Hi,
Just a quick question; were you configuring/building AmberTools from a
clean directory? If not, did you do a 'make clean' before 'make
install'?
It seems that (as you say) the library is not being generated
correctly on your system. I've been able to successfully build the
netcdf version that comes with AmberTools using both gnu 4.6 and intel
12 compilers. It may be that the issue has to do with the tools used
to generate the library itself. What versions of 'ar' and 'ranlib' do
you have?
Other than that, would you mind sending me the
$AMBERHOME/AmberTools/src/netcdf_config.log that is generated after
you run './configure' on your system with the original AmberTools
netcdf (i.e. not the one you downloaded and installed manually).
Thanks!
-Dan
On Tue, Nov 1, 2011 at 4:45 PM, Jan-Philip Gehrcke
<jgehrcke.googlemail.com> wrote:
> 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 Could you even switch to a newer version of the NetCDF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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Tue Nov 01 2011 - 20:00:03 PDT
