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:hdf-forum-boun...@lists.hdfgroup.org] On Behalf Of 
Sjaardema, Gregory D
Sent: Thursday, December 8, 2016 3:23 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
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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