Also,
can you try to send full log of installing amber from a tar file (as a
fresh install)
1. untar your amber
2.
cd amber14
export AMBERHOME=`pwd`
./configure gnu >& log.configure.serial
source amber.sh
make install >& log.install.serial
make clean
./configure -mpi gnu >& log.configure.mpi
make install >& log.install.mpi
3. attach the log.* files here
Hai
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_6
>> 4/4.8.2/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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Received on Wed Jan 18 2017 - 12:30:03 PST
