Mailman 3 October 2013 - yt-users

Re: [yt-users] yt-users Digest, Vol 68, Issue 22
by Alexander Philippov 21 Oct '13

21 Oct '13

Hi John, here is the public link to data: https://dl.dropboxusercontent.com/u/72536930/data.zip folders id* contain unjoined data, joined file is in directory comb. Thanks, Sasha On Oct 18, 2013, at 1:54 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. reading joined vtk from Athena in yt (Alexander Philippov) > 2. Re: reading joined vtk from Athena in yt (John ZuHone) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Oct 2013 01:38:35 -0400 > From: Alexander Philippov <philippo(a)astro.princeton.edu> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] reading joined vtk from Athena in yt > Message-ID: <7779567D-AB79-4A9A-B5C3-2866F3BF10C8(a)astro.princeton.edu> > Content-Type: text/plain; charset=us-ascii > > Hi, > > I have a problem reading joined vtk files from Athena in yt. > Here is the problem. I have 800x2000 2D grid decomposed > on 4 processors in a way that each output is 200x2000. > > I'm now joining vtks and trying to download it to yt. > > pf=load("khc.0001.vtk") > print pf.h.grids > [AthenaGrid_0000 ([ 200 2000 1])] > > So the size of the grid I get is as if it is not joined file. > Tricks listed here https://bitbucket.org/yt_analysis/yt/issue/616/loading-vtk-files-from-athen… > do not work. > Hope someone can help with that. > > Thanks in advance, > Sasha > > ------------------------------ > > Message: 2 > Date: Thu, 17 Oct 2013 18:43:58 -0400 > From: John ZuHone <jzuhone(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] reading joined vtk from Athena in yt > Message-ID: <1DC37F0C-5B3E-44ED-95A7-09C029B52E51(a)gmail.com> > Content-Type: text/plain; charset=us-ascii > > Hi Sasha, > > Sorry to hear about the trouble... > > Is there any way you can post a dataset somewhere that demonstrates this behavior that I can check out? > > Best, > > John > > On Oct 17, 2013, at 1:38 AM, Alexander Philippov <philippo(a)astro.princeton.edu> wrote: > >> Hi, >> >> I have a problem reading joined vtk files from Athena in yt. >> Here is the problem. I have 800x2000 2D grid decomposed >> on 4 processors in a way that each output is 200x2000. >> >> I'm now joining vtks and trying to download it to yt. >> >> pf=load("khc.0001.vtk") >> print pf.h.grids >> [AthenaGrid_0000 ([ 200 2000 1])] >> >> So the size of the grid I get is as if it is not joined file. >> Tricks listed here https://bitbucket.org/yt_analysis/yt/issue/616/loading-vtk-files-from-athen… >> do not work. >> Hope someone can help with that. >> >> Thanks in advance, >> Sasha >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > ------------------------------ > > _______________________________________________ > 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 68, Issue 22 > ****************************************

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yt-3.0 devel with RAMSES
by Romain Teyssier 20 Oct '13

20 Oct '13

I have now installed yt-3.0 properly. But I am having issues reading a file with 7 hydro variables. r=load("mike/ramses/output_00040/info_00040.txt",fields=["Density","x-velocity","y-velocity","z-velocity","Pressure","Metal","g"]) yt : [WARNING ] 2013-10-19 18:59:51,239 RAMSES frontend assumes all simulations are cosmological! yt : [INFO ] 2013-10-19 18:59:51,240 Parameters: current_time = 2.88490981599e+15 yt : [INFO ] 2013-10-19 18:59:51,240 Parameters: domain_dimensions = [128 128 128] yt : [INFO ] 2013-10-19 18:59:51,241 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2013-10-19 18:59:51,242 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2013-10-19 18:59:51,242 Parameters: cosmological_simulation = 1 yt : [INFO ] 2013-10-19 18:59:51,243 Parameters: current_redshift = 0.0 yt : [INFO ] 2013-10-19 18:59:51,243 Parameters: omega_lambda = 0.0 yt : [INFO ] 2013-10-19 18:59:51,243 Parameters: omega_matter = 1.0 yt : [INFO ] 2013-10-19 18:59:51,244 Parameters: hubble_constant = 0.01 p=ProjectionPlot(r,'z','Density') You are running with the wrong number of fields. Please specify these in the load command. We are looking for 6 fields. The last set of field sizes was: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] --------------------------------------------------------------------------- AssertionError Traceback (most recent call last) <ipython-input-39-c02d2ecd2249> in <module>() ----> 1 p=ProjectionPlot(r,'z','Density') /Users/teyssier/yt-3.0/yt/visualization/plot_window.py in __init__(self, pf, axis, fields, center, width, axes_unit, weight_field, max_level, origin, fontsize, field_parameters, data_source) 1439 proj = pf.h.proj(fields, axis, weight_field=weight_field, 1440 center=center, data_source=data_source, -> 1441 field_parameters = field_parameters) 1442 PWViewerMPL.__init__(self, proj, bounds, fields=fields, origin=origin, 1443 fontsize=fontsize) /Users/teyssier/yt-3.0/yt/data_objects/construction_data_containers.py in __init__(self, field, axis, weight_field, center, pf, data_source, style, field_parameters) 232 self.data_source = data_source 233 self.weight_field = weight_field --> 234 self.get_data(field) 235 236 @property /Users/teyssier/yt-3.0/yt/data_objects/construction_data_containers.py in get_data(self, fields) 276 # This needs to be parallel_objects-ified 277 for chunk in parallel_objects(self.data_source.chunks( --> 278 chunk_fields, "io")): 279 mylog.debug("Adding chunk (%s) to tree (%0.3e GB RAM)", chunk.ires.size, 280 get_memory_usage()/1024.) /Users/teyssier/yt-3.0/yt/utilities/parallel_tools/parallel_analysis_interface.py in parallel_objects(objects, njobs, storage, barrier, dynamic) 432 # this will prevent intermediate objects from being created. 433 oiter = itertools.islice(enumerate(objects), my_new_id, None, njobs) --> 434 for obj_id, obj in oiter: 435 result_id = obj_id * njobs + my_new_id 436 if storage is not None: /Users/teyssier/yt-3.0/yt/data_objects/data_containers.py in chunks(self, fields, chunking_style, **kwargs) 451 for chunk in self.hierarchy._chunk(self, chunking_style, **kwargs): 452 with self._chunked_read(chunk): --> 453 self.get_data(fields) 454 # NOTE: we yield before releasing the context 455 yield self /Users/teyssier/yt-3.0/yt/data_objects/data_containers.py in get_data(self, fields) 529 # need to be generated. 530 read_fluids, gen_fluids = self.hierarchy._read_fluid_fields( --> 531 fluids, self, self._current_chunk) 532 self.field_data.update(read_fluids) 533 /Users/teyssier/yt-3.0/yt/geometry/geometry_handler.py in _read_fluid_fields(self, fields, dobj, chunk) 512 selector, 513 fields_to_read, --> 514 chunk_size) 515 for field in fields_to_read: 516 ftype, fname = field /Users/teyssier/yt-3.0/yt/frontends/ramses/io.py in _read_fluid_selection(self, chunks, selector, fields, size) 39 # and pick off the right vectors 40 content = cStringIO.StringIO(f.read()) ---> 41 rv = subset.fill(content, fields, selector) 42 for ft, f in fields: 43 d = rv.pop(f) /Users/teyssier/yt-3.0/yt/frontends/ramses/data_structures.py in fill(self, content, fields, selector) 302 for field in fields: 303 tr[field] = np.zeros(cell_count, 'float64') --> 304 for level, offset in enumerate(self.domain.hydro_offset): 305 if offset == -1: continue 306 content.seek(offset) /Users/teyssier/yt-3.0/yt/frontends/ramses/data_structures.py in hydro_offset(self) 100 ('file_ncache', 1, 'I') ) 101 try: --> 102 hvals = fpu.read_attrs(f, header, "=") 103 except AssertionError: 104 print "You are running with the wrong number of fields." /Users/teyssier/yt-3.0/yt/utilities/fortran_utils.py in read_attrs(f, attrs, endian) 72 if s1 != s2: 73 size = struct.calcsize(endian + "I" + "".join(n*[t]) + "I") ---> 74 assert(s1 == s2) 75 if n == 1: v = v[0] 76 if type(a)==tuple: AssertionError:

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yt-3.0 ramses
by Romain Teyssier 19 Oct '13

19 Oct '13

I rebooted my mac and now it works ! Thanks to everyone ! Here is my first Ramses yt-image. Romain

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yt-3.0 install issue
by Romain Teyssier 19 Oct '13

19 Oct '13

I have built and installed yt-3.0 When I try to import the modules I have this: Any clue ? Romain

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Ramses data support
by Romain Teyssier 19 Oct '13

19 Oct '13

I am using yt from the bitbucket version. When I read, project and plot a Ramses snapshot (density) I get this: any ideas ? Romain

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reading joined vtk from Athena in yt
by Alexander Philippov 18 Oct '13

18 Oct '13

Hi, I have a problem reading joined vtk files from Athena in yt. Here is the problem. I have 800x2000 2D grid decomposed on 4 processors in a way that each output is 200x2000. I'm now joining vtks and trying to download it to yt. pf=load("khc.0001.vtk") print pf.h.grids [AthenaGrid_0000 ([ 200 2000 1])] So the size of the grid I get is as if it is not joined file. Tricks listed here https://bitbucket.org/yt_analysis/yt/issue/616/loading-vtk-files-from-athen… do not work. Hope someone can help with that. Thanks in advance, Sasha

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multiply a function of a field with another field
by Reju Sam John 17 Oct '13

17 Oct '13

Dear All, I want to multiply a function of a field in YT (function of MachNumber ) with another field in YT. How can I proceed? -- Reju Sam John

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Example of volume rendering on >1 field
by Chris Beaumont 15 Oct '13

15 Oct '13

Hi yt, Can someone point me to an example script that does a volume rendering using more than one field? I essentially want to make an isosurface rendering with two surfaces from different fields. From the docs I suspect this uses MultiVariateTransferFunction, but I'm finding the usage docstrings a bit opaque Thanks! chris

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install script failure
by Elizabeth Tasker 15 Oct '13

15 Oct '13

Hi, I was trying to re-install yt on my macbook and I get: /Users/Elizabeth/yt/bin/python2.7: can't open file '/distribute_setup.py': [Errno 2] No such file or directory … what did I break? Elizabeth

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install script failure (swig)
by Semyeong Oh 15 Oct '13

15 Oct '13

Hi, I'm trying to install yt on OS X 1.8.5, and get the following error: ******************************************** FAILURE REPORT: ******************************************** adding 'build/src.macosx-10.4-x86_64-2.7' to include_dirs. building extension "scipy.sparse.linalg.dsolve._superlu" sources building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack" sources creating build/src.macosx-10.4-x86_64-2.7/scipy/sparse/linalg/dsolve creating build/src.macosx-10.4-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack adding 'scipy/sparse/linalg/dsolve/umfpack/umfpack.i' to sources. swig: scipy/sparse/linalg/dsolve/umfpack/umfpack.i swig -python -I/opt/local/include -I/opt/local/include -I/opt/local/include -o build/src.macosx-10.4-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c -outdir build/src.macosx-10.4-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack scipy/sparse/linalg/dsolve/umfpack/umfpack.i unable to execute swig: No such file or directory error: command 'swig' failed with exit status 1 ******************************************** ******************************************** I've tried both stable and development, and both fail at the same point. Any ideas on how to fix it? Thank you, Semyeong

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