Hi Jan-Philip,
Did you run the AT15_Amber.py script?
i.e.
cd $AMBERHOME/AmberTools/src
./configure intel
make
cd ../../
./AT15_Amber.py
cd src
make
All the best
Ross
> -----Original Message-----
> From: Jan-Philip Gehrcke [mailto:jgehrcke.googlemail.com]
> Sent: Tuesday, November 01, 2011 1:46 PM
> To: AMBER Mailing List
> Subject: [AMBER] AmberTools 1.5 build fails due to undefined symbols in
> libnetcdf.a
>
> 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 Could you even switch to a newer version of the NetCDF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 - 15:00:04 PDT
