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)
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Message: 1 Date: Tue, 28 Nov 2017 11:55:56 +0200 From: Tomer Nussbaum
mailto:tomer.nussbaum@mail.huji.ac.il> To: yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org Subject: [yt-users] Fwd: Cluster best configurations for YT Message-ID:
mailto:XhqEFvnp-6g17FUv6aDN2vSvqWg@mail.gmail.com> Content-Type: text/plain; charset="utf-8" ---------- Forwarded message ---------- From: Tomer Nussbaum
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 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2017... http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2017...>
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Message: 2 Date: Tue, 28 Nov 2017 12:42:40 +0000 From: Nathan Goldbaum
mailto:nathan12343@gmail.com> To: Discussion of the yt analysis package mailto:yt-users@lists.spacepope.org> Subject: Re: [yt-users] Fwd: Cluster best configurations for YT Message-ID:
mailto:CAJXewOk9tCL-TCTQef9Up-mTj-qgVFJp6yHZXmwQ8SReoV4h8A@mail.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> wrote:
> > ---------- Forwarded message ---------- > From: Tomer Nussbaum
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 > > > > 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@lists.spacepope.org mailto:yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2017... http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2017...> ------------------------------
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