Opened 8 years ago
Closed 7 years ago
#52289 closed defect (fixed)
hdf5, hdf5-18 header & library runtime error
Reported by: | almage (Roy Miller) | Owned by: | tenomoto (Takeshi Enomoto) |
---|---|---|---|
Priority: | Normal | Milestone: | |
Component: | ports | Version: | 2.3.4 |
Keywords: | Cc: | mamoll (Mark Moll), dershow, aaschwanden (Andy Aschwanden), Dave-Allured (Dave Allured) | |
Port: | hdf5 hdf5-18 netcdf ncarg |
Description
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
Change History (12)
comment:1 Changed 8 years ago by mf2k (Frank Schima)
Cc: | mmoll@… added; takeshi@… removed |
---|---|
Owner: | changed from macports-tickets@… to takeshi@… |
comment:2 Changed 8 years ago by dershow
Cc: | dersh@… added |
---|
comment:3 Changed 8 years ago by aaschwanden (Andy Aschwanden)
Cc: | aaschwanden added |
---|
comment:4 follow-ups: 7 8 Changed 8 years ago by aaschwanden (Andy Aschwanden)
That's been a constant source of frustration for me too.
As far as I can tell, there is not good reason to keep hdf5-18 around anymore, since the latest release of hdf5 is now compatible with netcdf. Can't we just get rid of the hdf5-18 port?
As a work around, I've replaced "hdf5-18" with "hdf5" in all port files that request hdf5-18 (netcdf, py-tables). Works for me, but it's not a nice solution.
comment:5 Changed 8 years ago by mf2k (Frank Schima)
Here are all the ports that depend on hdf5-18. They must be updated to use hdf5 and tested first.
$ port echo depends:hdf5-18 h4h5tools hdfeos5 netcdf octave-devel py27-tables py34-tables py35-tables py36-tables ncarg
comment:6 Changed 8 years ago by mamoll (Mark Moll)
hdf5 1.10 is still not supported in py-tables: https://github.com/PyTables/PyTables/issues/545
comment:7 Changed 8 years ago by mf2k (Frank Schima)
Replying to aaschwanden:
As far as I can tell, there is not good reason to keep hdf5-18 around anymore, since the latest release of hdf5 is now compatible with netcdf. Can't we just get rid of the hdf5-18 port?
I have created ticket:54101 for this issue.
comment:8 Changed 8 years ago by Dave-Allured (Dave Allured)
Replying to aaschwanden:
As far as I can tell, there is not good reason to keep hdf5-18 around anymore, since the latest release of hdf5 is now compatible with netcdf. Can't we just get rid of the hdf5-18 port?
(2017 May 10) Hdf5-18 solves two particular problems: creation of backward incompatible hdf5 data files, and broken network file access with hdf5 version 1.10.0. The first problem was solved only in netcdf-4.4.1, and not necessarily in any other hdf5-using packages. AFIK, the second problem is still extant for many if not all Macs using network file servers. Hdf5 version 1.10.1 provides an improved solution for the network file problem.
I urge caution. Please see ticket:54101 for more details.
comment:9 Changed 8 years ago by Dave-Allured (Dave Allured)
Cc: | Dave-Allured added |
---|
comment:10 follow-up: 11 Changed 7 years ago by mf2k (Frank Schima)
Now that no port depends on hdf5-18 anymore (#54101), can we close this ticket?
comment:11 Changed 7 years ago by Dave-Allured (Dave Allured)
comment:12 Changed 7 years ago by mf2k (Frank Schima)
Resolution: | → fixed |
---|---|
Status: | new → closed |
Cc Me!