Re: [yt-users] yt-users Digest, Vol 117, Issue 33

29 Nov 2017

      On 11/29/2017 05:19 AM, Tomer Nussbaum wrote:
...
Hi,
Hi again,
...
Thank for answering,
My question is what are you doing now in order to have fast
computations, without changing any YT code.
Is there something That can be solved by change in the YT
configurations? (Do I understand from your answer that no?)
No, there is not.
...
How are you handling many group members using the same files together?
I don't think that's a typical use case scenario. Apart from occasions
such as workshops/schools, it's usually a single person (or a few at
most) doing the analysis. However, I'm pretty sure that even a single
person can cause similar i/o load by using yt in parallel. I'm not aware
of any previous reports of such a significant performance degradation
though.
...
Do you use SSD drives?
Possibly, I don't know. It's always whatever cluster provides.
...
Do you copy each snapshot to the node and then
compute?
I've personally never done that. I've always used parallel networking
filesystem that was available.
...
Do you do some of what I asked about? Do you have any other special tricks?
I'm afraid there are no special "tricks", we can only understand what's
going on and try to fix it.

If you're willing to share the data and the script you're using to
measure the performance, I can run some tests. We have 2 clusters that
are using GPFS here.

Cheers,
Kacper
...
Thank,
Tomer
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Today's Topics:
1. Re: yt-users Digest, Vol 117, Issue 31 (Matthew Turk)
----------------------------------------------------------------------
Message: 1
    Date: Tue, 28 Nov 2017 11:52:57 -0600
    From: Matthew Turk <matthewturk@gmail.com
    <mailto:matthewturk@gmail.com>>
    To: Discussion of the yt analysis package
            <yt-users@lists.spacepope.org
    <mailto:yt-users@lists.spacepope.org>>
    Subject: Re: [yt-users] yt-users Digest, Vol 117, Issue 31
    Message-ID:
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Hi Tomer,
Both the ARTIO frontend and the NMSU-ART frontends could definitely be
    improved in their number of disk accesses, but like Kacper said,
    getting a
    handle on where they are occurring would be the best first step, I
    think.
    Then we can take it from there.
On Tue, Nov 28, 2017 at 11:25 AM, Kacper Kowalik
    <xarthisius.kk@gmail.com <mailto:xarthisius.kk@gmail.com>>
    wrote:
> 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,
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    > >     Today's Topics:
    > >
    > >        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@mail.huji.ac.il
    <mailto:tomer.nussbaum@mail.huji.ac.il>
    > >     <mailto:tomer.nussbaum@mail.huji.ac.il
    <mailto:tomer.nussbaum@mail.huji.ac.il>>>
    > >     To: yt-users@lists.spacepope.org
    <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists
    <mailto:yt-users@lists>.
    > spacepope.org <http://spacepope.org>>
    > >     Subject: [yt-users] Fwd: Cluster best configurations for YT
    > >     Message-ID:
    > >
    > >   
     <CAOGC2jACH1Q4QLfFNi8h7p=XhqEFvnp-6g17FUv6aDN2vSvqWg@mail.gmail.com
    <mailto:XhqEFvnp-6g17FUv6aDN2vSvqWg@mail.gmail.com>
    > >     <mailto:XhqEFvnp-6g17FUv6aDN2vSvqWg@mail.gmail.com
    <mailto:XhqEFvnp-6g17FUv6aDN2vSvqWg@mail.gmail.com>>>
    > >     Content-Type: text/plain; charset="utf-8"
    > >
    > >     ---------- Forwarded message ----------
    > >     From: Tomer Nussbaum <tomer.nussbaum@mail.huji.ac.il
    <mailto:tomer.nussbaum@mail.huji.ac.il>
    > >     <mailto:tomer.nussbaum@mail.huji.ac.il
    <mailto:tomer.nussbaum@mail.huji.ac.il>>>
    > >     Date: Thu, Nov 23, 2017 at 6:08 PM
    > >     Subject: Cluster best configurations for YT
    > >     To: yt-users@lists.spacepope.org
    <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists
    <mailto:yt-users@lists>.
    > spacepope.org <http://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@gmail.com
    <mailto:nathan12343@gmail.com>
    > >     <mailto:nathan12343@gmail.com <mailto:nathan12343@gmail.com>>>
    > >     To: Discussion of the yt analysis package
    > >             <yt-users@lists.spacepope.org
    <mailto:yt-users@lists.spacepope.org>
    > >     <mailto:yt-users@lists.spacepope.org
    <mailto:yt-users@lists.spacepope.org>>>
    > >     Subject: Re: [yt-users] Fwd: Cluster best configurations for YT
    > >     Message-ID:
    > >
    > >   
     <CAJXewOk9tCL-TCTQef9Up-mTj-qgVFJp6yHZXmwQ8SReoV4h8A@mail.gmail.com
    <mailto:CAJXewOk9tCL-TCTQef9Up-mTj-qgVFJp6yHZXmwQ8SReoV4h8A@mail.gmail.com>
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    <mailto:CAJXewOk9tCL-TCTQef9Up-mTj-qgVFJp6yHZXmwQ8SReoV4h8A@mail>.
    > gmail.com <http://gmail.com>>>
    > >     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@mail.huji.ac.il
    <mailto:tomer.nussbaum@mail.huji.ac.il>
    > >     <mailto:tomer.nussbaum@mail.huji.ac.il
    <mailto:tomer.nussbaum@mail.huji.ac.il>>> wrote:
    > >
    > >     >
    > >     > ---------- Forwarded message ----------
    > >     > From: Tomer Nussbaum <tomer.nussbaum@mail.huji.ac.il
    <mailto:tomer.nussbaum@mail.huji.ac.il>
    > >     <mailto:tomer.nussbaum@mail.huji.ac.il
    <mailto:tomer.nussbaum@mail.huji.ac.il>>>
    > >     > Date: Thu, Nov 23, 2017 at 6:08 PM
    > >     > Subject: Cluster best configurations for YT
    > >     > To: yt-users@lists.spacepope.org
    <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists
    <mailto:yt-users@lists>.
    > spacepope.org <http://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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