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

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