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
Received on Thu Sep 16 2010 - 20:30:03 PDT
