Hey,
on Ubuntu 10.04, I have the same problem building ptraj with NetCDF
support as described in these threads:
http://archive.ambermd.org/201004/0680.html
http://archive.ambermd.org/201106/0731.html
The error for me looks like:
icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ncgen main.o load.o
ncgentab.o escapes.o getfill.o init.o genlib.o
../libsrc/.libs/libnetcdf.a
../libsrc/.libs/libnetcdf.a(attr.o): In function `nc_put_att_text':
attr.c:(.text+0x179a): undefined reference to `ncx_pad_putn_text'
and many more of "undefined references".
> nm libnetcdf.a | grep ncx_pad_putn_text
> U ncx_pad_putn_text
> U ncx_pad_putn_text
This shows that libnetcdf.a has been built with undefined symbols like
`ncx_pad_putn_text`. I've reproduced this by running configure/make in
the AmberTools/src/netcdf/src directory. `configure --disable-utils`
deactivates the `ncgen` compilation which works around the problem.
However, during make of AmberTools, libnetcdf.a is used in different
contexts and therefore `--disable-utils`` does not help for building
AmberTools.
I think that libnetcdf.a is somehow built wrong on "newer" systems. What
do you suggest? Could you even switch to a newer version of the NetCDF
library in AmberTools? I will try building a newer version of
libnetcdf.a and see if AmberTools builds against it...
Any hint is appreciated!
Jan-Philip
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Received on Tue Nov 01 2011 - 14:00:03 PDT
