yt-users November 2017

yt-users@python.org

21 participants
24 discussions

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

6 8

3-D Mass power spectra
by 梁家豪 03 Jun '19

03 Jun '19

Dear yt Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....? Thanks in advance

4 7

Volume rendering
by Андрей Парамонов 04 Dec '17

04 Dec '17

Hello! I've recently discovered yt, and I found the rendering examples really encouraging. I'm now trying to visualize a large 3D dataset via volume rendering technique. I have come up with the following script that is intended to plot a part of the dataset: --- import yt from yt.config import ytcfg import h5py f = h5py.File('ims-p.hdf5') intens = f['intensity'][:256,:256,:256] print(intens.shape) ds = yt.load_uniform_grid({'Intensity': intens}, intens.shape) print(ds) sc = yt.create_scene(ds, ('Intensity'), lens_type = 'perspective') sc[0].set_log(True) sc[0].tfh.plot('transfer_function.png', profile_field = 'Intensity') sc.camera.resolution = 1024 sc.annotate_axes(alpha = 0.1) sc.annotate_domain(ds, color = [1, 1, 1, 0.1]) sc.save_annotated('vr_grids.png', sigma_clip = 4) --- I get some really fascinating rendering (attached), and now I want to tweak it. I would be really happy if you could help me with the following questions: 1) What is the best way to configure the camera viewpoint so the complete data cube fits into the view? How to quickly render the domain axes without performing the costly volume rendering (to find the "optimal" viewpoint experimentally)? 2) What is the best way to specify axes scales, so that rendered volume appears as cuboid, not cube? I want the resulting cuboid to be scaled as 3:2:2. How to specify resulting image size, e.g. how to get image of 1600x1200 pixels? 3) In my dataset, the grid is not in fact uniform, but rather X coordinates are specified by (non-decreasing) array rettime, Y coordinates are specified by (non-decreasing) array mz. What is the best way to pass this information (to load_uniform_grid)? 4) Is it possible to use inverse transfer function model, i.e. white background? 5) My complete dataset is rather large and doesn't readily fit into RAM. However it seems that for ray-tracing algorithm, it shouldn't be required that all data is available simultaneously. Is it possible to feed dataset by chunks? Your help is greatly appreciated! Best wishes, Andrey Paramonov -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Re: [yt-users] yt-users Digest, Vol 117, Issue 33
by Tomer Nussbaum 29 Nov '17

29 Nov '17

Hi, 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?) How are you handling many group members using the same files together? Do you use SSD drives? Do you copy each snapshot to the node and then compute? Do you do some of what I asked about? Do you have any other special tricks? Thank, Tomer On Tue, Nov 28, 2017 at 7:53 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > 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(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] yt-users Digest, Vol 117, Issue 31 > Message-ID: > <CALO3=5Hu9VJLYA9yAZEPdACLUi+RfYwhABD78du+vsacJW=wXA@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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(a)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, <yt-users-request(a)lists.spacepope.org > > > <mailto:yt-users-request@lists.spacepope.org>> wrote: > > > > > > Send yt-users mailing list submissions to > > > yt-users(a)lists.spacepope.org > > > <mailto:yt-users@lists.spacepope.org> > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> > > > or, via email, send a message with subject or body 'help' to > > > yt-users-request(a)lists.spacepope.org > > > <mailto:yt-users-request@lists.spacepope.org> > > > > > > You can reach the person managing the list at > > > yt-users-owner(a)lists.spacepope.org > > > <mailto:yt-users-owner@lists.spacepope.org> > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of yt-users digest..." > > > > > > > > > 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(a)mail.huji.ac.il > > > <mailto:tomer.nussbaum@mail.huji.ac.il>> > > > To: yt-users(a)lists.spacepope.org <mailto:yt-users@lists. > > 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>> > > > Content-Type: text/plain; charset="utf-8" > > > > > > ---------- Forwarded message ---------- > > > From: Tomer Nussbaum <tomer.nussbaum(a)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(a)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/20171128/cde38586/attachment-0001.html > > > <http://lists.spacepope.org/pipermail/yt-users-spacepope. > > org/attachments/20171128/cde38586/attachment-0001.html>> > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Tue, 28 Nov 2017 12:42:40 +0000 > > > From: Nathan Goldbaum <nathan12343(a)gmail.com > > > <mailto:nathan12343@gmail.com>> > > > To: Discussion of the yt analysis package > > > <yt-users(a)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>> > > > 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(a)mail.huji.ac.il > > > <mailto:tomer.nussbaum@mail.huji.ac.il>> wrote: > > > > > > > > > > > ---------- Forwarded message ---------- > > > > From: Tomer Nussbaum <tomer.nussbaum(a)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(a)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(a)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/20171128/854b8a3d/attachment-0001.html > > > <http://lists.spacepope.org/pipermail/yt-users-spacepope. > > org/attachments/20171128/854b8a3d/attachment-0001.html>> > > > > > > ------------------------------ > > > > > > Subject: Digest Footer > > > > > > _______________________________________________ > > > yt-users mailing list > > > yt-users(a)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> > > > > > > > > > ------------------------------ > > > > > > End of yt-users Digest, Vol 117, Issue 31 > > > ***************************************** > > > > > > > > > > > > > > > _______________________________________________ > > > yt-users mailing list > > > yt-users(a)lists.spacepope.org > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.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/20171128/1708bea9/attachment.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 117, Issue 33 > ***************************************** >

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Trouble Installing Yt with Rockstar
by Sean Larkin 28 Nov '17

28 Nov '17

I have been trying to install Rockstar with yt onto a computer running macOS sierra 10.12, using both the install script and manually. For the install script, I get this error: Building Rockstar ******************************************** FAILURE REPORT: ******************************************** config=config) File "/Users/user1/Rockstar/yt-conda/lib/python3.6/site-packages/conda_build/build.py", line 1147, in build utils.check_call_env(cmd, env=env, cwd=src_dir) File "/Users/user1/Rockstar/yt-conda/lib/python3.6/site-packages/conda_build/utils.py", line 628, in check_call_env return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, **kwargs) File "/Users/user1/Rockstar/yt-conda/lib/python3.6/site-packages/conda_build/utils.py", line 624, in _func_defaulting_env_to_os_environ return func(_args, **kwargs) File "/Users/user1/Rockstar/yt-conda/lib/python3.6/subprocess.py", line 291, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/bin/bash', '-x', '-e', '/Users/user1/Rockstar/yt-conda/conda-bld/rockstar_1511919771484/work/conda_build.sh']' returned non-zero exit status 2. ******************************************** ******************************************** Failure. Check /Users/user1/Rockstar/yt-conda/yt_install.log. The last 10 lines are above. And when installing manually, after stating "make lib" i get this error: /bin/sh: pkg-config: command not found gcc -m64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_BSD_SOURCE -D_POSIX_SOURCE -D_POSIX_C_SOURCE=200809L -D_SVID_SOURCE -D_DARWIN_C_SOURCE -Wall -fno-math-errno -fPIC -shared rockstar.c check_syscalls.c fof.c groupies.c subhalo_metric.c potential.c nfw.c jacobi.c fun_times.c interleaving.c universe_time.c hubble.c integrate.c distance.c config_vars.c config.c bounds.c inthash.c io/read_config.c client.c server.c merger.c inet/socket.c inet/rsocket.c inet/address.c io/meta_io.c io/io_internal.c io/io_ascii.c io/stringparse.c io/io_gadget.c io/io_generic.c io/io_art.c io/io_tipsy.c io/io_bgc2.c io/io_util.c io/io_arepo.c io/io_hdf5.c -o librockstar.so -lm -O3 -std=c99 In file included from server.c:241: *./load_balance.c:8:21: **warning: **using floating point absolute value function* * 'fabs' when argument is of integer type [-Wabsolute-value]* i = ceil(sqrt(fabs(in)))+1; * ^* *./load_balance.c:8:21: **note: *use function 'llabs' instead i = ceil(sqrt(fabs(in)))+1; * ^~~~* llabs 1 warning generated. Undefined symbols for architecture x86_64: "_GROUPIES_fast3tree_box_inside_sphere", referenced from: _GROUPIES_fast3tree_find_sphere_offset in groupies-eb1fe8.o ld: symbol(s) not found for architecture x86_64 clang: *error: *linker command failed with exit code 1 (use -v to see invocation) make: *** [lib] Error 1 I am not sure what is causing the error for install script, but for the manual install, I think it is clang using the wrong c++ standard library. I have attempted to change the library used, but nothing has worked for me so far.

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Re: [yt-users] yt-users Digest, Vol 117, Issue 31
by Tomer Nussbaum 28 Nov '17

28 Nov '17

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(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > 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(a)mail.huji.ac.il> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] Fwd: Cluster best configurations for YT > Message-ID: > <CAOGC2jACH1Q4QLfFNi8h7p=XhqEFvnp-6g17FUv6aDN2vSvqWg@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > ---------- Forwarded message ---------- > From: Tomer Nussbaum <tomer.nussbaum(a)mail.huji.ac.il> > Date: Thu, Nov 23, 2017 at 6:08 PM > Subject: Cluster best configurations for YT > To: yt-users(a)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/20171128/cde38586/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Tue, 28 Nov 2017 12:42:40 +0000 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Fwd: Cluster best configurations for YT > Message-ID: > <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(a)mail.huji.ac.il> wrote: > > > > > ---------- Forwarded message ---------- > > From: Tomer Nussbaum <tomer.nussbaum(a)mail.huji.ac.il> > > Date: Thu, Nov 23, 2017 at 6:08 PM > > Subject: Cluster best configurations for YT > > To: yt-users(a)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(a)lists.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/20171128/854b8a3d/attachment-0001.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 117, Issue 31 > ***************************************** >

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Fwd: Cluster best configurations for YT
by Tomer Nussbaum 28 Nov '17

28 Nov '17

---------- Forwarded message ---------- From: Tomer Nussbaum <tomer.nussbaum(a)mail.huji.ac.il> Date: Thu, Nov 23, 2017 at 6:08 PM Subject: Cluster best configurations for YT To: yt-users(a)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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Exodus file Couldn't figure out output type
by Jaron Senecal 22 Nov '17

22 Nov '17

Hi, I just installed yt and immediately ran into the following problem. The following script #viz1.py import yt from yt.mods import * ds = yt.load("stnd_2d_out.e", step=-1) gives this error: yt : [ERROR ] 2017-11-21 09:34:33,950 Couldn't figure out output type for stnd_2d_out.e Traceback (most recent call last): File "viz1.py", line 27, in <module> ds = yt.load("stnd_2d_out.e", step=-1) File "/home/jaron/.conda/envs/py36/lib/python3.6/site-packages/yt/convenience.py", line 98, in load raise YTOutputNotIdentified(args, kwargs) yt.utilities.exceptions.YTOutputNotIdentified: Supplied ('stnd_2d_out.e',) {'step': -1}, but could not load! Please let me know how to resolve this. -Jaron

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Readline on Pleiades
by David Collins 21 Nov '17

21 Nov '17

Hi, Everybody! I'm running yt on Pleiades, and I'm running into a readline error (below) Has anyone else run into this, and do you know what I can do to fix this? This is a recent build, not from source. Thanks! pleiades:~/yt3_scripts>python Python 2.7.13 | packaged by conda-forge | (default, May 2 2017, 12:48:11) [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2 Type "help", "copyright", "credits" or "license" for more information. Traceback (most recent call last): File "/etc/pythonstart", line 7, in <module> import readline ImportError: /u/dccolli1/local-yt-2017-09-28/yt-conda/lib/python2.7/lib- dynload/../../libreadline.so.6: undefined symbol: PC >>> -- -- Sent from a computer.

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yt-users November 2017