[gradsusr] How to read HDF5 data by using the latest version of GrADS?

Arlindo da Silva dasilva at alum.mit.edu
Wed Jan 12 21:33:16 EST 2011


On Wed, Jan 12, 2011 at 11:13 AM, muhammad hasan ali baig <
mhasanbaig at gmail.com> wrote:

> Dear Zablone, Rafael and other kind researchers,
>                                                                       I
> tried to follow your advice and tried to use the lats4d command but error
> message occurred "Command not found". Then I started to install different
> libraries from http://iges.org/grads/gadoc/supplibs.html but when i
> installed the zlib by following the steps:
>

1) Lats4d is not able to write GRIB2 datasets, only GRIB-1.

2) Lats4d is not available with the standard grads v2 from COLA; you will
need an opengrads bundle release for that:


http://opengrads.org/wiki/index.php?title=Installing_the_OpenGrADS_Bundle

3) For reading HDF-5, consult the grads documentation on the subject:

      http://grads.iges.org/grads/gadoc/SDFdescriptorfile.html

          Arlindo





> cd $HOME/supplibs/src/
> tar xvfz ./tarfiles/zlib-1.2.3.tar.gz
> ln -sf zlib-1.2.3 zlib
> cd zlib
> ./configure --prefix=$HOME/supplibs/src/zlib
> make
> make install
> cp ./lib/libz.a $HOME/supplibs/lib
> mkdir $HOME/supplibs/include/zlib
> cp ./include/zlib.h $HOME/supplibs/include/zlib
>
> following output could be seen on my terminal of the linux fedora having
> version 2.0.a9 of grads after running the above mentioned commands:
> [Hasan at localhost zlib]$ make
> gcc -O3 -DUSE_MMAP   -c -o example.o example.c
> gcc -O3 -DUSE_MMAP   -c -o adler32.o adler32.c
> gcc -O3 -DUSE_MMAP   -c -o compress.o compress.c
> gcc -O3 -DUSE_MMAP   -c -o crc32.o crc32.c
> gcc -O3 -DUSE_MMAP   -c -o gzio.o gzio.c
> gcc -O3 -DUSE_MMAP   -c -o uncompr.o uncompr.c
> gcc -O3 -DUSE_MMAP   -c -o deflate.o deflate.c
> gcc -O3 -DUSE_MMAP   -c -o trees.o trees.c
> gcc -O3 -DUSE_MMAP   -c -o zutil.o zutil.c
> gcc -O3 -DUSE_MMAP   -c -o inflate.o inflate.c
> gcc -O3 -DUSE_MMAP   -c -o infback.o infback.c
> gcc -O3 -DUSE_MMAP   -c -o inftrees.o inftrees.c
> gcc -O3 -DUSE_MMAP   -c -o inffast.o inffast.c
> ar rc libz.a adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o
> trees.o zutil.o inflate.o infback.o inftrees.o inffast.o
> gcc -O3 -DUSE_MMAP -o example example.o -L. libz.a
> gcc -O3 -DUSE_MMAP   -c -o minigzip.o minigzip.c
> gcc -O3 -DUSE_MMAP -o minigzip minigzip.o -L. libz.a
> [Hasan at localhost zlib]$ make install
> cp zlib.h zconf.h /home/Hasan/supplibs/src/zlib/include
> chmod 644 /home/Hasan/supplibs/src/zlib/include/zlib.h
> /home/Hasan/supplibs/src/zlib/include/zconf.h
> cp libz.a /home/Hasan/supplibs/src/zlib/lib
> cd /home/Hasan/supplibs/src/zlib/lib; chmod 755 libz.a
> cd /home/Hasan/supplibs/src/zlib/lib; if test -f libz.so.1.2.3; then \
>       rm -f libz.so libz.so.1; \
>       ln -s libz.so.1.2.3 libz.so; \
>       ln -s libz.so.1.2.3 libz.so.1; \
>       (ldconfig || true)  >/dev/null 2>&1; \
>     fi
> cp zlib.3 /home/Hasan/supplibs/src/zlib/share/man/man3
> chmod 644 /home/Hasan/supplibs/src/zlib/share/man/man3/zlib.3
> [Hasan at localhost zlib]$ cp ./lib/libz.a $HOME/supplibs/lib
> [Hasan at localhost zlib]$ mkdir $HOME/supplibs/include/zlib
> [Hasan at localhost zlib]$ cp ./include/zlib.h $HOME/supplibs/include/zlib
>
>
> After it, I tried to install libpng by using the following commands:
> cd $HOME/supplibs/src/
> tar xvfz tarfiles/libpng-1.2.18.tar.gz
> ln -sf libpng-1.2.18 libpng
> cd libpng
> ./configure --disable-shared --prefix=$HOME/supplibs/src/libpng
> make
> make install
> cp ./lib/libpng12.a $HOME/supplibs/lib
> mkdir $HOME/supplibs/include/libpng12
> cp ./include/libpng12/*.h $HOME/supplibs/include/libpng12
>
> But after executing the configure command, i received following message
> that zlib had not been installed:
>
> [Hasan at localhost libpng]$ ./configure --disable-shared
> --prefix=$HOME/supplibs/src/libpng
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking whether to enable maintainer-specific portions of Makefiles... no
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking for style of include used by make... GNU
> checking dependency style of gcc... gcc3
> checking for a sed that does not truncate output... /bin/sed
> checking build system type... i686-pc-linux-gnu
> checking host system type... i686-pc-linux-gnu
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for ld used by gcc... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking how to run the C preprocessor... gcc -E
> checking for sed... /bin/sed
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for /usr/bin/ld option to reload object files... -r
> checking for BSD-compatible nm... /usr/bin/nm -B
> checking how to recognise dependent libraries... pass_all
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking dlfcn.h usability... yes
> checking dlfcn.h presence... yes
> checking for dlfcn.h... yes
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking dependency style of g++... gcc3
> checking how to run the C++ preprocessor... g++ -E
> checking for g77... g77
> checking whether we are using the GNU Fortran 77 compiler... yes
> checking whether g77 accepts -g... yes
> checking the maximum length of command line arguments... 32768
> checking command to parse /usr/bin/nm -B output from gcc object... ok
> checking for objdir... .libs
> checking for ar... ar
> checking for ranlib... ranlib
> checking for strip... strip
> checking if gcc supports -fno-rtti -fno-exceptions... no
> checking for gcc option to produce PIC... -fPIC
> checking if gcc PIC flag -fPIC works... yes
> checking if gcc static flag -static works... no
> checking if gcc supports -c -o file.o... yes
> checking whether the gcc linker (/usr/bin/ld) supports shared libraries...
> yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> configure: creating libtool
> appending configuration tag "CXX" to libtool
> checking for ld used by g++... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking whether the g++ linker (/usr/bin/ld) supports shared libraries...
> yes
> checking for g++ option to produce PIC... -fPIC
> checking if g++ PIC flag -fPIC works... yes
> checking if g++ static flag -static works... no
> checking if g++ supports -c -o file.o... yes
> checking whether the g++ linker (/usr/bin/ld) supports shared libraries...
> yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> appending configuration tag "F77" to libtool
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking for g77 option to produce PIC... -fPIC
> checking if g77 PIC flag -fPIC works... yes
> checking if g77 static flag -static works... no
> checking if g77 supports -c -o file.o... yes
> checking whether the g77 linker (/usr/bin/ld) supports shared libraries...
> yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking for ANSI C header files... (cached) yes
> checking malloc.h usability... yes
> checking malloc.h presence... yes
> checking for malloc.h... yes
> checking for stdlib.h... (cached) yes
> checking for string.h... (cached) yes
> checking for strings.h... (cached) yes
> checking for an ANSI C-conforming const... yes
> checking for size_t... yes
> checking whether struct tm is in sys/time.h or time.h... time.h
> checking for working strtod... yes
> checking for memset... yes
> checking for pow... no
> checking for pow in -lm... yes
> checking for zlibVersion in -lz... no
> configure: error: zlib not installed
> [Hasan at localhost libpng]$ make
> make: *** No targets specified and no makefile found.  Stop.
> [Hasan at localhost libpng]$ make install
> make: *** No rule to make target `install'.  Stop.
>
>
> I am very worried how to proceed now? Could you help me in this regard?
>
>
>
> ==================================================================
>
> *Muhammad Hasan Ali Baig,
> *
>
> *Key Laboratory of Meteorological Disaster of Ministry of Education,
> Nanjing*
>
> *University of Information Science & Technology, Nanjing 210044, P. R.
> China*
> *School of Atmospheric Physics*
> *Nanjing University of Information Science & Technology 210044, P. R.
> China*
> *Mobile: +8615251705047
> ==================================================================
> *
>
>
> On 12 January 2011 11:12, Zablone Owiti <zowiti at ncst.go.ke> wrote:
>
>>
>>
>> > Dear Ali,
>> > You can use the following LATS4D command to convert your Data:
>> >
>> > lats4d -v -q -i inputfile -o outputfile -format grads_grib
>> >
>> > Where: inputfile is the name of the name of your hdf file (if it is not
>> in the Grads default file, then you need to give the path)
>> >          outputfile is the name of the GRIB file that will be created
>> (it
>> is saved in the default GRADS directory).
>> >
>> > There are more options you can choose. Note that the option -q above
>> makes GRADS to quite after running the command.
>> >
>> > You can get more about LATS4D
>> here:http://opengrads.org/doc/scripts/lats4d/
>> >
>> > Hope this will be of assistance to you.
>> >
>> > Wish you the best.
>> >
>> > ----------------------------
>> >
>> >  ZABLONE OWITIy
>> >
>> >  GRADUATE STUDENT
>> >
>> > College of Atmospheric Science
>> >
>> > Nanjing University of Information, Science and Technology
>> >
>> > Add: 219 Ning Liu Rd, Nanjing, Jiangsu, 21004, P.R. China
>> >
>> >  Tel: +86-25-58731402
>> >
>> > Fax: +86-25-58731456
>> > Mob. 15077895632
>> > Website:  www.nuist.edu.cn
>> >
>> > ====================================================
>> >
>> > DO NOT PRINT THIS E-MAIL UNLESS NECESSARY. THE ENVIRONMENT CONCERNS US
>> ALL.
>> >
>> > -------- Original Message --------
>> > > From: "muhammad hasan ali baig" <mhasanbaig at gmail.com>
>> > > Sent: Wednesday, January 12, 2011 1:32 AM
>> > > To: gradsusr at gradsusr.org
>> > > Subject: [gradsusr] How to read HDF5 data by using the latest version
>> of GrADS?
>> > >
>> > > Hi dear all!
>> >                I am using the latest version of GrADS. I tried to use it
>> in
>> > converting SST data of Chinese satellite FY2C which is available in HDF5
>> > format into grib2 format. But unfortunately, it couldnt read the HDF5
>> > format. What should i do?
>> > ==================================================================
>> > *Muhammad Hasan Ali Baig,
>> > *
>> >
>> > *Key Laboratory of Meteorological Disaster of Ministry of
>> Education,Nanjing*
>> >
>> > *University of Information Science & Technology, Nanjing 210044, P. R.
>> China
>> > *
>> > *School of Atmospheric Physics*
>> > *Nanjing University of Information Science & Technology 210044, P. R.
>> China*
>> > *Mobile: +8615251705047
>> > ==================================================================
>> > *
>> > _______________________________________________
>> > > gradsusr mailing list
>> > > gradsusr at gradsusr.org
>> > > http://gradsusr.org/mailman/listinfo/gradsusr
>>
>>
>>
>
> _______________________________________________
> gradsusr mailing list
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>
>


-- 
Arlindo da Silva
dasilva at alum.mit.edu
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