[netcdfgroup] netcdf-4.1.2beta build fails with hdf5 on OSX 10.6.3

  • To: John Helly <hellyj@xxxxxxxx>
  • Subject: [netcdfgroup] netcdf-4.1.2beta build fails with hdf5 on OSX 10.6.3
  • From: John Helly <hellyj@xxxxxxxx>
  • Date: Sun, 1 Aug 2010 19:09:27 -0700
Cheers.
--------------
John Helly, UCSD / San Diego Supercomputer Center / Scripps Institution of 
Oceanography, Climate, Atmospheric Science, and Physical Oceanography / +01 760 
840 8660 mobile / stonesteps (Skype) / stonesteps7 (iChat) / 
/www.sdsc.edu/~hellyj




On Aug 1, 2010, at 7:04 PM, John Helly wrote:

Same result with the beta as well.

checking hdf5.h presence... yes
checking for hdf5.h... yes
checking whether we should try to build netCDF-4... yes
checking for H5Fflush in -lhdf5... no
configure: error: Can't find or link to the hdf5 library. Configure with 
--disable-netcdf-4 or see config.log for errors.
NeptuneStonesteps.local:~/src/netcdf-4.1.2-beta1>


Cheers.
--------------
John Helly, UCSD / San Diego Supercomputer Center / Scripps Institution of 
Oceanography, Climate, Atmospheric Science, and Physical Oceanography / +01 760 
840 8660 mobile / stonesteps (Skype) / stonesteps7 (iChat) / 
/www.sdsc.edu/~hellyj




On Aug 1, 2010, at 7:01 PM, John Helly wrote:

Greetings.

I am struggling to compile netcdf-4.1.1 on OSX 10.6.4 with hdf5 and fortran so 
I can build Dave Pierce's new ncview.  I have worked my way through some 
earlier problems and have come to this script:

#!/bin/bash                                                                     
                                                                                
                                                                 
make distclean                                                                  
                                                                                
                                                                  
#export LDFLAGS="-L/usr/local/hdf5-1.8.5-macosx32-static"                       
                                                                                
                                                                 
export CC=/usr/bin/cc                                                           
                                                                                
                                                                 
export CFLAGS='-m32'                                                            
                                                                                
                                                                  
#export CPPFLAGS=-Df2cFortran                                                   
                                                                                
                                                                 
export F77=gfortran                                                             
                                                                                
                                                                 
export FC=gfortran                                                              
                                                                                
                                                                  
export FCFLAGS=-qsuffix=cpp=f90                                                 
                                                                                
                                                                 
./configure --prefix=/usr/local/netcdf-4.1.1 --enable-netcdf-4 --enable-f90 
--with-hdf5=/usr/local/hdf5-1.8.5-macosx32-static                               
                                                                     
#                                                                               
                                                                                
                                                                 
#export LDFLAGS="-L/usr/local/hdf5-1.8.5-macosx64-static"                       
                                                                                
                                                                 
#./configure --prefix=/usr/local/netcdf-4.1.1 --enable-netcdf-4 --enable-f90 
--with-hdf5=/usr/local/hdf5-1.8.5-macosx64-static                     


This got me past some earlier problems with 32-bit fortran libraries (I think) 
but now I'm getting complaints about the hdf5 libraries even though they seem 
to be found for some things.  

checking for manual-page index command... 
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking whether we should try to build netCDF-4... yes
checking for H5Fflush in -lhdf5... no
configure: error: Can't find or link to the hdf5 library. Configure with 
--disable-netcdf-4 or see config.log for errors.


I'm attaching the config.log for those who might care to look.  In the script 
above, you can see that I experimented with defining the LDFLAGS and this 
solved the problem of the missing -lhdf5 but introduced a bunch of other even 
stranger problems that made me think I was overriding some more basic library 
paths by specifying LDFLAGS.  Anyway, I couldn't figure out what those problems 
were so I backed up to this in hoping that someone out there would have a 
suggestion.

Any help would be appreciated.

Cheers.
--------------
John Helly, UCSD / San Diego Supercomputer Center / Scripps Institution of 
Oceanography, Climate, Atmospheric Science, and Physical Oceanography / +01 760 
840 8660 mobile / stonesteps (Skype) / stonesteps7 (iChat) / 
/www.sdsc.edu/~hellyj
<config.log>




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