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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