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
>>
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue Nov 01 2011 - 16:00:04 PDT
