yayahjb
commented
4 years ago Dear John, The hdf5 library is, unfortunately, fragile. Some combinations work on some systems and not on others. Things got worse with hdf5-1.10.1 through hdf5-1.10.4, then a little better with hdf5-1.10.5 and still better with hdf5-1.10.6. Now hdf5-1.12 is out, so I'll be investigating that next. Other destabilizing issues are use or no use of dlfnc, gcc and gfortran versions or use of intel compilers. Yes there is a deep problem here. Got a student who likes a challenge? Regards, Herbert
On Wed, Apr 29, 2020 at 6:29 PM John Bollinger notifications@github.com wrote:
I am building and CBFLib 0.9.6 from the distribution package available at SourceForge, on CentOS Linux 8 (x86_64), using the distribution's GCC toochain version 8.3.1. The library, wrappers, and example programs all built successfully, but when I ran the tests, nexus2cbf crashed:
LD_LIBRARY_PATH=/home/jbolling/tmp/cbflib-CBFlib-0.9.6/solib:$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; cd /home/jbolling/tmp/cbflib-CBFlib-0.9.6/minicbf_test; time /home/jbolling/tmp/cbflib-CBFlib-0.9.6/bin/nexus2cbf \ -o i19-1.cbf i19-1.h5 HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 0:
000: H5D.c line 342 in H5Dopen2(): no name
major: Invalid arguments to routine minor: Bad valueHDF5-DIAG: Error detected in HDF5 (1.8.18) thread 0:
000: H5L.c line 1183 in H5Literate(): link iteration failed
major: Symbol table minor: Iteration failed001: H5Gint.c line 844 in H5G_iterate(): error iterating over links
major: Symbol table minor: Iteration failed002: H5Gobj.c line 708 in H5G__obj_iterate(): can't iterate over symbol table
major: Symbol table minor: Iteration failed003: H5Gstab.c line 566 in H5G__stab_iterate(): iteration operator failed
major: Symbol table minor: Can't move to next iterator location004: H5B.c line 1221 in H5B_iterate(): B-tree iteration failed
major: B-Tree node minor: Iteration failed005: H5B.c line 1177 in H5B_iterate_helper(): B-tree iteration failed
major: B-Tree node minor: Iteration failed006: H5Gnode.c line 1039 in H5G__node_iterate(): iteration operator failed
major: Symbol table minor: Can't move to next iterator locationHDF5-DIAG: Error detected in HDF5 (1.8.18) thread 0:
000: H5L.c line 1183 in H5Literate(): link iteration failed
major: Symbol table minor: Iteration failed001: H5Gint.c line 844 in H5G_iterate(): error iterating over links
major: Symbol table minor: Iteration failed002: H5Gobj.c line 708 in H5G__obj_iterate(): can't iterate over symbol table
major: Symbol table minor: Iteration failed003: H5Gstab.c line 566 in H5G__stab_iterate(): iteration operator failed
major: Symbol table minor: Can't move to next iterator location004: H5B.c line 1221 in H5B_iterate(): B-tree iteration failed
major: B-Tree node minor: Iteration failed005: H5B.c line 1177 in H5B_iterate_helper(): B-tree iteration failed
major: B-Tree node minor: Iteration failed006: H5Gnode.c line 1039 in H5G__node_iterate(): iteration operator failed
major: Symbol table minor: Can't move to next iterator locationHDF5-DIAG: Error detected in HDF5 (1.8.18) thread 0:
000: H5L.c line 1183 in H5Literate(): link iteration failed
major: Symbol table minor: Iteration failed001: H5Gint.c line 844 in H5G_iterate(): error iterating over links
major: Symbol table minor: Iteration failed002: H5Gobj.c line 708 in H5G__obj_iterate(): can't iterate over symbol table
major: Symbol table minor: Iteration failed003: H5Gstab.c line 566 in H5G__stab_iterate(): iteration operator failed
major: Symbol table minor: Can't move to next iterator location004: H5B.c line 1221 in H5B_iterate(): B-tree iteration failed
major: B-Tree node minor: Iteration failed005: H5B.c line 1177 in H5B_iterate_helper(): B-tree iteration failed
major: B-Tree node minor: Iteration failed006: H5Gnode.c line 1039 in H5G__node_iterate(): iteration operator failed
major: Symbol table minor: Can't move to next iterator locationAn error occured, will not try to write the file 'i19-1.cbf' Time to convert 'i19-1.cbf': 0.006s
real 0m0.008s user 0m0.006s sys 0m0.002s make: *** [Makefile_LINUX_64:2230: extra] Error 1
I found, however, that if I used the default Makefile instead of Makefile_LINUX_64, then the same test ran successfully. Ultimately, I traced the issue to optimization level. nexus2cbf works if everything is built with optimization -O3 (default Makefile), but not if everything is built with optimization -O2 (Makefile_LINUX_64 and Makefile_LINUX).
There is a clear workaround here, of course, but optimization-dependent misbehavior is usually a sign of a deeper problem, especially when it is the more aggressive optimization level that is required for (apparently) correct behavior.
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jcbollinger
I am building and CBFLib 0.9.6 from the distribution package available at SourceForge, on CentOS Linux 8 (x86_64), using the distribution's GCC toochain version 8.3.1. The library, wrappers, and example programs all built successfully, but when I ran the tests, nexus2cbf crashed:
I found, however, that if I used the default Makefile instead of Makefile_LINUX_64, then the same test ran successfully. Ultimately, I traced the issue to optimization level. nexus2cbf works if everything is built with optimization
-O3(default Makefile), but not if everything is built with optimization-O2(Makefile_LINUX_64 and Makefile_LINUX).There is a clear workaround here, of course, but optimization-dependent misbehavior is usually a sign of a deeper problem, especially when it is the more aggressive optimization level that is required for (apparently) correct behavior.