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[netCDF #TJB-572859]: Trouble with building parallel netcdf

Excellent news, I'm happy to hear it.  I will close out the issue, let 
me know if I can provide any additional help!

-Ward
On 4/17/14, 1:55 PM, John Blaas wrote:
> New Client Reply: Trouble with building parallel netcdf
>
> Great success!
>
> I got it to build not after adding -lgpfs to LIBS, since both the
> library and header file for gpfs is in a standard place, but after
> swapping in the entire path to where HDF5 is instead of using the
> H5DIR variable to shorten the LDFLAGS and CPPFLAGS variables.  Not
> sure why they were not evaluated correctly but it has built correctly.
>
> Thanks for your help!
> John
>
> On Thu, Apr 17, 2014 at 1:30 PM, Unidata netCDF Support
> <address@hidden> wrote:
>> Hi John,
>>
>> Thank you for fixing this; we're moving in the right direction!
>>
>> Looking at the config.log now, when configure is testing for hdf5, I see
>> the following:
>>
>> configure:16382: mpicc -o conftest -g -O2
>> -I/soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/include
>> -L/soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/lib conftest.c
>> -lhdf5  -lm -lz -ldl >&5
>> /soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/lib/libhdf5.a(H5FDmpiposix.o):
>> In function `H5FD_mpiposix_open':
>> H5FDmpiposix.c:(.text+0xa8e): undefined reference to `gpfs_fcntl'
>> /soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/lib/libhdf5.a(H5FDmpiposix.o):
>> In function `H5FD_mpiposix_write':
>> H5FDmpiposix.c:(.text+0x166e): undefined reference to `gpfs_fcntl'
>>
>> When configure is linking the libhdf5 test program, it is failing
>> because of this 'undefined reference to gpfs_fcntl'.  I am unfamiliar
>> with gpfs_fcntl, but I found the following from a search on Google:
>>
>> https://publib.boulder.ibm.com/infocenter/clresctr/vxrx/index.jsp?topic=%2Fcom.ibm.cluster.gpfs.v3r5.gpfs100.doc%2Fbl1adm_fcntl.htm
>>
>> I appears that in order to use the libhdf5 you are compiling against,
>> you will need to have netcdf link against 'libgpfs'.  You can do this by
>> adjusting your LDFLAGS to include  '-lgpfs'; depending on where it
>> lives, you may need to add its library path as well.
>>
>> Give this a shot and let me know what happens, thanks!
>>
>> -Ward
>>
>> On 4/17/14, 11:38 AM, John Blaas wrote:
>>> New Client Reply: Trouble with building parallel netcdf
>>>
>>> Here is the config log after fixing the library linking.
>>>
>>> Still the same error
>>>
>>> checking for library containing H5Fflush... no
>>> configure: error: Can't find or link to the hdf5 library. Use
>>> --disable-netcdf-4, or see config.log for errors.
>>>
>>> All things remained the same.
>>>
>>> John
>>>
>>> On Thu, Apr 17, 2014 at 11:43 AM, Unidata netCDF Support
>>> <address@hidden> wrote:
>>>> Hi John,
>>>>
>>>> I'm finding a couple of issues in the config.log; thank you very much for 
>>>> providing it. I apologize in the delay responding to you.
>>>>
>>>>    I had expected to see a line in the config.log telling me that the hdf5 
>>>> library was found, but could not be linked against due to an unmet 
>>>> downstream dependency, as is often the case.  However, your config.log 
>>>> indicates that it simply cannot find a libhdf5 library at all.
>>>>
>>>> As Russ pointed out, the difference between '-I' and '-L' in the LDFLAGS 
>>>> setting is fairly important.  It appears that it was not corrected for 
>>>> this configuration attempt; if you search the config.log for 
>>>> '-I/soft/hdf5/1.8.12-parallel/../lib' you will find that it is still 
>>>> treating the directory as an include directory, not a link directory.  If 
>>>> you correct this so that it uses -L, and then confirm in your config.log 
>>>> that it is in fact using -L, I am hopeful that it will find the hdf5 
>>>> library.  If it does not, please send me the new config.log and I will see 
>>>> what new information it provides.
>>>>
>>>> Thank you, have a good day,
>>>>
>>>> -Ward
>>>>
>>>>
>>>>> While true I still get the same error on configure with the corrected 
>>>>> LDFLAGS.
>>>>>
>>>>> - JB
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Apr 15, 2014 at 3:50 PM, Unidata netCDF Support
>>>>> <address@hidden> wrote:
>>>>>> Also, I noticed a typo in your environment settings.  You have:
>>>>>>
>>>>>>>> [wilshire@blogin1 1.8.12-parallel]$ env
>>>>>>>> MODULE_VERSION_STACK=3.2.9
>>>>>>>> LDFLAGS=-I/soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/lib
>>>>>> which should instead be:
>>>>>>
>>>>>>       LDFLAGS=-L/soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/lib
>>>>>>
>>>>>> ("-L" instead of "-I")
>>>>>>
>>>>>> --Russ
>>>>>>
>>>>>> Ticket Details
>>>>>> ===================
>>>>>> Ticket ID: TJB-572859
>>>>>> Department: Support netCDF
>>>>>> Priority: Normal
>>>>>> Status: Closed
>>>>>>
>>>> Ticket Details
>>>> ===================
>>>> Ticket ID: TJB-572859
>>>> Department: Support netCDF
>>>> Priority: Normal
>>>> Status: Closed
>>>>
>>>
>>> Ticket Details
>>> ===================
>>> Ticket ID: TJB-572859
>>> Department: Support netCDF
>>> Priority: Normal
>>> Status: Open
>>> Link:  
>>> https://www.unidata.ucar.edu/esupport/staff/index.php?_m=tickets&_a=viewticket&ticketid=23800
>>
>>
>> Ticket Details
>> ===================
>> Ticket ID: TJB-572859
>> Department: Support netCDF
>> Priority: Normal
>> Status: Open
>>
>
>
> Ticket Details
> ===================
> Ticket ID: TJB-572859
> Department: Support netCDF
> Priority: Normal
> Status: Open
> Link:  
> https://www.unidata.ucar.edu/esupport/staff/index.php?_m=tickets&_a=viewticket&ticketid=23800



Ticket Details
===================
Ticket ID: TJB-572859
Department: Support netCDF
Priority: Normal
Status: Open