<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr">Hey Max,<div><br></div><div>I just tried running the development version of the install script on a linux box to try and replicate your environment as closely as possible.</div><div><br></div><div>Unfortunately, I'm still not able to trigger your error (specifically, I'm running the script I pasted higher up the thread, using the dataset you uploaded). This is just a guess, but I think there's something strange about the environment on your cluster that is causing an outdated yt installation to be loaded somehow, but in a very confusing way that prevents us from easily seeing that it's happening.</div><div><br></div><div>Are you able to get the script to run when you install yt elsewhere?</div><div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jan 19, 2016 at 8:52 AM, Max Katz <span dir="ltr"><<a href="mailto:maxpkatz@gmail.com" target="_blank">maxpkatz@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I also tried removing yt and reinstalling the latest version on the development branch, but I see the same behavior.<br></div><div class="gmail_extra"><span class=""><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">Max Katz<br>Ph.D. Candidate, Department of Physics and Astronomy<br>Stony Brook University<br><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__astro.sunysb.edu_mkatz_&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=mIW5Q2E4mUngzPLmz2PgZtyXaK38QM_hlZA1epIBw5s&s=2AoYuB0svTc2WYBLJcCjALQr6d7JK-iEYHsJCJ-LxnE&e=" target="_blank">http://astro.sunysb.edu/mkatz/</a></div></div></div></div></div></div></div>
<br></span><div><div class="h5"><div class="gmail_quote">On Mon, Jan 18, 2016 at 5:37 PM, Max Katz <span dir="ltr"><<a href="mailto:maxpkatz@gmail.com" target="_blank">maxpkatz@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div style="margin-left:40px">The current version and changeset for the code is:<br><br>---<br>Version = 3.2.2<br>Changeset = d7acb82ef450 (stable) @<br>---<br></div><br></div><div class="gmail_extra"><span><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">Max Katz<br>Ph.D. Candidate, Department of Physics and Astronomy<br>Stony Brook University<br><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__astro.sunysb.edu_mkatz_&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=mIW5Q2E4mUngzPLmz2PgZtyXaK38QM_hlZA1epIBw5s&s=2AoYuB0svTc2WYBLJcCjALQr6d7JK-iEYHsJCJ-LxnE&e=" target="_blank">http://astro.sunysb.edu/mkatz/</a></div></div></div></div></div></div></div>
<br></span><div><div><div class="gmail_quote">On Mon, Jan 18, 2016 at 5:26 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Which yt version are you using? I'm able to create a covering grid of your dataset with the following script using the latest dev version of yt.<div><br></div><div><div>import yt</div><div>ds = yt.load('plt00000/')</div><div>ds.periodicity = (True, True, True)<br></div><div><br></div><div>cg = ds.covering_grid(0, [0, 0, 0], ds.domain_dimensions)</div><div>cg['density']</div></div><div><br></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jan 18, 2016 at 4:20 PM, Max Katz <span dir="ltr"><<a href="mailto:maxpkatz@gmail.com" target="_blank">maxpkatz@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Sure, here's the link to the dataset (10 MB, tgz format): <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__use.yt_upload_7bcd9429&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=mIW5Q2E4mUngzPLmz2PgZtyXaK38QM_hlZA1epIBw5s&s=VTjfSQSdHbexlczvhw6ihv-1AFy5KKCfLEvpWzS5q8E&e=" target="_blank">http://use.yt/upload/7bcd9429</a><br></div><div class="gmail_extra"><span><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">Max Katz<br>Ph.D. Candidate, Department of Physics and Astronomy<br>Stony Brook University<br><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__astro.sunysb.edu_mkatz_&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=mIW5Q2E4mUngzPLmz2PgZtyXaK38QM_hlZA1epIBw5s&s=2AoYuB0svTc2WYBLJcCjALQr6d7JK-iEYHsJCJ-LxnE&e=" target="_blank">http://astro.sunysb.edu/mkatz/</a></div></div></div></div></div></div></div>
<br></span><div><div><div class="gmail_quote">On Mon, Jan 18, 2016 at 5:08 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I'm not able to reproduce this with any of the 2D datasets I have on hand.<div><br></div><div>Would it be ok to share the dataset you're having trouble with or a test dataset that triggers the same error? You can use the curldrop Kacper set up to do this, which allows you to upload a file using:</div><div><br></div><div>$ curl -T <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__file.name&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=mIW5Q2E4mUngzPLmz2PgZtyXaK38QM_hlZA1epIBw5s&s=E1Gyazjm34vkM2AkPjUh6KfxhXe6hRcuMpHEOU1FboI&e=" target="_blank">file.name</a> <span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__use.yt_upload_&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=mIW5Q2E4mUngzPLmz2PgZtyXaK38QM_hlZA1epIBw5s&s=4VKrOl5v5ASQbO3V_3HfriKQFGaOjsfPm-o1fzioHME&e=" target="_blank">http://use.yt/upload/</a></span><br></div><div><p>You could also use e.g. dropbox or google drive.</p><span><font color="#888888"><p>-Nathan</p></font></span></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jan 18, 2016 at 3:40 PM, Max Katz <span dir="ltr"><<a href="mailto:maxpkatz@gmail.com" target="_blank">maxpkatz@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">That results in the following:<br><br><div style="margin-left:40px"><span>Traceback (most recent call last):<br> File "analyze.py", line 78, in <module><br> wdmerger.rho_T_scatterplot(eps_filename, output_dir + pltfile)<br></span> File "/home/mkatz/codes/wdmerger/analysis/wdmerger.py", line 617, in rho_T_scatterplot<br> grid = ds.covering_grid(level=0, left_edge = problo, dims = [1024, 2048, 1])<br> File "/gpfs/home/mkatz/codes/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 506, in __init__<br> rdx[np.where(np.array(dims) - 2 * num_ghost_zones <= 1)] = 1 # issue 602<br>IndexError: index 2 is out of bounds for axis 1 with size 2<br></div><br></div><div class="gmail_extra"><span><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">Max Katz<br>Ph.D. Candidate, Department of Physics and Astronomy<br>Stony Brook University<br><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__astro.sunysb.edu_mkatz_&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=mIW5Q2E4mUngzPLmz2PgZtyXaK38QM_hlZA1epIBw5s&s=2AoYuB0svTc2WYBLJcCjALQr6d7JK-iEYHsJCJ-LxnE&e=" target="_blank">http://astro.sunysb.edu/mkatz/</a></div></div></div></div></div></div></div>
<br></span><div><div><div class="gmail_quote">On Mon, Jan 18, 2016 at 3:32 PM, Kacper Kowalik <span dir="ltr"><<a href="mailto:xarthisius.kk@gmail.com" target="_blank">xarthisius.kk@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div>On 01/18/2016 11:59 AM, Max Katz wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
I'm trying to use yt for analysis of a 2D axisymmetric (R-z) dataset using<br>
the BoxLib frontend. After I load the dataset I am trying to make a<br>
covering grid with the following commands:<br>
<br>
ds = yt.load(pltfile)<br>
<br>
problo = ds.domain_left_edge.v<br>
probhi = ds.domain_right_edge.v<br>
dim = ds.domain_dimensions<br>
<br>
grid = ds.covering_grid(level=0, left_edge = problo, dims = dim)<br>
<br>
That leads to the following output at the terminal:<br>
<br>
yt : [INFO ] 2016-01-18 01:35:47,516 Parameters:<br>
current_time = 0.0<br>
yt : [INFO ] 2016-01-18 01:35:47,516 Parameters:<br>
domain_dimensions = [1024 2048]<br>
yt : [INFO ] 2016-01-18 01:35:47,517 Parameters:<br>
domain_left_edge = [ 0.00000000e+00 -5.12000000e+09<br>
0.00000000e+00]<br>
yt : [INFO ] 2016-01-18 01:35:47,517 Parameters:<br>
domain_right_edge = [ 5.12000000e+09 5.12000000e+09<br>
6.28318531e+00]<br>
Traceback (most recent call last):<br>
File "analyze.py", line 78, in <module><br>
wdmerger.rho_T_scatterplot(eps_filename, output_dir + pltfile)<br>
File "/home/mkatz/codes/wdmerger/analysis/wdmerger.py", line 615, in<br>
rho_T_scatterplot<br>
grid = ds.covering_grid(level=0, left_edge = problo, dims = dim)<br>
File<br>
"/gpfs/home/mkatz/codes/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",<br>
line 503, in __init__<br>
self.ActiveDimensions = self._sanitize_dims(dims)<br>
File<br>
"/gpfs/home/mkatz/codes/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",<br>
line 552, in _sanitize_dims<br>
"Length of dims must match the dimensionality of the dataset")<br>
RuntimeError: Length of dims must match the dimensionality of the dataset<br>
<br>
Thoughts? It seems like the code has some inconsistency in what the<br>
dimensionality of the dataset is. The Castro plot file in question doesn't<br>
provide that third angular dimension of size 2*pi.<br>
</blockquote>
<br></div></div>
Could you try dims=[1024, 2048, 1] ?<br>
<br>
Cheers,<br>
Kacper<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span>
Max Katz<br>
Ph.D. Candidate, Department of Physics and Astronomy<br>
Stony Brook University<br>
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<br>
<br>
<br></span>
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