[gradsusr] Build GrADS 2.20 from Source, Errors with GRIB2 and gribmap

Wed Jan 31 09:50:49 EST 2018

Hi William,

This line has me concerned:

|    GRIB2 I/O Error: Predefined bitmap applies (ibmap=47244640267)

The grib standard allows predefined bitmaps in order to save space.
However, I am not aware of any grib file that uses predefined bitmaps,
and I am not aware of any center that has made predefined bitmaps
available.  I suspect that your grib file has problems.  Try running your
file through wgrib2 to confirm that a predefined bitmap is being used.

Wesley

On Tue, Jan 30, 2018 at 4:01 PM, William Daniel Scheftic <
scheftic at email.arizona.edu> wrote:

> Hi,
>
> I have built GrADS-2.2.0 from source for OpenSuse Leap 42.3 on the Windows
> Subsystem for Linux.
>
> I have tested reading netcdf and GRIB1 files and they work fine. However,
> I am not able to read GRIB2 files. I get the following error if I try to
> open a GRIB2 file that already had a .idx file produced:
>
> GRIB2 I/O Error: Predefined bitmap applies (ibmap=47244640267)
> Data Request Error:  Error for variable 'tmp2m'
>   Error ocurred at column 1
> DISPLAY error:  Invalid expression
>   Expression = tmp2m
>
> If I rerun the built gribmap on the file to produce a new .idx file I get
> a different error:
> Cannot contour grid - all undefined values
>
> This file worked fine with the SUSE-12.1 binaries using the gribmap in
> that distribution.  I had a different issue with the binaries regarding
> gxprint that is working now that I've built from source.
>
> I should point out that the built gribmap gives a segmentation fault on
> verbose (-v) mode.
>
> After some struggles I got all the libraries to build.  I do get some
> ignored errors due to permission problems.  I install in user permitted
> areas but it seems some parts of the installation want access to system
> areas.
>
> Here is a rundown of the various errors and the associated libraries.
> *** ncurses-5.7 ***
> /sbin/ldconfig: Can't create temporary cache file /etc/ld.so.cache~:
> Permission denied
> Makefile:658: recipe for target '/home/bill/grads/supplibs/lib/libncurses.so.5.7'
> failed
> make[1]: [/home/bill/grads/supplibs/lib/libncurses.so.5.7] Error 1
> (ignored)
>
> /sbin/ldconfig: Can't create temporary cache file /etc/ld.so.cache~:
> Permission denied
> Makefile:259: recipe for target '/home/bill/grads/supplibs/lib/libpanel.so.5.7'
> failed
> make[1]: [/home/bill/grads/supplibs/lib/libpanel.so.5.7] Error 1 (ignored)
>
> /sbin/ldconfig: Can't create temporary cache file /etc/ld.so.cache~:
> Permission denied
> Makefile:290: recipe for target '/home/bill/grads/supplibs/lib/libmenu.so.5.7'
> failed
> make[1]: [/home/bill/grads/supplibs/lib/libmenu.so.5.7] Error 1 (ignored)
>
> /sbin/ldconfig: Can't create temporary cache file /etc/ld.so.cache~:
> Permission denied
> Makefile:314: recipe for target '/home/bill/grads/supplibs/lib/libform.so.5.7'
> failed
> make[1]: [/home/bill/grads/supplibs/lib/libform.so.5.7] Error 1 (ignored)
>
> make[1]: Entering directory '/mnt/c/Libraries/grads-2.2.0/
> supplibs/src/ncurses-5.7/test'
> make[1]: Nothing to be done for 'install'.
>
> *** readline-5.0 ***
> make[1]: Leaving directory '/mnt/c/Libraries/grads-2.2.0/
> supplibs/src/readline-5.0/doc'
> mv /home/bill/grads/supplibs/lib/libreadline.a
> /home/bill/grads/supplibs/lib/libreadline.old
> mv: cannot stat '/home/bill/grads/supplibs/lib/libreadline.a': No such
> file or directory
> Makefile:221: recipe for target 'install-static' failed
> make: [install-static] Error 1 (ignored)
> /usr/bin/install -c -m 644 libreadline.a /home/bill/grads/supplibs/lib/
> libreadline.a
> test -n "ranlib" && ranlib /home/bill/grads/supplibs/lib/libreadline.a
> mv /home/bill/grads/supplibs/lib/libhistory.a
> /home/bill/grads/supplibs/lib/libhistory.old
> mv: cannot stat '/home/bill/grads/supplibs/lib/libhistory.a': No such
> file or directory
> Makefile:221: recipe for target 'install-static' failed
> make: [install-static] Error 1 (ignored)
> /usr/bin/install -c -m 644 libhistory.a /home/bill/grads/supplibs/lib/
> libhistory.a
>
> *** udunits-1.11.7 ***
> make[2]: Entering directory '/mnt/c/Libraries/grads-2.2.0/
> supplibs/src/udunits-1.11.7/src/port/cfortran'
> make[2]: Nothing to be done for 'all'.
> make[2]: Entering directory '/mnt/c/Libraries/grads-2.2.0/
> supplibs/src/udunits-1.11.7/src/port/cfortran'
> make[2]: Nothing to be done for 'install'.
> make[2]: Entering directory '/mnt/c/Libraries/grads-2.2.0/
> supplibs/src/udunits-1.11.7/src/lib'
> make[2]: Nothing to be done for 'installed_manual'.
>
> *** freetype-2.4.10 ***
> rmdir: failed to remove '/home/bill/grads/supplibs/inc
> lude/freetype2/freetype/internal': No such file or directory
> /home/bill/grads/supplibs/src/freetype-2.4.10/builds/unix/install.mk:31:
> recipe for target 'install' failed
> make: [install] Error 1 (ignored)
>
> *** cairo-1.14.10 ***
> /usr/bin/install: cannot stat './html/index.sgml': No such file or
> directory
> which: no gtkdoc-rebase in (/home/bill/grads/supplibs/bin
> :/home/bill/grads/bin:/home/bill/bin:/usr/local/sbin:/usr/
> local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/
> local/games:/mnt/c/Windows/System32:/mnt/c/Windows:/mnt/
> c/Windows/System32/wbem:/mnt/c/Windows/System32/
> WindowsPowerShell/v1.0:/usr/bin/X11:/usr/lib/mit/bin:/usr/lib/mit/sbin)
> Makefile:1882: recipe for target 'install-data-local' failed
> make[6]: [install-data-local] Error 1 (ignored)
>
>
> I also frequently get the following for various libraries and grads
> install:
> make[2]: Nothing to be done for 'install-exec-am'.
> make[2]: Nothing to be done for 'install-data-am'.
>
>
> Configure Output for GrADS install:
> -----------------------------------
> bill at Bill-PC:~/grads/supplibs/src/grads-2.2.0> ./configure
> --prefix=$HOME/grads
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> /home/bill/grads/supplibs/src/grads-2.2.0/etc/missing: Unknown
> `--is-lightweight' option
> Try `/home/bill/grads/supplibs/src/grads-2.2.0/etc/missing --help' for
> more information
> configure: WARNING: 'missing' script is too old or missing
> checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking whether make supports nested variables... yes
> checking whether to enable maintainer-specific portions of Makefiles... no
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking how to print strings... printf
> checking for gcc... gcc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> 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 a sed that does not truncate output... /usr/bin/sed
> checking for grep that handles long lines and -e... /usr/bin/grep
> checking for egrep... /usr/bin/grep -E
> checking for fgrep... /usr/bin/grep -F
> checking for ld used by gcc... /usr/x86_64-suse-linux/bin/ld
> checking if the linker (/usr/x86_64-suse-linux/bin/ld) is GNU ld... yes
> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
> checking the name lister (/usr/bin/nm -B) interface... BSD nm
> checking whether ln -s works... yes
> checking the maximum length of command line arguments... 1572864
> checking whether the shell understands some XSI constructs... yes
> checking whether the shell understands "+="... yes
> checking how to convert x86_64-unknown-linux-gnu file names to
> x86_64-unknown-linux-gnu format... func_convert_file_noop
> checking how to convert x86_64-unknown-linux-gnu file names to toolchain
> format... func_convert_file_noop
> checking for /usr/x86_64-suse-linux/bin/ld option to reload object
> files... -r
> checking for objdump... objdump
> checking how to recognize dependent libraries... pass_all
> checking for dlltool... no
> checking how to associate runtime and link libraries... printf %s\n
> checking for ar... ar
> checking for archiver @FILE support... @
> checking for strip... strip
> checking for ranlib... ranlib
> checking command to parse /usr/bin/nm -B output from gcc object... ok
> checking for sysroot... no
> checking for mt... mt
> checking if mt is a manifest tool... no
> checking how to run the C preprocessor... gcc -E
> 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 for dlfcn.h... yes
> checking for objdir... .libs
> checking if gcc supports -fno-rtti -fno-exceptions... no
> checking for gcc option to produce PIC... -fPIC -DPIC
> checking if gcc PIC flag -fPIC -DPIC works... yes
> checking if gcc static flag -static works... no
> checking if gcc supports -c -o file.o... yes
> checking if gcc supports -c -o file.o... (cached) yes
> checking whether the gcc linker (/usr/x86_64-suse-linux/bin/ld -m
> elf_x86_64) supports shared libraries... yes
> checking whether -lc should be explicitly linked in... no
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking for shl_load... no
> checking for shl_load in -ldld... no
> checking for dlopen... no
> checking for dlopen in -ldl... yes
> checking whether a program can dlopen itself... yes
> checking whether a statically linked program can dlopen itself... yes
> checking whether stripping libraries is possible... yes
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... no
>
> Checking for programs
> ---------------------
> checking for gawk... (cached) gawk
> checking whether we are using the GNU C compiler... (cached) yes
> checking whether gcc accepts -g... (cached) yes
> checking for gcc option to accept ISO C89... (cached) none needed
> checking for xlc++... no
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking how to run the C++ preprocessor... g++ -E
> checking for ld used by g++... /usr/x86_64-suse-linux/bin/ld -m elf_x86_64
> checking if the linker (/usr/x86_64-suse-linux/bin/ld -m elf_x86_64) is
> GNU ld... yes
> checking whether the g++ linker (/usr/x86_64-suse-linux/bin/ld -m
> elf_x86_64) supports shared libraries... yes
> checking for g++ option to produce PIC... -fPIC -DPIC
> checking if g++ PIC flag -fPIC -DPIC works... yes
> checking if g++ static flag -static works... no
> checking if g++ supports -c -o file.o... yes
> checking if g++ supports -c -o file.o... (cached) yes
> checking whether the g++ linker (/usr/x86_64-suse-linux/bin/ld -m
> elf_x86_64) supports shared libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether ln -s works... yes
>
> Setting host specific options
> -----------------------------
> Host machine: x86_64-unknown-linux-gnu
>
> Checking system libraries, headers, and compiler features
> ---------------------------------------------------------
> checking for cos in -lm... yes
> checking for X... libraries , headers
> checking for gethostbyname... yes
> checking for connect... yes
> checking for remove... yes
> checking for shmat... yes
> checking for IceConnectionNumber in -lICE... yes
>
> checking for ANSI C header files... (cached) yes
> checking malloc.h usability... yes
> checking malloc.h presence... yes
> checking for malloc.h... yes
> checking sys/file.h usability... yes
> checking sys/file.h presence... yes
> checking for sys/file.h... yes
> checking for unistd.h... (cached) yes
>
> checking for an ANSI C-conforming const... yes
> checking whether byte ordering is bigendian... no
> checking for off_t... yes
> checking for special C compiler options needed for large files... no
> checking for _FILE_OFFSET_BITS value needed for large files... no
> checking for _LARGEFILE_SOURCE value needed for large files... no
>
> Checking for optional feature support
> -------------------------------------
> checking for supplibs directory... /home/bill/grads/supplibs
> Checking in /home/bill/grads/supplibs for libraries to support extra
> features ...
>
> readline
> --------
> checking readline/readline.h usability... yes
> checking readline/readline.h presence... yes
> checking for readline/readline.h... yes
> checking readline/history.h usability... yes
> checking readline/history.h presence... yes
> checking for readline/history.h... yes
> checking for tgetent in -lreadline... no
> checking for tgetent in -lncurses... yes
>
> geotiff
> -------
> checking geotiff.h usability... yes
> checking geotiff.h presence... yes
> checking for geotiff.h... yes
> checking geotiffio.h usability... yes
> checking geotiffio.h presence... yes
> checking for geotiffio.h... yes
> checking xtiffio.h usability... yes
> checking xtiffio.h presence... yes
> checking for xtiffio.h... yes
> checking for main in -ltiff... yes
> checking for main in -lgeotiff... yes
>
> shapefiles
> ----------
> checking shapefil.h usability... yes
> checking shapefil.h presence... yes
> checking for shapefil.h... yes
> checking for main in -lshp... yes
>
> png
> ---
> checking for main in -lpng15... yes
>
> zlib
> ----
> checking zlib.h usability... yes
> checking zlib.h presence... yes
> checking for zlib.h... yes
> checking for compress in -lz... yes
>
> jpeg
> ----
> checking for main in -ljpeg... yes
>
> jasper
> ------
> checking jasper.h usability... yes
> checking jasper.h presence... yes
> checking for jasper.h... yes
> checking for main in -ljasper... yes
>
> gd
> --
> checking gd.h usability... yes
> checking gd.h presence... yes
> checking for gd.h... yes
> checking for gdImageCreate in -lgd... yes
> checking for gdImageJpeg in -lgd... yes
>
> grib2
> -----
> checking grib2.h usability... yes
> checking grib2.h presence... yes
> checking for grib2.h... yes
> checking for main in -lgrib2c... yes
>
> xml2
> ----
> checking for main in -lxml2... yes
>
> Cairo
> -----
> checking cairo.h usability... yes
> checking cairo.h presence... yes
> checking for cairo.h... yes
> checking cairo-xlib.h usability... yes
> checking cairo-xlib.h presence... yes
> checking for cairo-xlib.h... yes
> checking ft2build.h usability... yes
> checking ft2build.h presence... yes
> checking for ft2build.h... yes
> checking for main in -lpixman-1... yes
> checking for main in -lfontconfig... yes
> checking for main in -lfreetype... yes
> checking for main in -lXrender... yes
> checking for main in -lcairo... yes
>
> udunits
> -------
> checking udunits.h usability... yes
> checking udunits.h presence... yes
> checking for udunits.h... yes
> checking for utInit in -ludunits... yes
>
> curl
> ----
> checking for main in -lcurl... yes
>
> hdf5
> ----
> checking hdf5.h usability... yes
> checking hdf5.h presence... yes
> checking for hdf5.h... yes
> checking for main in -lhdf5... yes
> checking for main in -lhdf5_hl... yes
>
> hdf4
> ----
> checking mfhdf.h usability... yes
> checking mfhdf.h presence... yes
> checking for mfhdf.h... yes
> checking for main in -ldf... yes
> checking for main in -lmfhdf... yes
>
> netcdf
> ------
> checking netcdf.h usability... yes
> checking netcdf.h presence... yes
> checking for netcdf.h... yes
> checking for main in -lnetcdf... yes
>
> gadap
> -----
> checking gadap.h usability... yes
> checking gadap.h presence... yes
> checking for gadap.h... yes
> checking for main in -lgadap... yes
> checking for main in -ldap... yes
> checking for main in -ldapclient... yes
> configure: creating src/VERSION
> configure: creating src/buildinfo.h
> checking that generated files are newer than configure... done
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating src/Makefile
> config.status: creating src/config.h
> config.status: executing libtool commands
>
> +===========================================================
> ==============+
>    GrADS 2.2.0 : Configured on 01/28/18 for x86_64-unknown-linux-gnu
> +===========================================================
> ==============+
>
>   +-------------------------------+
>   |                               |
>   |  GrADS will be built with:    |
>   |                               |
>   |  - GUI disabled               |
>   |  + READLINE enabled           |
>   |  + GEOTIFF enabled            |
>   |  + SHAPEFILE enabled          |
>   |  + GD enabled                 |
>   |  + CAIRO enabled              |
>   |  + GRIB2 enabled              |
>   |  + HDF4 enabled               |
>   |  + HDF5 enabled               |
>   |  + NETCDF4 enabled            |
>   |  + OPeNDAP enabled            |
>   |     for grids and stn data    |
>   |                               |
>   +-------------------------------+
>
> Run 'make && make install' to build GrADS.
> Executables will be installed to bin/ in current dir, unless prefix was
> specified.
>
> _______________________________________________
> gradsusr mailing list
> gradsusr at gradsusr.org
> http://gradsusr.org/mailman/listinfo/gradsusr
>
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