Then perhaps try installing byacc? I had this problem and installed
both bison and byacc (perhaps redundant, but they're small packages),
and this error was resolved.
On Tue, Jan 12, 2010 at 1:13 PM, Cihan Aydin <cihan.aydin.umassmed.edu> wrote:
> Bison is present and i directed yacc to bison on the makefile for
> ncgen...
>
> On Tue, 2010-01-12 at 13:08 -0500, Jason Swails wrote:
>> 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
>> >
>>
>>
>>
>
>
>
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> 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 - 10:30:07 PST
