#52289: hdf5, hdf5-18 header & library runtime error ----------------------------+--------------------------------------- Reporter: gryphon.csd8@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: | Port: hdf5 hdf5-18 netcdf ncarg ----------------------------+--------------------------------------- Hi, we are experiencing runtime errors with netcdf and nacre (ncl commands) that have to do with the hdf5 headers used for compilation, and the hdf5-18 library used during compilation of netcdf. system on which this occurs: Mac OS X 10.10.5 Xcode 7.2.1 The runtime error can be generated by doing a simple "ncdump" on a netcdf4 format file, shown here below: {{{ Tue Sep 20 10:45:33 beowulf test> ncdump tro3_Amon_reanalysis_ENS_198101-201012.3D.cg.ltm.nc 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 1.10.0, library is 1.8.16 SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.8.16 Configured on: Wed Aug 3 06:43:51 PDT 2016 Configured by: macports@tenten-slave.macports.org Configure mode: production Host system: i386-apple-darwin14.5.0 Uname information: Darwin tenten-slave.macports.org 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 Byte sex: little-endian Libraries: static, shared Installation point: /opt/local/lib/hdf5-18 Compiling Options: ------------------ Compilation Mode: production C Compiler: /usr/bin/clang CFLAGS: -pipe -Os H5_CFLAGS: AM_CFLAGS: CPPFLAGS: -I/opt/local/include H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: Shared C Library: yes Static C Library: yes Statically Linked Executables: no LDFLAGS: -L/opt/local/lib -Wl,-headerpad_max_install_names H5_LDFLAGS: 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/clang++ C++ Flags: -pipe -Os -stdlib=libc++ H5 C++ Flags: AM C++ Flags: Shared C++ Library: yes Static C++ Library: yes 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) MPE: no Direct VFD: no dmalloc: no Clear file buffers before write: yes Using memory checker: no Function Stack Tracing: no Strict File Format Checks: no Optimization Instrumentation: no Bye... Abort trap: 6 }}} It appears that hdf5-18 is necessary for the netcdf and hdfeos5 ports, while hdf5 is necessary for a handful of others. These are the ports we are using that are dependent upon a version of hdf5: {{{ Tue Sep 20 12:26:35 beowulf ~> port depend hdf5 cdo depends on hdf5 grads depends on hdf5 grib_api depends on hdf5 nco depends on hdf5 ncview depends on hdf5 wgrib2 depends on hdf5 Tue Sep 20 12:26:42 beowulf ~> port depend hdf5-18 hdfeos5 depends on hdf5-18 netcdf depends on hdf5-18 }}} I've been unable to get all these dependent ports to install, using only one of the hdf5 ports, it appears I must use both for the compilations. Then we have the runtime headers/library problem. ideas? thanks, Roy -- Ticket URL: <https://trac.macports.org/ticket/52289> MacPorts <https://www.macports.org/> Ports system for macOS