Yeah. I've thought about this and I probably should create an API call. I was just hoping to avoid that.
Dana -----Original Message----- From: Hdf-forum [mailto:[email protected]] On Behalf Of Werner Benger Sent: Tuesday, May 17, 2016 5:30 AM To: [email protected] Subject: Re: [Hdf-forum] HDF5-1.10.0 and flock() Hi Elena & Dana, shouldn't disabling file locking rather be a runtime mechanism? What if you want to use the same binary on the same hardware with different file system configurations, or one the same hardware writing to different file systems, or if the sysadmin changes their mind on a daily basis to enable or disable file locking? Werner On 16.05.2016 18:03, Dana Robinson wrote: > 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.o >> r >> 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.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.or > g > Twitter: https://twitter.com/hdf5 -- ___________________________________________________________________________ Dr. Werner Benger Visualization Research Center for Computation & Technology at Louisiana State University (CCT/LSU) 2019 Digital Media Center, Baton Rouge, Louisiana 70803 Tel.: +1 225 578 4809 Fax.: +1 225 578-5362 _______________________________________________ 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
