Mailman 3 June 2015 - yt-users

An error when using yt on PLUTO 4.1
by 方军 16 Jun '15

16 Jun '15

Dear everyone, I recently used yt to plot the slice files for the hdf5 file from PLUTO 4.1. An error exists when ploting, i.e., [('chombo', 'rho'), ('chombo', 'vx1'), ('chombo', 'vx2'), ('chombo', 'vx3'), ('chombo', 'prs')] Traceback (most recent call last): File "simple_slice.py", line 18, in <module> p = yt.ProjectionPlot(ds, "y", "density") File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1227, in __init__ field_parameters = field_parameters, method = method) File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 250, in __init__ self.get_data(field) File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 295, in get_data chunk_fields, "io", local_only = True)): File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 506, in parallel_objects for obj_id, obj in oiter: File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 592, in chunks self.get_data(fields) File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 681, in get_data fluids, self, self._current_chunk) File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/geometry/geometry_handler.py", line 252, in _read_fluid_fields chunk_size) File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/frontends/chombo/io.py", line 147, in _read_fluid_selection data = self._read_data(g, fname) File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/frontends/chombo/io.py", line 104, in _read_data shape = grid.ActiveDimensions + 2*self.ghost AttributeError: 'IOHandlerPlutoHDF5' object has no attribute 'ghost' Could you give some instructions on it? Best wishes, Jun

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Re: [yt-users] Subtracting datasets
by bh11e 16 Jun '15

16 Jun '15

Hi Matthew and Jonah, Firstly, thanks to Matt for the answer! Secondly, to add to the answer to Johah's question - without knowing the details, I've heard about "covering grid" in yt that interpolates the data from the existing grid hierarchy onto a uniform mesh. Perhaps someone else can elaborate. I already tried something like Matt suggested: ds1.index.grids[0][field] = ds1.index.grids[0][field] - ds2.index.grids[0][field] print ds1.index.grids[0][field] plot = SlicePlot(ds1, "y", field) It printed the modified values but SlicePlot didn't know about it. Some time ago I noticed that derived fields don't preserve the calculated values if they are being accessed more than once. I wonder if it is for the same reason. Best regards, --Boyan > Today's Topics (Digest, Vol 88, Issue 38, Jun 16, 2015, at 9:57) > > 1. Subtracting datasets (bh11e) > 2. An error when using yt on PLUTO 4.1 (=?GBK?B?t72+/A==?=) > 3. Re: Subtracting datasets (Matthew Turk) > 4. Re: Subtracting datasets (Jonah Miller) > 5. Re: Subtracting datasets (Matthew Turk) > 6. Re: Subtracting datasets (Jonah Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 16 Jun 2015 00:05:52 -0400 > From: bh11e <bh11e(a)my.fsu.edu> > To: <yt-users(a)lists.spacepope.org> > Subject: [yt-users] Subtracting datasets > Message-ID: <D0CA8853-F36E-4FA8-815C-93676BF4E6EC(a)my.fsu.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I was wondering if someone could advise on the following problem. Consider two (Enzo) datasets with identical grids. What is the way to plot the difference between a field in one set and a field in the other. Alternatively is there a way to create a new dataset with the calculated difference, after which plotting will be as usual. > > Thanks, > > --Boyan Hristov > > ------------------------------ > > Message: 2 > Date: Tue, 16 Jun 2015 20:57:22 +0800 > From: "=?GBK?B?t72+/A==?=" <fangjun(a)ynu.edu.cn> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] An error when using yt on PLUTO 4.1 > Message-ID: <15061620572294f6197f024e15786d70ba0f25fa12a9(a)ynu.edu.cn> > Content-Type: text/plain; charset="gbk" > > Dear everyone, > I recently used yt to plot the slice files for the hdf5 file from PLUTO 4.1. > An error exists when ploting, i.e., > [('chombo', 'rho'), ('chombo', 'vx1'), ('chombo', 'vx2'), ('chombo', 'vx3'), ('chombo', 'prs')] > Traceback (most recent call last): > File "simple_slice.py", line 18, in <module> > p = yt.ProjectionPlot(ds, "y", "density") > File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1227, in __init__ > field_parameters = field_parameters, method = method) > File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 250, in __init__ > self.get_data(field) > File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 295, in get_data > chunk_fields, "io", local_only = True)): > File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 506, in parallel_objects > for obj_id, obj in oiter: > File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 592, in chunks > self.get_data(fields) > File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 681, in get_data > fluids, self, self._current_chunk) > File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/geometry/geometry_handler.py", line 252, in _read_fluid_fields > chunk_size) > File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/frontends/chombo/io.py", line 147, in _read_fluid_selection > data = self._read_data(g, fname) > File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/frontends/chombo/io.py", line 104, in _read_data > shape = grid.ActiveDimensions + 2*self.ghost > > AttributeError: 'IOHandlerPlutoHDF5' object has no attribute 'ghost' > > Could you give some instructions on it? > Best wishes, > Jun >

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Subtracting datasets
by bh11e 16 Jun '15

16 Jun '15

Hi, I was wondering if someone could advise on the following problem. Consider two (Enzo) datasets with identical grids. What is the way to plot the difference between a field in one set and a field in the other. Alternatively is there a way to create a new dataset with the calculated difference, after which plotting will be as usual. Thanks, --Boyan Hristov

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wired square in enzo DM slice map
by Junhwan Choi (최준환) 15 Jun '15

15 Jun '15

Hi yt users, I have asked a similar question previously but I did get partial answer so that I ask again. I have made cosmological IC from MUSIC and run with enzo. I made the DM density map with velocity arrow at z=200 which is initial redshift using yt (and attach the figure). It shows the wired square feature. Previously, John wise suggested me to use enzo SPH smoothing to remove this issue and it worked. But, after test a few more run, I have couple more fundamental questions on this issue. 1) Is this wired square effect is real effect in enzo or visualization in yt? If this is an intrinsic enzo effect, we can say that DM gravity calculation at high-z some kind of error. If this is an visualization effect, I found that other enzo simulation using different IC generator does not show this effect (see question 2). This difference makes me very confused. 2) I tested with other IC generator and I do not see the wired square feature. I found that other IC generator output real DM position while MUSIC IC generate displacement of DM particle position. Can it be the origin of issue? I think this inquiry can go to enzo mailing list or MUSIC developer. If it is necessary, I can ask it to other place. Thank you in advance, Junhwan

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wired square in enzo DM slice map
by Junhwan Choi (최준환) 15 Jun '15

15 Jun '15

Hi yt users, I have asked a similar question previously but I did get partial answer so that I ask again. I have made cosmological IC from MUSIC and run with enzo. I made the DM density map with velocity arrow at z=200 which is initial redshift using yt (and attach the figure). It shows the wired square feature. Previously, John wise suggested me to use enzo SPH smoothing to remove this issue and it worked. But, after test a few more run, I have couple more fundamental questions on this issue. 1) Is this wired square effect is real effect in enzo or visualization in yt? If this is an intrinsic enzo effect, we can say that DM gravity calculation at high-z some kind of error. If this is an visualization effect, I found that other enzo simulation using different IC generator does not show this effect (see question 2). This difference makes me very confused. 2) I tested with other IC generator and I do not see the wired square feature. I found that other IC generator output real DM position while MUSIC IC generate displacement of DM particle position. Can it be the origin of issue? I think this inquiry can go to enzo mailing list or MUSIC developer. If it is necessary, I can ask it to other place. Thank you in advance, Junhwan

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changing units for data in a projection container
by mc knabbits 11 Jun '15

11 Jun '15

hi, I have the simple problem that I cant figure out how to change the units for data within a|||YTQuadTreeProjBase. so I'm stuck with code units all along. heres my script part: ds = yt.load(some ramses data) prj = ds.proj("Density", 2) prj.apply_units(arr,'g/cm**2') #maybe it's all because I dont know what to put in for "arr" frb=prj.to_frb((10,'pc'),(1024,1024)) surfdense=np.array(frb[density]) as you can see the unit I need is g/cm**2 but the method applied above dont work!? thanx for your help phil |||

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YT: Rockstar Halo Finder
by Jacob Kneibel 11 Jun '15

11 Jun '15

Hello, I've been trying to run the Rockstar Halo finder on a 1536^3 unigrid Enzo simulation and have been running into a few issues. I am using the Blue waters machine and when I run the finder with multiple readers, the process is killed by the OOM killer, and when I run it with one reader there is a Network IO error. My yt version is 3.2-dev, changeset= 8ad62b624390 Here is the python script I am running: http://paste.yt-project.org/show/5631/ and here is the job script I'm submitting to blue waters: http://paste.yt-project.org/show/5632/ I've tried different node and ppn settings, with no luck. Does anyone have an idea on how to get rockstar to run on the blue waters system with this large simulation? Or is there a recommended number of readers based on the number of nodes I set? Thank you for any help you can give, Jacob Kneibel

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FLASH and Off Axis Projections
by Jeffrey Alan Gritton 11 Jun '15

11 Jun '15

Hi all, I'm having a bit of a problem with off axis projections and my FLASH domains. I want to create an off axis projection for the entire domain. However, I try to follow the Cookbook I run into one of two errors. The first being: ds = yt.load("4.2.1_hdf5_plt_cnt_0150") prj = yt.OffAxisProjectionPlot(ds, [-1,1,0], 'dens') ... ... YTUnitOperationError: The subtraction operator for YTArrays with units (code_length) and (1) is not well defined. The second I can't recreate at the moment but yt throws an error back complaining about accessing indicies outside of the array and suggests overriding periodic boundaries. My domain has no periodic boundaries. Has anyone ever run into this? Thank you for your help, Jeff

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Bug Report: Memory leak when rendering projection plots in parallel
by Gabriel Goodwin 10 Jun '15

10 Jun '15

Hello, I believe I have found a memory leak when iterating through a DatasetSeries in parallel to render projection plots of each data file in the series. I work in a CFD research group and our code is built on boxlib, so I have been using yt to generate images of my simulations. The DatasetSeries's I work with are fairly large, on the order of 6000 to 7000 data sets per series. To expedite the image rendering process, I have been using yt's parallelism to iterate through the series with openmpi. The ram usage, per mpi process, increases steadily throughout the duration of the script's runtime. When running my attached script with 16 mpi processes on a 16 core machine (1 process per core) the ram usage starts at about 2.56 GB per process and gradually increases to over 25 GB per process, at which time the script typically crashes due to insufficient ram on the machine to continue running. My simulations do involve data sets of increasing memory requirements versus simulation time, but not to the scale mentioned above in the corresponding ram increases. I determined that the crashing is due to a memory leak by starting the script over after it crashed, using only the data set files that had not yet been processed (to ensure that the memory required to render the projection of each data set is the same as it was before it crashed by starting over at the same time in the simulation as when it crashed). I also ran this script on my university's cluster, using several different openmpi implementations, and always got the same result. Additionally, the crashes always occur at approximately the same script runtime. Attached to this email is a copy of a script I'm using. I run the script on my 16 core mini-cluster using the command: mpirun -np 16 --cpus-per-proc 1 br0.05_temp.py I also attached a sample image of the projection plots I'm generating. Any help with this bug is appreciated! Thanks very much, Gabe

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Using eps_writer with ProfilePlot causes AttributeError
by Anni Järvenpää 09 Jun '15

09 Jun '15

Hi all, I'm trying to use eps_writer to create figure that has both projections and profiles as subplots, but every time I try to create one with profiles the program crashes with following stack trace: Traceback (most recent call last): File "myprogram.py", line 14, in <module> multiplot = eps.multiplot(cols, rows, plots) File "/.../yt-x86_64/src/yt-hg/yt/visualization/eps_writer.py", line 1120, in multiplot field=fields[index]) File ".../yt-x86_64/src/yt-hg/yt/visualization/eps_writer.py", line 505, in insert_image_yt plot._redraw_image() AttributeError: 'ProfilePlot' object has no attribute '_redraw_image' Here is a minimal example of a program that produces that error: http://paste.yt-project.org/show/5617/. One plot could of course be saved without eps_writer but if I want multiple plots to the same figure, I don't know any other way of doing it if some of them are profiles. I took a look at the source code of eps_writer and it seems that it is intended to work with projections also because there are lines like line 504 which explicitly handles profiles: "elif isinstance(plot, ProfilePlot):". I was able to work my way around the error by getting the figure from the plot similarly to what is done in ProfilePlot source when the plot is saved: I create an iterator to iterate through plot.figures.iteritems() and get the figure to _p1. Unfortunately, then I get errors from similar calls to functions and attributes that don't exist, for example in code block starting from line 358, so I haven't been able to get profiles to work. Of course it is also possible that my workaround does not work correctly, because my understanding of yt source is not very comprehensive. Am I doing something wrong with eps_writer or profile creation? Or has anyone else run into a similar problem and if so, how have you managed to get around it? Is there any other way to get both profiles and projections to same figure? Thanks for your help Anni Järvenpää Summer Trainee Division of Particle Physics and Astrophysics University of Helsinki

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