pseudo netcdf calls in the HDF4 library, that if the two are compiled and
linked together (netcdf3, hdf4) there are collisions and things fail.
yes, HDF4 has a netCDF3 version included in it (version around 1996 ? )
...probably little know fact.
There is an option in the HDF4 configure that you need to set when you
are going to be linking both libraries, but I can't remember which.
HDF4 has this option
--enable-netcdf
but I got the same netCDF4 linking errors with either option
(--enable-netcdf /disable-netcdf )
there are some warnings in netCDF with
--enable-hdf4
checking mfhdf.h usability... yes
checking mfhdf.h presence... no
configure: WARNING: mfhdf.h: accepted by the compiler, rejected by the
preprocessor!
configure: WARNING: mfhdf.h: proceeding with the compiler's result
checking for mfhdf.h... yes
checking for Hclose in -ldf... no
checking for SDcreate in -lmfhdf... no
------
Pedro Vicente, Earth System Science
University of California, Irvine
http://www.ess.uci.edu/
----- Original Message -----
From: "Roy Mendelssohn - NOAA Federal" <roy.mendelssohn@xxxxxxxx>
To: "Charlie Zender" <zender@xxxxxxx>
Cc: "netCDF Mail List" <netcdfgroup@xxxxxxxxxxxxxxxx>
Sent: Wednesday, March 20, 2013 11:34 AM
Subject: Re: [netcdfgroup] installing netCDF with --enable-hdf4
Oops I sent the following to Chris, meant to send to all:
My memory (and I am old and don't remember too well) is because of the
pseudo netcdf calls in the HDF4 library, that if the two are compiled and
linked together (netcdf3, hdf4) there are collisions and things fail.
There is an option in the HDF4 configure that you need to set when you are
going to be linking both libraries, but I can't remember which. You might
do better posting this to the hdf help list.
-Roy
On Mar 20, 2013, at 11:31 AM, "Lynnes, Christopher S. (GSFC-6102)"
<christopher.s.lynnes@xxxxxxxx> wrote:
On Mar 20, 2013, at 11:46 AM, Charlie Zender wrote:
Hi netCDFers,
I'm trying to install netCDF with the optional HDF4 support.
Is there a site that illustrates the procedure?
I'm closer than before, stymied by a linking error.
A summary of my attempt follows.
Any help appreciated,
Clearly the main HDF4 libraries, -lmfhdf and -ldf, are not getting into
the link specification, though they are getting picked up at preprocessor
time.
I tried an opposite approach to yours, starting with the
near-minimum, --enable-netcdf4 --enable-hdf4, and it compiled all the way
through, including ncgen3. However, one of the make checks failed to
compile, interops3. Anyway, perhaps that is worth trying: start with
just --enable-hdf4 and then add in options after that until it fails.
If the minimal approch still doesn't work, note that your LDFLAGS
environment has to be set to find the HDF4 libraries, e.g.,
LDFLAGS=-L/wherever/your/libdf.a/is/located.
cz
I build and install HDF5, then HDF4, then (attempt to build) netCDF4:
# HDF5 ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/hdf5-1.8.9.tar.gz
./configure --prefix=/usr/local --enable-cxx --enable-fortran
make;sudo make install
# HDF4 http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.9.tar.gz
./configure --prefix=/usr/local --enable-fortran
make;sudo make install
# netCDF4
LDFLAGS='-L/usr/local/lib' ./configure --prefix=/usr/local
--enable-shared --enable-dap --enable-hdf4 --enable-logging
--enable-netcdf4 --enable-v2
make
The steps above all work fine with the simple change to --disable-hdf4.
With --enable-hdf4 the netCDF make command fails in the ncgen3 section:
Making check in libsrc4
make[1]: entrant dans le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/libsrc4 »
make[1]: Rien à faire pour « check ».
make[1]: quittant le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/libsrc4 »
Making check in libdap2
make[1]: entrant dans le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/libdap2 »
make[1]: Rien à faire pour « check ».
make[1]: quittant le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/libdap2 »
Making check in liblib
make[1]: entrant dans le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/liblib »
make[1]: Rien à faire pour « check ».
make[1]: quittant le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/liblib »
make[1]: Rien à faire pour « check ».
make[1]: entrant dans le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/ncgen3 »
/bin/bash ../libtool --tag=CC --mode=link gcc -fPIC -m64
-L/usr/local/lib -o ncgen3 main.o load.o escapes.o getfill.o init.o
genlib.o ncgentab.o
../liblib/libnetcdf.la -lhdf5_hl -lhdf5 -lm -lz -lcurl
libtool: link: gcc -fPIC -m64 -o .libs/ncgen3 main.o load.o escapes.o
getfill.o init.o genlib.o ncgentab.o -L/usr/local/lib
../liblib/.libs/libnetcdf.so /usr/local/lib/libhdf5_hl.so
/usr/local/lib/libhdf5.so -lm -lz
/usr/lib/x86_64-linux-gnu/libcurl-gnutls.so
../liblib/.libs/libnetcdf.so: undefined reference to `SDstart'
../liblib/.libs/libnetcdf.so: undefined reference to `SDend'
../liblib/.libs/libnetcdf.so: undefined reference to `SDattrinfo'
../liblib/.libs/libnetcdf.so: undefined reference to `SDfileinfo'
../liblib/.libs/libnetcdf.so: undefined reference to `SDreadattr'
../liblib/.libs/libnetcdf.so: undefined reference to `SDselect'
../liblib/.libs/libnetcdf.so: undefined reference to `SDreaddata'
../liblib/.libs/libnetcdf.so: undefined reference to `SDdiminfo'
../liblib/.libs/libnetcdf.so: undefined reference to `SDgetfillvalue'
../liblib/.libs/libnetcdf.so: undefined reference to `SDgetinfo'
../liblib/.libs/libnetcdf.so: undefined reference to `SDgetdimid'
collect2: error: ld returned 1 exit status
make[1]: *** [ncgen3] Erreur 1
make[1]: quittant le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/ncgen3 »
make: *** [check-recursive] Erreur 1
--
Charlie Zender, Earth System Sci. & Computer Sci.
University of California, Irvine 949-891-2429 )'(
_______________________________________________
netcdfgroup mailing list
netcdfgroup@xxxxxxxxxxxxxxxx
For list information or to unsubscribe, visit:
http://www.unidata.ucar.edu/mailing_lists/
--
Dr. Christopher Lynnes NASA/GSFC, Code 610.2 phone: 301-614-5185
_______________________________________________
netcdfgroup mailing list
netcdfgroup@xxxxxxxxxxxxxxxx
For list information or to unsubscribe, visit:
http://www.unidata.ucar.edu/mailing_lists/
On Mar 20, 2013, at 11:31 AM, "Lynnes, Christopher S. (GSFC-6102)"
<christopher.s.lynnes@xxxxxxxx> wrote:
On Mar 20, 2013, at 11:46 AM, Charlie Zender wrote:
Hi netCDFers,
I'm trying to install netCDF with the optional HDF4 support.
Is there a site that illustrates the procedure?
I'm closer than before, stymied by a linking error.
A summary of my attempt follows.
Any help appreciated,
Clearly the main HDF4 libraries, -lmfhdf and -ldf, are not getting into
the link specification, though they are getting picked up at preprocessor
time.
I tried an opposite approach to yours, starting with the
near-minimum, --enable-netcdf4 --enable-hdf4, and it compiled all the way
through, including ncgen3. However, one of the make checks failed to
compile, interops3. Anyway, perhaps that is worth trying: start with
just --enable-hdf4 and then add in options after that until it fails.
If the minimal approch still doesn't work, note that your LDFLAGS
environment has to be set to find the HDF4 libraries, e.g.,
LDFLAGS=-L/wherever/your/libdf.a/is/located.
cz
I build and install HDF5, then HDF4, then (attempt to build) netCDF4:
# HDF5 ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/hdf5-1.8.9.tar.gz
./configure --prefix=/usr/local --enable-cxx --enable-fortran
make;sudo make install
# HDF4 http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.9.tar.gz
./configure --prefix=/usr/local --enable-fortran
make;sudo make install
# netCDF4
LDFLAGS='-L/usr/local/lib' ./configure --prefix=/usr/local
--enable-shared --enable-dap --enable-hdf4 --enable-logging
--enable-netcdf4 --enable-v2
make
The steps above all work fine with the simple change to --disable-hdf4.
With --enable-hdf4 the netCDF make command fails in the ncgen3 section:
Making check in libsrc4
make[1]: entrant dans le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/libsrc4 »
make[1]: Rien à faire pour « check ».
make[1]: quittant le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/libsrc4 »
Making check in libdap2
make[1]: entrant dans le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/libdap2 »
make[1]: Rien à faire pour « check ».
make[1]: quittant le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/libdap2 »
Making check in liblib
make[1]: entrant dans le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/liblib »
make[1]: Rien à faire pour « check ».
make[1]: quittant le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/liblib »
make[1]: Rien à faire pour « check ».
make[1]: entrant dans le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/ncgen3 »
/bin/bash ../libtool --tag=CC --mode=link gcc -fPIC -m64
-L/usr/local/lib -o ncgen3 main.o load.o escapes.o getfill.o init.o
genlib.o ncgentab.o
../liblib/libnetcdf.la -lhdf5_hl -lhdf5 -lm -lz -lcurl
libtool: link: gcc -fPIC -m64 -o .libs/ncgen3 main.o load.o escapes.o
getfill.o init.o genlib.o ncgentab.o -L/usr/local/lib
../liblib/.libs/libnetcdf.so /usr/local/lib/libhdf5_hl.so
/usr/local/lib/libhdf5.so -lm -lz
/usr/lib/x86_64-linux-gnu/libcurl-gnutls.so
../liblib/.libs/libnetcdf.so: undefined reference to `SDstart'
../liblib/.libs/libnetcdf.so: undefined reference to `SDend'
../liblib/.libs/libnetcdf.so: undefined reference to `SDattrinfo'
../liblib/.libs/libnetcdf.so: undefined reference to `SDfileinfo'
../liblib/.libs/libnetcdf.so: undefined reference to `SDreadattr'
../liblib/.libs/libnetcdf.so: undefined reference to `SDselect'
../liblib/.libs/libnetcdf.so: undefined reference to `SDreaddata'
../liblib/.libs/libnetcdf.so: undefined reference to `SDdiminfo'
../liblib/.libs/libnetcdf.so: undefined reference to `SDgetfillvalue'
../liblib/.libs/libnetcdf.so: undefined reference to `SDgetinfo'
../liblib/.libs/libnetcdf.so: undefined reference to `SDgetdimid'
collect2: error: ld returned 1 exit status
make[1]: *** [ncgen3] Erreur 1
make[1]: quittant le répertoire «
/data/zender/tmp/netcdf-4.3.0-rc3/ncgen3 »
make: *** [check-recursive] Erreur 1
--
Charlie Zender, Earth System Sci. & Computer Sci.
University of California, Irvine 949-891-2429 )'(
_______________________________________________
netcdfgroup mailing list
netcdfgroup@xxxxxxxxxxxxxxxx
For list information or to unsubscribe, visit:
http://www.unidata.ucar.edu/mailing_lists/
--
Dr. Christopher Lynnes NASA/GSFC, Code 610.2 phone: 301-614-5185
_______________________________________________
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"
"the arc of the moral universe is long, but it bends toward justice" -MLK
Jr.
_______________________________________________
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