Even if you are using independent datasets or groups from each process, the file metadata will need to be updated collectively for the HDF5 library to work correctly. Dataset identifiers, chunk locations, group information, attributes, etc. all need to be coordinated among all processes writing to the file for the file to have the correct data.
This page has a list of all the calls that need to be used collectively for the file to be written correctly.
https://www.hdfgroup.org/HDF5/doc/RM/CollectiveCalls.html
Jarom
*From:*Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] *On Behalf Of *Chris Green
*Sent:* Tuesday, July 26, 2016 8:33 AM
*To:* HDF Users Discussion List
*Subject:* Re: [Hdf-forum] Parallel dataset resizing strategies
Hi,
Thanks for continuing the conversation. I believe files will be *either* read from, *or* written to, but not both simultaneously, at least in the scenario I'm working on right now. I'd like to be able to write to the same file from different ranks simultaneously, but only to different datasets. If that's not possible without propagating dataset extension operations collectively to ranks not writing to that dataset, then I will start looking at the virtual dataset solution you suggested in your first reply.
Thanks again,
Chris.
On 7/25/16 7:41 PM, Nelson, Jarom wrote:
If you want to have multiple ranks write to the same file, you’ll
need to open the file in read-write and use parallel HDF5 with the
associated overhead and complexity of the collective calls. I
think the only way to avoid the overhead of the collective calls
is to open separate files for each rank.
If you are going to have a multi-file approach, and read from
files which are open in write mode by another process, you’ll need
to have some way to get the metadata updated in the reading
processes. It sounds like you might try another 1.10.x addition,
the single-writer multiple-reader. If each rank can open its own
output file in read-write, and all the other ranks’ files in
read-only, you can avoid the parallel overhead. I haven’t tried
this approach, and you’ll have to be careful of race conditions
and keep the file metadata correct in all the ranks, but it sounds
like it might fit your parallel I/O model.
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html
Jarom
*From:*Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] *On
Behalf Of *Chris Green
*Sent:* Monday, July 25, 2016 3:41 PM
*To:* HDF Users Discussion List
*Subject:* Re: [Hdf-forum] Parallel dataset resizing strategies
Hi,
Thanks for this. Comments inline.
On 7/22/16 12:13 PM, Nelson, Jarom wrote:
If you can move to HDF5 1.10, I would recommend independent files
for each MPI rank, and then create a master file (created
independently perhaps by rank 0) with Virtual Datasets linking in
the data from each rank in the format you need. Virtual Datasets
can be created with file matching patterns for dynamically
increasing datasets, so you might look into using that feature.
We don't have existing tools relying on a particular version, so
we are nominally free to move to HDF5 1.10.x. However, it won't be
completely straightforward because I have been relying for now on
using the homebrew version, which is currently 1.18.16. I'd have
to dink the recipe to use 1.10.x, which is not a showstopper.
I found this approach much faster than creating a collective
file (~5-10x speedup on a Lustre filesystem). You don’t need
to do any collective reads or writes, and I think we could
even bypass using parallel HDF5 altogether. Note, this will
only work if you only ever need to open the Virtual Dataset in
parallel (i.e. by more than one process) as non-collective
read-only. If you need to have read-write access to the master
file, you can’t access a Virtual Dataset using collective
operations. You can, however, have as many processes as you
like read from a virtual dataset from a file opened as read-only.
If you have other tools that use your data but can’t move to
HDF5 1.10, you can h5repack a file with Virtual Datasets to
remove the Virtual Datasets, and it should be compatible with
HDF5 1.8 (use h5repack from HDF5 1.10 patch 1 or later). This
also worked well for us and I was able to load a repacked file
in IDL under a 1.8 HDF5 library. However h5repack is not a
parallel application, so it can be slow to repack a very large
file, on the order minutes per GB.
After having thought a little more about likely parallel models, I
think now we can arrange that:
·Only one rank will write to a particular dataset.
·A dataset will not be read from in the same job in which it was
written.
·A dataset may be read by one or more ranks.
I *think* if that's the case, we could use a hierarchical
multi-file format without resorting to virtual datasets, no? I
still have some reading and experimenting to do, but if you have
particular information that would speak to the likely success of
this approach, I'd be happy to hear it.
Thanks,
Chris.
Jarom
*From:*Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org]
*On Behalf Of *Chris Green
*Sent:* Friday, July 22, 2016 9:32 AM
*To:* hdf-forum@lists.hdfgroup.org
<mailto:hdf-forum@lists.hdfgroup.org>
*Subject:* [Hdf-forum] Parallel dataset resizing strategies
Hi,
I am relatively new to HDF5 and HDF5/parallel, and although I
have experience with MPI it is not extensive. We are exploring
ways of saving data in parallel using HDF5 in a field in which
it is practically unknown up to now.
Our paradigm is "parallel modular event processing:"
* A typical job processes many "events."
* An event contains all of the interesting data (raw and
processed) associated with some time interval.
* Each event can be processed independently of all other events.
* Each event's data can be subdivided into internal
components, "data products."
* "Modules" are processing subunits which read or generate
one or more data products for each event.
* One can calculate a data dependency graph specifying the
allowed ordering and/or parallelism of modules processing
one or more events simultaneously for a given job
configuration and event structure.
We have been using h5py with HDF5 and OpenMPI to explore
different strategies for parallel I/O in a future parallel
event-processing framework. One of the approaches we have come
up with so far is to have one HDF5 dataset per unique data
product / writer module combination, keeping track of the
different relevant sections of each dataset via (for now) an
external database. This works well in serial tests, but in
parallel tests we are running up against the constraint that
dataset resizing is a collective operation, meaning that all
ranks including non-writers will have to become aware of and
duplicate dataset resizing operations required by other
writers. The problem seems to get even worse if there's a
possibility that two or more instances of a module would need
to extend and write to the same dataset at the same time
(while processing different events, say), since they will have
to coordinate and agree on the new size of the dataset and
their respective sections thereof.
Are we misunderstanding the problem, or is it really this
hard? Has anyone else hit upon a reasonable strategy for
handling this or something like it?
Any pointers appreciated.
Thanks,
Chris Green.
--
Chris Green<greenc@fnal.gov> <mailto:greenc@fnal.gov>, FNAL CS/SCD/ADSS/SSI/TAC;
'phone (630) 840-2167; Skype: chris.h.green;
IM:greenc@jabber.fnal.gov <mailto:greenc@jabber.fnal.gov>, chissgreen (AIM),
chris.h.green (Google Talk).
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Twitter:https://twitter.com/hdf5
--
Chris Green<greenc@fnal.gov> <mailto:greenc@fnal.gov>, FNAL CS/SCD/ADSS/SSI/TAC;
'phone (630) 840-2167; Skype: chris.h.green;
IM:greenc@jabber.fnal.gov <mailto:greenc@jabber.fnal.gov>, chissgreen (AIM),
chris.h.green (Google Talk).
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org <mailto:Hdf-forum@lists.hdfgroup.org>
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter:https://twitter.com/hdf5
--
Chris Green<greenc@fnal.gov> <mailto:greenc@fnal.gov>, FNAL CS/SCD/ADSS/SSI/TAC;
'phone (630) 840-2167; Skype: chris.h.green;
IM:greenc@jabber.fnal.gov <mailto:greenc@jabber.fnal.gov>, chissgreen (AIM),
chris.h.green (Google Talk).
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
