[yt-users] yt-users Digest, Vol 117, Issue 31
Kacper Kowalik
xarthisius.kk at gmail.com
Tue Nov 28 09:25:59 PST 2017
Hi Tomer,
unfortunately we don't have any means of fine tuning yt's i/o on a low
level. Short of profiling ART frontend and trying to decrease the number
of iops, I'm afraid there's not much to be done.
Having said that, I'd try to debug your GPFS too with something
different than yt and simpler. Maybe a single hdf5 file with a large
array and simultaneous access to a random row/column with each process?
20 concurrent reads sounds like something that GPFS should handle
without degradation of performance from 10s to hours.
Cheers,
Kacper
On 11/28/2017 11:01 AM, Tomer Nussbaum wrote:
> Hi Nathan,
>
> Thank you for answering,
>
> 1. Does it take hours to load these files on a laptop?
> # Ans: Nope, It take 10 sec.
> # It takes us lots of time on the cluster when we parallel the jobs,
> above 20 yt.load calls toghter.
> # We toke a look at our GPFS, it looks like there are many IOP that
> flood the GPFS, (it is currently a serial reading at our GPFS)
>
> 2. What sort of data are you working with? How big are the data files?
> # Ans: We are working on Vela sims, it's ART simulations, 5GB per
> snapshot ruffly.
>
> 3. When you say ?load? the data, is that just doing yt.load or are you
> doing any I/O?
> # Ans: load=yt.load and then creating a sphere obj and reading gas
> particles from it.
>
> Thank,
> Tomer
> On Tue, Nov 28, 2017 at 6:31 PM, <yt-users-request at lists.spacepope.org
> <mailto:yt-users-request at lists.spacepope.org>> wrote:
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> Today's Topics:
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> 1. Fwd: Cluster best configurations for YT (Tomer Nussbaum)
> 2. Re: Fwd: Cluster best configurations for YT (Nathan Goldbaum)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 28 Nov 2017 11:55:56 +0200
> From: Tomer Nussbaum <tomer.nussbaum at mail.huji.ac.il
> <mailto:tomer.nussbaum at mail.huji.ac.il>>
> To: yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
> Subject: [yt-users] Fwd: Cluster best configurations for YT
> Message-ID:
>
> <CAOGC2jACH1Q4QLfFNi8h7p=XhqEFvnp-6g17FUv6aDN2vSvqWg at mail.gmail.com
> <mailto:XhqEFvnp-6g17FUv6aDN2vSvqWg at mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
>
> ---------- Forwarded message ----------
> From: Tomer Nussbaum <tomer.nussbaum at mail.huji.ac.il
> <mailto:tomer.nussbaum at mail.huji.ac.il>>
> Date: Thu, Nov 23, 2017 at 6:08 PM
> Subject: Cluster best configurations for YT
> To: yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
>
>
>
> Hi,
>
> We have updated our cluster lately, but our YT platform works very slow
> (loads one snapshot an hour, when couple of people run together...).
> I wanted to ask you if you can help solving this issue from your
> experience.
>
> We use infiniband, and we see that the main problem is lots of
> request in
> random access to our hard drives,
> so the problem can be in fine tuning YT on the Nodes, or fine tuning the
> file system
>
> This brings up this couple of issues (maybe more, if you have
> another idea,
> I would be thankful to know):
>
> 1. *IO readings - *Is there a way to optimize the io readings
> requests
> to the file server?
> 2. *YT configurations -* Are there specific parameters in the YT
> configuration for this status?
> 3. *File server behavior -* Can we set reading server functions
> (we use
> hard drives, serial reading status)?
> 4. *Metadata cache -* Does using metadata cache will solve the issue?
> 5. *zlib usage - *How can I check if this feature is activated,
> how much
> is it important in the YT platform?
>
>
> I will really appreciate any help with it,
> Thanx,
> Tomer
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> ------------------------------
>
> Message: 2
> Date: Tue, 28 Nov 2017 12:42:40 +0000
> From: Nathan Goldbaum <nathan12343 at gmail.com
> <mailto:nathan12343 at gmail.com>>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org
> <mailto:yt-users at lists.spacepope.org>>
> Subject: Re: [yt-users] Fwd: Cluster best configurations for YT
> Message-ID:
>
> <CAJXewOk9tCL-TCTQef9Up-mTj-qgVFJp6yHZXmwQ8SReoV4h8A at mail.gmail.com
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> Content-Type: text/plain; charset="utf-8"
>
> Hi Tomer,
>
> A couple questions:
>
> 1. Does it take hours to load these files on a laptop?
>
> 2. What sort of data are you working with? How big are the data files?
>
> 3. When you say ?load? the data, is that just doing yt.load or are you
> doing any I/O?
>
> Nathan
>
> On Tue, Nov 28, 2017 at 4:56 AM Tomer Nussbaum <
> tomer.nussbaum at mail.huji.ac.il
> <mailto:tomer.nussbaum at mail.huji.ac.il>> wrote:
>
> >
> > ---------- Forwarded message ----------
> > From: Tomer Nussbaum <tomer.nussbaum at mail.huji.ac.il
> <mailto:tomer.nussbaum at mail.huji.ac.il>>
> > Date: Thu, Nov 23, 2017 at 6:08 PM
> > Subject: Cluster best configurations for YT
> > To: yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
> >
> >
> >
> > Hi,
> >
> > We have updated our cluster lately, but our YT platform works very
> slow
> > (loads one snapshot an hour, when couple of people run together...).
> > I wanted to ask you if you can help solving this issue from your
> > experience.
> >
> > We use infiniband, and we see that the main problem is lots of
> request in
> > random access to our hard drives,
> > so the problem can be in fine tuning YT on the Nodes, or fine
> tuning the
> > file system
> >
> > This brings up this couple of issues (maybe more, if you have another
> > idea, I would be thankful to know):
> >
> > 1. *IO readings - *Is there a way to optimize the io readings
> requests
> > to the file server?
> > 2. *YT configurations -* Are there specific parameters in the YT
> > configuration for this status?
> > 3. *File server behavior -* Can we set reading server functions (we
> > use hard drives, serial reading status)?
> > 4. *Metadata cache -* Does using metadata cache will solve the
> issue?
> > 5. *zlib usage - *How can I check if this feature is activated, how
> > much is it important in the YT platform?
> >
> >
> > I will really appreciate any help with it,
> > Thanx,
> > Tomer
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> >
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