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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