I did exactly the way you mentioned.
Do you have any suggestions that I may try.
On Thu, Sep 16, 2010 at 10:09 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> Did you make clean? This also looks like a parallel build in AmberTools,
> which I'd suggest against doing if you're having problems with it. Build
> in
> serial, then ./configure -mpi {compiler} in $AMBERHOME/AmberTools/src, then
> cd ../../src and make parallel in the amber source directory.
>
> Hope this helps,
> Jason
>
> On Thu, Sep 16, 2010 at 10:15 PM, Anuradha Mittal <
> anuradha.mittal.gmail.com
> > wrote:
>
> > Thanks for your reply. I actually intended to compile Amber11 in
> parallel,
> > hence was compiling Ambertools in parallel too.
> >
> > Anyways, I just compiled Ambertools in serial and am now trying to
> install
> > Amber11. But I get this error:
> >
> > cd ../lib && make sys.a
> > make[2]: Entering directory `/home/amittal/amber11/AmberTools/src/lib'
> > cpp -traditional -P -DMKL -DBINTRAJ -DMPI sys.f > _sys.f
> > mpif90 -c -O0 -o sys.o _sys.f
> > mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -o
> > wallclock.o wallclock.c
> > wallclock.c(25): error: incomplete type is not allowed
> > struct timezone tz;
> > ^
> >
> > wallclock.c(42): error: incomplete type is not allowed
> > struct timezone tz;
> > ^
> >
> > compilation aborted for wallclock.c (code 2)
> > make[2]: *** [wallclock.o] Error 2
> > make[2]: Leaving directory `/home/amittal/amber11/AmberTools/src/lib'
> > make[1]: *** [syslib] Error 2
> > make[1]: Leaving directory `/home/amittal/amber11/src/sander'
> > make: *** [parallel] Error 2
> >
> >
> > Thanks
> > Anu
> >
> >
> > On Thu, Sep 16, 2010 at 6:42 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > 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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > 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
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 16 2010 - 20:30:06 PDT
