Hai,
I was thinking about doing that, but I am not sure if the syntax will be
the same for the two yaccs.
Ada
On Wed, Jan 18, 2017 at 1:44 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> may be try
>
> export YACC=/usr/bin/yacc
>
> to force amber to use your system yacc?
>
> Hai
>
> On Wed, Jan 18, 2017 at 1:19 PM, Ada Sedova <ada.a.sedova.gmail.com>
> wrote:
>
> > Hi, I have not received any responses about this problem since my last
> > reply. There is also another reply from me in a previous thread which
> > provided the requested logfiles and other info.
> >
> > I am still trying (unsuccessfully) to solve this problem. I think I can
> be
> > pretty confident that the mpi make is rebuilding the byacc binary,
> however,
> > and that is what is causing errors.
> >
> >
> > Thanks,
> >
> > Ada
> >
> >
> > ---------- Forwarded message ----------
> > From: Ada Sedova <ada.a.sedova.gmail.com>
> > Date: Tue, Jan 17, 2017 at 2:42 PM
> > Subject: some clues about yacc errors on OLCF rhea
> > To: david.case.rutgers.edu
> >
> >
> > Hi David,
> >
> > I'm guessing you guys are building yacc as part of the amber build. When
> I
> > run
> >
> > /ccs/home/adaa/AMBER/amber14/bin/yacc -v -d cifparse.y
> >
> > from the serial-build folder,
> >
> > I get no error.
> >
> >
> > However, when I run the same command from the parallel build folder,
> >
> > I get the same error that crashes the make install:
> >
> >
> > bash-4.1$ /ccs/home/adaa/AMBER/AMBER_PARALLEL/amber14/bin/yacc -v -d
> > cifparse.y
> >
> > yacc:39196 terminated with signal 11 at PC=40abac SP=7ffed5cb7530.
> > Backtrace:
> >
> > /ccs/home/adaa/AMBER/AMBER_PARALLEL/amber14/bin/yacc[0x40abac]
> >
> > /ccs/home/adaa/AMBER/AMBER_PARALLEL/amber14/bin/yacc[0x40ce6b]
> >
> > /ccs/home/adaa/AMBER/AMBER_PARALLEL/amber14/bin/yacc[0x404dfd]
> >
> > /lib64/libc.so.6(__libc_start_main+0xfd)[0x7fcb1871ed1d]
> >
> > /ccs/home/adaa/AMBER/AMBER_PARALLEL/amber14/bin/yacc[0x400ea9]
> >
> >
> > Also. when I try it using the system yacc in the parallel folder, I get
> no
> > error:
> >
> > -bash-4.1$ which yacc
> >
> > /usr/bin/yacc
> >
> > -bash-4.1$ /usr/bin/yacc -v -d cifparse.y
> >
> > (no error)
> >
> >
> > I'm guessing that building byacc with mpicc is incompatible with our
> > system, and I should try to get the cifparse workflow to use the system
> > yacc, if that would work.
> >
> >
> > What do you think?
> >
> >
> > Ada
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
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Received on Wed Jan 18 2017 - 12:00:04 PST
