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-- 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 >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Nov 01 2011 - 16:30:02 PDT