I have been unsuccessful in building a parallel version of hdf5-1.10.0-patch1
on a blue gene q system (rzuseq). I have used both the yod-configure approach
and manually changing all ./conftest to srun –n1 ./conftest and although both
approaches configure and build correctly, I am unable to run the testhdf5 or
testphdf5. The testhdf5 gives errors of the sort:
Linked with hdf5 version 1.10 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)
*** UNEXPECTED RETURN from H5Fcreate is -1 at line 187 in tfile.c
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
#000: H5F.c line 491 in H5Fcreate(): unable to create file
major: File accessibilty
minor: Unable to open file
#001: H5Fint.c line 1168 in H5F_open(): unable to lock the file or initialize
file structure
major: File accessibilty
minor: Unable to open file
#002: H5FD.c line 1821 in H5FD_lock(): driver lock request failed
major: Virtual File Layer
minor: Can't update object
#003: H5FDsec2.c line 939 in H5FD_sec2_lock(): unable to flock file, errno =
38, error message = 'Function not implemented'
major: File accessibilty
minor: Bad file ID accessed
*** UNEXPECTED RETURN from H5Fclose is -1 at line 198 in tfile.c
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
#000: H5F.c line 749 in H5Fclose(): not a file ID
major: Invalid arguments to routine
minor: Inappropriate type
This happens on both a lustre and nfs filesystem. When I build hdf5-1.8.16
using same procedure; everything works correctly. I have also used the
bulid_hdf5 in the CGNS distribution with no change in behavior.
I need hdf5-1.10.0-patch1 or later to investigate the collective metadata
changes.
If anyone on the list or any of the hdf5 developers or support people have
successfully bult on a blue gene q system, your help would be very much
appreciated.
..Greg
--
"A supercomputer is a device for turning compute-bound problems into I/O-bound
problems”
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