Well, I guess that's because he did not reply to me with a cc to the
mailing list. I simply hit reply, and the thread was already, I thought, to
the mailing list, as it was initiated as such.
On Wed, Jan 18, 2017 at 2:54 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> hi
>
> side note: It's clearly that you did not attach two_par.out and one_par.out
> files to amber mailing list.
> You only sent to David.
>
> Hai
>
> On Wed, Jan 18, 2017 at 2:44 PM, Ada Sedova <ada.a.sedova.gmail.com>
> wrote:
>
> > This was sent a few days ago with no response.
> >
> > Today I was told this info was not given.
> >
> > Here it is again.
> >
> >
> > AS
> >
> >
> > ---------- Forwarded message ----------
> > From: Ada Sedova <ada.a.sedova.gmail.com>
> > Date: Tue, Jan 17, 2017 at 11:19 AM
> > Subject: Re: [AMBER] amber14 parallel build problems
> > To: david.case.rutgers.edu
> >
> >
> > Yes, I would like to continue to debug this, as getting OLCF to update to
> > amber16 may be difficult, as it requires a purchase and thus a bunch of
> > paperwork and bureaucratic steps.
> >
> > The output logs form sdtout and stderr from the failed mpi build are
> > attached.
> >
> > The complete output from mpicc -show was given above in this thread, but
> I
> > will repeat for convenience:
> >
> > -bash-4.1$ mpicc -show
> > >
> > > gcc -I/sw/rhea/openmpi/1.8.4/rhel6.6_gcc4.8.2/include -pthread
> > > -L/usr/lib64
> > > -Wl,-rpath -Wl,/usr/lib64 -Wl,-rpath
> > > -Wl,/sw/rhea/openmpi/1.8.4/rhel6.6_gcc4.8.2/lib -Wl,--enable-new-dtags
> > > -L/sw/rhea/openmpi/1.8.4/rhel6.6_gcc4.8.2/lib -lmpi
> > >
> >
> > serial build:
> >
> > -bash-4.1$ ldd ./yacc
> >
> > linux-vdso.so.1 => (0x00007ffe30bfd000)
> >
> > libc.so.6 => /lib64/libc.so.6 (0x00007f3b7805c000)
> >
> > /lib64/ld-linux-x86-64.so.2 (0x00007f3b7841b000)
> >
> >
> > parallel build:
> >
> > -bash-4.1$ ldd ./yacc
> >
> > linux-vdso.so.1 => (0x00007ffe86cf6000)
> >
> > libmpi.so.1 => /sw/rhea/openmpi/1.8.4/rhel6.6_gcc4.8.2/lib/libmpi.so.1
> > (0x00007f29e89ac000)
> >
> > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f29e8764000)
> >
> > libc.so.6 => /lib64/libc.so.6 (0x00007f29e83d0000)
> >
> > librdmacm.so.1 => /usr/lib64/librdmacm.so.1 (0x00007f29e81bb000)
> >
> > libosmcomp.so.3 => /usr/lib64/libosmcomp.so.3 (0x00007f29e7fad000)
> >
> > libibverbs.so.1 => /usr/lib64/libibverbs.so.1 (0x00007f29e7d9b000)
> >
> > libpsm_infinipath.so.1 => /usr/lib64/libpsm_infinipath.so.1
> > (0x00007f29e7b47000)
> >
> > libopen-rte.so.7 => /sw/rhea/openmpi/1.8.4/rhel6.
> > 6_gcc4.8.2/lib/libopen-rte.so.7 (0x00007f29e7856000)
> >
> > libtorque.so.2 => /usr/lib64/libtorque.so.2 (0x00007f29e6f65000)
> >
> > libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x00007f29e6c12000)
> >
> > libz.so.1 => /lib64/libz.so.1 (0x00007f29e69fb000)
> >
> > libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x00007f29e6617000)
> >
> > libssl.so.10 => /usr/lib64/libssl.so.10 (0x00007f29e63aa000)
> >
> > libopen-pal.so.6 => /sw/rhea/openmpi/1.8.4/rhel6.
> > 6_gcc4.8.2/lib/libopen-pal.so.6 (0x00007f29e60b9000)
> >
> > libnuma.so.1 => /usr/lib64/libnuma.so.1 (0x00007f29e5eae000)
> >
> > libdl.so.2 => /lib64/libdl.so.2 (0x00007f29e5caa000)
> >
> > librt.so.1 => /lib64/librt.so.1 (0x00007f29e5aa1000)
> >
> > libm.so.6 => /lib64/libm.so.6 (0x00007f29e581d000)
> >
> > libutil.so.1 => /lib64/libutil.so.1 (0x00007f29e561a000)
> >
> > /lib64/ld-linux-x86-64.so.2 (0x00007f29e8ec1000)
> >
> > libibumad.so.3 => /usr/lib64/libibumad.so.3 (0x00007f29e5412000)
> >
> > libgcc_s.so.1 => /ccs/compilers/gcc/rhel6-x86_
> 64/4.8.2/lib64/libgcc_s.so.1
> > (0x00007f29e51fc000)
> >
> > libnl.so.1 => /lib64/libnl.so.1 (0x00007f29e4faa000)
> >
> > libinfinipath.so.4 => /usr/lib64/libinfinipath.so.4 (0x00007f29e4d9b000)
> >
> > libuuid.so.1 => /lib64/libuuid.so.1 (0x00007f29e4b97000)
> >
> > libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f29e4891000)
> >
> > libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x00007f29e464c000)
> >
> > libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00007f29e4365000)
> >
> > libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00007f29e4161000)
> >
> > libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00007f29e3f34000)
> >
> > libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x00007f29e3d29000)
> >
> > libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00007f29e3b25000)
> >
> > libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f29e390b000)
> >
> > libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f29e36ec000)
> >
> >
> > Thanks for your continued assistance.
> >
> >
> > Ada
> >
> > On Tue, Jan 17, 2017 at 9:10 AM, David Case <david.case.rutgers.edu>
> > wrote:
> >
> > > On Sun, Jan 15, 2017, Ada Sedova wrote:
> > >
> > > > Here are the results of the checks you suggested:
> > > >
> > > > 1) mpicc -show shows the correct gcc (4.8.2) that I used for serial
> > > compile
> > >
> > > I'm not sure if you still want to try to debug this problem or not. If
> > you
> > > do, please save the complete log of the "make install" run that fails,
> > and
> > > send it as an attachment. So far, I think we have only seen snippets
> of
> > > the
> > > end of the error messages.
> > >
> > > Also: run the serial install, cd $AMBERHOME/bin and report the output
> > > from "ldd ./yacc". Do the same after the (failed) parallel install.
> > > Are there any differences in what libraries are loaded?
> > >
> > > Finally, please provide the full output from "mpicc -show", and let us
> > know
> > > which MPI version you are using, and how you installed it.
> > >
> > > As best I can understand things, when you compile byacc with gcc, the
> > > resulting executable works, but when you later compile it with mpicc,
> the
> > > resulting executable tries to load a library that is not in your
> > > LD_LIBRARY_PATH. If this is correct, it is something we should be able
> > to
> > > track down.
> > >
> > > [An alternative workaround is to comment out the line in the Makefile
> > > that (re-)makes yacc during the parallel compilation step. But if your
> > > mpicc
> > > is failing with yacc, it seems likely to fail at some other step as
> > well.]
> > >
> > > Trying the whole procedure again with AmberTools16 is probably a good
> > > sanity
> > > check (removes some possible sources of problems).
> > >
> > > Sorry for all the problems you are seeing: I don't recall having ever
> > seen
> > > this particular problem before.
> > >
> > > ...dac
> > >
> >
> > _______________________________________________
> > 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 - 12:00:06 PST
