On Wed, Mar 10, 2010 at 1:24 AM, Scott Brozell <sbrozell.rci.rutgers.edu> wrote:
> Hi,
>
> On Tue, Mar 09, 2010 at 06:28:44PM -0500, Jason Swails wrote:
>> On Sat, Mar 6, 2010 at 3:23 PM, case <case.biomaps.rutgers.edu> wrote:
>> > On Sat, Mar 06, 2010, Ross Walker wrote:
>> >
>> >> That might be useful although right now the 'actual' limitation is that you
>> >> can't do:
>> >> make -f Makefile_at parallel
>> >> without AMBERHOME/exe/yacc
>> >
>> > I'll work on removing this dependency...not only does it (appear to) involve
>> > a piece of pnetcdf that we don't actually use, but according to Jason, the
>> > code doesn't even accept yacc.
>>
>> As a follow-up to this (since I said I would try to verify my past
>> claims): I removed bison/byacc from my ubuntu machine, then checked
>> out a new version of Amber today. Serial installation/test went fine.
>> Parallel install of ambertools yielded the same error for me as it
>> did when it was first introduced:
>>
>> make[5]: Entering directory
>> `/home/swails/newamber/03.09.10/amber11/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
>> flex ./ncgen.l; \
>> mv lex.yy.c ncgenyy.c
>> yacc -d ./ncgen.y; \
>> mv y.tab.c ncgentab.c; \
>> mv y.tab.h ncgentab.h
>> yacc: e - line 10 of "./ncgen.y", syntax error
>> %expect 1
>> ^
>> mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
>> -I./../../../src/lib -I. -I. -DNDEBUG ncgentab.c
>
> Apparently, the yacc syntax error is not fatal since ncgentab.c compiles.?
> %expect is a bison-ism and seems only to quell messages regarding
> shift/reduce conflicts:
> http://dinosaur.compilertools.net/bison/bison_6.html#SEC54
> http://dinosaur.compilertools.net/yacc/index.html
>
> What happens if you delete the %expect line ?
Magic. It works now. (I uninstalled bison first to check). But
still, this issue wasn't really found for 7 months after the initial
pnetcdf was released officially (and it's been in CVS for even longer
than that). Perhaps we just list bison as a prereq and/or try and get
rid of the dependency altogether? This is a decision for the
higher-ups though.
Thanks!
Jason
>
>> 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
>> main.o: In function `main':
>> main.c:(.text+0x527): undefined reference to `yyin'
>> main.c:(.text+0x52c): undefined reference to `yyparse'
>> init.o: In function `init_netcdf':
>> init.c:(.text+0x2): undefined reference to `clearout'
>> make[5]: *** [ncmpigen] Error 1
>>
>> which yacc returns: /home/swails/newamber/03.09.10/amber11/bin/yacc
>>
>> After re-installing bison from aptitude (so that there is a yacc in
>> /usr/bin), the compilation finishes successfully. My system uses
>> intel11 compilers with MKL.
>
> Scott
>
>
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Mar 10 2010 - 08:00:06 PST
