I am getting confusing results with the file-locking patch. The parallel tests
(check-p) seem to run correctly, but the serial tests fail on the low level
file i/o tests (file) with an error that looks related to the file locking. I
have verified that the patch applied correctly. Here is the results of the
test output:
For help use:
/usr/workspace/wsrzc/gdsjaar/seacas/TPL/hdf5/hdf5-1.10.0-patch1/test/./testhdf5
-help
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 3158 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
*** UNEXPECTED RETURN from H5Dcreate2 is -1 at line 3180 in tfile.c
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
#000: H5D.c line 121 in H5Dcreate2(): not a location ID
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
*** UNEXPECTED RETURN from H5Dclose is -1 at line 3183 in tfile.c
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
#000: H5D.c line 334 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
*** UNEXPECTED RETURN from H5Dcreate2 is -1 at line 3180 in tfile.c
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
#000: H5D.c line 121 in H5Dcreate2(): not a location ID
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
*** UNEXPECTED RETURN from H5Dclose is -1 at line 3183 in tfile.c
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
#000: H5D.c line 334 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
*** UNEXPECTED RETURN from H5Dcreate2 is -1 at line 3180 in tfile.c
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
#000: H5D.c line 121 in H5Dcreate2(): not a location ID
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
*** UNEXPECTED RETURN from H5Dclose is -1 at line 3183 in tfile.c
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
#000: H5D.c line 334 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
*** UNEXPECTED RETURN from H5Dcreate2 is -1 at line 3180 in tfile.c
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
#000: H5D.c line 121 in H5Dcreate2(): not a location ID
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
*** UNEXPECTED RETURN from H5Dclose is -1 at line 3183 in tfile.c
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
#000: H5D.c line 334 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
*** UNEXPECTED RETURN from H5Dcreate2 is -1 at line 3180 in tfile.c
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
#000: H5D.c line 121 in H5Dcreate2(): not a location ID
/
--
"A supercomputer is a device for turning compute-bound problems into I/O-bound
problems”
From: Hdf-forum <[email protected]> on behalf of Dana
Robinson <[email protected]>
Reply-To: HDF Users Discussion List <[email protected]>
Date: Thursday, December 8, 2016 at 1:46 PM
To: HDF Users Discussion List <[email protected]>
Subject: [EXTERNAL] Re: [Hdf-forum] Building hdf5-1.10.0-patch 1 on Blue Gene Q
Hi Greg,
It looks like you are bumping into the "file locking not implemented" issue.
There is a small source patch here that disables file locking:
https://support.hdfgroup.org/HDF5/release/obtainsrc5110.html
Note that file locking was implemented solely to help users get concurrent file
opening semantics right. There's no actual loss of HDF5 or SWMR functionality.
In the upcoming HDF5 1.10.1, file locking can be disabled via an environment
variable and we have a more informative error message when we detect that file
locking is not implemented on a file system.
Let me know if that doesn't work for you and we can diagnose further.
Cheers,
Dana Robinson
Software Engineer
The HDF Group
From: Hdf-forum [mailto:[email protected]] On Behalf Of
Sjaardema, Gregory D
Sent: Thursday, December 8, 2016 3:23 PM
To: HDF Users Discussion List <[email protected]>
Subject: [Hdf-forum] Building hdf5-1.10.0-patch 1 on Blue Gene Q
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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