Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 1 Nov 2011 19:20:28 -0400

Yes it's necessary. It's what does the patchwork necessary to accommodate the build changes reflected in AmberTools 1.5 to be compatible with Amber 11.

HTH,
Jason

PS the configure script should tell you this needs to be done after it finishes

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Nov 1, 2011, at 6:52 PM, Jan-Philip Gehrcke <jgehrcke.googlemail.com> wrote:
> Dear Ross,
> 
> I did not invoke that script. First of all, I am pretty sure it is not
> mentioned in the Amber 11 and AmberTools 1.5 PDF manuals. Second, I
> see that one should first make AmberTools, then invoke that script and
> then make Amber. The error I was talking about occurred in the first
> step; during making AmberTools.
> 
> I solved that problem by simply replacing AmberTools/src/netcdf/src
> with the version 4.1.3 (from
> http://www.unidata.ucar.edu/downloads/netcdf/index.jsp) of the library
> and then adding "--disable-netcdf-4" to the netcdf configure command
> in the AmberTools/src/configure script. As far as I can see, the
> NetCDF libary releases are fully backwards compatible to each other,
> so there shouldn't be any disadvantage in using a newer version. The
> changelogs mention several bug fixes and performance improvements.
> Hence, you could consider using a newer version of netcdflib in the
> next release.
> 
> Now I have successfully built AmberTools. Next, I will follow your
> instructions and apply this AT15_Amber.py script and try building
> pmemd/sander. But I am still a bit confused... I only found
> AT15_Amber.py mentioned in the context of GPUs at
> http://ambermd.org/gpus/ and in these instructions:
> http://sites.google.com/site/dxulab/wiki/amber11installation.
> 
> When is it actually really necessary to execute AT15_Amber.py?
> 
> Thanks,
> 
> Jan-Philip
> 
> 2011/11/1 Ross Walker <ross.rosswalker.co.uk>:
>> 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
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> 
>> 
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Received on Tue Nov 01 2011 - 16:30:02 PDT
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