ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/hdf5-1.8.4-patch1.tar.gz
-Roy
On Aug 2, 2010, at 9:10 AM, John Helly wrote:
> 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"
>>
>> _______________________________________________
>> netcdfgroup mailing list
>> netcdfgroup@xxxxxxxxxxxxxxxx
>> For list information or to unsubscribe, visit:
>> http://www.unidata.ucar.edu/mailing_lists/
>>
>> _______________________________________________
>> netcdfgroup mailing list
>> netcdfgroup@xxxxxxxxxxxxxxxx
>> For list information or to unsubscribe, visit:
>> http://www.unidata.ucar.edu/mailing_lists/
>>
>> _______________________________________________
>> netcdfgroup mailing list
>> netcdfgroup@xxxxxxxxxxxxxxxx
>> For list information or to unsubscribe, visit:
>> http://www.unidata.ucar.edu/mailing_lists/
>>
>> _______________________________________________
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>> 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"
>
> _______________________________________________
> 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"
