Re: [netcdfgroup] netcdf-4.1.1 build succeeds with hdf5 on OSX 10.6.3 using Xcode 3.2.2 and gfortran-42-5659.pkg

  • To: John Helly <hellyj@xxxxxxxx>
  • Subject: Re: [netcdfgroup] netcdf-4.1.1 build succeeds with hdf5 on OSX 10.6.3 using Xcode 3.2.2 and gfortran-42-5659.pkg
  • From: John Helly <hellyj@xxxxxxxx>
  • Date: Mon, 2 Aug 2010 08:36:05 -0700
Hi.

I copied all the source (netcdf-beta.tar and hdf5-1.8.5) to another mac and 
upgraded Xcode and then installed the gfortran you specified and bingo.

+-------------------------------------------------------------+
| Congratulations! You have successfully installed netCDF!    |
|                                                             |
| You can use script "nc-config" to find out the relevant     |
| compiler options to build your application. Enter           |
|                                                             |
|     nc-config --help                                        |
|                                                             |
| for additional information.                                 |
|                                                             |
| CAUTION:                                                    |
|                                                             |
| If you have not already run "make check", then we strongly  |
| recommend you do so. It does not take very long.            |
|                                                             |
| Before using netCDF to store important data, test your      |
| build with "make check".                                    |
|                                                             |
| NetCDF is tested nightly on many platforms at Unidata       |
| but your platform is probably different in some ways.       |
|                                                             |
| If any tests fail, please see the netCDF web site:          |
| http://www.unidata.ucar.edu/software/netcdf/                |
|                                                             |
| NetCDF is developed and maintained at the Unidata Program   |
| Center. Unidata provides a broad array of data and software |
| tools for use in geoscience education and research.         |
| http://www.unidata.ucar.edu                                 |
+-------------------------------------------------------------+

iceberg:netcdf-4.1.2-beta1 hellyj$ 

Here's the script I used.  Note that this is a 64bit build since I turned off 
the -m32 option.  At least I think it defaults to 64-bit. 

#!/bin/bash                                                                     
                                                                                
                                                                                
                       
make distclean
#export LDFLAGS="-L/usr/local/hdf5-1.8.5-macosx32-static"                       
                                                                                
                                                                                
                       
#export 
DYLD_LIBRARY_PATH=/usr/local/hdf5-1.8.5-macosx32-static:$DYLD_LIBRARY_PATH      
                                                                                
                                                                                
                
export DYLD_LIBRARY_PATH=/usr/local/hdf5-1.8.5:$DYLD_LIBRARY_PATH
#export LD_LIBRARY_PATH=/usr/local/hdf5-1.8.5-macosx32-static:$LD_LIBRARY_PATH  
                                                                                
                                                                                
                        
#                                                                               
                                                                                
                                                                                
                       
echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH"
echo "DYLD_LIBRARY_PATH:$DYLD_LIBRARY_PATH"
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-4.1.2beta --enable-netcdf-4 --enable-f90 
--with-hdf5=/usr/local/hdf5-1.8.5

#./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                               
                                                                                
                           

I'm going to try to reproduce this on my laptops where I was having the 
previous problems.

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 2, 2010, at 8:20 AM, John Helly wrote:

Thanks, Roy.  Sounds like just the kind of black magic I need.
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 2, 2010, at 7:52 AM, Roy Mendelssohn wrote:

Hi John:

I notice you are using HDF-1.8.5.  A few days ago I emailed the list about 
that, and Ed replied that at the moment they do not work with HDF-1.8.5  (i 
can't find the email but look at the archives).  You need to use the version of 
HDF 1.8.4 that is on the netcdf ftp site.  I have been able to compile that 
with:

1.  the gcc and gfortran from fink

2. the gcc from apple and the gfortran from R at:  
http://r.research.att.com/tools/  - make certain you scroll down and get the 
gfortran for Snwo Leopard, not the one at the top of the page.

HTH,

-Roy




> 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>
> 
> _______________________________________________
> netcdfgroup mailing list
> netcdfgroup@xxxxxxxxxxxxxxxx
> For list information or to unsubscribe,  visit: 
> http://www.unidata.ucar.edu/mailing_lists/ 

**********************
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
1352 Lighthouse Avenue
Pacific Grove, CA 93950-2097

e-mail: Roy.Mendelssohn@xxxxxxxx (Note new e-mail address)
voice: (831)-648-9029
fax: (831)-648-8440
www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 

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