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

[Xiabing Xu]

If you was building netcdf using VPATH build, you may try to combine your source tree and build tree to see whether the zlib will be found.

If it is still not found, you could set up the following flags to enforce the compiler to compile your code with zlib:

export CFLAGS=-IZLIB-INSTALL-PATH/include //for c
export CXXFLAGS=-IZLIB-INSTALL-PATH/include // for c++
export LDFLAGS=-LZLIB-INSTALL-PATH/lib
export LIBS=-lz

Xiabing

On Oct 13, 2011, at 10:33 AM, Hong-Jun Kim 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
>>> *******************************************