a mac, be configured with -DpgiFortran. This
usually seems to be correctly guessed, but with the combination of the gcc
compiler and the -m32 flag, it will not be. Thus, I have ensured that if we
are building on a Mac, this compiler flag will be added explicitly."

But, as far as I can see, the current version of configure does not in fact
add -DpgiFortran.

Anyway...does anyone recoginize the problem? I guess I can debug it
myself, but am hoping that it will be recognized. We've had *lots* of
changes to the configure script over the past few days, which continues
to scare me, since I am pretty sure these are not being tested on lots of
platforms. Also, please don't tweak the configure scripts just to get the
absolute last millisecond of performance out of the codes.


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Received on Mon Nov 16 2009 - 08:00:02 PST
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