I believe the default behavior in many things changed between 10.5.x and
10.6.x. I needed the -m32 flag for my compile (on 10.6.4) because HDF did
default to 32 bit while netcdf did not.
-Roy
On Aug 2, 2010, at 11:00 AM, Larry Baker wrote:
> My Mac is a 64-bit Mac Pro with 12 GB RAM. The kernel may be 32-bit (uname
> -a says i386), but that may not be definitive (OS X configures the kernel
> dynamically at boot.) (I never paid that much attention to it.) Regardless,
> 64-bit applications are supported. The Intel compilers (icc/icpc/ifort)
> default to 64-bit, but the GNU compilers (gcc/g++/g95/gfortran) do not.
>
> Larry Baker
> US Geological Survey
> 650-329-5608
> baker@xxxxxxxx
>
> On Aug 2, 2010, at 10:47 AM, John Helly wrote:
>
>> Thanks, Larry. I think that's true if you install the 32-bit Snow Leopard
>> kernel. I'll check what this is actually compiling as if I can figure out
>> how to do that on OSX.
>>
>>
>> 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 10:22 AM, Larry Baker wrote:
>>
>> John,
>>
>> My recollection using gcc and gfortran on Mac OS X 10.5 (Leopard) is that
>> they both default to 32-bit. My makefiles define CC (and, sometimes, LD) as
>> "gcc -m64", plus FC as "gfortran -m64" to get things to work. Note: the
>> -m64 flag is NOT in defined in the CFLAGS, FCFLAGS and LDFLAGS variables --
>> since -m64 is really selecting a different compiler/linker, it should be
>> defined as part of those variables, regardless of the rest of the options.
>>
>> For example, here's my (non-HDF) make configure of netCDF using
>> gcc/g++/gfortran:
>>
>> cd netcdf-$(VERSION) ; \
>> ./configure >configure.log 2>&1 \
>> CC="gcc -m64" \
>> CFLAGS="-g -O2" \
>> CXX="g++ -m64" \
>> CXXFLAGS="-g -O2" \
>> CPPFLAGS="-DNDEBUG -DgFortran" \
>> FC="gfortran -m64" \
>> FCFLAGS="-g -O2"
>>
>> (I haven't tried -O3, which supposedly invokes the gcc vectorizer/sse code
>> generator.)
>>
>> Larry Baker
>> US Geological Survey
>> 650-329-5608
>> baker@xxxxxxxx
>>
>> On Aug 2, 2010, at 8:36 AM, John Helly wrote:
>>
>>> Hi.
>>>
>>> I copied all the source (netcdf-beta.tar and hdf5-1.8.5) to another mac and
>>> upgraded Xcode and then installed the gfortran you specified and bingo.
>>>
>>> +-------------------------------------------------------------+
>>> | Congratulations! You have successfully installed netCDF! |
>>> | |
>>> | You can use script "nc-config" to find out the relevant |
>>> | compiler options to build your application. Enter |
>>> | |
>>> | nc-config --help |
>>> | |
>>> | for additional information. |
>>> | |
>>> | CAUTION: |
>>> | |
>>> | If you have not already run "make check", then we strongly |
>>> | recommend you do so. It does not take very long. |
>>> | |
>>> | Before using netCDF to store important data, test your |
>>> | build with "make check". |
>>> | |
>>> | NetCDF is tested nightly on many platforms at Unidata |
>>> | but your platform is probably different in some ways. |
>>> | |
>>> | If any tests fail, please see the netCDF web site: |
>>> | http://www.unidata.ucar.edu/software/netcdf/ |
>>> | |
>>> | NetCDF is developed and maintained at the Unidata Program |
>>> | Center. Unidata provides a broad array of data and software |
>>> | tools for use in geoscience education and research. |
>>> | http://www.unidata.ucar.edu |
>>> +-------------------------------------------------------------+
>>>
>>> iceberg:netcdf-4.1.2-beta1 hellyj$
>>>
>>> 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>
>>>>
>>>> _______________________________________________
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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/
>>>
>>> _______________________________________________
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>>>
>>> _______________________________________________
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>>> netcdfgroup@xxxxxxxxxxxxxxxx
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>>> http://www.unidata.ucar.edu/mailing_lists/
>>
>> _______________________________________________
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>> netcdfgroup@xxxxxxxxxxxxxxxx
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>> 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"
