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[netCDF #YSY-473903]: make check fails with HDF5/netCDF4-beta1

Howdy Charlie!

No, netCDF-4 will not work well if HDF5 does not work.

Have you contacted the HDF5 support people? They will be very interested in 
this bug I think.

Funny, HDF5 beta1 has never failed "make check" on any machine I've tried here 
at Unidata. You're just lucky I guess!

I have forwarded this email to address@hidden, hopefully they can tell us what 
is going wrong on your HDF5 build...



> Hi All,
> 
> I have been unable to build netcdf4-beta1 on my Linux boxen.
> These intel machines run fully patched Ubuntu Feisty.
> The HDF5 'make check' does not succeed---the errors are below.
> I'll hold off on posting the netcdf4 'make check' errors
> until I learn whether the HDF ones are expected or not.
> 
> Here is how I built HDF5:
> export CC='gcc'
> export CXX='g++'
> export CPPFLAGS='-DNDEBUG'
> export CFLAGS='-O -g'
> export FC='g95'
> export F90='g95'
> export FFLAGS='-O -g'
> export F90FLAGS='-O -g'
> export NETCDF4_ROOT=/usr/local/netcdf4
> export HDF5_ROOT=${NETCDF4_ROOT}
> ./configure --prefix=${HDF5_ROOT} --enable-cxx --enable-fortran
> make
> 
> Things seem to build normally.
> Here is the tail of the 'make check':
> 
> zender@virga:/data/zender/tmp/hdf5-1.8.0-beta1$ make check
> Making check in src
> make[1]: Entering directory `/data/zender/tmp/hdf5-1.8.0-beta1/src'
> make  check-TESTS
> make[2]: Entering directory `/data/zender/tmp/hdf5-1.8.0-beta1/src'
> make[3]: Entering directory `/data/zender/tmp/hdf5-1.8.0-beta1/src'
> make[4]: Entering directory `/data/zender/tmp/hdf5-1.8.0-beta1/src'
> make[4]: Nothing to be done for `_exec_check-s'.
> make[4]: Leaving directory `/data/zender/tmp/hdf5-1.8.0-beta1/src'
> make[3]: Leaving directory `/data/zender/tmp/hdf5-1.8.0-beta1/src'
> make[3]: Entering directory `/data/zender/tmp/hdf5-1.8.0-beta1/src'
> make[3]: Leaving directory `/data/zender/tmp/hdf5-1.8.0-beta1/src'
> make[2]: Leaving directory `/data/zender/tmp/hdf5-1.8.0-beta1/src'
> make[1]: Leaving directory `/data/zender/tmp/hdf5-1.8.0-beta1/src'
> Making check in test
> make[1]: Entering directory `/data/zender/tmp/hdf5-1.8.0-beta1/test'
> make  testhdf5 lheap ohdr stab gheap cache cache_api pool hyperslab
> istore bittests dt_arith dtypes dsets cmpd_dset extend external objcopy
> links unlink big mtime fillval mount flush1 flush2 enum set_extent
> ttsafe stream_test getname vfd ntypes dangle dtransform reserved
> cross_read btree2 fheap error_test err_compat testmeta ../test/testerror.sh
> make[2]: Entering directory `/data/zender/tmp/hdf5-1.8.0-beta1/test'
> make[2]: `testhdf5' is up to date.
> make[2]: `lheap' is up to date.
> make[2]: `ohdr' is up to date.
> make[2]: `stab' is up to date.
> make[2]: `gheap' is up to date.
> make[2]: `cache' is up to date.
> make[2]: `cache_api' is up to date.
> make[2]: `pool' is up to date.
> make[2]: `hyperslab' is up to date.
> make[2]: `istore' is up to date.
> make[2]: `bittests' is up to date.
> make[2]: `dt_arith' is up to date.
> make[2]: `dtypes' is up to date.
> make[2]: `dsets' is up to date.
> make[2]: `cmpd_dset' is up to date.
> make[2]: `extend' is up to date.
> make[2]: `external' is up to date.
> make[2]: `objcopy' is up to date.
> make[2]: `links' is up to date.
> make[2]: `unlink' is up to date.
> make[2]: `big' is up to date.
> make[2]: `mtime' is up to date.
> make[2]: `fillval' is up to date.
> make[2]: `mount' is up to date.
> make[2]: `flush1' is up to date.
> make[2]: `flush2' is up to date.
> make[2]: `enum' is up to date.
> make[2]: `set_extent' is up to date.
> make[2]: `ttsafe' is up to date.
> make[2]: `stream_test' is up to date.
> make[2]: `getname' is up to date.
> make[2]: `vfd' is up to date.
> make[2]: `ntypes' is up to date.
> make[2]: `dangle' is up to date.
> make[2]: `dtransform' is up to date.
> make[2]: `reserved' is up to date.
> make[2]: `cross_read' is up to date.
> make[2]: `btree2' is up to date.
> make[2]: `fheap' is up to date.
> make[2]: `error_test' is up to date.
> make[2]: `err_compat' is up to date.
> make[2]: `testmeta' is up to date.
> make[2]: Nothing to be done for `../test/testerror.sh'.
> make[2]: Leaving directory `/data/zender/tmp/hdf5-1.8.0-beta1/test'
> make  check-TESTS
> make[2]: Entering directory `/data/zender/tmp/hdf5-1.8.0-beta1/test'
> make[3]: Entering directory `/data/zender/tmp/hdf5-1.8.0-beta1/test'
> ===Serial tests in test begin Sat May  5 19:27:30 PDT 2007===
> make[4]: Entering directory `/data/zender/tmp/hdf5-1.8.0-beta1/test'
> ============================
> Testing  testhdf5
> ============================
> testhdf5  Test Log
> ============================
> 
> For help use: /data/zender/tmp/hdf5-1.8.0-beta1/test/.libs/lt-testhdf5 -help
> Linked with hdf5 version 1.8 release 0
> Testing  -- Configure definitions (config)
> Testing  -- Encoding/decoding metadata (metadata)
> Testing  -- Checksum algorithm (checksum)
> Testing  -- Ternary Search Trees (tst)
> Testing  -- Memory Heaps (heap)
> Testing  -- Skip Lists (skiplist)
> Testing  -- Reference Counted Strings (refstr)
> Testing  -- Low-Level File I/O (file)
> Testing  -- Generic Object Functions (objects)
> Testing  -- Dataspaces (h5s)
> Command terminated by signal 11
> 0.04user 0.02system 0:00.19elapsed 34%CPU (0avgtext+0avgdata 0maxresident)k
> 0inputs+0outputs (0major+5114minor)pagefaults 0swaps
> make[4]: *** [testhdf5.chkexe_] Error 1
> make[4]: Leaving directory `/data/zender/tmp/hdf5-1.8.0-beta1/test'
> make[3]: *** [build-check-s] Error 2
> make[3]: Leaving directory `/data/zender/tmp/hdf5-1.8.0-beta1/test'
> make[2]: *** [test] Error 2
> make[2]: Leaving directory `/data/zender/tmp/hdf5-1.8.0-beta1/test'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory `/data/zender/tmp/hdf5-1.8.0-beta1/test'
> make: *** [check-recursive] Error 1
> zender@virga:/data/zender/tmp/hdf5-1.8.0-beta1$
> 
> I then run the recommended test to learn more:
> 
> zender@virga:/data/zender/tmp/hdf5-1.8.0-beta1$
> /data/zender/tmp/hdf5-1.8.0-beta1/test/.libs/lt-testhdf5
> 
> For help use: /data/zender/tmp/hdf5-1.8.0-beta1/test/.libs/lt-testhdf5 -help
> Linked with hdf5 version 1.8 release 0
> Testing  -- Configure definitions (config)
> Testing  -- Encoding/decoding metadata (metadata)
> Testing  -- Checksum algorithm (checksum)
> Testing  -- Ternary Search Trees (tst)
> Testing  -- Memory Heaps (heap)
> Testing  -- Skip Lists (skiplist)
> Testing  -- Reference Counted Strings (refstr)
> Testing  -- Low-Level File I/O (file)
> Testing  -- Generic Object Functions (objects)
> Testing  -- Dataspaces (h5s)
> *** UNEXPECTED RETURN from H5Fopen is -1 line  189 in th5s.c
> HDF5-DIAG: Error detected in HDF5 (1.8.0-beta1) thread 0:
> #000: H5F.c line 1539 in H5Fopen(): unable to open file
> major: File accessability
> minor: Unable to open file
> #001: H5F.c line 1197 in H5F_open(): unable to open file
> major: File accessability
> minor: Unable to open file
> #002: H5FD.c line 1042 in H5FD_open(): open failed
> major: Virtual File Layer
> minor: Unable to initialize object
> #003: H5FDsec2.c line 368 in H5FD_sec2_open(): unable to open file
> major: File accessability
> minor: Unable to open file
> #004: H5FDsec2.c line 368 in H5FD_sec2_open(): No such file or directory
> major: Internal error (too specific to document in detail)
> minor: System error message
> ***cannot open the pre-created H5S_MAX_RANK test file (th5s.h5)
> Segmentation fault (core dumped)
> zender@virga:/data/zender/tmp/hdf5-1.8.0-beta1$
> 
> Any help appreciated.
> 
> Thanks,
> Charlie
> --
> Charlie Zender, address@hidden, Department of Earth System Science
> 3228 Croul Hall, UC Irvine, Irvine CA 92697-3100. (949) 824-2987 :)
> 
> 


Ticket Details
===================
Ticket ID: YSY-473903
Department: Support netCDF
Priority: Normal
Status: Open