If a suitable way to lock files cannot be determined at configure time, a no-op function is substituted. This is currently the case on Windows. File locking is just advisory, so this isn't a big deal.
As for disabling file locking, we talked about this and will try to get a configure-time mechanism for disabling file locking implemented for HDF5 1.10.1. Dana Robinson Software Engineer The HDF Group -----Original Message----- From: Hdf-forum [mailto:[email protected]] On Behalf Of Elena Pourmal Sent: Sunday, May 15, 2016 9:01 PM To: HDF Users Discussion List <[email protected]> Subject: Re: [Hdf-forum] HDF5-1.10.0 and flock() Hi Tim, On May 13, 2016, at 10:55 AM, Timothy Brown <[email protected]> wrote: > Hi all, > > I was wondering if HDF5 was going to be keep the 1.8.x branch going? Or is it > recommend to move to the 1.10.x? Yes, we will keep 1.8 going until we are satisfied with the quality of 1.10.x. Transition from 1.8 to 1.10 should be seamless for our users :-) > > I'm asking as we all know for SWMR you need flock() and that you can not > disable SWMR at compile time (I don't need it in my day to day use). Hmm... HDF5 implements file locking in 1.10.x to prevent unauthorized access to an HDF5 file (for example, file is opened for writing (non-SWMR) and another process tries to write to it it). File locking is enabled if flock (or similar) is available on the system. Configure checks if file locking is available, but I think, we failed to check if it is disabled. We will take a look into this situation. Thank you for reporting! Elena > > On one of the clusters I run on we've got a Lustre file-system. However the > admin's have deemed that file locking is too expensive and have disabled it. > Here's the mount information: > > mds01ib@o2ib1:mds02ib@o2ib1:/scratch on /lustre/janus_scratch type > lustre (rw,noauto,_netdev) > > So when I run a very simple test to create a HDF5 with version 1.10.0 on this > file system it fails: > > janus-compile1 ~$ ./test /lustre/janus_scratch/tibr1099/foo.h5 > HDF5-DIAG: Error detected in HDF5 (1.10.0) 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 > Unable to open: /lustre/janus_scratch/tibr1099/foo.h5: -1 > 1 > > When I strace the program I see it's because flock() failed: > > open("/lustre/janus_scratch/tibr1099/foo.h5", O_RDWR) = 3 fstat(3, > {st_mode=S_IFREG|0644, st_size=0, ...}) = 0 > close(3) = 0 > open("/lustre/janus_scratch/tibr1099/foo.h5", O_RDWR|O_CREAT|O_TRUNC, > 0666) = 3 fstat(3, {st_mode=S_IFREG|0644, st_size=0, ...}) = 0 > flock(3, LOCK_EX|LOCK_NB) = -1 ENOSYS (Function not implemented) > close(3) = 0 > > Versus if I trace the program with version 1.8.15: > > open("/lustre/janus_scratch/tibr1099/foo.h5", O_RDWR) = 3 fstat(3, > {st_mode=S_IFREG|0644, st_size=0, ...}) = 0 > close(3) = 0 > open("/lustre/janus_scratch/tibr1099/foo.h5", O_RDWR|O_CREAT|O_TRUNC, > 0666) = 3 fstat(3, {st_mode=S_IFREG|0644, st_size=0, ...}) = 0 > brk(0x235a000) = 0x235a000 > mmap(NULL, 528384, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, > -1, 0) = 0x7f17252b8000 > > So my long winded example leads to three questions. > 1) Do other HPC sites enable flock() on lustre? If so is it only localflock > so as not to have the burden of a cluster wide flock? > 2) Is there a path forward for sites that don't enable flock? > 3) Is there the opposite of H5Fstart_swmr_write? > > Thanks! > Tim<test.f90>_______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.or > g > Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
