fritzo
commented
9 years ago I suspect HDF5 has a bug whereby empty datasets cannot be written. This bug was encountered when infering NCLOSED in SK, which has no proven NCLOSED elements, and thus must save an empty dataset.
$ make test ... ------------------------------------------------------------------------------ Testing sk cd /home/fritz/fritzo/pomagma/data/test/debug/atlas/sk POMAGMA_SIZE=1023 \ POMAGMA_LOG_FILE=/home/fritz/fritzo/pomagma/data/test/debug/atlas/sk/test.log \ POMAGMA_LOG_LEVEL=2 \ /home/fritz/fritzo/pomagma/build/debug/src/surveyor/sk.init \ /home/fritz/fritzo/pomagma/data/test/debug/atlas/sk/0.h5 \ /home/fritz/fritzo/pomagma/pomagma/theory/sk.compiled \ /home/fritz/fritzo/pomagma/pomagma/language/sk.language \ 8 # took 21.5 sec ==== LOG FILE ==== 29803 21.1967 INFO sampler.m_arity_sample_count.load() = 1153 29803 21.1967 INFO sampler.m_compound_arity_sample_count.load() = 766 29803 21.1967 INFO Dumping structure to file /home/fritz/fritzo/pomagma/data/test/debug/atlas/sk/0.h5 29803 21.1981 ERROR HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 47574156267328: #000: ../../../src/H5Dio.c line 234 in H5Dwrite(): can't prepare for writing data major: Dataset minor: Write failed #001: ../../../src/H5Dio.c line 355 in H5D__pre_write(): no output buffer major: Invalid arguments to routine minor: Bad value /home/fritz/fritzo/pomagma/include/pomagma/platform/hdf5.hpp : 516 void pomagma::hdf5::Dataset::write_all(const std::vector<_RealType>&) [with T = short unsigned int] 56 ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory. warning: File "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.20-gdb.py" auto-loading has been declined by your `auto-load safe-path' set to "$debugdir:$datadir/auto-load". ==== STACK TRACE ==== [New LWP 29803] [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". Core was generated by `/home/fritz/fritzo/pomagma/build/debug/src/surveyor/sk.init /home/fritz/fritzo/'. Program terminated with signal SIGABRT, Aborted. #0 0x00002b44ba8c2cc9 in __GI_raise (sig=sig@entry=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:56 To enable execution of this file add add-auto-load-safe-path /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.20-gdb.py line to your configuration file "/home/fritz/.gdbinit". To completely disable this security protection add set auto-load safe-path / line to your configuration file "/home/fritz/.gdbinit". For more information about this security protection see the "Auto-loading safe path" section in the GDB manual. E.g., run from the shell: info "(gdb)Auto-loading safe path" Thread 1 (Thread 0x2b44b8af4f40 (LWP 29803)): #0 0x00002b44ba8c2cc9 in __GI_raise (sig=sig@entry=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:56 #1 0x00002b44ba8c60d8 in __GI_abort () at abort.c:89 #2 0x00002b44b8f67579 in pomagma::hdf5::Dataset::write_all (this=this@entry=0x7fff01cd1970, source=...) at /home/fritz/fritzo/pomagma/include/pomagma/platform/hdf5.hpp:510
#3 0x00002b44b8f749a5 in pomagma::detail::dump (carrier=..., rel=..., file=..., name=...) at /home/fritz/fritzo/pomagma/include/pomagma/platform/structure.hpp:339
#4 0x00002b44b8f75f13 in pomagma::detail::dump (signature=..., file=...) at /home/fritz/fritzo/pomagma/include/pomagma/platform/structure.hpp:505
#5 0x00002b44b8f763d9 in pomagma::dump (signature=..., filename=...) at /home/fritz/fritzo/pomagma/include/pomagma/platform/structure.hpp:538
#6 0x00002b44b8f63989 in pomagma::Structure::dump (this=this@entry=0x2b44b8f05640 , filename=...) at /home/fritz/fritzo/pomagma/src/microstructure/structure.cpp:36
#7 0x00002b44b8ce003f in pomagma::dump_structure (filename=...) at /home/fritz/fritzo/pomagma/src/surveyor/theory.hpp:24
#8 0x0000000000401f0c in main (argc=, argv=) at /home/fritz/fritzo/pomagma/src/surveyor/init_main.cpp:66
cd /home/fritz/fritzo/pomagma
make[1]: *** [batch-test] Error 250
make[1]: Leaving directory `/home/fritz/fritzo/pomagma'
make: *** [test] Error 2