Hello,
Install the packages bison or byacc to your system. If you are using
Ubuntu, a simple "apt-get install byacc" or "apt-get install bison"
should fix the problem.
Good luck!
Jason
On Tue, Jan 12, 2010 at 1:01 PM, Cihan Aydin <cihan.aydin.umassmed.edu> wrote:
> Greetings community,
>
> I was trying to compile parallel AT 1.3 w/intel compilers and bintraj
> support but I got the following error...
>
> cd ncgen && make
> make[6]: Entering directory
> `/home/aydinc/MicroEnv/amber-11/src/pnetcdf/src/utils/ncgen'
> mpicc -o ncmpigen -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE main.o
> load.o ncgentab.o escapes.o getfill.o init.o genlib.o -L../../../src/lib
> -lpnetcdf
> /home/aydinc/MicroEnv/intel-11.1.064/lib/intel64/libimf.so: warning:
> warning: feupdateenv is not implemented and will always fail
> main.o: In function `main':
> main.c:(.text+0x54b): undefined reference to `yyin'
> main.c:(.text+0x550): undefined reference to `yyparse'
> init.o: In function `init_netcdf':
> init.c:(.text+0x2): undefined reference to `clearout'
> make[6]: *** [ncmpigen] Error 1
> make[6]: Leaving directory
> `/home/aydinc/MicroEnv/amber-11/src/pnetcdf/src/utils/ncgen'
> make[5]: *** [ncmpigen] Error 2
> make[5]: Leaving directory
> `/home/aydinc/MicroEnv/amber-11/src/pnetcdf/src/utils'
> make[4]: *** [all] Error 2
> make[4]: Leaving directory
> `/home/aydinc/MicroEnv/amber-11/src/pnetcdf/src'
> make[3]: *** [subdir_target] Error 1
> make[3]: Leaving directory `/home/aydinc/MicroEnv/amber-11/src/pnetcdf'
> make[2]: *** [src/lib/all] Error 2
> make[2]: Leaving directory `/home/aydinc/MicroEnv/amber-11/src/pnetcdf'
> make[1]: *** [../pnetcdf/lib/libpnetcdf.a] Error 2
> make[1]: Leaving directory `/home/aydinc/MicroEnv/amber-11/src/ptraj'
> make: *** [parallel] Error 2
>
> Following this error, I made the compilation without bintraj support and
> everything was OK.
>
> What may be the cause of the problem, in case I would like to use binary
> trajectories?
>
> Thank you,
>
> Cihan
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jan 12 2010 - 10:30:04 PST
