Thanks for that emphasis. I tried finding the link to hdf5-1.8.4 on the netcdf
pages but couldn't. Can you send it pls?
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 8:48 AM, Roy Mendelssohn wrote:
Ed's email the other day implied that while netcdf4.1.2 might compile with
HDF-1.8.5, that there are memory issues and that it can produce incorrect
results ( can not find the email and I can't find it in the archives either).
based on that email, I would strongly suggest you use hdf-1.8.4 at least patch
1, not hdf-1.8.5. Perhaps Russ or Dennis can find Ed's email about that.
-Roy
On Aug 2, 2010, at 8:38 AM, John Helly wrote:
> Sorry. Meant that this is the beta.
> 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 8:36 AM, John Helly wrote:
>
> 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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> For list information or to unsubscribe, visit:
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>
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**********************
"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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