Hello,
It actually looks like your MPI is providing its own byacc/bison routines.
Your best bet may be to simply skip the pnetcdf compilation. This will
really only effect parallel ptraj, since nothing else uses it.
What do you need parallel AmberTools for? Parallel NAB or ptraj?
Hopefully others will be more helpful, but from the looks of it I think
you'll actually have to tinker with the pnetcdf install, which isn't
technically part of amber.
Good luck!
Jason
On Thu, Sep 16, 2010 at 6:36 PM, Anuradha Mittal <amitta2.uic.edu> wrote:
> Hi,
>
> I am trying to compile parallel Ambertools 1.4 with intel processor on
> 64bit
> RHEL v4.
> (icc -g -O2 -D_XOPEN_SOURCE=600 -L/usr/local/ofed/lib64
> -I/usr/local/packages/mvapich2/1.4/intel-11.1/include
> -L/usr/local/packages/mvapich2/1.4/intel-11.1/lib -lmpich -lpthread
> -lrdmacm
> -libverbs -libumad -lrt)
>
> But I get the following error
>
> cd ncgen && make
> make[5]: Entering directory
> `/home/amittal/amber11/AmberTools/src/pnetcdf/src/utils/ncgen'
> mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I./../../../src/lib
> -I.
> -I. -DNDEBUG main.c
> mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I./../../../src/lib
> -I.
> -I. -DNDEBUG load.c
> bison -y -d ./ncgen.y; \
> mv y.tab.c ncgentab.c; \
> mv y.tab.h ncgentab.h
> conflicts: 1 shift/reduce
> mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I./../../../src/lib
> -I.
> -I. -DNDEBUG ncgentab.c
> mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I./../../../src/lib
> -I.
> -I. -DNDEBUG escapes.c
> mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I./../../../src/lib
> -I.
> -I. -DNDEBUG getfill.c
> mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I./../../../src/lib
> -I.
> -I. -DNDEBUG init.c
> mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I./../../../src/lib
> -I.
> -I. -DNDEBUG genlib.c
> 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
>
> /usr/local/packages/mvapich2/1.4/intel-11.1/lib/libmpich.a(parser.o)(.bss+0x18):
> In function `mvapich_yylex':
>
> /home/auto_build/sources/mvapich2-1.4/src/mpid/ch3/channels/mrail/src/plpa/parser.c:570:
> multiple definition of `yyin'
> ncgentab.o(.bss+0x1438):./ncgen.y:258: first defined here
>
> /usr/local/packages/mvapich2/1.4/intel-11.1/lib/libmpich.a(parser.o)(.bss+0x20):
> In function `mvapich_yylex':
>
> /home/auto_build/sources/mvapich2-1.4/src/mpid/ch3/channels/mrail/src/plpa/parser.c:578:
> multiple definition of `yyout'
> ncgentab.o(.bss+0x1440):./ncgen.y:258: first defined here
>
> /usr/local/packages/mvapich2/1.4/intel-11.1/lib/libmpich.a(parser.o)(.text+0xbf0):
> In function `yyrestart':
>
> /home/auto_build/sources/mvapich2-1.4/src/mpid/ch3/channels/mrail/src/plpa/parser.c:1148:
> multiple definition of `yyrestart'
>
> ncgentab.o(.text+0x3430):/home/amittal/amber11/AmberTools/src/pnetcdf/src/utils/ncgen/lex.yy.c:1567:
> first defined here
> ...
>
> /usr/local/packages/mvapich2/1.4/intel-11.1/lib/libmpich.a(parser.o)(.text+0x1010):
> In function `yy_flush_buffer':
>
> /home/auto_build/sources/mvapich2-1.4/src/mpid/ch3/channels/mrail/src/plpa/parser.c:1287:
> multiple definition of `yy_flush_buffer'
>
> ncgentab.o(.text+0x3850):/home/amittal/amber11/AmberTools/src/pnetcdf/src/utils/ncgen/lex.yy.c:1706:
> first defined here
>
> /usr/local/packages/mvapich2/1.4/intel-11.1/lib/libmpich.a(parser.o)(.text+0x1080):
> In function `yy_scan_buffer':
>
> /home/auto_build/sources/mvapich2-1.4/src/mpid/ch3/channels/mrail/src/plpa/parser.c:1317:
> multiple definition of `yy_scan_buffer'
>
> ncgentab.o(.text+0x38c0):/home/amittal/amber11/AmberTools/src/pnetcdf/src/utils/ncgen/lex.yy.c:1736:
> first defined here
>
> /usr/local/packages/mvapich2/1.4/intel-11.1/lib/libmpich.a(parser.o)(.text+0x1190):
> In function `yy_scan_string':
>
> /home/auto_build/sources/mvapich2-1.4/src/mpid/ch3/channels/mrail/src/plpa/parser.c:1354:
> multiple definition of `yy_scan_string'
>
> ncgentab.o(.text+0x39d0):/home/amittal/amber11/AmberTools/src/pnetcdf/src/utils/ncgen/lex.yy.c:1773:
> first defined here
>
> /usr/local/packages/mvapich2/1.4/intel-11.1/lib/libmpich.a(parser.o)(.text+0x1410):
> In function `yy_scan_bytes':
>
> /home/auto_build/sources/mvapich2-1.4/src/mpid/ch3/channels/mrail/src/plpa/parser.c:1372:
> multiple definition of `yy_scan_bytes'
>
> ncgentab.o(.text+0x3c50):/home/amittal/amber11/AmberTools/src/pnetcdf/src/utils/ncgen/lex.yy.c:1791:
> first defined here
>
> /usr/local/packages/mvapich2/1.4/intel-11.1/lib/libmpich.a(parser.o)(.text+0x1900):
> In function `yy_init_buffer':
>
> /home/auto_build/sources/mvapich2-1.4/src/mpid/ch3/channels/mrail/src/plpa/parser.c:1261:
> multiple definition of `yy_init_buffer'
>
> ncgentab.o(.text+0x3ec0):/home/amittal/amber11/AmberTools/src/pnetcdf/src/utils/ncgen/lex.yy.c:1680:
> first defined here
> make[5]: *** [ncmpigen] Error 1
> make[5]: Leaving directory
> `/home/amittal/amber11/AmberTools/src/pnetcdf/src/utils/ncgen'
> make[4]: *** [ncmpigen] Error 2
> make[4]: Leaving directory
> `/home/amittal/amber11/AmberTools/src/pnetcdf/src/utils'
> make[3]: *** [all] Error 2
> make[3]: Leaving directory
> `/home/amittal/amber11/AmberTools/src/pnetcdf/src'
> make[2]: *** [subdir_target] Error 1
> make[2]: Leaving directory `/home/amittal/amber11/AmberTools/src/pnetcdf'
> make[1]: *** [src/lib/all] Error 2
> make[1]: Leaving directory `/home/amittal/amber11/AmberTools/src/pnetcdf'
> make: *** [../pnetcdf/lib/libpnetcdf.a] Error 2
>
>
>
> I have both the packages bison and byacc installed on the system.
> Any help will be much appreciated.
>
> Thanks
> Anu
> _______________________________________________
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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 Thu Sep 16 2010 - 17:00:03 PDT
