Mexnc and OPeNDAP: What Works

Baseline system

• Debian GNU/Linux 4.0
• libdap-3.7.8
• libnc-dap-3.7.0
• mexnc 2.0.29

1. Compiled libdap 3.7.8 with

   CFLAGS="-fPIC" CXXFLAGS="-fPIC" ./configure --disable-shared --prefix=/local/opendap-static
   

2. Compiled libnc-dap 3.7.0 with

   export PATH=/local/opendap-static/bin:${PATH}
   CFLAGS="-fPIC" CXXFLAGS="-fPIC" ./configure --disable-shared --prefix=/local/opendap-static
   

3. Edit the bottom of mexopts.sh, make it read as follows

   #############################################################################
   #
   # Architecture independent lines:
   #
   #     Set and uncomment any lines which will apply to all architectures.
   #
   #----------------------------------------------------------------------------
   OPENDAP="/local/opendap-static"
   EXTRA_CFLAGS="-I${OPENDAP}/include/libnc-dap -I${OPENDAP}/include/libdap "
   EXTRA_CLIBS="-L${OPENDAP}/lib -lnc-dap -ldapclient -ldap -lstdc++ -lcurl -lgssapi_krb5 -lkrb5 -lk5crypto -lkrb5support -lcom_err -lresolv -lidn -ldl -lssl -lcrypto -lxml2 -lz -lm -lpthread "
   CFLAGS="-g $CFLAGS ${EXTRA_CFLAGS}"
   CLIBS="$CLIBS ${EXTRA_CLIBS} "
   

   The way to figure out what the EXTRA_CLIBS are is to look at how ncdump is linked in the previous step.
4. From the unix command line, issue a "make"
5. And finally, test it with

   >> url = 'http://tashtego.marine.rutgers.edu:8080/thredds/dodsC/philex/gridb/averages'      ;
   >> nc_dump ( url );
   

   ... and it works.

Baseline system

• Darwin Kernel Version 8.8.1
• curl-7.13.1
• libxml2-2.6.16
• SSL unknown
• gcc 4.0.1
• mexnc 2.0.21

1. Compiled libdap 3.6.2 with

   ./configure --prefix=/Users/jevans/local
   

2. Compiled libnc-dap 3.6.0 with

   export PATH=/opt/compiled/gnu/dods-3.6.2:${PATH}
   ./configure --prefix=/Users/jevans/local
   

3. Edit the bottom of mexopts.sh, make it read as follows

   #############################################################################
   #
   # Architecture independent lines:
   #
   #     Set and uncomment any lines which will apply to all architectures.
   #
   #----------------------------------------------------------------------------
   	OPENDAP="/Users/jevans/local"
   	EXTRA_CFLAGS="-I${OPENDAP}/include/libnc-dap -I${OPENDAP}/include/libdap "
       EXTRA_CLIBS="-L${OPENDAP}/lib -lnc-dap -ldap -lcurl -lssl -lcrypto -lxml2 -lz  -lm -lpthread "
   	CFLAGS="-g $CFLAGS ${EXTRA_CFLAGS}"
   	CLIBS="$CLIBS ${EXTRA_CLIBS} "
   

4. From the unix command line, issue a "make"
5. And finally, test it with

   >> url = 'http://queequeg.marine.rutgers.edu:9876/thredds/dodsC/roms/nena/in/frc_nena_2004_ncep_rain.nc'
   >> nc_dump ( url );
   

   ... and it works.

Baseline system

• kernel 2.6.12-19mdk
• curl-7.14.0-2.2.20060mdk
• libxml2-2.6.21-3mdk
• libidn11-0.5.18-2mdk
• libopenssl0.9.7-0.9.7g-2.1.20060mdk
• gcc-4.0.1-5mdk

1. Compiled libdap 3.6.2 with

   ./configure --prefix=/opt/compiled/gnu/dods-3.6.2 --disable-shared
   

2. Compiled libnc-dap 3.6.0 with

   export PATH=/opt/compiled/gnu/dods-3.6.2:${PATH}
   LD_FLAGS="-lstdc++" ./configure --prefix=/opt/compiled/gnu/dods-3.6.2 --disable-shared
   

3. Edit the bottom of mexopts.sh, make it read as follows

   #############################################################################
   #
   # Architecture independent lines:
   #
   #     Set and uncomment any lines which will apply to all architectures.
   #
   #----------------------------------------------------------------------------
   	OPENDAP="/opt/compiled/gnu/dods-3.6.2"
   	EXTRA_CFLAGS="-I${OPENDAP}/include/libnc-dap -I${OPENDAP}/include/libdap "
   	EXTRA_CLIBS="-L${OPENDAP}/lib -lnc-dap -ldap -lcurl -lidn -lssl -lcrypto -ldl -lssl -lcrypto -ldl -lz -lxml2 -lz -lm -lpthread  -lstdc++ "
   	CFLAGS="-g $CFLAGS ${EXTRA_CFLAGS}"
   	CLIBS="$CLIBS ${EXTRA_CLIBS} "
   

4. From the unix command line, issue a "make"
5. And finally, test it with

   >> url = 'http://queequeg.marine.rutgers.edu:9876/thredds/dodsC/roms/nena/in/frc_nena_2004_ncep_rain.nc'
   >> nc_dump ( url );
   

   ... and it works.

Baseline system

• kernel 2.6.15-1.2054_FC5
• glibc-2.4-4
• libstdc++-4.1.0-3
• curl-7.15.1-1.2.1
• libidn-0.6.2-1.1
• openssl-0.9.8a-5.2
• zlib-devel-.2.3-1.2.1
• libxml2-2.6.23-1.2
• libgcc-4.1.0-3
• krb5-libs-1.4.3-4.1
• e2fsprogs-libs-1.38-12

The mex-file referenced above would not work on this system. The error message given was

??? Invalid MEX-file '/home/jevans/matlab/mexcdf/mexnc-opendap/mexnc/mexnc.mexglx': 
	libssl.so.0.9.7: cannot open shared object file: No such file or directory.

Baseline system

• kernel 2.6.12-18mdksmp
• glibc-2.3.5-5mdk
• libstdc++6-4.0.1-5mdk
• lib64curl3-7.14.0-2.2.20060mdk
• lib64idn11-0.5.18-2mdk
• lib64openssl0.9.7-0.9.7g-2.1.20060mdk
• zlib1-devel-1.2.3-1mdk
• lib64xml2-2.6.21-3mdk
• libgcc1-4.0.1-5mdk
• gcc-4.0.1-5mdk

The difference to notice between this case and that above is the requirement for the -fPIC flag.

1. Compiled libdap 3.6.2 with

   CFLAGS="-fPIC" CXXFLAGS="-fPIC" ./configure --prefix=/opt/compiled/gnu/dods-3.6.2 --disable-shared
   

2. Compiled libnc-dap 3.6.0 with

   export PATH=/opt/compiled/gnu/dods-3.6.2:${PATH}
   CFLAGS="-fPIC" CXXFLAGS="-fPIC"  LDFLAGS="-lstdc++" ./configure --prefix=/opt/compiled/gnu/dods-3.6.2 --disable-shared
   

3. Edit the bottom of mexopts.sh, make it read as follows

   #############################################################################
   #
   # Architecture independent lines:
   #
   #     Set and uncomment any lines which will apply to all architectures.
   #
   #----------------------------------------------------------------------------
   	OPENDAP="/opt/compiled/gnu/dods-3.6.2"
   	EXTRA_CFLAGS="-I${OPENDAP}/include/libnc-dap -I${OPENDAP}/include/libdap "
   	EXTRA_CLIBS="-L${OPENDAP}/lib -lnc-dap -ldap -lcurl -lidn -lssl -lcrypto -ldl -lssl -lcrypto -ldl -lz -lxml2 -lz -lm -lpthread  -lstdc++ "
   	CFLAGS="-g $CFLAGS ${EXTRA_CFLAGS}"
   	CLIBS="$CLIBS ${EXTRA_CLIBS} "
   

4. From the unix command line, issue a "make"
5. And finally, test it with

   >> url = 'http://queequeg.marine.rutgers.edu:9876/thredds/dodsC/roms/nena/in/frc_nena_2004_ncep_rain.nc'
   >> nc_dump ( url );
   

   ... and it works.

The above x86-64 setup did not work for this system. I know I've been harping on this, but you really have to source-compile mexnc-opendap on each system rather than trade pre-compiled mex-files.

Baseline system

• kernel-2.4.29-295r0048.Scyld
• glibc-2.3.2-295r0048.Scyld
• libstdc++-3.2.3-42_scyld
• curl-7.10.6-4.1
• openssl-0.9.7a-33.12
• zlib-devel-1.1.4-8.1
• libxml2-2.5.10-5
• krb5-libs-1.2.7-19
• gcc-3.2.3-42_scyld

CFLAGS="-fPIC" CXXFLAGS="-fPIC" ./configure --prefix=/p/om/compiled/gnu/dods-3.6.2 --disable-shared

export PATH=/opt/compiled/gnu/dods-3.6.2:${PATH}
CFLAGS="-fPIC" CXXFLAGS="-fPIC"  LDFLAGS="-lstdc++" ./configure --prefix=/p/om/compiled/gnu/dods-3.6.2 --disable-shared

#############################################################################
#
# Architecture independent lines:
#
#     Set and uncomment any lines which will apply to all architectures.
#
#----------------------------------------------------------------------------
	OPENDAP="/p/om/gnu/compiled/dods-3.6.2"
	EXTRA_CFLAGS="-I${OPENDAP}/include/libnc-dap -I${OPENDAP}/include/libdap "
	EXTRA_CLIBS="-L${OPENDAP}/lib -lnc-dap -ldap -lcurl -lssl -lcrypto -lssl -lcrypto -ldl -lz -lxml2 -lz -lm -lpthread  -lstdc++ "
	CFLAGS="-g $CFLAGS ${EXTRA_CFLAGS}"
	CLIBS="$CLIBS ${EXTRA_CLIBS} "

>> url = 'http://queequeg.marine.rutgers.edu:9876/thredds/dodsC/roms/nena/in/frc_nena_2004_ncep_rain.nc'
>> nc_dump ( url );

1. The existing system came with gcc at version 2.95.2, which is too old, so the gnu toolchain was updated. First of all, the installed solaris version of make would not compile gcc, so make-3.81 was installed.

   GCC was then configured as

   Using built-in specs.
   Target: sparc-sun-solaris2.9
   Configured with: ../gcc-4.1.1/configure --with-as=/usr/ccs/bin/as 
   	--with-ld=/usr/ccs/bin/ld --enable-threads=posix --disable-nls 
   	--enable-languages=c,c++ 
   	--prefix=/m1/gnu
   Thread model: posix
   gcc version 4.1.1
   

2. Once gcc was compiled, the environment had to be modified just so:

   export PATH=/m1/gnu/bin:/m1/opendap/bin:${PATH}
   export LD_LIBRARY_PATH=/m1/gnu/lib:/m1/opendap/lib:${LD_LIBRARY_PATH}
   

3. Other GNU packages were then installed ...

   • make-3.81
   • libiconv-1.9.2
   • coreutils-5.0
   all using the same configure target

   ./configure --prefix=/m1/gnu
   

4. The following packages were then compiled, using the configuration command

   CFLAGS="-fPIC -I/m1/opendap/include"   \
   CXXFLAGS="-fPIC -I/m1/opendap/include" \
   LDFLAGS="-L/m1/opendap/lib"            \
   ./configure --prefix=/m1/gnu
   

   • libz-1.2.3
   • curl-7.15.3
   • libxml2-2.6.24
5. Compiled libdap 3.6.2 with

   ./configure --prefix=/m1/opendap
   

   However, this failed to compile the files tests/TestFloat64.cc and tests/TestFloat32.cc . In both cases, it was necessary to insert the line

   double trunc(double x);
   

   close to the area where the error occurs.
6. Compiled libncdap 3.6.0 with

   ./configure --prefix=/m1/opendap
   

7. Since curl was not compiled so as to depend upon SSL, the settings in mexopts.sh are a little easier...

   #############################################################################
   #
   # Architecture independent lines:
   #
   #     Set and uncomment any lines which will apply to all architectures.
   #
   #----------------------------------------------------------------------------
   	OPENDAP="/m1/opendap"
   	EXTRA_CFLAGS="-I${OPENDAP}/include/libnc-dap -I${OPENDAP}/include/libdap "
   	EXTRA_CLIBS="-L${OPENDAP}/lib -lnc-dap -ldap -lcurl -ldl -lz -lxml2 -lz -lm -lpthread  -lstdc++ "
   	CFLAGS="-g $CFLAGS ${EXTRA_CFLAGS}"
   	CLIBS="$CLIBS ${EXTRA_CLIBS} "
   

8. From the unix command line, issue a "make"
9. And finally, test it with

   >> url = 'http://queequeg.marine.rutgers.edu:9876/thredds/dodsC/roms/nena/in/frc_nena_2004_ncep_rain.nc'
   >> nc_dump ( url );
   

   ... and it works.