I should add that this error occurred with both, `configure gnu` and
`configure intel`.
These are my compiler --version outputs:
gcc: (Ubuntu 4.4.3-4ubuntu5) 4.4.3
icc/ifort: 12.1.0 20111011
2011/11/1 Jan-Philip Gehrcke <jgehrcke.googlemail.com>:
> 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 Could you even switch to a newer version of the NetCDF library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 - 15:00:03 PDT
