Mailman 3 October 2013 - yt-users

Parallel yt on Kraken
by Hilary Egan 10 Oct '13

10 Oct '13

Perhaps inadvisedly I'm trying to get parallel yt to work on kraken. As suggested in the docs faq I made sure I loaded the PrgEnv-gnu module and pip installed mpi4py with env MPICC=cc. Although this worked fine as is on my local machine, yt then complained about missing libraries, I guessed because of some sort of static linking/build problem, so I copied all of the libraries it complained about to $YT_DIR/lib (full list is below). Now it's giving me a completely indecipherable message about matplotlib which I've copied here: http://paste.yt-project.org/show/3939/. I only see this error when I try and run yt with the --parallel flag, so I'm guessing it must be related. Any advice would be greatly appreciated! Thanks, Hilary ______ Missing libraries yt complained about and I added: libgfortran.so.3 libscicpp_gnu.so.1 libsci_gnu_mp.so.1 libstdc++.so.6 libfttw3.so.3 libfftw3f.so.3 libmpich_gnu.so.gnu-46-1 libmpl.so.0 libpmi.so.0 libgomp.so.1 libquadmath.so.0 libmpich.so.1 libgcc_s.so.1 libportals.so.1 libalpsutil.so libalpslli.so

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(no subject)
by Hilary Egan 10 Oct '13

10 Oct '13

Setting HOME to the working directory worked! Thank you so much! -Hilary > Hi Hilary, > This is increasingly looking like a matplotlib bug -- but there is one > other thing you could try. Looking at the matplotlib source, it looks > like it checks HOME, USERPROFILE and TMP to see if they are None. So > you could try setting one of those three variables to the current > working directory of your script. Otherwise, maybe file an issue with > matplotlib? > Sorry ... :( > -Matt > On Thu, Oct 10, 2013 at 12:49 PM, Hilary Egan <hilaryye at gmail.com<http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > wrote: > >* Unfortunately setting XDG_CONFIG_HOME as the working directory didn't > work. > *>* I get this error message http://paste.yt-project.org/show/3941/ which > *>* appears to be the same problem as before. > *> > >* -Hilary > *> > >>* ________________________________ > *>> > >>* Hi Hilary, > *>> > >>* Yeah ... this is actually a problem with funny home directories and > *>>* Matplotlib 1.3.0. I think this is a problem specific to machines > *>>* where the home directories aren't visible. You may be able to either > *>>* set the environment variable XDG_CONFIG_HOME to the working directory > *>>* for some success. > *>> > >>* Additionally, I think that yt.pmods no longer works with matplotlib > *>>* 1.3.0, too, but it looks like you're using yt.mods, so that's good. > *>> > >>* Could you let us know if that works? > *>> > >>* -Matt > *>> > >>* On Wed, Oct 9, 2013 at 10:42 PM, Hilary Egan <hilaryye at gmail.com> > *>>* wrote: > *>>* > Perhaps inadvisedly I'm trying to get parallel yt to work on > kraken. As > *>>* > suggested in the docs faq I made sure I loaded the PrgEnv-gnu > module and > *>>* > pip > *>>* > installed mpi4py with env MPICC=cc. Although this worked fine as > is on > *>>* > my > *>>* > local machine, yt then complained about missing libraries, I > guessed > *>>* > because > *>>* > of some sort of static linking/build problem, so I copied all of > the > *>>* > libraries it complained about to $YT_DIR/lib (full list is below). > Now > *>>* > it's > *>>* > giving me a completely indecipherable message about matplotlib > which > *>>* > I've > *>>* > copied here: http://paste.yt-project.org/show/3939/.<http://paste.yt-project.org/show/3939/>I only see this > *>>* > error > *>>* > when I try and run yt with the --parallel flag, so I'm guessing it > must > *>>* > be > *>>* > related. Any advice would be greatly appreciated! > *>>* > > *>>* > Thanks, > *>>* > Hilary > *>>* > > *>>* > ______ > *>>* > > *>>* > Missing libraries yt complained about and I added: > *>>* > > *>>* > libgfortran.so.3 > *>>* > libscicpp_gnu.so.1 > *>>* > libsci_gnu_mp.so.1 > *>>* > libstdc++.so.6 > *>>* > libfttw3.so.3 > *>>* > libfftw3f.so.3 > *>>* > libmpich_gnu.so.gnu-46-1 > *>>* > libmpl.so.0 > *>>* > libpmi.so.0 > *>>* > libgomp.so.1 > *>>* > libquadmath.so.0 > *>>* > libmpich.so.1 > *>>* > libgcc_s.so.1 > *>>* > libportals.so.1 > *>>* > libalpsutil.so > *>>* > libalpslli.so > *>>* > > *>>* > > *>>* > _______________________________________________ > *>>* > yt-users mailing list > *>>* > yt-users at lists.spacepope.org > *>>* > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > *>> > >> > > > >* _______________________________________________ > *>* yt-users mailing list > *>* yt-users at lists.spacepope.org > <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> *>* > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > *> > ------------------------------ >

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starting yt notebook
by Stephanie Tonnesen 09 Oct '13

09 Oct '13

Hi users, A while ago I was using a yt notebook, and was running it with the command python2.7 notebook.py (I think). Now, I can't get a notebook to load! Can someone tell/remind me what the commands are? More specifically I am trying to get a tunnel for my notebook. When I type >python2.7 notebook.py Traceback (most recent call last): File "notebook.py", line 2, in <module> from IPython.frontend.html.notebook.notebookapp import NotebookApp File "/u/stonnes/Installs/yt-x86_64/lib/python2.7/site-packages/IPython/frontend/html/notebook/notebookapp.py", line 59, in <module> from IPython.frontend.consoleapp import IPythonConsoleApp File "/u/stonnes/Installs/yt-x86_64/lib/python2.7/site-packages/IPython/frontend/consoleapp.py", line 36, in <module> from IPython.lib.kernel import tunnel_to_kernel, find_connection_file, swallow_argv ImportError: cannot import name swallow_argv and when I type > yt notebook Traceback (most recent call last): File "/u/stonnes/Installs/yt-x86_64/bin/yt", line 9, in <module> load_entry_point('yt==2.6dev', 'console_scripts', 'yt')() File "/u/stonnes/Installs/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1695, in run_main args.func(args) File "/u/stonnes/Installs/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 84, in run self(args) File "/u/stonnes/Installs/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1454, in __call__ from IPython.frontend.html.notebook.notebookapp import NotebookApp File "/u/stonnes/Installs/yt-x86_64/lib/python2.7/site-packages/IPython/frontend/html/notebook/notebookapp.py", line 59, in <module> from IPython.frontend.consoleapp import IPythonConsoleApp File "/u/stonnes/Installs/yt-x86_64/lib/python2.7/site-packages/IPython/frontend/consoleapp.py", line 36, in <module> from IPython.lib.kernel import tunnel_to_kernel, find_connection_file, swallow_argv ImportError: cannot import name swallow_argv Thanks! Stephanie

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YT :: Failure Report :: h5py
by ABHIJIT BHATTACHARYYA 09 Oct '13

09 Oct '13

Hi! I find the present YT version is better. I wanted to install in Opensuse 12.3 in my laptop. I wanted to install as "ROOT" to install in /usr/local/YT-x64. Accordingly I modified yt_install.sh file. However, I find error dueing installation of h5py as shown in http://paste.yt-project.org/show/3926/ pastebin showing : cc -pthread -shared -L/usr/local/YT-x64/lib/ -L/usr/local/YT-x64/lib64/ -L/usr/local/YT-x64/lib/ -L/usr/local/YT-x64/lib64/ -L/usr/local/YT-x64/lib/ -L/usr/local/YT-x64/lib64/ -L/usr/local/YT-x64/lib/ -L/usr/local/YT-x64/lib64/ build/temp.linux-i686-2.7/h5py/defs.o -L/usr/local/YT-x64/lib -R/usr/local/YT-x64/lib -lhdf5 -lhdf5_hl -o build/lib.linux-i686-2.7/h5py/defs.so cc: error: unrecognized option ‘-R’ error: command 'cc' failed with exit status 1 ******************************************** ******************************************** Failure. Check /usr/local/YT-x64/yt_install.log. The last 10 lines are above. Aditya.site-> I have attached my yt_install.sh file. Please help me. Abhijit Bhattacharyya Mumbai, INDIA

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error on pmods import
by Morgan MacLeod 06 Oct '13

06 Oct '13

Dear YT developers, I'm having a slight yt parallelism issue on one cluster at UCSC, "Laozi". I just installed a fresh version of yt-3.0 on this machine. I'm pasting the full info below, but I will note that this is similar to an issue reported on the list: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2012-October/00… There was no published resolution on the list to this issue at that date. Have others seen this behavior since? If so, how should I proceed on this machine? The code below is a minimal example. In general, I would like to implement code similar to the examples here: http://yt-project.org/doc/advanced/parallel_computation.html using parallel_objects. The simple scripts I am trying to run proceed without warning or error on the other machines I have access to (Mac laptop, and ucsc cluster "hyades"). The error message mentions that the warning may be disabled. Is this the recommended setting for the cluster? Thanks for your advice. Morgan If I try to run this script: from yt.config import ytcfg from yt.pmods import * print range(10) I get this error output (related to the pmods import): (yt-x86_64)[morgan@laozi ytpar]$ mpirun -np 1 python test.py --parallel -------------------------------------------------------------------------- WARNING: There are more than one active ports on host 'laozi.ucsc.edu', but the default subnet GID prefix was detected on more than one of these ports. If these ports are connected to different physical IB networks, this configuration will fail in Open MPI. This version of Open MPI requires that every physically separate IB subnet that is used between connected MPI processes must have different subnet ID values. Please see this FAQ entry for more details: http://www.open-mpi.org/faq/?category=openfabrics#ofa-default-subnet-gid NOTE: You can turn off this warning by setting the MCA parameter btl_openib_warn_default_gid_prefix to 0. -------------------------------------------------------------------------- Beginning parallel import block. -------------------------------------------------------------------------- An MPI process has executed an operation involving a call to the "fork()" system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your MPI job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged. The process that invoked fork was: Local host: laozi.ucsc.edu (PID 31958) MPI_COMM_WORLD rank: 0 If you are *absolutely sure* that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0. -------------------------------------------------------------------------- Traceback (most recent call last): File "test.py", line 7, in <module> from yt.pmods import * File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 364, in <module> from yt.mods import * File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 235, in __import_hook__ m = __load_tail__(q, tail) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 339, in __load_tail__ m = __import_module__(head, mname, m) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 279, in __import_module__ m = imp.load_module(fqname, fp, pathname, stuff) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/mods.py", line 142, in <module> from yt.visualization.api import \ File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 235, in __import_hook__ m = __load_tail__(q, tail) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 339, in __load_tail__ m = __import_module__(head, mname, m) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 279, in __import_module__ m = imp.load_module(fqname, fp, pathname, stuff) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/visualization/api.py", line 31, in <module> from color_maps import \ File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 234, in __import_hook__ q, tail = __find_head_package__(parent, name) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 323, in __find_head_package__ q = __import_module__(head, qname, parent) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 279, in __import_module__ m = imp.load_module(fqname, fp, pathname, stuff) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/visualization/color_maps.py", line 26, in <module> import matplotlib File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 234, in __import_hook__ q, tail = __find_head_package__(parent, name) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 328, in __find_head_package__ q = __import_module__(head, qname, parent) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 279, in __import_module__ m = imp.load_module(fqname, fp, pathname, stuff) File "/share/work1/morgan/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/__init__.py", line 130, in <module> from matplotlib.compat import subprocess File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 239, in __import_hook__ __ensure_fromlist__(m, fromlist) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 357, in __ensure_fromlist__ submod = __import_module__(sub, subname, m) File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 279, in __import_module__ m = imp.load_module(fqname, fp, pathname, stuff) File "/share/work1/morgan/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/compat/subprocess.py", line 79, in <module> CalledProcessError = subprocess.CalledProcessError AttributeError: 'module' object has no attribute 'CalledProcessError' -------------------------------------------------------------------------- mpirun noticed that the job aborted, but has no info as to the process that caused that situation. -------------------------------------------------------------------------- (yt-x86_64)[morgan@laozi ytpar]$

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matplotlib backend install
by Semyeong Oh 04 Oct '13

04 Oct '13

Hi, I have anaconda python installed, and use this as my default python with Qt4Agg matplotlib backend in my home directory(It also has TKAgg and other backends). Yet when I install yt with the install script, it does not install any of the backends that allows me to view plots interactively. How can I properly install them? Best regards, Semyeong

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volume rendering with artio
by Owen Parry 04 Oct '13

04 Oct '13

Hi, I'm trying to do some volume rendering of artio outputs, but am running into problems setting up the camera. Seems like pf.h.grids is used when building the kd tree, but isn't defined for artio...? I'm using yt-3.0. Traceback here: http://paste.yt-project.org/show/2ouFxUS2MrGXbhxjLD6L/ My script is pretty much identical to the one in the volume rendering tutorial: http://paste.yt-project.org/show/3921/ Thanks, Owen

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Blocky Projections with RAMSES data when log=True
by Butler,Michael J 04 Oct '13

04 Oct '13

Hi everyone, I have been working with the stable branch of yt to look at RAMSES data and have run into a problem. When doing simple projections of e.g. Density with take_log=True, the projection becomes blocky (see attached image). This doesn't happen if I take out the take_log line. Here is what I am doing : pf = load("output_00427/info_00427.txt") pf.h pf.field_info['Density'].take_log = True p=SlicePlot(pf,2,"Density") Any ideas what is going on here? Thanks, Mike

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finding the Mach numbers?
by Reju Sam John 04 Oct '13

04 Oct '13

Hello, How we can find the Mach numbers for the full 128^3 region of a simulated clusters at a particular redshift(say Z=0) from ENZO output? Thanks -- Reju Sam John

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Problems with fields
by Cameron Hummels 02 Oct '13

02 Oct '13

Hello fellow yt'ers: I'm having some issues with some fields that I don't think are behaving the way they should be in yt. I'm encountering a number of problems with a simple 2D enzo dataset (x and y), so I put together a notebook demonstrating my various issues. https://hub.yt-project.org/nb/727j2j To summarize the weirdness from the notebook: 1) The 'dx' field doesn't seem to be able to be displayed (i.e. when I try to slice it), whereas the 'dy' field is fine. 'dz' even exists, but it's just uniformly 0, as is expected from a 2D dataset. 2) When I try to produce a new field which is 2^GridLevel, I get weird results (ignored levels and more). 3-5) I get strange behavior when trying to make a new field combining GridLevel and 'dy', since GridLevel has twice as many indices as any of the spatial fields (in the z direction no less). This results in some odd behavior when I try to pair various subsets of GridLevel with 'dy'. Any clarification of these ideas is welcome. The docs and source haven't yet revealed what is going on here. Thanks! Cameron -- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org

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yt-users October 2013