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

[Tim Tautges]

turning off netcdf4 shouldn't be a problem, most of us do that too.

- tim

On 10/13/2011 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
>>> *******************************************
>

-- 
================================================================
"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