This archive contains answers to questions sent to Unidata support through mid-2025. Note that the archive is no longer being updated. We provide the archive for reference; many of the answers presented here remain technically correct, even if somewhat outdated. For the most up-to-date information on the use of NSF Unidata software and data services, please consult the Software Documentation first.
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 > Hello, > > On the surface, it appears that it should be finding the hdf5 library. Would > it be possible for you to provide the config.log generated when you run the > 'configure' command? It may contain additional useful information as to what > exactly is happening when it fails to find the hdf5 library that is present, > or why it rejects the hdf5 library. > > Thanks, have a great day, > > -Ward > > > Following your instructions for building parallel Netcdf from here: > > https://www.unidata.ucar.edu/software/netcdf/docs/build_parallel.html > > > > I have ran into an issue where configure can't find the hdf5 library. > > > > ./configure --disable-shared > > =========== > > checking for floor in -lm... yes > > 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. > > =========== > > > > I would appreciate some help or insight that would lead to finally > > getting this built. > > > > Below are some things that should prove useful, but please let me know > > if I can supply any more information that would lead to a resolution. > > > > Thanks, > > John Blaas > > > > [wilshire@blogin1 netcdf-4.3.1.1]$ cat > > /soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/lib/libhdf5.settings > > SUMMARY OF THE HDF5 CONFIGURATION > > ================================= > > > > General Information: > > ------------------- > > HDF5 Version: 1.8.12 > > Configured on: Thu Apr 3 15:22:15 CDT 2014 > > Configured by: wilshire@blogin2 > > Configure mode: production > > Host system: x86_64-unknown-linux-gnu > > Uname information: Linux blogin2 2.6.32-431.3.1.el6.x86_64 > > #1 SMP Fri Jan 3 21:39:27 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > Byte sex: little-endian > > Libraries: static > > Installation point: /soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9 > > > > Compiling Options: > > ------------------ > > Compilation Mode: production > > C Compiler: > > /software/mvapich2-intel-psm-1.9.5/bin/mpicc -w -m64 ( Intel(R) C > > Intel(R) 64 Compiler Version 13.1.3.192 Build 20130607) > > CFLAGS: > > H5_CFLAGS: -std=c99 -O > > AM_CFLAGS: > > CPPFLAGS: > > H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L -DNDEBUG > > -UH5_DEBUG_API > > AM_CPPFLAGS: -D_LARGEFILE_SOURCE > > -D_LARGEFILE64_SOURCE -D_BSD_SOURCE > > Shared C Library: no > > Static C Library: yes > > Statically Linked Executables: no > > LDFLAGS: > > H5_LDFLAGS: > > AM_LDFLAGS: > > Extra libraries: -lz -ldl -lm -lgpfs > > Archiver: ar > > Ranlib: ranlib > > Debugged Packages: > > API Tracing: no > > > > Languages: > > ---------- > > Fortran: no > > > > C++: no > > > > Features: > > --------- > > Parallel HDF5: mpicc > > High Level library: yes > > Threadsafety: no > > Default API Mapping: v18 > > With Deprecated Public Symbols: yes > > I/O filters (external): deflate(zlib) > > I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset > > MPE: > > Direct VFD: no > > dmalloc: no > > Clear file buffers before write: yes > > Using memory checker: no > > Function Stack Tracing: no > > GPFS: yes > > Strict File Format Checks: no > > Optimization Instrumentation: no > > Large File Support (LFS): yes > > > > > > And of course environment at the time of building > > > > [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 > > MANPATH=/soft/intel/13.1.3/man/en_US:/software/mvapich2-intel-psm-1.9.5/share/man:/soft/autoconf/2.68/share/man:/soft/softenv/1.6.2/man:/soft/lcrc/man:/usr/man:/usr/share/man:/usr/local/man:/usr/X11R6/man:/home/wilshire/man > > HOSTNAME=blogin1 > > IPPROOT=/soft/intel/13.1.3/ipp > > TERM=xterm-256color > > SHELL=/bin/bash > > PSM_SHARECONTEXTS_MAX=16 > > HISTSIZE=1000 > > CPPFLAGS=-I/soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/include > > LIBRARY_PATH=/soft/intel/13.1.3/lib/intel64:/soft/intel/13.1.3/ipp/lib/intel64:/soft/intel/13.1.3/tbb/lib/intel64/gcc4.4:/soft/lcrc/lib > > OLDPWD=/soft/hdf5 > > SSH_TTY=/dev/pts/4 > > USER=wilshire > > INTEL_HOME=/soft/intel/13.1.3 > > LD_LIBRARY_PATH=/soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/lib:/soft/intel/13.1.3/lib/intel64:/soft/intel/13.1.3/composer_xe_2013.5.192/mpirt/lib/intel64:/soft/intel/13.1.3/ipp/lib/intel64:/soft/intel/13.1.3/tbb/lib/intel64/gcc4.4:/software/mvapich2-intel-psm-1.9.5/lib:/soft/lcrc/lib:/usr/lib64:/usr/lib > > IPATH_NO_CPUAFFINITY=1 > > CPATH=/soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/include:/soft/intel/13.1.3/tbb/include:/software/mvapich2-intel-psm-1.9.5/include > > CXXFLAGS=-I/soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/include > > NLSPATH=/soft/intel/13.1.3/lib/intel64/locale/%l_%t/%N:/soft/intel/13.1.3/ipp/lib/intel64/locale/%l_%t/%N:/soft/intel/13.1.3/composerxe/debugger/intel64/locale/%l_%t/%N > > MODULE_VERSION=3.2.9 > > PATH=/soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/bin:/soft/intel/13.1.3/bin:/software/mvapich2-intel-psm-1.9.5/bin:/soft/autoconf/2.68/bin:/soft/softenv/1.6.2/bin:/soft/lcrc/bin:/bin:/usr/bin:/usr/local/bin:/usr/X11R6/bin:/home/wilshire/bin:. > > FCFLAGS=-I/soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/include > > TBBROOT=/soft/intel/13.1.3/tbb > > LD_RUN_PATH=/soft/intel/13.1.3/lib/intel64:/soft/intel/13.1.3/composer_xe_2013.5.192/mpirt/lib/intel64:/soft/intel/13.1.3/ipp/lib/intel64:/soft/intel/13.1.3/tbb/lib/intel64/gcc4.4 > > PWD=/soft/hdf5/1.8.12-parallel > > IDB_HOME=/soft/intel/13.1.3/composer_xe_2013.5.192/bin/intel64 > > LANG=en_US.UTF-8 > > WHATAMI=linux-rhel6-x86_64 > > PLATFORM=linux-rhel6-x86_64 > > CXX=mpicxx > > HISTCONTROL=ignoredups > > SHLVL=1 > > HOME=/home/wilshire > > FC=mpif90 > > LIBS=-ldl > > H5DIR=/soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9 > > LOGNAME=wilshire > > CVS_RSH=ssh > > SSH_CONNECTION=140.221.13.25 49759 140.221.74.11 22 > > MODULESHOME=/software/Modules/3.2.9 > > MPI_HOME=/software/mvapich2-intel-psm-1.9.5 > > LESSOPEN=|/usr/bin/lesspipe.sh %s > > ARCH=linux-rhel6-x86_64 > > CC=mpicc > > LD_FLAGS=-L/soft/hdf5/1.8.12-parallel/intel-13.1/mvapich2-1.9/lib > > > > Russ Rew UCAR Unidata Program address@hidden http://www.unidata.ucar.edu Ticket Details =================== Ticket ID: TJB-572859 Department: Support netCDF Priority: Normal Status: Closed