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

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