<div dir="ltr"> Hello,<br><div><br>$ hg pull -r f4c5c13 <a href="https://bitbucket.org/yt_analysis/yt" target="_blank">https://bitbucket.org/yt_<wbr>analysis/yt</a><br></div><div>This is giving the following error:<br>pulling from <a href="https://bitbucket.org/yt_analysis/yt">https://bitbucket.org/yt_analysis/yt</a><br>abort: unknown revision 'f4c5c13'!<br><br></div><div>Alankar Dutta<br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Mar 4, 2017 at 10:46 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>To test my pull request you're going to want to build yt from a clone of the mercurial repository after pulling in my changes.</div><div><br></div><div>$ conda uninstall yt</div><div>$ hg clone <a href="https://bitbucket.org/yt_analysis/yt" target="_blank">https://bitbucket.org/yt_<wbr>analysis/yt</a></div><div>$ cd yt</div><div>$ hg pull -r f4c5c13 <a href="https://bitbucket.org/yt_analysis/yt" target="_blank">https://bitbucket.org/yt_<wbr>analysis/yt</a></div><div>$ hg update f4c5c13</div><div>$ python setup.py develop</div><div><br></div><div>You'll need a compilation environment set up for that to succeed. If you don't have compilers installed it will be less straightforward to test this. I'd urge you *not* to hand-edit your installed version of yt from conda, as that will create more headaches for you if you make a mistake and forget to correct it.</div><div class="HOEnZb"><div class="h5"><div><br></div><div><br><div class="gmail_quote"><div>On Sat, Mar 4, 2017 at 10:34 AM Alankar Dutta <<a href="mailto:dutta.alankar@gmail.com" target="_blank">dutta.alankar@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg">Hello,<br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg">I have modified the yt files as given in the pull request. I get the following error code:<br class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg">Traceback (most recent call last):<br class="m_-2072811568109207121gmail_msg"> File "dev.py", line 9, in <module><br class="m_-2072811568109207121gmail_msg"> import yt<br class="m_-2072811568109207121gmail_msg"> File "/home/alankar/anaconda3/lib/<wbr>python3.6/site-packages/yt/__<wbr>init__.py", line 133, in <module><br class="m_-2072811568109207121gmail_msg"> frontends = _frontend_container()<br class="m_-2072811568109207121gmail_msg"> File "/home/alankar/anaconda3/lib/<wbr>python3.6/site-packages/yt/<wbr>frontends/api.py", line 52, in __init__<br class="m_-2072811568109207121gmail_msg"> setattr(self, frontend, importlib.import_module(_mod))<br class="m_-2072811568109207121gmail_msg"> File "/home/alankar/anaconda3/lib/<wbr>python3.6/importlib/__init__.<wbr>py", line 126, in import_module<br class="m_-2072811568109207121gmail_msg"> return _bootstrap._gcd_import(name[<wbr>level:], package, level)<br class="m_-2072811568109207121gmail_msg"> File "/home/alankar/anaconda3/lib/<wbr>python3.6/site-packages/yt/<wbr>frontends/eagle/api.py", line 17, in <module><br class="m_-2072811568109207121gmail_msg"> from .data_structures import \<br class="m_-2072811568109207121gmail_msg"> File "/home/alankar/anaconda3/lib/<wbr>python3.6/site-packages/yt/<wbr>frontends/eagle/data_<wbr>structures.py", line 21, in <module><br class="m_-2072811568109207121gmail_msg"> from yt.frontends.gadget.data_<wbr>structures import \<br class="m_-2072811568109207121gmail_msg"> File "/home/alankar/anaconda3/lib/<wbr>python3.6/site-packages/yt/<wbr>frontends/gadget/data_<wbr>structures.py", line 28, in <module><br class="m_-2072811568109207121gmail_msg"> from yt.frontends.sph.data_<wbr>structures import \<br class="m_-2072811568109207121gmail_msg">ImportError: cannot import name 'SPHDataset'<br class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div>The following is my code:<br class="m_-2072811568109207121gmail_msg">import yt<br class="m_-2072811568109207121gmail_msg">ds = yt.load("snapshot_068.0")<br class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div></div><div class="m_-2072811568109207121gmail_msg">Alankar Dutta<br class="m_-2072811568109207121gmail_msg"></div><div class="gmail_extra m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"><div class="gmail_quote m_-2072811568109207121gmail_msg">On Sat, Mar 4, 2017 at 3:13 PM, Alankar Dutta <span class="m_-2072811568109207121gmail_msg"><<a href="mailto:dutta.alankar@gmail.com" class="m_-2072811568109207121gmail_msg" target="_blank">dutta.alankar@gmail.com</a>></span> wrote:<br class="m_-2072811568109207121gmail_msg"><blockquote class="gmail_quote m_-2072811568109207121gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="m_-2072811568109207121gmail_msg">Oh I missed telling that the full dataset is around 950 GB<br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121m_-4774300613610813270HOEnZb m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121m_-4774300613610813270h5 m_-2072811568109207121gmail_msg"><div class="gmail_extra m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"><div class="gmail_quote m_-2072811568109207121gmail_msg">On Sat, Mar 4, 2017 at 1:02 PM, Alankar Dutta <span class="m_-2072811568109207121gmail_msg"><<a href="mailto:dutta.alankar@gmail.com" class="m_-2072811568109207121gmail_msg" target="_blank">dutta.alankar@gmail.com</a>></span> wrote:<br class="m_-2072811568109207121gmail_msg"><blockquote class="gmail_quote m_-2072811568109207121gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg">Hello,<br class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg">This is only one part of the multipart snapshot of the simulation. I am sending you the header information from the snapshot file:<br class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"><pre style="box-sizing:border-box;overflow:auto;font-family:monospace;font-size:14px;display:block;padding:0px;margin:0px;line-height:inherit;word-break:break-all;color:rgb(0,0,0);background-color:rgb(255,255,255);border-width:0px;border-style:none;border-color:-moz-use-text-color;border-radius:0px;white-space:pre-wrap;vertical-align:baseline;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:left;text-indent:0px;text-transform:none;word-spacing:0px" class="m_-2072811568109207121gmail_msg">{'O0': 0.27500000000000002,
'Ol': 0.72499999999999998,
'boxsize': 100000.0,
'flag_age': 1,
'flag_cooling': 1,
'flag_delaytime': 0,
'flag_fb': 1,
'flag_fh2': 0,
'flag_metals': 1,
'flag_potential': 3,
'flag_sfr': 1,
'flag_tmax': 0,
'h': 0.70199999999999996,
'massTable': array([ 0. , 0.00110449, 0. , 0. , 0. , 0. ]),
'nbndry': 76247,
'nbulge': 0,
'ndisk': 0,
'ndm': 1459617792,
'nfiles': 1024,
'ngas': 1343721867,
'npartThisFile': array([10045237, 10239661, 0, 0, 451148, 67], dtype=uint32),
'npartTotal': array([1343721867, 1459617792, 0, 0, 503500456,
76247], dtype=uint32),
'npartTotalHW': array([1, 1, 0, 0, 0, 0], dtype=uint32),
'nstar': 503500456,
'redshift': 1.0000000010567627,
'rhocrit': 2.707660428120944e-29,
'time': 0.49999999973580939}</pre><br class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div>I extracted this information using a different python program.<span class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112HOEnZb m_-2072811568109207121gmail_msg"><font class="m_-2072811568109207121gmail_msg" color="#888888"><br class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></font></span></div><span class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112HOEnZb m_-2072811568109207121gmail_msg"><font class="m_-2072811568109207121gmail_msg" color="#888888">Alankar Dutta<br class="m_-2072811568109207121gmail_msg"></font></span></div><div class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112HOEnZb m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112h5 m_-2072811568109207121gmail_msg"><div class="gmail_extra m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"><div class="gmail_quote m_-2072811568109207121gmail_msg">On Sat, Mar 4, 2017 at 12:45 PM, Nathan Goldbaum <span class="m_-2072811568109207121gmail_msg"><<a href="mailto:nathan12343@gmail.com" class="m_-2072811568109207121gmail_msg" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br class="m_-2072811568109207121gmail_msg"><blockquote class="gmail_quote m_-2072811568109207121gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"><div class="gmail_extra m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"><div class="gmail_quote m_-2072811568109207121gmail_msg"><span class="m_-2072811568109207121gmail_msg">On Sat, Mar 4, 2017 at 12:25 AM, Nathan Goldbaum <span class="m_-2072811568109207121gmail_msg"><<a href="mailto:nathan12343@gmail.com" class="m_-2072811568109207121gmail_msg" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br class="m_-2072811568109207121gmail_msg"><blockquote class="gmail_quote m_-2072811568109207121gmail_msg" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"><div class="gmail_extra m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"><div class="gmail_quote m_-2072811568109207121gmail_msg"><span class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail- m_-2072811568109207121gmail_msg">On Sat, Mar 4, 2017 at 12:13 AM, Alankar Dutta <span class="m_-2072811568109207121gmail_msg"><<a href="mailto:dutta.alankar@gmail.com" class="m_-2072811568109207121gmail_msg" target="_blank">dutta.alankar@gmail.com</a>></span> wrote:<br class="m_-2072811568109207121gmail_msg"><blockquote class="gmail_quote m_-2072811568109207121gmail_msg" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="m_-2072811568109207121gmail_msg">Hello,<div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg">Modifying the GADGET simulation isn't possible the moment because it has already been developed by someone else who has a paper published on this simulation and I want to use that simulation snapshots to make mock xray map from it.</div></div></blockquote><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div></span><div class="m_-2072811568109207121gmail_msg">I'm talking about modifying yt, not Gadget.<div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg">Is the file you attached to your other e-mail just a single file in a multi-file dataset? How large is the full dataset? Do you not have a way to produce a full dataset in this output format that's not prohibitively large?</div></div></div></div></div></blockquote><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div></span><div class="m_-2072811568109207121gmail_msg">I've opened a pull request that allows me to do IO on the data you attached: <a href="https://bitbucket.org/yt_analysis/yt/pull-requests/2537" class="m_-2072811568109207121gmail_msg" target="_blank">https://bitbucket.<wbr>org/yt_analysis/yt/pull-<wbr>requests/2537</a></div><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg">This allows me to read your data in, getting sensible values for e.g. position. I suspect we're not using the correct field specification because I see this warning:</div><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg">yt : [WARNING ] 2017-03-04 01:06:09,109 Your Gadget-2 file may have extra columns or different precision! (1814947576 file vs 1486279952 computed)<br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg">yt supports a number of field specifications out of the box, see:</div><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg"><a href="https://bitbucket.org/yt_analysis/yt/src/3eca2ae80ab14a48b643d3055d7d3c0933fa77ae/yt/frontends/gadget/definitions.py?at=yt&fileviewer=file-view-default#definitions.py-50" class="m_-2072811568109207121gmail_msg" target="_blank">https://bitbucket.org/yt_<wbr>analysis/yt/src/<wbr>3eca2ae80ab14a48b643d3055d7d3c<wbr>0933fa77ae/yt/frontends/<wbr>gadget/definitions.py?at=yt&<wbr>fileviewer=file-view-default#<wbr>definitions.py-50</a><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg">Do you happen to know which fields are in your output file?</div><div class="m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112m_2054906823403235472h5 m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg"> </div><blockquote class="gmail_quote m_-2072811568109207121gmail_msg" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="m_-2072811568109207121gmail_msg"><div class="gmail_extra m_-2072811568109207121gmail_msg"><div class="gmail_quote m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-h5 m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg"> </div><blockquote class="gmail_quote m_-2072811568109207121gmail_msg" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg"><span class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-HOEnZb m_-2072811568109207121gmail_msg"><font class="m_-2072811568109207121gmail_msg" color="#888888"><br class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg">Alankar Dutta</div></font></span></div></div><div class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-HOEnZb m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-h5 m_-2072811568109207121gmail_msg"><div class="gmail_extra m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"><div class="gmail_quote m_-2072811568109207121gmail_msg">On Mar 4, 2017 11:38 AM, "Nathan Goldbaum" <<a href="mailto:nathan12343@gmail.com" class="m_-2072811568109207121gmail_msg" target="_blank">nathan12343@gmail.com</a>> wrote:<br type="attribution" class="m_-2072811568109207121gmail_msg"><blockquote class="gmail_quote m_-2072811568109207121gmail_msg" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="m_-2072811568109207121gmail_msg">I think the most straightforward thing to do here is to fix the Gadget frontend so it properly reads in gadget binary data with positions written in double precision.<div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg">Is there any chance you can generate a smallish test dataset in your Gadget output format that we can use for debugging purposes? With that available it should be straightforward to add support. You can share the dataset using the yt curldrop (<a href="https://docs.hub.yt/services.html#curldrop" class="m_-2072811568109207121gmail_msg" target="_blank">https://docs.hub.yt/services.<wbr>html#curldrop</a>) or a cloud filesharing service like dropbox or google drive.</div><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg">Unfortunately there isn't a way to load SPH data without a full-fledged frontend right now.</div><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg">We do have a load_particles function which allows creating a dataset from particle data loaded as numpy arrays, but it's currently not possible to use it to load SPH data. </div><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg">I'm currently actively working on improving support for SPH data in yt and adding the ability to load SPH data with load_particles is one of the things I've added in that branch of the code. Hopefully this work will be stabilized sometime in the next few months.<br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></div><div class="gmail_extra m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"><div class="gmail_quote m_-2072811568109207121gmail_msg">On Fri, Mar 3, 2017 at 11:45 PM, Alankar Dutta <span class="m_-2072811568109207121gmail_msg"><<a href="mailto:dutta.alankar@gmail.com" class="m_-2072811568109207121gmail_msg" target="_blank">dutta.alankar@gmail.com</a>></span> wrote:<br class="m_-2072811568109207121gmail_msg"><blockquote class="gmail_quote m_-2072811568109207121gmail_msg" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg"><div class="m_-2072811568109207121gmail_msg">Hello yt-community,<br class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg">I am a beginner on yt. I have an array of data which I have read from a Gadget simulation snapshot. It is not directly supported by yt at present (I have ensured this by already discussing this issue in the community before). The array has position,velocity, density, mass, internal energy and smoothing length information on the gas particles. Now how can I use this to make the slice plots or other useful visualizations?<span class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-m_5927581532522955128m_-3416413581748429304m_-832106199985279372HOEnZb m_-2072811568109207121gmail_msg"><font class="m_-2072811568109207121gmail_msg" color="#888888"><br class="m_-2072811568109207121gmail_msg"><br class="m_-2072811568109207121gmail_msg"></font></span></div><span class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-m_5927581532522955128m_-3416413581748429304m_-832106199985279372HOEnZb m_-2072811568109207121gmail_msg"><font class="m_-2072811568109207121gmail_msg" color="#888888">Alankar Dutta,<br class="m_-2072811568109207121gmail_msg"></font></span></div><span class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-m_5927581532522955128m_-3416413581748429304m_-832106199985279372HOEnZb m_-2072811568109207121gmail_msg"><font class="m_-2072811568109207121gmail_msg" color="#888888">Third year Undergraduate,<br class="m_-2072811568109207121gmail_msg"></font></span></div><span class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-m_5927581532522955128m_-3416413581748429304m_-832106199985279372HOEnZb m_-2072811568109207121gmail_msg"><font class="m_-2072811568109207121gmail_msg" color="#888888">Physics Department,<br class="m_-2072811568109207121gmail_msg"></font></span></div><span class="m_-2072811568109207121m_-4774300613610813270m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-m_5927581532522955128m_-3416413581748429304m_-832106199985279372HOEnZb m_-2072811568109207121gmail_msg"><font class="m_-2072811568109207121gmail_msg" color="#888888">Presidency University, India<br class="m_-2072811568109207121gmail_msg"></font></span></div>
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