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



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
> 
> 

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