Hi,
A note on practical approaches - if you follow Hai's advice to
define YACC then you need to use make -e
A note on the 'amber side bigger picture' - of course we are not
rebuilding yacc -- you have no yacc since you are building parallel
in a separate directory without having built serial...
A debugging comment - these parallely built yaccs work fine for building
cifparse :
mpicc -show -v
mpicc for MVAPICH2 version 2.1
gcc -v -I/usr/local/mvapich2/gnu/5.2/2.1/include -L/usr/local/mvapich2/gnu/5.2/2.1/lib -Wl,-rpath -Wl,/usr/local/mvapich2/gnu/5.2/2.1/lib -Wl,--enable-new-dtags -lmpi
and
mpicc for MVAPICH2 version 2.1
icc -v -I/usr/local/mvapich2/intel/15/2.1/include -L/usr/local/mvapich2/intel/15/2.1/lib -Wl,-rpath -Wl,/usr/local/mvapich2/intel/15/2.1/lib -Wl,--enable-new-dtags -lmpi
IMHO take a practical approach, document it for your future use, move on.
scott
On Wed, Jan 18, 2017 at 01:44:41PM -0500, Scott Brozell wrote:
>
> As a practical matter you could produce the serial yacc and change its
> permission to owner not writable and then build in parallel perhaps
> with make -i if a non writable amberhome/bin/yacc produces an error.
>
> FWIW i just checked this thread :
> [AMBER] amber14 parallel build problems
> and i do not see the verbose and verbatim details such as logfiles etc.
> Perhaps these did not make it into the list.
> Also the message below appears to have been sent to an individual not to
> the list.
>
> If we really really want to find the local problem then you may need to
> run the parallelly produced yacc in a debugger. I'll take a look at the
> amber side bigger picture - why rebuild yacc if a serial build already
> made it.
>
> scott
>
> On Wed, Jan 18, 2017 at 01:19:24PM -0500, Ada Sedova 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.
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Received on Wed Jan 18 2017 - 11:30:03 PST
