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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/~hellyjOn 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: $DYLD_LIBRARY_PATHexport DYLD_LIBRARY_PATH=/usr/local/hdf5-1.8.5:$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-staticI'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/~hellyjOn 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/~hellyjOn 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 fink2. 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, -RoyGreetings.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-staticThis 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... noconfigure: 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." 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