[MOAB-dev] moab-announce Digest, Vol 5, Issue 2

Thu Oct 13 17:05:48 CDT 2011

Revision 5195 from Jane solves your problem.
Please update and recompile the code.

Thank you, Jain.

Hong-Jun

----- Original Message -----
> From: "Tiantian Xu" <tiantianxu.88 at gmail.com>
> To: "Hong-Jun Kim" <hongjun at mcs.anl.gov>
> Sent: Thursday, October 13, 2011 2:22:00 PM
> Subject: Re: moab-announce Digest, Vol 5, Issue 2
> Yes, I enabled parallel when building HDF5. There is a test file
> "ph5example.c" in the HDF5 source code to test HDF5 parallel
> operations, it runs correctly so I think HDF5 library is good. Tests
> in netcdf "make check" are all passed, so netcdf should be good too,
> unless there are some hidden problems...
> Thanks!
> 
> Tiantian
> 
> 
> On Thu, Oct 13, 2011 at 2:47 PM, Hong-Jun Kim < hongjun at mcs.anl.gov >
> wrote:
> 
> 
> I am checking it, before that, are you using a parallel build of the
> HDF5 library?
> Thanks.
> 
> Hong-Jun
> 
> 
> 
> 
> 
> ----- Original Message -----
> > From: "Tiantian Xu" < tiantianxu.88 at gmail.com >
> > To: "Hong-Jun Kim" < hongjun at mcs.anl.gov >
> > Sent: Thursday, October 13, 2011 12:11:09 PM
> > Subject: Re: moab-announce Digest, Vol 5, Issue 2
> > Hi Hong-Jun,
> >
> > Yes, that machine is 64bit, however the Fedora installed is a 32-bit
> > version, I'm not sure if this is the problem... However I have
> > decided
> > not to dig into the problem on that machine any more...
> > I had reinstalled hdf5 and netcdf on a different machine, also 64
> > bit,
> > with 64-bit Fedora. Moab "configure", "make", "make check" and "make
> > install" were all successful. But the same error in parallel read
> > occurred:
> >
> > [tiantian at vis-pc2 bin]$ mpiexec -np 2 ./mbconvert -O
> > PARALLEL=READ_PART -O PARTITION=MATERIAL_SET -O
> > PARALLEL_RESOLVE_SHARED_ENTS -O PARALLEL_GHOSTS=3.0.1 -o
> > PARALLEL=WRITE_PART ./64bricks_512hex.h5m dummy.h5m
> > Read "./64bricks_512hex.h5m"
> >
> > =====================================================================================
> > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> > = EXIT CODE: 139
> > = CLEANING UP REMAINING PROCESSES
> > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> > =====================================================================================
> > APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
> > (signal 11)
> >
> > I'm very confused because now the "make check" works, all tests are
> > passed, same error still occurs. So it is very likely that there are
> > some subtle issues...
> > The config and make log from the installed lib directory are
> > attached.
> >
> > Thank you so much for the help.
> >
> > Tiantian
> >
> >
> > On Thu, Oct 13, 2011 at 11:33 AM, Hong-Jun Kim < hongjun at mcs.anl.gov
> > >
> > wrote:
> >
> >
> > Actually, I can not replicate the problem in my machine.
> > Can you check if your machine is 64bit with "uname -m" command?
> >
> > Could anyone have any idea about the question below?
> > Can "netcdf-4" disabled netcdf cause any segmentation error?
> >
> >
> > > Also, before I built MOAB, when I was trying to build netcdf,
> > > configure complained it could not find the z library, so I turned
> > > off
> > > "netcdf-4" feature, in other words, the netcdf library was not
> > > built
> > > on top of hdf5/zlib. Could this be the problem?
> >
> > Thanks.
> >
> > Hong-Jun
> >
> >
> >
> >
> >
> > > Hi Hong-Jun,
> > >
> > > I still have the same problems after chaning "LFLAGS=-static".
> > > "config.log", "mbcn_test.log" and "test-suite.log" are all
> > > attached.
> > > But I'm not sure what you mean by "error signs"..
> > > Also, before I built MOAB, when I was trying to build netcdf,
> > > configure complained it could not find the z library, so I turned
> > > off
> > > "netcdf-4" feature, in other words, the netcdf library was not
> > > built
> > > on top of hdf5/zlib. Could this be the problem? I'm still trying
> > > to
> > > fix the "can't find z lib" error with netcdf.
> > >
> > > Thanks for your help!
> > >
> > > Tiantian
> > >
> > >
> > > On Wed, Oct 12, 2011 at 1:19 PM, Hong-Jun Kim <
> > > hongjun at mcs.anl.gov
> > > >
> > > wrote:
> > >
> > >
> > > If you still have the same problems with Tim's suggestion as
> > > below,
> > > could you please send me your "config.log" and error signs for me
> > > to
> > > replicate it?
> > >
> > > In addition, can you use " moab-dev at mcs.anl.gov " for this kind of
> > > question?
> > > "moab-announce" is for announcing new things and upgrades and
> > > looks
> > > it
> > > has some latencies to get mail.(I just got Tim's message which
> > > looks
> > > sent yesterday)
> > >
> > > Thanks.
> > >
> > > -----------------------------
> > > Hong-Jun Kim
> > > Post-doc researcher
> > > MCS, Argonne National Laboratory
> > > 9700 S. Cass Ave. B240/R2147
> > > Argonne, IL 60439
> > > 630-252-4791
> > > hongjun at mcs.anl.gov
> > > -----------------------------
> > >
> > > > Hong-Jun,
> > > > Can you check this out? Tiantian, we haven't seen this problem
> > > > anywhere. The output from your configure looks like
> > > > you're on a 64bit machine, but can you verify that? The only
> > > > other
> > > > thing that looks strange in your configure is the
> > > > LFLAGS=-static; you should be able to get the same thing, in a
> > > > more
> > > > standard way, using --disable-shared
> > > > --enable-static. Could you try that? Thanks.
> > > >
> > > > - tim
> > > >
> > > > On 10/11/2011 12:58 PM, Tiantian Xu wrote:
> > > > >
> > > > > Hi,
> > > > >
> > > > > I was trying to build moab but met with the "mbcn_test fail"
> > > > > during
> > > > > make
> > > > > check.
> > > > > The commands I used to build the library were:
> > > > >
> > > > > ./configure LFLAGS=-static
> > > > > --with-mpi=/home/tiantian/ITL/mpich2-1.4.1p1/gcc
> > > > > --with-hdf5=/home/tiantian/hdf5
> > > > > --with-netcdf=/home/tiantian/ITL/netcdf-4.1.3/gcc
> > > > > --with-zlib=/home/tiantian/ITL/zlib-1.2.5/gcc
> > > > > --with-szip=/home/tiantian/ITL/szip-2.1/gcc
> > > > > --prefix=/home/tiantian/ITL/moab 2>&1 | tee configure.log
> > > > > make 2>&1 | make.log
> > > > > make check 2>&1 | tee make.check.log
> > > > >
> > > > > Looks like the mbcn_test is about query on entities, I don't
> > > > > know
> > > > > why
> > > > > this went wrong. Later I ignored the make check errors and did
> > > > > "make
> > > > > install". I tried to perform parallel read/write and found
> > > > > mbconvert
> > > > > went wrong too:
> > > > >
> > > > > $mpiexec -np 2 ./mbconvert -O PARALLEL=READ_PART -O
> > > > > PARTITION=MATERIAL_SET -O PARALLEL_RESOLVE_SHARED_ENTS -O
> > > > > PARALLEL_GHOSTS=3.0.1 -o PARALLEL=WRITE_PART
> > > > > ./64bricks_512hex.h5m
> > > > > dummy.h5m
> > > > > Read "./64bricks_512hex.h5m"
> > > > >
> > > > > =====================================================================================
> > > > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> > > > > = EXIT CODE: 139
> > > > > = CLEANING UP REMAINING PROCESSES
> > > > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> > > > > =====================================================================================
> > > > > APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation
> > > > > fault
> > > > > (signal 11)
> > > > >
> > > > > I suspect some fundamental functions in moab were not properly
> > > > > made?
> > > > > I had attached the log files. Please take a look.
> > > > >
> > > > > Thanks a lot for your help!
> > > > >
> > > > > Best,
> > > > > Tiantian
> > > > >
> > > >
> > > > --
> > > > ================================================================
> > > > "You will keep in perfect peace him whose mind is
> > > > steadfast, because he trusts in you." Isaiah 26:3
> > > >
> > > > Tim Tautges Argonne National Laboratory
> > > > ( tautges at mcs.anl.gov ) (telecommuting from UW-Madison)
> >
> >
> >
> > > > phone: (608) 263-8485 1500 Engineering Dr.
> > > > fax: (608) 263-4499 Madison, WI 53706
> > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > _______________________________________________
> > > > moab-announce mailing list
> > > > moab-announce at mcs.anl.gov
> > > > https://lists.mcs.anl.gov/mailman/listinfo/moab-announce
> > > >
> > > >
> > > > End of moab-announce Digest, Vol 5, Issue 2
> > > > *******************************************