Mailman 3 July 2015 - yt-users

Shock Finding
by Yuan Li July 9, 2015

July 9, 2015

Dear all, I am trying to figure out a way to mask out cells that contain shocks. One way I can think of is to create a derived field by identifying shocks. It seems that there are different ways of finding shocks: Enzo has a refinement criterion (refine by shocks) and there is also shock finding written by Sam. Has anybody tried to find shocks using yt? I would appreciate it if you would like to share your code/experience/advice. Thank you! Yuan

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YT 2.7 - Getting field values in code units
by James Larrue-Baulch July 6, 2015

July 6, 2015

Hello, I have been working on a system with YT 2.7-dev (changeset 1b93a1840f38) and trying to graph field values in code units, specifically the density, but I cannot figure out how to convert to code units in YT 2. My data is from an Enzo cosmology simulation (i.e. expansion ON). If I were using YT 3, I believe the following would work to convert to any units desired: dataSet = load(inputDataFileName); hierarchy = dataSet.index; maxValue = hierarchy.find_max(dataFieldName) ray = hierarchy.ortho_ray(0, (maxValue[1][1], maxValue[1][2])); ray[xFieldName].convert_to_units(xAxisUnit); // use "code_mass", "code_length", "code_time", etc. to get code units. With YT 2, I am trying: dataSet = load(inputDataFileName); hierarchy = dataSet.hierarchy; maxValue = hierarchy.find_max(dataFieldName) ray = hierarchy.ortho_ray(0, (maxValue[1][1], maxValue[1][2])); ray[xFieldName] = ray[xFieldName] * dataSet.units[xAxisUnit]; This works fine, if my "xAxisUnit" is a length unit, but no other units seem to be recognized. While testing density, I tried to convert from cgs to mks: KeyError: 'kg/m^3' I listed the values in dataSet.units and they look to be only length units. Should I just give up on YT 2 and move to a machine that has YT 3, or is it possible to convert density units with YT 2? Regards, James PS The full script I am using is: https://bitbucket.org/james_larrue/enzo-3.0-experimental/src/f425b7d5a10bf0… but it contains much more code than my immediate goal.

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Re: [yt-users] yt-users Digest, Vol 89, Issue 7
by rahul kashyap July 6, 2015

July 6, 2015

Thanks for the reply. I came to see your replies just now in the daily digest. Is there something I should do to get the replies instantly forwarded to my email ? As Greg suggested, it seems that this problem occurs only on login nodes. Using yt-3.1 and submission through job script solves the problem. Thanks again, r Rahul On Mon, 6 Jul 2015 1:53 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. Problem in running parallel yt on stampede (rahul kashyap) > 2. Re: Problem in running parallel yt on stampede (Nathan Goldbaum) > 3. Re: Problem in running parallel yt on stampede (Greg Meece) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 05 Jul 2015 22:43:29 +0000 > From: rahul kashyap <rahulkashyap411(a)gmail.com> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] Problem in running parallel yt on stampede > Message-ID: > < > CAMt8yfjzKDr50Nk0tYuiqPFDyr_wCTyMq4KaUwTwR3bS3MMG4A(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear yt-users, > > I'm trying to use parallel yt on stampede and got this error -- > LiMIC: (limic_open) file open fail > [unset]: aborting job: > Fatal error in PMPI_Init_thread: > Other MPI error, error stack: > MPIR_Init_thread(436)....: > MPID_Init(371)...........: channel initialization failed > MPIDI_CH3_Init(335)......: > MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file or > directory > > In the interactive ipython, import yt and import mpi4py works ok but, > yt.enable_parallelism() gives the same error. > Serial scripts runs perfectly fine. I've also tried building mpi4py by > specifying mpicc path; itdoesn't work. > > Any help would be highly appreciated. Thanks in advance. > > rahul > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Sun, 5 Jul 2015 16:02:55 -0700 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Problem in running parallel yt on stampede > Message-ID: > <CAJXewOmJbGaAwvHJx4DxLmg2F6U_+bgqE8vFHKf_NXmDX= > Rfmg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > How did mpi4py get installed? > > You may need to troubleshoot this with the Stampede sysadmins, since the > error is being raised by the MPI library you're using. > > On Sunday, July 5, 2015, rahul kashyap <rahulkashyap411(a)gmail.com> wrote: > > > Dear yt-users, > > > > I'm trying to use parallel yt on stampede and got this error -- > > LiMIC: (limic_open) file open fail > > [unset]: aborting job: > > Fatal error in PMPI_Init_thread: > > Other MPI error, error stack: > > MPIR_Init_thread(436)....: > > MPID_Init(371)...........: channel initialization failed > > MPIDI_CH3_Init(335)......: > > MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file or > > directory > > > > In the interactive ipython, import yt and import mpi4py works ok but, > > yt.enable_parallelism() gives the same error. > > Serial scripts runs perfectly fine. I've also tried building mpi4py by > > specifying mpicc path; itdoesn't work. > > > > Any help would be highly appreciated. Thanks in advance. > > > > rahul > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 3 > Date: Sun, 5 Jul 2015 22:56:42 -0400 > From: Greg Meece <meecegre(a)msu.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Problem in running parallel yt on stampede > Message-ID: > <CADDDyPC334pZ0H_bAe5F9uFj+SWF= > hVtCLHhuCSshQUqxO+Evg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Are you running on the login node? > > I've seen this too when I try to use mpi4py in a script on the Stampede > login ode. Specifically, it fails in the 'from mpi4py import MPI' step. > This happens even if I am not using yt or not running in parallel. > > mpi4py works fine (for me at least) in an interactive compute node. I > wonder if they have the login nodes set up to discourage parallel jobs. > > -- Greg > > On Sun, Jul 5, 2015 at 7:02 PM, Nathan Goldbaum <nathan12343(a)gmail.com> > wrote: > > > How did mpi4py get installed? > > > > You may need to troubleshoot this with the Stampede sysadmins, since the > > error is being raised by the MPI library you're using. > > > > On Sunday, July 5, 2015, rahul kashyap <rahulkashyap411(a)gmail.com> > wrote: > > > >> Dear yt-users, > >> > >> I'm trying to use parallel yt on stampede and got this error -- > >> LiMIC: (limic_open) file open fail > >> [unset]: aborting job: > >> Fatal error in PMPI_Init_thread: > >> Other MPI error, error stack: > >> MPIR_Init_thread(436)....: > >> MPID_Init(371)...........: channel initialization failed > >> MPIDI_CH3_Init(335)......: > >> MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file or > >> directory > >> > >> In the interactive ipython, import yt and import mpi4py works ok but, > >> yt.enable_parallelism() gives the same error. > >> Serial scripts runs perfectly fine. I've also tried building mpi4py by > >> specifying mpicc path; itdoesn't work. > >> > >> Any help would be highly appreciated. Thanks in advance. > >> > >> rahul > >> > >> > >> > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > > -- > Gregory Meece > Michigan State University > Department of Physics and Astronomy > http://galactica.pa.msu.edu/~gmeece > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > 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 89, Issue 7 > *************************************** >

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Problem in running parallel yt on stampede
by rahul kashyap July 5, 2015

July 5, 2015

Dear yt-users, I'm trying to use parallel yt on stampede and got this error -- LiMIC: (limic_open) file open fail [unset]: aborting job: Fatal error in PMPI_Init_thread: Other MPI error, error stack: MPIR_Init_thread(436)....: MPID_Init(371)...........: channel initialization failed MPIDI_CH3_Init(335)......: MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file or directory In the interactive ipython, import yt and import mpi4py works ok but, yt.enable_parallelism() gives the same error. Serial scripts runs perfectly fine. I've also tried building mpi4py by specifying mpicc path; itdoesn't work. Any help would be highly appreciated. Thanks in advance. rahul

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Installing yt 3.0
by Paco Holguin July 3, 2015

July 3, 2015

Hi, I want to install yt 3.0 instead of the current version. Is there a straightforward way to do this, or can someone point me to a relevant page with the info ? I have been looking at the documentation, but I don't quite understand how to do it. I originally used the all in one installation, but all I see in the documentation is the command to get the script for the current stable version. Thanks, Paco

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Off Axis Plot
by Chen Jingjing July 1, 2015

July 1, 2015

Hi yt users, I am trying to make multiple off-axis projection plots in the same figure, and I follow the example of http://yt-project.org/doc/cookbook/complex_plots.html#multi-plot-slice-and-… The example has these two lines: slc = yt.SlicePlots(...) slc_frb = slc.data_source.to_frb(...) So I did: proj = yt.OffAxisProjectionPlot(...) proj_frb = proj.data_source.to_frb(...) But I got this error: AttributeError: 'OffAxisProjectionDummyDataSource' object has no attribute 'to_frb' Can anyone tell me why and how to fix it? Thanks, Jingjing -- Jingjing Chen [ chenjj235(a)gmail.com ] Department of Astronomy Columbia University 550 West 120th Street New York, New York 10027 Cell Phone: +1(347)5746709

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yt in the 2015 John Hunter plotting contest
by Nathan Goldbaum July 1, 2015

July 1, 2015

Hi all, I'd like to direct your attention to the 2015 John Hunter plotting contest entries: http://stsdas.stsci.edu/download/mdroe/plotting-2015/ Three of the entries make use of yt! Hopefully like last year, the overall winner ( http://stsdas.stsci.edu/download/mdroe/plotting/entry6/index.html) will be one of the yt entries :) -Nathan

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Streamlines error
by Caroline Van Borm July 1, 2015

July 1, 2015

Hi yt users, I'm having a problem generating streamlines. I'm following the cookbook script and it works fine for the IsolatedGalaxy dataset, but not for my own data (also Enzo). The error I'm getting is the following: --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-20-d3a0fa7307d4> in<module>() 5 pos= c+pos_dx 6 ----> 7 streamlines = Streamlines(pf,pos,'x-velocity', 'y-velocity', 'z-velocity', length=1.0) 8 #streamlines = Streamlines(pf,pos,'x-velocity', 'y-velocity', 'z-velocity', length=pf.domain_width[0]) 9 streamlines.integrate_through_volume() /data/users/borm/YT/yt-x86_64/src/yt-hg/yt/visualization/streamlines.pyc in__init__(self, pf, positions, xfield, yfield, zfield, volume, dx, length, direction, get_magnitude) 102 volume = AMRKDTree(self.pf, fields=[self.xfield,self.yfield,self.zfield], 103 log_fields=[False,False,False]) --> 104 volume.join_parallel_trees() 105 self.volume= volume 106 if dxis None: /data/users/borm/YT/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc injoin_parallel_trees(self) 456 nid= np.array(nid) 457 new_tree = self.rebuild_tree_from_array(nid, pid, lid, --> 458 rid, les, res, gid, splitdims, splitposs) 459 460 def get_node_arrays(self): /data/users/borm/YT/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc inrebuild_tree_from_array(self, nids, pids, lids, rids, les, res, gids, splitdims, splitposs) 505 N= nids.shape[0] 506 for iin xrange(N): --> 507 n = self.get_node(nids[i]) 508 n.set_left_edge(les[i]) 509 n.set_right_edge(res[i]) /data/users/borm/YT/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc inget_node(self, nodeid) 212 for depthin range(1,len(path)): 213 if path[depth] == '0': --> 214 temp = temp.left 215 else: 216 temp= temp.right AttributeError: 'NoneType' object has no attribute 'left' Though sometimes with a different dataset I also get AttributeError: 'NoneType' object has no attribute 'right' I'm using yt 2.6, but I've also tried with yt 3.1 and I get the same error there (only it takes much, much longer before it crashes?) My datasets do not have particles, not sure if that may be relevant. Any help is much appreciated! Cheers, Caroline

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