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Hi Mohammad,<br>
<br>
This is not an answer to your question but there is a usage caveat
w/ VTK XML files that I want to make sure you're aware of. When you
use that format make sure you set mode to "appended" and "encode"
off. This is the combination to produce binary files which are going
to be faster and very likely smaller too. You probably already know
that, but just in case ...<br>
<br>
now to get to your question:<br>
<blockquote type="cite">1) Go with a single parallel HDF5 file that
includes data for all time-steps. This makes it all nice and
portable except there are two issues. i) It looks like doing
MPI-IO might not be as efficient as separate POSIX IO, especially
on large number of processors. ii) ParaView does not seem to be
able to read HDF5 files in parallel</blockquote>
comment: If I were you I'd avoid putting all time steps in a single
file, or any solution where files get too big. Once files occupy
more than ~80% of a tape drive you'll have very hard time getting
them on and off archive systems. see this:
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<a
href="http://www.nersc.gov/users/data-and-file-systems/hpss/storing-and-retrieving-data/mistakes-to-avoid/">http://www.nersc.gov/users/data-and-file-systems/hpss/storing-and-retrieving-data/mistakes-to-avoid/</a>
My comment assumes that you actually use such systems. But you
probably will need to if you generate large datasets at common HPC
centers.<br>
<br>
I've seen some AMR codes get elaborate in their HDF5 formats and run
into serious performance issues as a result. So my comment here is
that if you go with HDF5, keep the format as simple as possible! and
of course file sizes small enough to be archived ;-)<br>
<br>
Burlen<br>
<br>
<br>
<div class="moz-cite-prefix">On 05/05/2014 10:48 AM, Mohammad
Mirzadeh wrote:<br>
</div>
<blockquote
cite="mid:CAKsPKwm6ZaZDfbKoVotD8H+DbNWhx8KhWUBMiRJWfC=wsBbHgg@mail.gmail.com"
type="cite">
<div dir="ltr">They are represented as unstructured grid. As a
sample run, a 100M grid point on 256 proc produces almost 8.5G
file. We intent to push the limits close to 1B at most at this
time with # processors up to a few thousands. However, it would
be good to have something that could scale to larger problems as
well</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Sat, May 3, 2014 at 1:28 AM, Stephen
Wornom <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:stephen.wornom@inria.fr" target="_blank">stephen.wornom@inria.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Mohammad
Mirzadeh wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div class="h5">
Hi I am at a critical point in deciding I/O format for
my application. So far my conclusion is to use
parallel HDF5 for restart files as they are quite
flexible and portable across systems.<br>
<br>
When it comes to visualization, however, i'm not quite
sure. Up until now I've been using pvtu along with vtu
files and although they generally work fine, one
easily gets in trouble when running big simulations on
large number of processors as the number of files can
easily get out of control and even simplest utility
commands (e.g. ls) takes minutes to finish!<br>
<br>
After many thinking I've come to a point to decide
between two strategies:<br>
<br>
1) Go with a single parallel HDF5 file that includes
data for all time-steps. This makes it all nice and
portable except there are two issues. i) It looks like
doing MPI-IO might not be as efficient as separate
POSIX IO, especially on large number of processors.
ii) ParaView does not seem to be able to read HDF5
files in parallel<br>
<br>
2) Go with the same pvtu+vtu strategy except take
precautions to avoid file explosions. I can think of
two strategies here: i) use nested folders to separate
vtu files from pvtu and also each time step ii) create
an IO group communicator with much less processors
that do the actual IO.<br>
<br>
My questions are 1) Is the second approach necessarily
more efficient than MPI-IO used in HDF5? and 2) Is
there any plan to support parallel IO for HDF5 files
in paraview?<br>
<br>
<br>
</div>
</div>
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Are your meshes structured or unstructured? How many
vertices in your meshes?<span class="HOEnZb"><font
color="#888888"><br>
<br>
Stephen<br>
<br>
-- <br>
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href="mailto:stephen.wornom@inria.fr" target="_blank">stephen.wornom@inria.fr</a><br>
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Fax: 04 97 15 53 51<br>
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