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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