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mac_info.txt
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# Basic system info
-------------------------------------------------------------
Hardware Overview:
Model Name: Mac Pro
Model Identifier: MacPro4,1
Processor Name: Quad-Core Intel Xeon
Processor Speed: 2.26 GHz
Number Of Processors: 2
Total Number Of Cores: 8
Memory: 16 GB
System Software Overview:
System Version: Mac OS X 10.6.4 (10F569)
Kernel Version: Darwin 10.4.0
64-bit Kernel and Extensions: No
Xcode:
Version: 3.2.3
Kind: Universal
64-Bit (Intel): Yes
$ ifort -v
> Version 11.1
$ icc -v
> Version 11.1
$ gcc -v
> Using built-in specs.
> Target: i686-apple-darwin10
> Configured with: /var/tmp/gcc/gcc-5664~38/src/configure --disable-checking --enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-> slibdir=/usr/lib --build=i686-apple-darwin10 --program-prefix=i686-apple-darwin10- --host=x86_64-apple-darwin10 --target=i686-apple-darwin10 --with-gxx-include-dir=/include/c++/4.2.1
> Thread model: posix
> gcc version 4.2.1 (Apple Inc. build 5664)
# Turn on super user
-------------------------------------------------------------
Some make commands fail when issued as "sudo make XXX" so enable su
Here's how to enable root in Snow Leopard:
1) Open Directory Utility in its new home, which is /System/Library/CoreServices.
2) Unlock the application by clicking the padlock icon and entering your Administrator login.
3) Select Edit È Enable Root User.
4) Choose Edit È Change Root Password, and choose a password for the root user.
$ su
# Environmental Setup
-------------------------------------------------------------
I use macports and have versions of netcdf, HDF etc installed that are incompatible with COSP.
Thus I need a secondary install and a setup where they don't see each other.
Edit ~/.profile and temporarily alter path and other environmental items so the system doesn't look to /opt 1st but /usr/local
$ echo $PATH
> /usr/local:/opt/local/bin:É.
Set environmental variables (this can be in .bashrc) but be sure
$ source /opt/intel/Compiler/11.1/089/bin/ifortvars.sh intel64
$ source /opt/intel/Compiler/11.1/089/bin/iccvars.sh intel64
$ set
edited relevant output
CC=gcc
CFLAGS='-arch x86_64 -fPIC'
CPATH=/opt/intel/Compiler/11.1/089/Frameworks/ipp/Headers:/opt/intel/Compiler/11.1/089/Frameworks/mkl/include:/opt/intel/Compiler/11.1/089/Frameworks/tbb/include:/opt/intel/Compiler/11.1/089/Frameworks/ipp/Headers:/opt/intel/Compiler/11.1/089/Frameworks/mkl/include:/opt/intel/Compiler/11.1/089/Frameworks/tbb/include
CXX=g++
CXXFLAGS='-arch x86_64'
DYLD_LIBRARY_PATH=/usr/local/lib:/usr/local/hdf5/:/usr/local/netcdf4:/usr/local/szip/lib:/opt/intel/Compiler/11.1/089/lib:/opt/intel/Compiler/11.1/089/lib/intel64:/opt/intel/Compiler/11.1/089/Frameworks/ipp/Libraries:/opt/intel/Compiler/11.1/089/Frameworks/mkl/lib/em64t:/opt/intel/Compiler/11.1/089/Frameworks/tbb/ia32/cc4.0.1_os10.5.4/lib:/opt/intel/Compiler/11.1/089/lib:/opt/intel/Compiler/11.1/089/lib/intel64:/opt/intel/Compiler/11.1/089/Frameworks/ipp/Libraries:/opt/intel/Compiler/11.1/089/Frameworks/mkl/lib/em64t:/opt/intel/Compiler/11.1/089/Frameworks/tbb/ia32/cc4.0.1_os10.5.4/lib
F77=ifort
F90=ifort
F9X=ifort
FC=ifort
FFLAGS='-arch x86_64 -m64 -fPIC'
FPATH=/opt/intel/Compiler/11.1/089/Frameworks/mkl/include:/opt/intel/Compiler/11.1/089/Frameworks/mkl/include
INCLUDE=/opt/intel/Compiler/11.1/089/Frameworks/ipp/Headers:/opt/intel/Compiler/11.1/089/Frameworks/mkl/Headers:/opt/intel/Compiler/11.1/089/Frameworks/ipp/Headers:/opt/intel/Compiler/11.1/089/Frameworks/mkl/Headers
INTEL_LICENSE_FILE='/opt/intel/Compiler/11.1/089/licenses:/opt/intel/licenses:/Users/mbauer/intel/licenses:/Users/Shared/Library/Application Support/Intel/Licenses:/opt/intel/Compiler/11.1/089/licenses:/opt/intel/licenses:/Users/mbauer/intel/licenses:/Users/Shared/Library/Application Support/Intel/Licenses'
LDFLAGS='-arch x86_64'
LD_LIBRARY_PATH=/opt/intel/Compiler/11.1/089/Frameworks/tbb/ia32/cc4.0.1_os10.5.4/lib:/opt/intel/Compiler/11.1/089/Frameworks/tbb/ia32/cc4.0.1_os10.5.4/lib
LIB=/opt/intel/Compiler/11.1/089/Frameworks/ipp/lib:/opt/intel/Compiler/11.1/089/Frameworks/ipp/lib:
LIBRARY_PATH=/opt/intel/Compiler/11.1/089/lib:/opt/intel/Compiler/11.1/089/Frameworks/ipp/lib:/opt/intel/Compiler/11.1/089/Frameworks/mkl/lib/em64t:/opt/intel/Compiler/11.1/089/Frameworks/tbb/ia32/cc4.0.1_os10.5.4/lib:/opt/intel/Compiler/11.1/089/lib:/opt/intel/Compiler/11.1/089/Frameworks/ipp/lib:/opt/intel/Compiler/11.1/089/Frameworks/mkl/lib/em64t:/opt/intel/Compiler/11.1/089/Frameworks/tbb/ia32/cc4.0.1_os10.5.4/lib
MACHTYPE=x86_64-apple-darwin10.0
MACOSX_DEPLOYMENT_TARGET=10.6
This is in my .profile just in case
export CC=gcc
export F9X=ifort
export CXX=g++
export FC=ifort
export F77=ifort
export F90=ifort
# -arch x86_64 forces 64-bit compiles for gcc/icc
# -m64 forces 64-bit compiles for ifort
# -fPIC forces non-shared libraries (see below)
export CFLAGS="-arch x86_64 -fPIC"
export CXXFLAGS="-arch x86_64 -fPIC"
export FFLAGS="-arch x86_64 -m64 -fPIC"
export MACOSX_DEPLOYMENT_TARGET=10.6
export LDFLAGS="-arch x86_64"
export PATH=/usr/local:/opt/local/bin:$PATH
****NOTES from cmor INSTALL: it strongly recommend to use the --disable-shared argument to the
./configure when building udunits2, hdf5 and netcdf4.
# zlib 1.2.5
-------------------------------------------------------------
http://www.zlib.net/
$ cd /usr/local/src
$ mv ~/Downloads/zlib-1.2.5.tar.gz .
$ tar -zxvf zlib-1.2.5.tar.gz
$ cd zlib-1.2.5
$ vim README
$ ./configure -help
$ ./configure --static --64
Scan Makefile
$ more Makefile
$ make
gcc -arch x86_64 -fPIC -m64 -c -o example.o example.c
gcc -arch x86_64 -fPIC -m64 -c -o adler32.o adler32.c
gcc -arch x86_64 -fPIC -m64 -c -o compress.o compress.c
gcc -arch x86_64 -fPIC -m64 -c -o crc32.o crc32.c
gcc -arch x86_64 -fPIC -m64 -c -o deflate.o deflate.c
gcc -arch x86_64 -fPIC -m64 -c -o gzclose.o gzclose.c
gcc -arch x86_64 -fPIC -m64 -c -o gzlib.o gzlib.c
gcc -arch x86_64 -fPIC -m64 -c -o gzread.o gzread.c
gcc -arch x86_64 -fPIC -m64 -c -o gzwrite.o gzwrite.c
gcc -arch x86_64 -fPIC -m64 -c -o infback.o infback.c
gcc -arch x86_64 -fPIC -m64 -c -o inffast.o inffast.c
gcc -arch x86_64 -fPIC -m64 -c -o inflate.o inflate.c
gcc -arch x86_64 -fPIC -m64 -c -o inftrees.o inftrees.c
gcc -arch x86_64 -fPIC -m64 -c -o trees.o trees.c
gcc -arch x86_64 -fPIC -m64 -c -o uncompr.o uncompr.c
gcc -arch x86_64 -fPIC -m64 -c -o zutil.o zutil.c
ar rc libz.a adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o
gcc -arch x86_64 -fPIC -m64 -o example example.o -L. libz.a
gcc -arch x86_64 -fPIC -m64 -c -o minigzip.o minigzip.c
gcc -arch x86_64 -fPIC -m64 -o minigzip minigzip.o -L. libz.a
$ make check
hello world
zlib version 1.2.5 = 0x1250, compile flags = 0xa9
uncompress(): hello, hello!
gzread(): hello, hello!
gzgets() after gzseek: hello!
inflate(): hello, hello!
large_inflate(): OK
after inflateSync(): hello, hello!
inflate with dictionary: hello, hello!
*** zlib test OK ***
$ make install
cp libz.a /usr/local/lib
cp /usr/local/lib
cp: missing destination file operand after `/usr/local/lib'
Try `cp --help' for more information.
make: *** [install-libs] Error 1
The install partly fails because it expects a shared lib so do manually
$ cp zlib.h zconf.h /usr/local/include/
# SZIP 2.1
-------------------------------------------------------------
ftp://ftp.hdfgroup.org/lib-external/szip/
$ cd /usr/local/src
$ mv ~/Downloads/szip-2.1.tar.gz .
$ tar -zxvf szip-2.1.tar.gz
$ cd szip-2.1
$ vim INSTALL
Installation with encoder
$ ./configure -help
$ ./configure --prefix=/usr/local/szip --disable-shared
Scan Makefile
$ more Makefile
$ make
$ make check
> All test passed.
$ make install
Libraries have been installed in:
/usr/local/szip/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
during execution
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
-----------------------------------------------------------------
Add to .profile
export DYLD_LIBRARY_PATH=/usr/local/lib:/usr/local/szip/lib:${DYLD_LIBRARY_PATH}
Restart the terminal and check
$ echo $DYLD_LIBRARY_PATH
> /usr/local/lib:/usr/local/szip/lib:...
# UDUNITS2 2.1.19
-------------------------------------------------------------
http://www.unidata.ucar.edu/software/udunits/udunits-2/udunits2.html
ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.1.19.tar.gz
$ cd /usr/local/src
$ mv ~/Downloads/udunits-2.1.19.tar.gz .
$ tar -zxvf udunits-2.1.19.tar.gz
$ cd udunits-2.1.19
$ ./configure -help
$ ./configure --prefix=/usr/local --disable-shared
Scan Makefile
$ more Makefile
$ make
$ make check
$ make install
Libraries have been installed in:
/usr/local/lib
# ossp-uuid 1.6.2
-------------------------------------------------------------
http://www.ossp.org/pkg/lib/uuid/
$ cd /usr/local/src
$ mv ~/Downloads/uuid-1.6.2.tar.gz .
$ tar -zxvf uuid-1.6.2.tar.gz
$ cd uuid-1.6.2
$ vim INSTALL
$ ./configure -help
$ ./configure --disable-shared --without-perl --without-php --without-pgsql --includedir=/usr/local/include/ossp
Scan Makefile
$ more Makefile
$ makefile
$ make check
$ make install
Libraries have been installed in:
/usr/local/lib
Some Make files look for uuid.h in different placesÉ help them out
$ ln -s /usr/local/include/ossp/uuid.h /usr/local/include/uuid.h
# HDF5 hdf5-1.8.5-patch1
-------------------------------------------------------------
http://www.hdfgroup.org/HDF5/
$ cd /usr/local/src
$ mv ~/Downloads/hdf5-1.8.5-patch1.tar.bz2 .
$ tar -zxvf hdf5-1.8.5-patch1.tar.bz2
$ cd hdf5-1.8.5-patch1
$ vim release_docs/INSTALL
For some reason the icc compile link fails but the gcc one works. So I've used gcc throughout these installs.
$ ./configure -help
$ ./configure --prefix=/usr/local/hdf5 --disable-shared --enable-fortran --with-zlib=/usr/local --with-szlib=/usr/local/szip
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.5-patch1
Configured on: Tue Sep 14 10:17:45 EDT 2010
Configured by: [email protected]
Configure mode: production
Host system: i386-apple-darwin10.4.0
Uname information: Darwin boreas.giss.nasa.gov 10.4.0 Darwin Kernel Version 10.4.0: Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELEASE_I386 i386 i386 MacPro4,1 Darwin
Byte sex: little-endian
Libraries:
Installation point: /usr/local/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/gcc ( (GCC) 4.2.1 (Apple Inc. build 5664))
CFLAGS: -arch x86_64 -fPIC
H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O3 -fomit-frame-pointer -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -I/usr/local/szip/include -I/usr/local/include
Shared Libraries: no
Static Libraries: yes
Statically Linked Executables: no
LDFLAGS: -arch x86_64
AM_LDFLAGS: -L/usr/local/lib -L/usr/local/szip/lib
Extra libraries: -lsz -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: yes
Fortran Compiler: /opt/intel/Compiler/11.1/089/bin/intel64/ifort
Fortran Flags:
H5 Fortran Flags: -O3
AM Fortran Flags: -arch x86_64 -m64 -fPIC
C++: no
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
H5dump Packed Bits: yes
$ make > make.log 2>&1
$ more make.log
$ make check > make_check.log 2>&1
$ more make_check.log
All PASSED or SKIPPED including the fortran tests
$ make install > make_install.log 2>&1
$ more make_install.log
Libraries have been installed in:
/usr/local/hdf5/lib
$ make check-install
$ export HDF5_DIR=/usr/local/hdf5
$ export HDF5_LIB_DIR=/usr/local/lib
$ export HDF5DIR=/usr/local/hdf5
$ export DYLD_LIBRARY_PATH=/usr/local/hdf5/:${DYLD_LIBRARY_PATH}
Also modify .profile accordingly
$ echo $HDF5_DIR
> /usr/local/hdf5
$ echo $DYLD_LIBRARY_PATH
> /usr/local/hdf5/:/usr/local/lib:É.
# NetCDF4 4.1.1
-------------------------------------------------------------
http://www.unidata.ucar.edu/software/netcdf
$ cd /usr/local/src
$ mv ~/Downloads/netcdf.tar.gz .
$ tar -zxvf netcdf.tar.gz
$ cd netcdf-4.1.1
$ vim INSTALL
Warning:
A bug in the 4.1.1 release means the "make clean" wipes out the
documentation files, though it should not. This leads to a
need latex warning on make.
To fix, unpack the tarball again.
**** Ah, configure sees curl from macports and adds /opt/ to the link paths which sees the netcdf and hdf5 libraries there!
use --with-curl to stop this!
*** According to netcdf guys the file
libnetcdff.a
is not created if you follow the --disable-shared recommendation of the cmor INSTALL file
this can be over rode with --enable-separate-fortran
$ ./configure -help
$ ./configure --prefix=/usr/local/netcdf4 --with-curl-config=/usr/bin --with-curl=/usr/lib --disable-shared --enable-netcdf4 --enable-fortran --with-zlib=/usr/local --with-szlib=/usr/local/szip --with-hdf5=/usr/local/hdf5 --enable-separate-fortran
Scan Makefile
$ more Makefile
$ make > make.log 2>&1
$ more make.log
$ make check > make_check.log 2>&1
$ more make_check.log
All tests seemed to pass there are these warnings about the HDF5, but on the web I found that is is not an issue and the test passes in any event.
HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
#000: H5O.c line 717 in H5Oget_info_by_idx(): group not found
major: Symbol table
minor: Object not found
#001: H5Gloc.c line 591 in H5G_loc_find_by_idx(): can't find object
major: Symbol table
minor: Object not found
#002: H5Gtraverse.c line 964 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#003: H5Gtraverse.c line 887 in H5G_traverse_real(): traversal operator failed
major: Symbol table
minor: Can't move to next iterator location
#004: H5Gloc.c line 522 in H5G_loc_find_by_idx_cb(): link not found
major: Symbol table
minor: Object not found
#005: H5Gobj.c line 1204 in H5G_obj_lookup_by_idx(): no creation order index to query
major: Symbol table
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
#000: H5O.c line 717 in H5Oget_info_by_idx(): group not found
major: Symbol table
minor: Object not found
#001: H5Gloc.c line 591 in H5G_loc_find_by_idx(): can't find object
major: Symbol table
minor: Object not found
#002: H5Gtraverse.c line 964 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#003: H5Gtraverse.c line 887 in H5G_traverse_real(): traversal operator failed
major: Symbol table
minor: Can't move to next iterator location
#004: H5Gloc.c line 522 in H5G_loc_find_by_idx_cb(): link not found
major: Symbol table
minor: Object not found
#005: H5Gobj.c line 1204 in H5G_obj_lookup_by_idx(): no creation order index to query
major: Symbol table
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
#000: H5O.c line 717 in H5Oget_info_by_idx(): group not found
major: Symbol table
minor: Object not found
#001: H5Gloc.c line 591 in H5G_loc_find_by_idx(): can't find object
major: Symbol table
minor: Object not found
#002: H5Gtraverse.c line 964 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#003: H5Gtraverse.c line 887 in H5G_traverse_real(): traversal operator failed
major: Symbol table
minor: Can't move to next iterator location
#004: H5Gloc.c line 522 in H5G_loc_find_by_idx_cb(): link not found
major: Symbol table
minor: Object not found
#005: H5Gobj.c line 1204 in H5G_obj_lookup_by_idx(): no creation order index to query
major: Symbol table
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
#000: H5O.c line 717 in H5Oget_info_by_idx(): group not found
major: Symbol table
minor: Object not found
#001: H5Gloc.c line 591 in H5G_loc_find_by_idx(): can't find object
major: Symbol table
minor: Object not found
#002: H5Gtraverse.c line 964 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#003: H5Gtraverse.c line 887 in H5G_traverse_real(): traversal operator failed
major: Symbol table
minor: Can't move to next iterator location
#004: H5Gloc.c line 522 in H5G_loc_find_by_idx_cb(): link not found
major: Symbol table
minor: Object not found
#005: H5Gobj.c line 1204 in H5G_obj_lookup_by_idx(): no creation order index to query
major: Symbol table
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
#000: H5O.c line 717 in H5Oget_info_by_idx(): group not found
major: Symbol table
minor: Object not found
#001: H5Gloc.c line 591 in H5G_loc_find_by_idx(): can't find object
major: Symbol table
minor: Object not found
#002: H5Gtraverse.c line 964 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#003: H5Gtraverse.c line 887 in H5G_traverse_real(): traversal operator failed
major: Symbol table
minor: Can't move to next iterator location
#004: H5Gloc.c line 522 in H5G_loc_find_by_idx_cb(): link not found
major: Symbol table
minor: Object not found
#005: H5Gobj.c line 1204 in H5G_obj_lookup_by_idx(): no creation order index to query
major: Symbol table
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
#000: H5O.c line 717 in H5Oget_info_by_idx(): group not found
major: Symbol table
minor: Object not found
#001: H5Gloc.c line 591 in H5G_loc_find_by_idx(): can't find object
major: Symbol table
minor: Object not found
#002: H5Gtraverse.c line 964 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#003: H5Gtraverse.c line 887 in H5G_traverse_real(): traversal operator failed
major: Symbol table
minor: Can't move to next iterator location
#004: H5Gloc.c line 522 in H5G_loc_find_by_idx_cb(): link not found
major: Symbol table
minor: Object not found
#005: H5Gobj.c line 1204 in H5G_obj_lookup_by_idx(): no creation order index to query
major: Symbol table
minor: Bad value
*** Testing HDF5/NetCDF-4 interoperability...
*** Creating a HDF5 file with one var with two dimension scales...ok.
*** Checking that HDF5 file can be read by netCDF-4, and adding an att...ok.
*** Checking that one var, two dimscales, one att file can still be read by HDF5...ok.
*** Creating a HDF5 file with one var and no dimension scales...ok.
*** Creating a HDF5 file with one var and no dimension scales, without creation ordering...ok.
*** Creating a HDF5 file with two vars and no dimension scales, without creation ordering...ok.
*** Creating a HDF5 file with fixed length string...ok.
*** Checking a HDF5 file with scalar, fixed-length string dataset...ok.
*** Tests successful!
PASS: tst_interops
$ make install > make_install.log 2>&1
$ more make_install.log
Libraries have been installed in:
/usr/local/netcdf4/lib
+-------------------------------------------------------------+
| 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.
$ /usr/local/netcdf4/bin/nc-config --libs
> -L/usr/local/netcdf4/lib -lnetcdf -L/usr/local/hdf5/lib -lhdf5_hl -lhdf5 -L/usr/local/lib -lz -lm -L/usr/local/szip/lib -lsz -lcurl
$ /usr/local/netcdf4/bin/nc-config --fflags
> -arch x86_64 -m64 -fPIC -I/usr/local/netcdf4/include
$ /usr/local/netcdf4/bin/nc-config --cflags
> --I/usr/local/netcdf4/include
$ export NETCDF4_DIR=/usr/local/netcdf4
$ export DYLD_LIBRARY_PATH=/usr/local/netcdf4:${DYLD_LIBRARY_PATH}
Also modify .profile accordingly
$ echo $NETCDF4_DIR
> /usr/local/netcdf4
$ echo $DYLD_LIBRARY_PATH
> /usr/local/netcdf4:É
# for cmor 2.2 (9/8/2010)
-------------------------------------------------------------
http://www2-pcmdi.llnl.gov/cmor
$ cd /usr/local/src
$ git clone http://esgf.org/git/cmor.git
$ cd /usr/local/src/cmor
$ vim INSTALL
**WATCH OUT THIS REEFERS TO NETCDF, HDF ETC not COSP!
NOTES2: You only need to install the C libraries for these. Usually you can turn off
the fortran using --disable-fortran
$ ./configure -help
$ ./configure --prefix=/usr/local --with-netcdf=/usr/local/netcdf4 --with-hdf5=/usr/local/hdf5 --with-udunits2=/usr/local --with-uuid=/usr/local/
configure: ************************************************************************
configure: SUMMARY
configure: VERSION: 2.2.1 (commit: 4bbd53da1c465cd825e7c3150813dad699f6f894)
configure: ************************************************************************
configure:
configure: ........................................................................
configure: ... COMPILERS
configure: ........................................................................
configure:
configure: FORTRAN
configure: FC=ifort
configure: F77=ifort
configure: FFLAGS=-arch x86_64 -m64 -fPIC
configure: FCFLAGS=-g
configure: ........................................................................
configure: ... EXTERNALS ...
configure: ........................................................................
./configure: line 5667: test: !=: unary operator expected
configure:
configure: UUID
configure: CFLAGS : -I/usr/local//include
configure: LDFLAGS : -L/usr/local//lib -R/usr/local//lib -luuid
configure:
configure: UDUNITS2
configure: CFLAGS : -I/usr/local/include
configure: LDFLAGS : -L/usr/local/lib -R/usr/local/lib -ludunits2 -lexpat
configure:
configure: NetCDF4
configure: CFLAGS : -I/usr/local/netcdf4/include
configure: LDFLAGS : -L/usr/local/netcdf4/lib -lnetcdf -L/usr/local/hdf5/lib -lhdf5_hl -lhdf5 -L/usr/local/lib -lz -lm -L/usr/local/szip/lib -lsz -lcurl
configure:
configure: PYTHON
configure: Not built, not used it tests
configure:
configure: Type "make" to build cmor
configure: Type "make install" to build and install cmor to /usr/local
configure:
configure: Type "make test" to build and test cmor code only
configure: Type "make test_C" to build cmor and test C only
configure: Type "make test_fortran" to build cmor and test fortran only
configure:
configure: You can compile C or FORTRAN code using the compilation lines shown in file: compile_line.txt and printed bellow:
configure:
configure:
# The following line will compile "C" code mycode.c with cmor, additional libraries mycode.c may requires should be added to this line
gcc -g -DCOLOREDOUTPUT -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime mycode.c -L/usr/local/lib -I/usr/local/include -L. -lcmor -I/usr/local/netcdf4/include -L/usr/local/netcdf4/lib -lnetcdf -L/usr/local/hdf5/lib -lhdf5_hl -lhdf5 -L/usr/local/lib -lz -lm -L/usr/local/szip/lib -lsz -lcurl -L/usr/local/lib -R/usr/local/lib -ludunits2 -lexpat -I/usr/local/include -L/usr/local//lib -R/usr/local//lib -luuid -I/usr/local//include -o mycode
# The following line will compile "FORTRAN" code mycode.f90 with cmor, additional libraries mycode.f90 may requires should be added to this line
ifort -g -g mycode.f90 -L/usr/local/lib -L. -lcmor -I/usr/local/netcdf4/include -L/usr/local/netcdf4/lib -lnetcdf -L/usr/local/hdf5/lib -lhdf5_hl -lhdf5 -L/usr/local/lib -lz -lm -L/usr/local/szip/lib -lsz -lcurl -L/usr/local/lib -R/usr/local/lib -ludunits2 -lexpat -I/usr/local/include -L/usr/local//lib -R/usr/local//lib -luuid -I/usr/local//include -o mycode
Scan Makefile
$ more Makefile
**** Note no matter what I pass in for CFLAGS or FCFLAGS.FFLAGSsome tests fail in configure and I always get the default
CFLAGS=-g,CFFLAGS=-g
This helps for ifort but not gcc
$ ./configure --prefix=/usr/local --with-netcdf=/usr/local/netcdf4 --with-hdf5=/usr/local/hdf5 --with-udunits2=/usr/local --with-uuid=/usr/local/ "CFLAGS=-arch x86_64 -fPIC" "FFLAGS=-arch x86_64 -m64 -fPIC" "FCFLAGS=-arch x86_64 -m64 -fPIC" "FC=ifort" "CXXFLAGS=-arch x86_64 -fPIC"
also make test issues a bunch of
> ifort: command line warning #10006: ignoring unknown option '-R/usr/local/lib'
These being somesort of Sun computer specific things I don't need to worry about or affect the results
$ ./configure --prefix=/usr/local --with-netcdf=/usr/local/netcdf4 --with-hdf5=/usr/local/hdf5 --with-udunits2=/usr/local --with-uuid=/usr/local/
So force the matter by editing the Makefile as so
#!/usr/bin/env sh
FC=ifort
CPPFLAGS_USER=""
FFLAGS_USER="-fPIC"
#MODULE_SUFFIX="mod"
PREFIX=/usr/local
FCFLAGS=-arch x86_64 -m64 -fPIC -c -g
CFLAGS=-arch x86_64 -fPIC -c -g
PYTHONEXEC=
NO_COLOR2=\x1b[0m
OK_COLOR2=\x1b[2;34m
NO_COLOR=${NO_COLOR2}
OK_COLOR=${OK_COLOR2}
# Library name
LIBNAME = libcmor.a
# Library sources
#LIBSOURCES = Src/cmor.c Src/cmor_variables.c Src/cmor_axes.c Src/cmor_tables.c Src/cmor_grids.c Src/cdTime/cdTimeConv.c Src/cdTime/cdUtil.c Src/cdTime/timeConv.c Src/cdTime/timeArith.c
LIBSOURCES = Src/cmor.c Src/cmor_variables.c Src/cmor_axes.c Src/cmor_tables.c Src/cmor_grids.c Src/cdTime/cdTimeConv.c Src/cdTime/cdUtil.c Src/cdTime/timeConv.c Src/cdTime/timeArith.c Src/cmor_cfortran_interface.c Src/cmor_md5.c
LIBFSOURCES = Src/cmor_fortran_interface.f90
LIBFILES = cmor.o cmor_axes.o cmor_variables.o cmor_tables.o cdTimeConv.o cdUtil.o timeConv.o timeArith.o cmor_grids.o cmor_md5.o cmor_cfortran_interface.o cmor_fortran_interface.o
#Include Files
INCFILES = include/cmor.h include/cmor_func_def.h include/cmor_md5.h include/cdTime/cddrs.h include/cdTime/cddrsint.h include/cdTime/cdms.h include/cdTime/cdmsint.h include/cdTime/cdmsint_new.h include/cdTime/cdrra.h include/cdTime/cdunif.h include/cdTime/cdunifint.h include/cdTime/cdunifpp/cdunifpp.h include/cdTime/cdunifpp/cdunifpp_frename.h include/cdTime/cdunifpp/crayio.h include/cdTime/cdunifpp/util.h include/cdTime/cdunifpp/vardef.h include/cdTime/cfortran.h include/cdTime/drscdf.h include/cdTime/drsdef.h include/cdTime/fcddrs.h include/cdTime/gaussLats.h include/cdTime/grads.h include/cdTime/gx.h include/cdTime/isdb.h
# Temporary Files
TMPFILES = *~ $(LIBFILES) *.mod a.out *.stb Test/*.nc Test/IPCC_Fourth_Assessment *.LOG* *.dSYM Test/IPCC Test/CMIP5 CMIP5
DISTFILES = libcmor.a
DEPEND= makedepend $(CFLAGS) -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime -I/usr/local/netcdf4/include -I/usr/local/include -I/usr/local//include
all: cmor
@echo
depend: $(LIBSOURCES)
${DEPEND} $(LIBSOURCES)
cmor.o: Src/cmor.c include/cmor.h include/cmor_func_def.h
gcc $(CFLAGS) -DCOLOREDOUTPUT -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime -I/usr/local/netcdf4/include -I/usr/local/include -I/usr/local//include Src/cmor.c
cmor_variables.o: Src/cmor_variables.c include/cmor.h include/cmor_func_def.h
gcc $(CFLAGS) -DCOLOREDOUTPUT -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime -I/usr/local/netcdf4/include -I/usr/local/include -I/usr/local//include Src/cmor_variables.c
cmor_axes.o: Src/cmor_axes.c include/cmor.h include/cmor_func_def.h
gcc $(CFLAGS) -DCOLOREDOUTPUT -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime -I/usr/local/netcdf4/include -I/usr/local/include -I/usr/local//include Src/cmor_axes.c
cmor_tables.o: Src/cmor_tables.c include/cmor.h include/cmor_func_def.h
gcc $(CFLAGS) -DCOLOREDOUTPUT -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime -I/usr/local/netcdf4/include -I/usr/local/include -I/usr/local//include Src/cmor_tables.c
cmor_grids.o: Src/cmor_grids.c include/cmor.h include/cmor_func_def.h
gcc $(CFLAGS) -DCOLOREDOUTPUT -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime -I/usr/local/netcdf4/include -I/usr/local/include -I/usr/local//include Src/cmor_grids.c
cmor_md5.o: Src/cmor_md5.c include/cmor.h include/cmor_func_def.h include/cmor_md5.h
gcc $(CFLAGS) -DCOLOREDOUTPUT -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime -I/usr/local/netcdf4/include -I/usr/local/include -I/usr/local//include Src/cmor_md5.c
cmor_cfortran_interface.o: Src/cmor_cfortran_interface.c include/cmor.h include/cmor_func_def.h
gcc $(CFLAGS) -DCOLOREDOUTPUT -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime -I/usr/local/netcdf4/include -I/usr/local/include -I/usr/local//include Src/cmor_cfortran_interface.c
cdTimeConv.o: Src/cdTime/cdTimeConv.c include/cmor.h include/cmor_func_def.h
gcc $(CFLAGS) -DCOLOREDOUTPUT -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime -I/usr/local/netcdf4/include -I/usr/local/include -I/usr/local//include Src/cdTime/cdTimeConv.c
cdUtil.o: Src/cdTime/cdUtil.c include/cmor.h include/cmor_func_def.h
gcc $(CFLAGS) -DCOLOREDOUTPUT -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime -I/usr/local/netcdf4/include -I/usr/local/include -I/usr/local//include Src/cdTime/cdUtil.c
timeConv.o: Src/cdTime/timeConv.c include/cmor.h include/cmor_func_def.h
gcc $(CFLAGS) -DCOLOREDOUTPUT -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime -I/usr/local/netcdf4/include -I/usr/local/include -I/usr/local//include Src/cdTime/timeConv.c
timeArith.o:Src/cdTime/timeArith.c include/cmor.h include/cmor_func_def.h
gcc $(CFLAGS) -DCOLOREDOUTPUT -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime -I/usr/local/netcdf4/include -I/usr/local/include -I/usr/local//include Src/cdTime/timeArith.c
cmor_fortran_interface.o: Src/cmor_fortran_interface.f90
ifort $(FCFLAGS) -DCOLOREDOUTPUT Src/cmor_fortran_interface.f90
cmor: $(LIBFILES)
@ar crv $(LIBNAME) $(LIBFILES)
@ranlib $(LIBNAME)
clean:
@echo "Cleaning [$(WHEREAMI)] ..."
@rm -rf $(TMPFILES)
distclean: clean
@echo "Completely cleaning [$(WHEREAMI)]..."
@rm -f $(DISTFILES)
install: cmor
mkdir -p /usr/local/lib
mkdir -p /usr/local/include
mkdir -p /usr/local/include/cdTime
mkdir -p /usr/local/include/cdTime/cdunifpp
cp -p $(LIBNAME) /usr/local/lib
cp -pr include/*.h cmor_users_functions.* /usr/local/include
cp -pr include/cdTime/*.h /usr/local/include/cdTime
cp -pr include/cdTime/cdunifpp/*.h /usr/local/include/cdTime/cdunifpp
uninstall: distclean
rm /usr/local/lib/$(LIBNAME)
cd /usr/local ; rm $(INCFILES)
backup: clean
@echo "Creating full backup tar file..."
@(cd ..; \
@TGZNAME=$(TGZDIR)/cmor_`$(TIMESTAMP)`_full.tgz; \
@tar cfz $$TGZNAME Cmor; \
@touch $(TIMESTAMPDIR)/cmor_`$(TIMESTAMP)`_full.time; \
@echo "Full backup tar file created : $$TGZNAME")
test: cmor test_C test_fortran
@echo "All C and Fortran Test passed successfully"
test_C: cmor
@rm -f ./ipcc_test_code ; gcc $(CFLAGS) -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime Test/ipcc_test_code.c -L/usr/local/lib -I/usr/local/include -L. -lcmor -I/usr/local/netcdf4/include -L/usr/local/netcdf4/lib -lnetcdf -L/usr/local/hdf5/lib -lhdf5_hl -lhdf5 -L/usr/local/lib -lz -lm -L/usr/local/szip/lib -lsz -lcurl -L/usr/local/lib -R/usr/local/lib -ludunits2 -lexpat -I/usr/local/include -L/usr/local//lib -R/usr/local//lib -luuid -I/usr/local//include -o ipcc_test_code >/dev/null 2>/dev/null; ./ipcc_test_code >/dev/null 2>/dev/null
@rm -f test_grid ; gcc $(CFLAGS) -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime Test/test_grid.c -L/usr/local/lib -I/usr/local/include -L. -lcmor -I/usr/local/netcdf4/include -L/usr/local/netcdf4/lib -lnetcdf -L/usr/local/hdf5/lib -lhdf5_hl -lhdf5 -L/usr/local/lib -lz -lm -L/usr/local/szip/lib -lsz -lcurl -L/usr/local/lib -R/usr/local/lib -ludunits2 -lexpat -I/usr/local/include -L/usr/local//lib -R/usr/local//lib -luuid -I/usr/local//include -o test_grid >/dev/null 2>/dev/null; ./test_grid >/dev/null 2>/dev/null;
@rm -f test_lots_of_variables ; gcc $(CFLAGS) -I/usr/local/netcdf4/include -Iinclude -Iinclude/cdTime Test/test_lots_of_variables.c -L/usr/local/lib -I/usr/local/include -L. -lcmor -I/usr/local/netcdf4/include -L/usr/local/netcdf4/lib -lnetcdf -L/usr/local/hdf5/lib -lhdf5_hl -lhdf5 -L/usr/local/lib -lz -lm -L/usr/local/szip/lib -lsz -lcurl -L/usr/local/lib -R/usr/local/lib -ludunits2 -lexpat -I/usr/local/include -L/usr/local//lib -R/usr/local//lib -luuid -I/usr/local//include -o test_lots_of_variables >/dev/null 2>/dev/null; ./test_lots_of_variables >/dev/null 2>/dev/null;
python:
@echo "Building Python interface"
@${PYTHONEXEC} setup.py install
test_a_python:
@echo "${OK_COLOR}Testing ${TEST_NAME} ${NO_COLOR}"
${PYTHONEXEC} ${TEST_NAME} >/dev/null 2>/dev/null
test_python: python
@env TEST_NAME=Test/test_python_direct_calls.py make test_a_python
@env TEST_NAME=Test/test_python_user_interface_00.py make test_a_python
@env TEST_NAME=Test/test_python_user_interface_01.py make test_a_python
@env TEST_NAME=Test/test_python_user_interface_03.py make test_a_python
@env TEST_NAME=Test/test_python_common.py make test_a_python
@env TEST_NAME=Test/cmor_speed_and_compression.py make test_a_python
@env TEST_NAME=Test/cmor_speed_and_compression_01.py make test_a_python
# @env TEST_NAME=Test/cmor_speed_and_compression_02.py make test_a_python
@env TEST_NAME=Test/test_compression.py make test_a_python
@env TEST_NAME=Test/test_python_appending.py make test_a_python
@env TEST_NAME=Test/test_python_bounds_request.py make test_a_python
@env TEST_NAME=Test/test_python_new_tables.py make test_a_python
# @env TEST_NAME=Test/test_python_index_coord.py make test_a_python
@env TEST_NAME=Test/test_python_jamie.py make test_a_python
@env TEST_NAME=Test/test_python_jamie_2.py make test_a_python
@env TEST_NAME=Test/test_python_jamie_3.py make test_a_python
@env TEST_NAME=Test/test_python_jamie_4.py make test_a_python
@env TEST_NAME=Test/test_python_jamie_6.py make test_a_python
@env TEST_NAME=Test/test_python_memory_check.py make test_a_python
@env TEST_NAME=Test/test_python_open_close_cmor_multiple.py make test_a_python
@env TEST_NAME=Test/test_python_jamie_7.py make test_a_python
@env TEST_NAME=Test/test_python_joerg_1.py make test_a_python
@env TEST_NAME=Test/test_python_joerg_2.py make test_a_python
@env TEST_NAME=Test/test_python_joerg_3.py make test_a_python
@env TEST_NAME=Test/test_python_YYYMMDDHH_exp_fmt.py make test_a_python
@env TEST_NAME=Test/test_python_region.py make test_a_python
test_case:
@echo "${OK_COLOR}Testing: "${TEST_NAME}" with input file: ${INPUT_FILE}${NO_COLOR}"
@rm -f ./${TEST_NAME} 2>/dev/null ; ifort $(FCFLAGS) Test/${TEST_NAME}.f90 -L/usr/local/lib -L. -lcmor -I/usr/local/netcdf4/include -L/usr/local/netcdf4/lib -lnetcdf -L/usr/local/hdf5/lib -lhdf5_hl -lhdf5 -L/usr/local/lib -lz -lm -L/usr/local/szip/lib -lsz -lcurl -L/usr/local/lib -I/usr/local/include -L/usr/local//lib -luuid -I/usr/local//include -o ${TEST_NAME} ;
@./${TEST_NAME} >/dev/null 2>/dev/null < ${INPUT_FILE} ;
@ rm ./${TEST_NAME}
ifeq ( ,python)
@env TEST_NAME="Test/check_results.py ${TEST_NAME}" make test_a_python
endif
test_case_old_cmor_tables:
@echo "Testing: "${TEST_NAME}" with input file: "${INPUT_FILE}
@rm -f ./${TEST_NAME} 2>/dev/null ; ifort $(FCFLAGS) Test/old_cmor_tables/${TEST_NAME}.f90 -L/usr/local/lib -L. -lcmor -I/usr/local/netcdf4/include -L/usr/local/netcdf4/lib -lnetcdf -L/usr/local/hdf5/lib -lhdf5_hl -lhdf5 -L/usr/local/lib -lz -lm -L/usr/local/szip/lib -lsz -lcurl -L/usr/local/lib -ludunits2 -lexpat -I/usr/local/include -L/usr/local//lib -luuid -I/usr/local//include -o ${TEST_NAME} ;
@./${TEST_NAME} >/dev/null 2>/dev/null < ${INPUT_FILE} ;
@ rm ./${TEST_NAME}
ifeq ( ,python)
@env TEST_NAME="Test/check_results.py old_cmor_tables_${TEST_NAME}" make test_a_python
endif
test_fortran_old_cmor_tables: cmor
@env TEST_NAME="test_any_from_asc" INPUT_FILE="Test/tas_3D_noreorder.input" make test_case_old_cmor_tables
@env TEST_NAME="test_any_from_asc" INPUT_FILE="Test/3D_txy.input" make test_case_old_cmor_tables
@env TEST_NAME="test_any_from_asc" INPUT_FILE="Test/3D_txy_split_lon.input" make test_case_old_cmor_tables
@env TEST_NAME="test_any_from_asc" INPUT_FILE="Test/3D_xty_split_lon.input" make test_case_old_cmor_tables
@env TEST_NAME="test_any_from_asc_d" INPUT_FILE="Test/tas_3D_noreorder.input" make test_case_old_cmor_tables
@env TEST_NAME="test_any_from_asc_d" INPUT_FILE="Test/3D_txy.input" make test_case_old_cmor_tables
@env TEST_NAME="test_any_from_asc_d" INPUT_FILE="Test/3D_txy_split_lon.input" make test_case_old_cmor_tables
@env TEST_NAME="test_any_from_asc_d" INPUT_FILE="Test/3D_xty_split_lon.input" make test_case_old_cmor_tables
@env TEST_NAME="karls_test" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test1" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test2" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test3" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test4" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="main_prog" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test_any_from_asc_i" INPUT_FILE="Test/tas_mytest_3d_i.input" make test_case_old_cmor_tables
@env TEST_NAME="mytest_4d_r" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="rewrite_harvardf_data" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test_3h" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test_dimensionless" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test_fortran_example_00" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test_fortran_example_01" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test_station_data" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test_region" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test_sigma" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test_singleton" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="mytest_4d_r_big_array" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="mytest_4d_d_big_array_2" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="mytest_4d_d_big_array_3" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="mytest_4d_d_big_array_4" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="mytest_4d_d_big_array_5" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="climatology_test_code" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test_lots_of_variables" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test_shrt_exp_nm_set_att_initi" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
@env TEST_NAME="test_sophie" INPUT_FILE="Test/noinput" make test_case_old_cmor_tables
test_fortran: cmor
@env TEST_NAME="test_any_from_asc" INPUT_FILE="Test/tas_3D_noreorder.input" make test_case
@env TEST_NAME="test_any_from_asc" INPUT_FILE="Test/3D_txy.input" make test_case
@env TEST_NAME="test_any_from_asc" INPUT_FILE="Test/3D_txy_split_lon.input" make test_case
@env TEST_NAME="test_any_from_asc" INPUT_FILE="Test/3D_xty_split_lon.input" make test_case
@env TEST_NAME="test_any_from_asc_d" INPUT_FILE="Test/tas_3D_noreorder.input" make test_case
@env TEST_NAME="test_any_from_asc_d" INPUT_FILE="Test/3D_txy.input" make test_case
@env TEST_NAME="test_any_from_asc_d" INPUT_FILE="Test/3D_txy_split_lon.input" make test_case
@env TEST_NAME="test_any_from_asc_d" INPUT_FILE="Test/3D_xty_split_lon.input" make test_case
@env TEST_NAME="karls_test" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test1" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test2" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test3" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test4" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="main_prog" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_any_from_asc_i" INPUT_FILE="Test/tas_mytest_3d_i.input" make test_case
@env TEST_NAME="mytest_4d_r" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="rewrite_harvardf_data" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_3h" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_dimensionless" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_fortran_example_00" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_fortran_example_01" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_station_data" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_cmor_grid_alejandro" INPUT_FILE="Test/alejandro.txt" make test_case
@env TEST_NAME="test_cmor_grid_alejandro" INPUT_FILE="Test/alejandro_1.txt" make test_case
@env TEST_NAME="test_cmor_grid_alejandro" INPUT_FILE="Test/alejandro_2.txt" make test_case
@env TEST_NAME="test_region" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_sigma" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_singleton" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="mytest_4d_r_big_array" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="mytest_4d_d_big_array_2" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="mytest_4d_d_big_array_3" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="mytest_4d_d_big_array_4" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="mytest_4d_d_big_array_5" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="climatology_test_code" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_lots_of_variables" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_shrt_exp_nm_set_att_initi" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_sophie" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="ipcc_test_code" INPUT_FILE="Test/noinput" make test_case
atest: cmor
# @env TEST_NAME="mytest_4d_d_big_array_2" INPUT_FILE="Test/noinput" make test_case
@env TEST_NAME="test_lots_of_variables" INPUT_FILE="Test/noinput" make test_case
# @env TEST_NAME="wegner_test" INPUT_FILE="Test/noinput" make test_case
$ make > make.log 2>&1
$ more make.log
$ make test > make_test.log 2>&1
$ more make_test.log
> make: *** [test_C] Error 126
Okay, well let's go back to the default Makefile
$ rm Makefile
$ ./configure --prefix=/usr/local --with-netcdf=/usr/local/netcdf4 --with-hdf5=/usr/local/hdf5 --with-udunits2=/usr/local --with-uuid=/usr/local/ "CFLAGS=-arch x86_64 -fPIC" "FFLAGS=-arch x86_64 -m64 -fPIC" "FCFLAGS=-arch x86_64 -m64 -fPIC" "FC=ifort" "CXXFLAGS=-arch x86_64 -fPIC"
$ make > make.log 2>&1
$ more make.log
$ make test > make_test.log 2>&1
$ more make_test.log
> All C and Fortran Test passed successfully
Well, the C libraries don't seem like they are the same as those from netcdf/hdf but the fortran ones should beÉ.
$ make install
> cp -p libcmor.a /usr/local/lib
> cp -pr include/*.h cmor_users_functions.* /usr/local/include
> cp -pr include/cdTime/*.h /usr/local/include/cdTime
> cp -pr include/cdTime/cdunifpp/*.h /usr/local/include/cdTime/cdunifpp
$ grep "cmor_users_functions" /usr/local/lib/*
> Binary file libcmor.a matches
so it seems the fortran API is working.
# COSP 1.3
-------------------------------------------------------------
http://cfmip.metoffice.com/COSP.html
$ cd /usr/local/src
$ tar -zxvf cosp.v1.3.rev597.tar.gz
$ cd COSP
$ vim README.txt
$ vim Makefile
Start Modify Makefile
########################################################################
# Adapt these variables to your environment
########################################################################
F90 = ifort
F90FLAGS = -arch x86_64 -m64 -fPIC
# -------- Third Party Libraries -----------
NCDF_INC = /usr/local/netcdf4/include
NCDF_LIB = /usr/local/netcdf4/lib
UDUNITS_LIB = /usr/local/lib
UUID_INC = /usr/local/include
UUID_LIB = /usr/local/lib
HDF5_INC = /usr/local/hdf5/include
HDF5_LIB = /usr/local/hdf5/lib
CMOR_INC = /usr/local/include
CMOR_LIB = /usr/local/lib
# These are to find the szip library
INC = /usr/local/szip/include
LIB = /usr/local/szip/lib
# Help the linker
LD_LIBRARY_PATH=/usr/local/lib:/usr/local/hdf5/:/usr/local/netcdf4:/usr/local/szip/lib
# ---------------- RTTOV ---------------------
RTTOV_PATH = /usr/local/src/rttov93
RTTOV_LIB_PATH = $(RTTOV_PATH)/lib
RTTOV_INC_PATH = $(RTTOV_PATH)/include
RTTOV_MOD_PATH = $(RTTOV_PATH)/mod
# --------- Non-optional simulators ----------
RS_PATH = quickbeam
CS_PATH = actsim
LLNL_PATH = llnl
ISCCP_PATH = icarus-scops-4.1-bsd
MISR_PATH = MISR_simulator
MODIS_PATH = MODIS_simulator
########################################################################
# End of modifications
########################################################################
also modify the line
-L${RTTOV_LIB_PATH} -lrttov9.1 \
to
-L${RTTOV_LIB_PATH} -lrttov9.3 \
END Modify Makefile
Get RTTOV WorkingÉ.
# for RTTOV 9.3
-------------------------------------------------------------
http://research.metoffice.gov.uk/research/interproj/nwpsaf/rtm/rtm_rttov9.html
$ cd /usr/local/src
$ tar -zxvf rttov93.tar.gz
$ cd rttov93
$ vim readme.txt
Downloaded (9/9/2010)
$ tar -zxvf rttov93_bugfixes.tar.gz
$ cd rttov93_bugfixes
$ mv rttov_id.ksh ../scripts
$ mv *.F90 ../src
copied contents over originals
/scripts/rttov_id.ksh