<div dir="ltr"><div>Hello all.<br><br></div><div>So I have decided to test my code on a smaller box ( 20 Mpc/h @ level 7, one of my previous runs with 430 snapshots ) and I am getting halos (i.e Rockstar is working) within the earlier snapshots with Rockstar. I am currently running rockstar all the way through on that run now.<br><br></div><div>A part of me now is suspecting that I am doing something wrong with the resolution side of things maybe? I have kept the particle number the same, but increased the box size (thus decreased the spatial resolution).<br><br></div><div>Basically, rockstar is working. But I need to relax some initial conditions somewhere with a larger box by the sounds of it.<br><br></div><div>Currently running some more tests on the 20 Mpc box series (i.e seeing what happens when you allow for the spatial (but not particle mass) resolution to increase., rather than having a uniform grid run spatially<br><br></div><div>Any thoughts, suggestions on why it might be complaining about the larger box size runs?<br></div><div><br>Ben<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Oct 4, 2014 at 8:53 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">If you are comfortable sharing the data, one of us could probably help out with debugging. It's hard to debug these things remotely but if we have the dataset you're using and the script you're running it becomes much easier to quickly figure out what's going wrong.<span></span><div><br></div><div>In the past we've found sharing data via Dropbox or Google drive to work pretty well.<div><div class="h5"><br><br>On Saturday, October 4, 2014, Ben Thompson <<a href="mailto:bthompson2090@gmail.com" target="_blank">bthompson2090@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Reinstalling YT did not resolve the problem (although now I am on the latest version of YT which is cool :) )<br><br></div>I will have a serious debug with it on Monday.<br><br></div><div>Ben.<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 3, 2014 at 11:29 PM, Britton Smith <span dir="ltr"><<a>brittonsmith@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>My guess is that this is a units issue. It might be worth it to stick some debugging statements into yt/analysis_modules/halo_finding/rockstar/rockstar.py where the particles are loaded up to be sent to rockstar. I believe the units that rockstar is expecting are positions in Mpc/h, masses in Msun/h, and velocities in km/s.<span><font color="#888888"><br></font></span></div><span><font color="#888888"><div><br></div><div>Britton</div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 3, 2014 at 11:39 AM, Ben Thompson <span dir="ltr"><<a>bthompson2090@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><div>I am using Ramses v3.11<br><br>The current version and changeset of YT I am using is:<br>---<br>Version = 3.0.1<br>Changeset = f66765a58a61 (stable) @<br>---<br><br></div>And yes, I have produced a projection plot of the simulation, and halo structures exist (in z=0). The halos have also been identified by running another halo finder independently (AHF)<br><br></div>I will run the updates to see that helps.<br><br>Will be back later.<span><font color="#888888"><br><br>Ben.<br><div><div><br></div></div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 3, 2014 at 5:30 PM, Cameron Hummels <span dir="ltr"><<a>chummels@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's odd. Could you produce a projection of the dark matter particles to identify if halos actually exist? Try something like this:<div><br></div><div><a href="http://paste.yt-project.org/show/5145/" target="_blank">http://paste.yt-project.org/show/5145/</a><br></div><div><br></div><div>Also, what simulation code are you using?</div><div><br></div><div>And what version of yt are you using? To determine your yt version, type:</div><div><br></div><div>$ yt version</div><div><br></div><div>I know that recently there were some changes in the output format of rockstar that broke yt's interaction with it. Perhaps that is related to the problem you're experiencing. You could try upgrading to the newest version of yt and rockstar with this:</div><div><br></div><div>$ yt update --all</div><div><br></div><div>This may resolve your problems.</div><span><font color="#888888"><div><br></div><div>Cameron</div><div><br></div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 3, 2014 at 9:22 AM, Ben Thompson <span dir="ltr"><<a>bthompson2090@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><div><div>Hello.<br><br></div>My simulation runs to z=0. Only with 10 timesteps though (purely a test run). It identifies no halos in halos_0 (expected with it being the first snapshot) and halos_9 (the final snapshot).. All files are the same size too with no data.<br><br></div>My code is (with the filters taken out... it's a dark matter only one anyway)<br><br><br>from mpi4py import MPI<br>import yt, sys, os<br>yt.enable_parallelism()<br>from yt.config import ytcfg<br>from yt.analysis_modules.halo_finding.rockstar.api import \<br> RockstarHaloFinder<br>from yt.data_objects.particle_filters import \<br> particle_filter<br>from yt.data_objects.time_series import DatasetSeries<br>import numpy as np<br><br>ncpu = MPI.COMM_WORLD.Get_size()<br>ytcfg.set('yt', '__global_parallel_size', str(ncpu))<br><br>outputs = np.arange(1, 11)<br>dirs = []<br>#Add the datasets<br>for ioutput in outputs:<br> ds = yt.load('../output_%05d/info_%05d.txt'%(ioutput, ioutput))<br> dirs.append(ds)<br><br>es = DatasetSeries(dirs)<br>readers = int(ncpu/4.)<span><br>writers = ncpu - readers - 1<br></span>rh = RockstarHaloFinder(es, num_readers=readers, num_writers=writers)<br>rh.run()<span><font color="#888888"><br><br><br></font></span></div><span><font color="#888888">Ben<br><div><br></div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 3, 2014 at 5:09 PM, Cameron Hummels <span dir="ltr"><<a>chummels@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">Hi Ben,<div><br></div><div>No, you don't need to have halos in the first timestep. Rockstar will find the halos when they exist, so if you run it on all of the outputs and you get to a later redshift then 5 or so, rockstar will start to identify halos. Does your simulation run to z=0? If so, just look at the output file associated with that redshift and see if it identifies any halos. It doesn't matter your starting redshift.</div><span><font color="#888888"><div><br></div><div>Cameron</div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 3, 2014 at 9:02 AM, Ben Thompson <span dir="ltr"><<a>bthompson2090@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>Hi Cameron.<br><br></div>So it is dependent as of what timestep I start my run at? I start my run (i.e there needs to be halos in the snapshot that you start with)? This is the first time I have used Rockstar before (figured that since the package is there, for free, I should use it) I have DM only runs that start at z=50 (of which I am not expecting to find halos there, as part of the loading script I loop over all the snapshots)<br><div><br></div><div>This is what I have<br></div><div><span><br>cat halos_0.0.ascii<br>#id num_p mvir mbound_vir rvir vmax rvmax vrms x y z vx vy vz Jx Jy Jz E Spin PosUncertainty VelUncertainty bulk_vx bulk_vy bulk_vz BulkVelUnc n_core m200b m200c m500c m2500c Xoff Voff spin_bullock b_to_a c_to_a A[x] A[y] A[z] b_to_a(500c) c_to_a(500c) A[x](500c) A[y](500c) A[z](500c) Rs Rs_Klypin T/|U| M_pe_Behroozi M_pe_Diemer idx i_so i_ph num_cp mmetric<br></span>#a = 0.019608<br>#Bounds: (0.000000, 0.000000, 0.000000) - (99.816002, 99.816002, 19.807144)<br>#Om = 0.300000; Ol = 0.700000; h = 0.700000<span><br>#FOF linking length: 0.280000<br>#Unbound Threshold: 0.500000; FOF Refinement Threshold: 0.700000<br></span>#Particle mass: 2.87164e+10 Msun/h<br>#Box size: 99.816005 Mpc/h<br>#Total particles processed: 419422<br>#Force resolution assumed: 0.780498 Mpc/h<span><br>#Units: Masses in Msun / h<br>#Units: Positions in Mpc / h (comoving)<br>#Units: Velocities in km / s (physical, peculiar)<br>#Units: Halo Distances, Lengths, and Radii in kpc / h (comoving)<br>#Units: Angular Momenta in (Msun/h) * (Mpc/h) * km/s (physical)<br>#Units: Spins are dimensionless<br>#Units: Total energy in (Msun/h)*(km/s)^2 (physical)<br>#Note: idx, i_so, and i_ph are internal debugging quantities<br>#Np is an internal debugging quantity.<br>#Rockstar Version: 0.99.9-RC3<br><br></span>(yt-x86_64)[bthompson1@leopard rockstar_halos]$ cat halos_9.0.ascii<span><br>#id num_p mvir mbound_vir rvir vmax rvmax vrms x y z vx vy vz Jx Jy Jz E Spin PosUncertainty VelUncertainty bulk_vx bulk_vy bulk_vz BulkVelUnc n_core m200b m200c m500c m2500c Xoff Voff spin_bullock b_to_a c_to_a A[x] A[y] A[z] b_to_a(500c) c_to_a(500c) A[x](500c) A[y](500c) A[z](500c) Rs Rs_Klypin T/|U| M_pe_Behroozi M_pe_Diemer idx i_so i_ph num_cp mmetric<br></span>#a = 1.000879<br>#Bounds: (0.000000, 0.000000, 0.000000) - (99.816002, 99.816002, 19.667080)<br>#Om = 0.300000; Ol = 0.700000; h = 0.700000<span><br>#FOF linking length: 0.280000<br>#Unbound Threshold: 0.500000; FOF Refinement Threshold: 0.700000<br></span>#Particle mass: 2.87164e+10 Msun/h<br>#Box size: 99.816005 Mpc/h<br>#Total particles processed: 419437<br>#Force resolution assumed: 0.779813 Mpc/h<span><br>#Units: Masses in Msun / h<br>#Units: Positions in Mpc / h (comoving)<br>#Units: Velocities in km / s (physical, peculiar)<br>#Units: Halo Distances, Lengths, and Radii in kpc / h (comoving)<br>#Units: Angular Momenta in (Msun/h) * (Mpc/h) * km/s (physical)<br>#Units: Spins are dimensionless<br>#Units: Total energy in (Msun/h)*(km/s)^2 (physical)<br>#Note: idx, i_so, and i_ph are internal debugging quantities<br>#Np is an internal debugging quantity.<br>#Rockstar Version: 0.99.9-RC3<br><br></span></div><div>Both exactly the same pretty much.<br><br></div><div>If it is because I am starting at an early timestep, then I will cut out the earlier ones from the initial setup.<br><br></div><div>Thanks.<span><font color="#888888"><br></font></span></div><span><font color="#888888"><div><br>Ben,<br></div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 3, 2014 at 4:55 PM, Cameron Hummels <span dir="ltr"><<a>chummels@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">Hi Ben,<div><br></div><div>Oftentimes, rockstar cannot find any halos for the first few snapshots of a cosmology DM-only sim because things have not collapsed enough. In that case, you'll get files like this:</div><div><br></div><div>$ % cat halos_0.0.ascii</div><div>#id num_p mvir mbound_vir rvir vmax rvmax vrms x y z vx vy vz Jx Jy Jz E Spin PosUncertainty VelUncertainty bulk_vx bulk_vy bulk_vz BulkVelUnc n_core m200b m200c m500c m2500c Xoff Voff spin_bullock b_to_a c_to_a A[x] A[y] A[z] b_to_a(500c) c_to_a(500c) A[x](500c) A[y](500c) A[z](500c) Rs Rs_Klypin T/|U| M_pe_Behroozi M_pe_Diemer idx i_so i_ph num_cp mmetric</div><div>#a = 0.009901</div><div>#Bounds: (0.000000, 0.000000, 0.000000) - (40.000000, 40.000000, 3.099222)</div><div>#Om = 0.282000; Ol = 0.718000; h = 0.697000</div><div>#FOF linking length: 0.280000</div><div>#Unbound Threshold: 0.500000; FOF Refinement Threshold: 0.700000</div><div>#Particle mass: 2.98630e+08 Msun/h</div><div>#Box size: 40.000000 Mpc/h</div><div>#Total particles processed: 1290100</div><div>#Force resolution assumed: 0.15625 Mpc/h</div><div>#Units: Masses in Msun / h</div><div>#Units: Positions in Mpc / h (comoving)</div><div>#Units: Velocities in km / s (physical, peculiar)</div><div>#Units: Halo Distances, Lengths, and Radii in kpc / h (comoving)</div><div>#Units: Angular Momenta in (Msun/h) * (Mpc/h) * km/s (physical)</div><div>#Units: Spins are dimensionless</div><div>#Units: Total energy in (Msun/h)*(km/s)^2 (physical)</div><div>#Note: idx, i_so, and i_ph are internal debugging quantities</div><div>#Np is an internal debugging quantity.</div><div>#Rockstar Version: 0.99.9-RC3</div><div><br></div><div><br></div><div>Is this what you're seeing or are your files truly empty? If you're seeing this, you may just need to run Rockstar on data files that are more evolved in time, so as to allow for more non-linear collapse of the halos. For my DM-only runs, depending on the mass resolution that I use, I may not start to see halos until after z=10 to z=5, with the first outputs all looking like the stuff above: empty.</div><div><br></div><div>Cameron</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Fri, Oct 3, 2014 at 8:46 AM, Ben Thompson <span dir="ltr"><<a>bthompson2090@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div><div><div><div>P.S sorry if I sent the same email twice.. this is the actual email... accidental press send before I sent the email out.<br></div><div><div><div><br>Hello everyone.<br><br>I am currently using YT to run rockstar on my simulation.<br><br></div><div>I have been following the instructions which are around and about and have managed to write a script to run rockstar via MPI<br></div><div><br>readers = int(ncpu/4.)<br>#Reserve one cpu for the server<br>writers = ncpu - readers - 1<br>print 'Running rockstar with %i writers and %i readers'%(writers, readers)<br>rh = RockstarHaloFinder(es, num_readers=readers, num_writers=writers,<br> particle_type="dark_matter", dm_only=True)<br>rh.run()<br><br></div><div>using a particle filter on the datasets<br><br>@yt.particle_filter("dark_matter", requires=[('particle_mass')])<br>def dark_matter(pfilter, data):<br> if ('all', 'particle_age') in data.ds.field_list:<br> return data[("all", "particle_age")] == 0.0<br> else:<br> arr = np.zeros(len(data['particle_mass']))<br> return arr == 0.0<br><br>def setup_ds(ds):<br> #Return only dark matter particles, and assert that the filter holds<br> print 'Here'<br> assert(ds.add_particle_filter("dark_matter"))<br><br><br></div>It seems to run fine.... e.g<br><br><br></div></div>[ 111s] Sending projection requests...<br>[ 112s] Transferring particles to writers...<br>[ 116s] Analyzing for FoF groups...<br>[ 116s] Transferring boundary particles between writers...<br>[ 117s] Linking boundary particles...<br>[ 117s] Analyzing for halos / subhalos...<br>[ 119s] Loading merger tree information...<br>[ 120s] Constructing merger tree...<br>[ 121s] [Success] Done with snapshot 7.<br>[ 121s] Reading 6 blocks for snapshot 8...<br>P001 yt : [INFO ] 2014-10-03 16:19:28,101 Loading field plugins.<br>P002 yt : [INFO ] 2014-10-03 16:19:28,101 Loading field plugins.<br>P001 yt : [INFO ] 2014-10-03 16:19:28,101 Loaded angular_momentum (8 new fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,101 Loaded astro (14 new fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,102 Loaded cosmology (20 new fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,102 Loaded fluid (56 new fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,103 Loaded fluid_vector (88 new fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,103 Loaded geometric (102 new fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,103 Loaded local (102 new fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,104 Loaded magnetic_field (108 new fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,104 Loaded species (108 new fields)<br>P006 yt : [INFO ] 2014-10-03 16:19:28,127 Loading field plugins.<br>P005 yt : [INFO ] 2014-10-03 16:19:28,128 Loading field plugins.<br>P003 yt : [INFO ] 2014-10-03 16:19:28,128 Loading field plugins.<br>P004 yt : [INFO ] 2014-10-03 16:19:28,135 Loading field plugins.<br>[ 129s] Sending projection requests...<br>[ 130s] Transferring particles to writers...<br>[ 132s] Analyzing for FoF groups...<br>[ 133s] Transferring boundary particles between writers...<br>[ 133s] Linking boundary particles...<br>[ 134s] Analyzing for halos / subhalos...<br>[ 137s] Loading merger tree information...<br>[ 138s] Constructing merger tree...<br>[ 139s] [Success] Done with snapshot 8.<br>[ 139s] Reading 6 blocks for snapshot 9...<br>[ 143s] Sending projection requests...<br>[ 144s] Transferring particles to writers...<br>[ 146s] Analyzing for FoF groups...<br>[ 147s] Transferring boundary particles between writers...<br>[ 147s] Linking boundary particles...<br>[ 148s] Analyzing for halos / subhalos...<br>[ 150s] Loading merger tree information...<br>[ 151s] Constructing merger tree...<br>[ 152s] Constructing merger tree...<br>[ 153s] [Success] Done with snapshot 9.<br>[ 153s] [Finished]<br><br></div>generates the outputs<br><br><br>halos_0.0.ascii halos_1.14.bin halos_2.4.ascii halos_3.9.bin halos_5.14.ascii halos_6.3.bin halos_7.9.ascii halos_9.13.bin<br>halos_0.0.bin halos_1.15.ascii halos_2.4.bin halos_4.0.ascii halos_5.14.bin halos_6.4.ascii halos_7.9.bin halos_9.14.ascii<br>halos_0.10.ascii halos_1.15.bin halos_2.5.ascii halos_4.0.bin halos_5.15.ascii halos_6.4.bin halos_8.0.ascii halos_9.14.bin<br>halos_0.10.bin halos_1.16.ascii halos_2.5.bin halos_4.10.ascii halos_5.15.bin halos_6.5.ascii halos_8.0.bin halos_9.15.ascii<br>halos_0.11.ascii halos_1.16.bin halos_2.6.ascii halos_4.10.bin halos_5.16.ascii halos_6.5.bin halos_8.10.ascii halos_9.15.bin<br><br><br></div>but they are all empty.... yet within profiling, it seems to imply that there were some particles submitted to be analised<br><br><br>[Prof] S0,C0 0s: 10191 fofs, 123365 particles, 0s for conf.<br>[Prof] S0,C0: 0p,0h,0w; wt:0s; rcv:0s,0s; snd:0s; wk:0s; idl:1s<br>[Prof] S1,C0 0s: 10377 fofs, 123363 particles, 0s for conf.<br>[Prof] S1,C0: 1814p,73h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s<br>[Prof] S2,C0 0s: 9843 fofs, 123353 particles, 0s for conf.<br>[Prof] S2,C0: 5115p,139h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s<br>[Prof] S3,C0 0s: 9616 fofs, 123359 particles, 0s for conf.<br>[Prof] S3,C0: 9637p,221h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s<br>[Prof] S4,C0 1s: 9256 fofs, 123367 particles, 0s for conf.<br>[Prof] S4,C0: 14849p,314h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:0s<br>[Prof] S5,C0 0s: 9233 fofs, 123361 particles, 0s for conf.<br>[Prof] S5,C0: 17771p,369h,1w; wt:0s; rcv:0s,0s; snd:1s; wk:0s; idl:0s<br>[Prof] S6,C0 0s: 8964 fofs, 123365 particles, 0s for conf.<br>[Prof] S6,C0: 19888p,388h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:0s<br>[Prof] S7,C0 0s: 8996 fofs, 123356 particles, 0s for conf.<br>[Prof] S7,C0: 22352p,426h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s<br>[Prof] S8,C0 0s: 8801 fofs, 123361 particles, 0s for conf.<br>[Prof] S8,C0: 22553p,441h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s<br>[Prof] S9,C0 1s: 8806 fofs, 123361 particles, 0s for conf.<br>[Prof] S9,C0: 22685p,440h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s<br><br><br></div>Is there anything I should consider looking at to debug this problem? Any suggestions of what to look at?<br><br>Thanks<span><font color="#888888"><br><br>Ben<br><div><div><br><br><div><br><br></div></div></div></font></span></div>
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<br></blockquote></div><span><font color="#888888"><br><br clear="all"><div><br></div>-- <br>Cameron Hummels<div>Postdoctoral Researcher</div><div>Steward Observatory</div><div>University of Arizona</div><div><a href="http://chummels.org" target="_blank">http://chummels.org</a></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Cameron Hummels<div>Postdoctoral Researcher</div><div>Steward Observatory</div><div>University of Arizona</div><div><a href="http://chummels.org" target="_blank">http://chummels.org</a></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Cameron Hummels<div>Postdoctoral Researcher</div><div>Steward Observatory</div><div>University of Arizona</div><div><a href="http://chummels.org" target="_blank">http://chummels.org</a></div>
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