Re: HDF5 error with gmt 4.5.12
Chenjian Fu <[email protected]> Fri, 15 Aug 2014 18:21:01 -0400
| Newsgroups | gmane.comp.gis.gmt.user |
|---|---|
| Message-ID | <CAHtkriVmb=m-zhGWM6m=17TiWqVSn-E+_DNDUwfyem_4VJZh7w@mail.gmail.com> |
Oops, sorry, re-install your gmt4. -cj On Fri, Aug 15, 2014 at 6:19 PM, Chenjian Fu <[email protected]> wrote: > Hi Gery, > > Try this: go back to hdf5 1.8.12. Then re-install gmt5. > > Cheers, > Chenjian > > On Fri, Aug 15, 2014 at 12:57 PM, Gery . <[email protected]> wrote: >> Sorry for the last noisy message, but things were smooth finally, the >> solution was to install without gdal. Now things work, but I received this >> message about HDF5: >> >> ----------------------------------------------------------- >> >> $ pscoast -R-71.2/-70.9/42.25/42.45 -JM6.0 -Ba0.05f0.01SWen -Ia -Na -W3 -K > >> ps >> >> Warning! ***HDF5 library version mismatched error*** >> >> The HDF5 header files used to compile this application do not match >> >> the version used by the HDF5 library to which this application is linked. >> >> Data corruption or segmentation faults may occur if the application >> continues. >> >> This can happen when an application was compiled by one version of HDF5 but >> >> linked with a different version of static or shared HDF5 library. >> >> You should recompile the application or check your shared library related >> >> settings such as 'LD_LIBRARY_PATH'. >> >> You can, at your own risk, disable this warning by setting the environment >> >> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. >> >> Setting it to 2 or higher will suppress the warning messages totally. >> >> Headers are 1.8.12, library is 1.8.13 >> >> SUMMARY OF THE HDF5 CONFIGURATION >> >> ================================= >> >> General Information: >> >> ------------------- >> >> HDF5 Version: 1.8.13 >> >> Configured on: Wed Jun 4 15:04:57 CEST 2014 >> >> Configured by: marco@GE-MATZERI-EU >> >> Configure mode: production >> >> Host system: i686-pc-cygwin >> >> Uname information: CYGWIN_NT-6.1-WOW64 GE-MATZERI-EU 1.7.30(0.272/5/3) >> 2014-05-23 10:36 i686 Cygwin >> >> Byte sex: little-endian >> >> Libraries: shared >> >> Installation point: /usr >> >> Compiling Options: >> >> ------------------ >> >> Compilation Mode: production >> >> C Compiler: /usr/bin/gcc >> >> CFLAGS: -ggdb -O2 -pipe -Wimplicit-function-declaration >> -fdebug-prefix-map=/pub/devel/hdf5/hdf5-1.8.13-1/ >> build=/usr/src/debug/hdf5-1.8.13-1 >> -fdebug-prefix-map=/pub/devel/hdf5/hdf5-1.8.13-1/src/hdf5-1.8.13=/usr/src/debug/hdf5-1.8.13-1 >> >> 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 -Wre dundant-decls -Wnested-externs -Winline >> -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked >> -Wdisabled-optimizati on -Wformat=2 -Wunreachable-code -Wendif-labels >> -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch >> -Wvariadic-macr os -Winit-self -Wmissing-include-dirs -Wswitch-default >> -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wst >> rict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand >> -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overfl ow=5 >> -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion >> -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 >> -Wvector-operation-performance -Wsuggest-attribute=pure >> -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -O3 -fomit-frame- >> pointer -finline-functions >> >> AM_CFLAGS: >> >> CPPFLAGS: >> >> H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API >> >> AM_CPPFLAGS: >> >> Shared C Library: yes >> >> Static C Library: no >> >> Statically Linked Executables: no >> >> LDFLAGS: >> >> H5_LDFLAGS: -no-undefined >> >> AM_LDFLAGS: >> >> Extra libraries: -lz -ldl -lm >> >> Archiver: ar >> >> Ranlib: ranlib >> >> Debugged Packages: >> >> API Tracing: no >> >> Languages: >> >> ---------- >> >> Fortran: no >> >> C++: yes >> >> C++ Compiler: /usr/bin/g++ >> >> C++ Flags: -ggdb -O2 -pipe >> -fdebug-prefix-map=/pub/devel/hdf5/hdf5-1.8.13-1/build=/usr/src/debug/hdf5-1.8.13 >> -1 >> -fdebug-prefix-map=/pub/devel/hdf5/hdf5-1.8.13-1/src/hdf5-1.8.13=/usr/src/debug/hdf5-1.8.13-1 >> >> H5 C++ Flags: >> >> AM C++ Flags: >> >> Shared C++ Library: yes >> >> Static C++ Library: 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) >> >> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset >> >> MPE: no >> >> Direct VFD: yes >> >> dmalloc: no >> >> Clear file buffers before write: yes >> >> Using memory checker: no >> >> Function Stack Tracing: no >> >> Strict File Format Checks: no >> >> Optimization Instrumentation: no >> >> Large File Support (LFS): yes >> >> Bye... >> >> Aborted (core dumped) >> >> ----------------------------------------------------------- >> >> I have the latest Cygwin 32-bit version. Which HDF5 version should I use? >> this Cygwin comes with hdf5 1.8.13-1, netcdf 4.3.2-1 and zlib 1.2.8-1. >> >> Any ideas?? thank.. >> >> Gery >> >> Mailing list for GMT discussions of all kinds. If you are not sure you have >> found a bug, discuss it here first. To formally report bugs or request >> features, please register and add New Issue on gmt.soest.hawaii.edu To >> unsubscribe, send the message "signoff gmt-help" to >> [email protected] Note: gmt-help will become obsolete on Sept 1, >> 2014 - please use forum on gmt.soest.hawaii.edu instead. Mailing list for GMT discussions of all kinds. If you are not sure you have found a bug, discuss it here first. To formally report bugs or request features, please register and add New Issue on gmt.soest.hawaii.edu To unsubscribe, send the message "signoff gmt-help" to [email protected] Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.