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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Received on Thu Sep 16 2010 - 16:00:03 PDT
