Hi,
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.
>
>
> What do you think?
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Received on Wed Jan 18 2017 - 11:00:02 PST
