Mailman 3 April 2013 - yt-users

Install Issue with SQLite
by Drummond Fielding April 10, 2013

April 10, 2013

Hello everyone, I am trying to run the latest version of the install script and getting the following failure: Installing SQLite3 ******************************************** FAILURE REPORT: ******************************************** configure: creating ./config.status config.status: creating Makefile config.status: creating sqlite3.pc config.status: executing depfiles commands if /bin/sh ./libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"sqlite\" -DPACKAGE_TARNAME=\"sqlite\" -DPACKAGE_VERSION=\"3.7.5\" -DPACKAGE_STRING=\"sqlite\ 3.7.5\" -DPACKAGE_BUGREPORT=\"http://www.sqlite.org\" -DPACKAGE=\"sqlite\" -DVERSION=\"3.7.5\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_FDATASYNC=1 -DHAVE_USLEEP=1 -DHAVE_LOCALTIME_R=1 -DHAVE_GMTIME_R=1 -DHAVE_READLINE=1 -I. -I. -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -MT sqlite3.lo -MD -MP -MF ".deps/sqlite3.Tpo" -c -o sqlite3.lo sqlite3.c; \ then mv -f ".deps/sqlite3.Tpo" ".deps/sqlite3.Plo"; else rm -f ".deps/sqlite3.Tpo"; exit 1; fi mkdir .libs gcc -DPACKAGE_NAME=\"sqlite\" -DPACKAGE_TARNAME=\"sqlite\" -DPACKAGE_VERSION=\"3.7.5\" "-DPACKAGE_STRING=\"sqlite 3.7.5\"" -DPACKAGE_BUGREPORT=\"http://www.sqlite.org\" -DPACKAGE=\"sqlite\" -DVERSION=\"3.7.5\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_FDATASYNC=1 -DHAVE_USLEEP=1 -DHAVE_LOCALTIME_R=1 -DHAVE_GMTIME_R=1 -DHAVE_READLINE=1 -I. -I. -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -MT sqlite3.lo -MD -MP -MF .deps/sqlite3.Tpo -c sqlite3.c -fno-common -DPIC -o .libs/sqlite3.o gcc.exec: error: 3.7.5": No such file or directory make: *** [sqlite3.lo] Error 1 ******************************************** ******************************************** It was my understanding that all of the sqlite configuration is contained in sqlite-autoconf-3070500 so I am not really sure what is going wrong. Any thoughts? Thanks in advance Drummond

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Installing yt-dev on OS X 10.8.3
by Brian Crosby April 9, 2013

April 9, 2013

Hi everyone, I've run into a problem installing yt-dev. It appears to be having problems while installing matplotlib, and is failing as follows: Installing matplotlib-1.2.0 (arguments: 'matplotlib-1.2.0') ******************************************** FAILURE REPORT: ******************************************** building 'matplotlib.ft2font' extension gcc-4.2 -DNDEBUG -g -fwrapv -O3 -Wall -mmacosx-version-min=10.7 -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/Users/crosby/yt-dev-x86_64/include -I/Users/crosby/yt-dev-x86_64/lib/python2.7/site-packages/numpy/core/include -I/Users/crosby/yt-dev-x86_64/include/freetype2 -I/Users/crosby/yt-dev-x86_64/include -I. -I/Users/crosby/yt-dev-x86_64/include/python2.7 -c src/ft2font.cpp -o build/temp.macosx-10.4-x86_64-2.7/src/ft2font.o gcc-4.2 -DNDEBUG -g -fwrapv -O3 -Wall -mmacosx-version-min=10.7 -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/Users/crosby/yt-dev-x86_64/include -I/Users/crosby/yt-dev-x86_64/lib/python2.7/site-packages/numpy/core/include -I/Users/crosby/yt-dev-x86_64/include/freetype2 -I/Users/crosby/yt-dev-x86_64/include -I. -I/Users/crosby/yt-dev-x86_64/include/python2.7 -c src/mplutils.cpp -o build/temp.macosx-10.4-x86_64-2.7/src/mplutils.o gcc-4.2 -DNDEBUG -g -fwrapv -O3 -Wall -mmacosx-version-min=10.7 -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/Users/crosby/yt-dev-x86_64/include -I/Users/crosby/yt-dev-x86_64/lib/python2.7/site-packages/numpy/core/include -I/Users/crosby/yt-dev-x86_64/include/freetype2 -I/Users/crosby/yt-dev-x86_64/include -I. -I/Users/crosby/yt-dev-x86_64/include/python2.7 -c CXX/cxx_extensions.cxx -o build/temp.macosx-10.4-x86_64-2.7/CXX/cxx_extensions.o gcc-4.2 -DNDEBUG -g -fwrapv -O3 -Wall -mmacosx-version-min=10.7 -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/Users/crosby/yt-dev-x86_64/include -I/Users/crosby/yt-dev-x86_64/lib/python2.7/site-packages/numpy/core/include -I/Users/crosby/yt-dev-x86_64/include/freetype2 -I/Users/crosby/yt-dev-x86_64/include -I. -I/Users/crosby/yt-dev-x86_64/include/python2.7 -c CXX/cxxsupport.cxx -o build/temp.macosx-10.4-x86_64-2.7/CXX/cxxsupport.o gcc-4.2 -DNDEBUG -g -fwrapv -O3 -Wall -mmacosx-version-min=10.7 -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/Users/crosby/yt-dev-x86_64/include -I/Users/crosby/yt-dev-x86_64/lib/python2.7/site-packages/numpy/core/include -I/Users/crosby/yt-dev-x86_64/include/freetype2 -I/Users/crosby/yt-dev-x86_64/include -I. -I/Users/crosby/yt-dev-x86_64/include/python2.7 -c CXX/IndirectPythonInterface.cxx -o build/temp.macosx-10.4-x86_64-2.7/CXX/IndirectPythonInterface.o gcc-4.2 -DNDEBUG -g -fwrapv -O3 -Wall -mmacosx-version-min=10.7 -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/Users/crosby/yt-dev-x86_64/include -I/Users/crosby/yt-dev-x86_64/lib/python2.7/site-packages/numpy/core/include -I/Users/crosby/yt-dev-x86_64/include/freetype2 -I/Users/crosby/yt-dev-x86_64/include -I. -I/Users/crosby/yt-dev-x86_64/include/python2.7 -c CXX/cxxextensions.c -o build/temp.macosx-10.4-x86_64-2.7/CXX/cxxextensions.o g++-4.2 -bundle -undefined dynamic_lookup -L/Users/crosby/yt-dev-x86_64/lib/ -L/Users/crosby/yt-dev-x86_64/lib64/ -L/Users/crosby/yt-dev-x86_64/lib/ -L/Users/crosby/yt-dev-x86_64/lib64/ -L/Users/crosby/yt-dev-x86_64/lib/ -L/Users/crosby/yt-dev-x86_64/lib64/ -L/Users/crosby/yt-dev-x86_64/lib/ -L/Users/crosby/yt-dev-x86_64/lib64/ -mmacosx-version-min=10.7 build/temp.macosx-10.4-x86_64-2.7/src/ft2font.o build/temp.macosx-10.4-x86_64-2.7/src/mplutils.o build/temp.macosx-10.4-x86_64-2.7/CXX/cxx_extensions.o build/temp.macosx-10.4-x86_64-2.7/CXX/cxxsupport.o build/temp.macosx-10.4-x86_64-2.7/CXX/IndirectPythonInterface.o build/temp.macosx-10.4-x86_64-2.7/CXX/cxxextensions.o -L/Users/crosby/yt-dev-x86_64/lib -L/Users/crosby/yt-dev-x86_64/lib -lfreetype -lz -lstdc++ -lm -o build/lib.macosx-10.4-x86_64-2.7/matplotlib/ft2font.so unable to execute g++-4.2: No such file or directory error: command 'g++-4.2' failed with exit status 1 I'm installing on OS X 10.8.3, and am now using a fresh install of Xcode tools in an earlier attempt to solve this. I have also set the environment variables CC=gcc-4.2 and CXX=g++-4.2, as suggested by the install script. Has anyone encountered this before, or have any suggestions for solving it? Thanks, Brian

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Projection Question
by david collins April 9, 2013

April 9, 2013

Hi, Everybody! I have a probably dumb question. I keep getting the following error when projecting. I get this from a variety of methods, but what I'm trying to do is project a region. What I used to do was something like this, but it's no longer working (with or without the source.) reg = pf.h.region(center,left,right) pf = load(thing) pc = PlotCollection(pf) proj = pf.h.proj(0,'Density',center=Center) #,source=reg) prooj = pc.add_projection('Density','x') #,data_source=reg) So my question is: with the recent developments to yt, what's the best mechanism to do this? I'm on a self install that was done fresh pretty recently, the hash is 34b95297062b Thanks, d. prooj = pc.add_projection('Density','x',data_source=reg) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_collection.py", line 786, in add_projection size=fig_size, periodic=periodic)) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py", line 326, in __init__ self.__init_temp_image(use_colorbar) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py", line 358, in __init_temp_image shrink=0.95) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/figure.py", line 1387, in colorbar cb = cbar.colorbar_factory(cax, mappable, **kw) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 1173, in colorbar_factory cb = Colorbar(cax, mappable, **kwargs) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 854, in __init__ ColorbarBase.__init__(self, ax, **kw) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 298, in __init__ self.draw_all() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 323, in draw_all self._config_axes(X, Y) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 409, in _config_axes self.update_ticks() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 345, in update_ticks ticks, ticklabels, offset_string = self._ticker() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 560, in _ticker ticks = self._locate(b) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 808, in _locate z = np.take(y, i0) + (xn-np.take(b,i0))*dy/db

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Projection issue
by Elizabeth Tasker April 5, 2013

April 5, 2013

Hello, I have 2 problems, but possibly I only need the solution to one :) (1) If I calculate the total mass in a simulation via the projection: projection = pf.h.proj(2, 'CellMass') sum(projection["CellMass"]/projection["pdx"]/2.0/3.08568025e18) (i.e. sum(sum(m_i*dl)/dl) ) I get: 1.4855032022312827e+43 However, if I just sum it directly: dd = pf.h.all_data() sum(dd["CellMass"]) I get: 6.3279045575257765e+42 I was expecting those two numbers to be approximately the same. Why are they very different? Have I misunderstood the value of pdx? I think it should be equal to half the integration step. (2) The second problem occurred when I tried to fix this by using a fixed resolution projection (in case a variable dl was the issue). I tried: proj = pf.h.fixed_res_proj(2, 0, [0, 0, 0], [128,128,128]) (My root grid is 128^3) but I get: ValueError Traceback (most recent call last) /home/tasker/yt-new/src/yt-hg/scripts/iyt in <module>() ----> 1 proj = pf.h.fixed_res_proj(2, 0, [0, 0, 0], [128,128,128]) /home/tasker/yt-new/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, level, left_edge, dims, fields, pf, **kwargs) 2460 self.domain_width = np.rint((self.pf.domain_right_edge - 2461 self.pf.domain_left_edge)/self.dds).astype('int64') -> 2462 self._refresh_data() 2463 2464 def _get_list_of_grids(self): /home/tasker/yt-new/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 318 """ 319 self.clear_data() --> 320 self.get_data() 321 322 def keys(self): /home/tasker/yt-new/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields) 2494 Iterates over the list of fields and generates/reads them all. 2495 """ -> 2496 self._get_list_of_grids() 2497 if not self.has_key('pdx'): 2498 self._generate_coords() /home/tasker/yt-new/src/yt-hg/yt/data_objects/data_containers.pyc in _get_list_of_grids(self) 2470 else: 2471 grids,ind = self.pf.hierarchy.get_box_grids( -> 2472 self.left_edge, self.right_edge) 2473 level_ind = (self.pf.hierarchy.grid_levels.ravel()[ind] <= self.level) 2474 sort_ind = np.argsort(self.pf.h.grid_levels.ravel()[ind][level_ind]) /home/tasker/yt-new/src/yt-hg/yt/data_objects/object_finding_mixin.pyc in get_box_grids(self, left_edge, right_edge) 201 eps = np.finfo(np.float64).eps 202 grid_i = np.where((np.all((self.grid_right_edge - left_edge) > eps, axis=1) --> 203 & np.all((right_edge - self.grid_left_edge) > eps, axis=1)) == True) 204 205 return self.grids[grid_i], grid_i ValueError: operands could not be broadcast together with shapes (3,3) (7100,3) What did I do wrong? Thank you! Elizabeth

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yt-3.0 question: find_field_value_at_point()
by nick moeckel April 4, 2013

April 4, 2013

Hi there, I've been working with yt-3.0 and Ramses over the past few days. One thing that seems to not be working (or rather, to not be existing) is pf.h.find_field_value_at_point() I'm not sure if this is a problem or a design choice for 3.0- if the latter, is there a new way to do the same thing? best, Nick

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Problem with BinnedProfile1D
by trobolo dinni April 2, 2013

April 2, 2013

Dear yt users, I would like to ask you a suggestion about an error I am getting. I have a set of outputs from an Enzo simulation and the basis of my code is the following: *from yt.mods import ** *import matplotlib.pyplot as plt* *import numpy as np* *import math* *import os* * * *pf = load("/home/cthulhu/Downloads/DD0000/data0000")* * * *common_envelope = pf.h.all_data()* * * *radial_profile = BinnedProfile1D(common_envelope, 200, "Radius", 0.0, 0.5, log_space=False)* * * * * but when creating the binned profile yt gives me this error: *EmptyProfileData Traceback (most recent call last) * * * */home/cthulhu/Repository/Python/yt scripts/5.common_envelope_INCOMPLETE.pyin <module>() * * 12 * * 13 #creating binned profiles to evaluate v,rho,P,T in function of the radius* * * *---> 14 radial_profile = BinnedProfile1D(common_envelope, 200, "Radius", 0.0, 0.5, log_space=False)* * 15 * * 16 * * * */usr/local/lib/python2.7/dist-packages/yt-2.5-py2.7-linux-x86_64.egg/yt/data_objects/profiles.pyc in __init__(self, data_source, n_bins, bin_field, lower_bound, upper_bound, log_space, lazy_reader, end_collect)* * 251 # and the inverse indices right now.* * * * 252 if not lazy_reader:* *--> 253 self._args = self._get_bins(data_source)* * 254 * * 255 def _get_empty_field(self):* * * */usr/local/lib/python2.7/dist-packages/yt-2.5-py2.7-linux-x86_64.egg/yt/data_objects/profiles.pyc in save_state(*args, **kwargs)* * 53 old_params = source.field_parameters* * 54 source.field_parameters = prof._data_source.field_parameters* *---> 55 tr = func(*args, **kwargs)* * 56 source.field_parameters = old_params* * 57 else:* * * */usr/local/lib/python2.7/dist-packages/yt-2.5-py2.7-linux-x86_64.egg/yt/data_objects/profiles.pyc in _get_bins(self, source, check_cut)* * 300 sd = source_data[mi]* * 301 if sd.size == 0:* *--> 302 raise EmptyProfileData()* * 303 # Stick the bins into our fixed bins, set at initialization * * * * 304 bin_indices = np.digitize(sd, self._bins)* * * *EmptyProfileData: * * * It is not clear to me what is the problem at the basis of this error, do you have an idea of what to do? Thanks, Roberto

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