Mailman 3 September 2014 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 15 Aug '22

15 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

3 2

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

8 14

Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

6 8

Python SSL failure, yt3, osx
by David Collins 01 Oct '14

01 Oct '14

Hi, Everybody-- I have a potentially dumb question. I'm installing yt3.0 (a fresh install) on osx 10.9, and I get the following error. It looks like the error is coming from the hg clone, for some reason the newly installed python can't find SSL. I can use another install of hg on this machine just fine. Has anyone else seen this, and do you know if there's an easy fix? Thanks! d. Using curl Using shasum -a 512 Cloning yt Setting YT_DIR=/Users/dcollins/local-2014-09-23-yt3/src/yt-hg/ Installing distribute ******************************************** FAILURE REPORT: ******************************************** abort: repository /Users/dcollins/local-2014-09-23-yt3/src/yt-hg/ not found! /Users/dcollins/local-2014-09-23-yt3/bin/python2.7: can't open file '/Users/dcollins/local-2014-09-23-yt3/src/yt-hg//distribute_setup.py': [Errno 2] No such file or directory using https://bitbucket.org/yt_analysis/yt-supplemental/ sending capabilities command abort: Python SSL support not found using https://bitbucket.org/yt_analysis/yt/ sending capabilities command abort: Python SSL support not found abort: repository /Users/dcollins/local-2014-09-23-yt3/src/yt-hg/ not found! /Users/dcollins/local-2014-09-23-yt3/bin/python2.7: can't open file '/Users/dcollins/local-2014-09-23-yt3/src/yt-hg//distribute_setup.py': [Errno 2] No such file or directory -- -- Sent from a computer.

5 12

Stuck on installing Forthon
by 杨蕾(Lei Yang) 29 Sep '14

29 Sep '14

Hi all, I am following the introductions to setup Parallel HOP but I got stuck at "cd into yt/utilities/kdtree". I dont have a folder name "kdtree" in yt/utilities. Is it because I installed the yt in a wrong way? I installed the yt using "All-in-One Installation Script", and when I was installing it, everything went smoothly. But I knew that before I installed yt, there is a python already on my Mac. Any tips? Thanks a lot! Lei

2 1

Fwd: install failure
by Mordecai-Mark Mac Low 29 Sep '14

29 Sep '14

Here’s are examples of the problem. yt fails immediately with any usage. As you can see, I don’t have a lot of information here! [yt-x86_64] sagittariusb 1 % yt Abort [yt-x86_64] sagittariusb 2 % yt --help Abort [yt-x86_64] sagittariusb 3 % python Python 2.7.8 (default, Sep 28 2014, 20:55:56) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.51)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import yt Abort [yt-x86_64] sagittariusb 4 % I tried your suggestion of using the bash activate script: [yt-x86_64] sagittariusB 40 % bash yt-x86_64/bin/activate [yt-x86_64] sagittariusB 41 % yt Abort [yt-x86_64] sagittariusB 42 % FWIW, I do note that the “Abort” appears to be appearing a lot faster with the readline problem corrected. - Mordecai Begin forwarded message: > From: Nathan Goldbaum <nathan12343(a)gmail.com> > Subject: Re: [yt-users] install failure > Date: September 28, 2014 at 21:38:36 EDT > To: Mordecai-Mark Mac Low <mordecai(a)amnh.org> > Cc: <teuben(a)astro.umd.edu> > > > In your original message you said that you were using activate.csh - can you under bash with the bash activate script? > > When you say "on startup", can you copy/paste a session where the error happens? Are you saying that python is failing to start or do you get the abort error when you import yt? > > On Sun, Sep 28, 2014 at 6:35 PM, Mordecai-Mark Mac Low <mordecai(a)amnh.org> wrote: > I’m taking this off the general list for the moment… > > I have replaced readline with gnureadline as you suggested, and that does eliminate the error during installation (see https://dl.dropboxusercontent.com/u/31830722/yt_install-v2.log). Unfortunately, it doesn’t change the behavior on startup: Abort, with no further errors. > > At Peter Teuben’s suggestion, I also ran dtruss on this, but he saw nothing obviously wrong — just a whole lot of files being opened (around 900 at his estimate). > > - Mordecai > > > On Sep 28, 2014, at 20:45, Nathan Goldbaum <nathan12343(a)gmail.com> wrote: > >> >> ---------- Forwarded message ---------- >> From: Nathan Goldbaum <nathan12343(a)gmail.com> >> Date: Sun, Sep 28, 2014 at 5:29 PM >> Subject: Re: [yt-users] install failure >> To: Discussion of the yt analysis package <yt-users(a)lists.spacepope.org> >> >> >> So looking at the install log, it's actually the install script that's trying to build readline, right here: https://bitbucket.org/yt_analysis/yt/src/4cf5c5369df9b012759ab979330d8e356d… >> >> I'm actually able to reproduce this on my OSX Mavericks laptop when I do "pip install readline". It seems that the readline package on pypi hasn't been updated since 2012: https://pypi.python.org/pypi/readline. >> >> I never noticed this issue because I use homebrew's python, and homebrew links against the gnu readline library when they build python. >> >> It seems the gnureadline package has supplanted the old readline package: https://pypi.python.org/pypi/gnureadline >> >> I've gone ahead and created a pull request to make the install script install gnureadline instead of readline: https://bitbucket.org/yt_analysis/yt/pull-request/1225/install-gnureadline-… >> >> You can probably just modify your local copy of the install script to use "pip install gnureadline" instead of "pip install readline". >> >> Hope that fixes your issue, thanks very much for the report. >> >> -Nathan >> >> On Sun, Sep 28, 2014 at 5:00 PM, Mordecai-Mark Mac Low <mordecai(a)amnh.org> wrote: >> Nathan, >> >> I’ve posted the full install log to >> >> https://dl.dropboxusercontent.com/u/31830722/yt_install.log >> >> It does look like ipython is trying to compile readline. >> >> I have the regular Mac Python installation, but would have to learn anaconda or canopy before using them for an installation, which I was hoping to avoid for the moment by using the install script. >> >> Best, >> >> Mordecai >> >> >> On Sep 28, 2014, at 19:33, yt-users-request(a)lists.spacepope.org wrote: >> > Message: 1 >> > Date: Sun, 28 Sep 2014 13:57:47 -0700 >> > From: Nathan Goldbaum <nathan12343(a)gmail.com> >> > To: Discussion of the yt analysis package >> > <yt-users(a)lists.spacepope.org> >> > Subject: Re: [yt-users] install failure >> > Message-ID: >> > <CAJXewO=G9M7V0deBGtU46s68kdKPVTqsmhEBxV+yG7-K=8HcgQ(a)mail.gmail.com> >> > Content-Type: text/plain; charset="utf-8" >> > >> > Hi Mordecai, >> > >> > We've had some reports about incompatibilities with the install script on >> > OS X Mavericks recently, but I don't think this error has been reported >> > before. Unfortunately getting the install script to work portably in all >> > cases is a labor of love and sometimes errors like these crop up. >> > >> > Googling for your error returns this discussion on the readline mailing >> > list: https://lists.gnu.org/archive/html/bug-readline/2013-12/msg00002.html. >> > Apparently the version you're compiling needs to be patched to compile >> > cleanly on mavericks. I haven't checked whether the patch has made its way >> > into a readline release. >> > >> > I'm not sure what exactly is compiling readline (IPython maybe?), but >> > earlier in the install script we should have installed a pure-python >> > version of the readline library from pypi if we were unable to import it. >> > It would help to figure out what went wrong if you could upload the full >> > install log somewhere. >> > >> > Do you have a python environment setup on your laptop already? It's very >> > straightforward to install yt using anaconda, canopy, or a manually >> > configured python environment, bypassing all the bootstrapping that the >> > install script must do. Take a look at the following page in the >> > documentation: >> > >> > http://yt-project.org/doc/installing.html#installing-yt-using-anaconda >> > http://yt-project.org/doc/installing.html#installing-yt-using-pip-or-from-s… >> > >> > Hope that's helpful. >> > >> > -Nathan >> > >> > >> > On Sun, Sep 28, 2014 at 12:36 PM, Mordecai-Mark Mac Low <mordecai(a)amnh.org> >> > wrote: >> > >> >> Hi, I am having a fatal problem installing yt on my MacBook Pro running OS >> >> X v10.9.4. I am using the install script, with the options set as follows: >> >> >> >> >> >> # Here's where you put the HDF5 path if you like; otherwise it'll download >> >> it >> >> # and install it on its own >> >> #HDF5_DIR=/opt/local/lib >> >> >> >> # If you need to supply arguments to the NumPy or SciPy build, supply them >> >> here >> >> # This one turns on gfortran manually: >> >> #NUMPY_ARGS="--fcompiler=gnu95" >> >> # If you absolutely can't get the fortran to work, try this: >> >> #NUMPY_ARGS="--fcompiler=fake" >> >> >> >> INST_HG=0 # Install Mercurial or not? If hg is not already >> >> # installed, yt cannot be installed. >> >> INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with >> >> # the system zlib, which is compiled statically. >> >> # If need be, you can turn this off. >> >> INST_BZLIB=1 # On some systems, libbzip2 is missing. This can >> >> # lead to broken mercurial installations. >> >> INST_PNG=1 # Install a local libpng? Same things apply as with zlib. >> >> INST_FTYPE=1 # Install FreeType2 locally? >> >> INST_ENZO=0 # Clone a copy of Enzo? >> >> INST_SQLITE3=1 # Install a local version of SQLite3? >> >> INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without a >> >> # working TeX installation. >> >> INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings? >> >> INST_ROCKSTAR=1 # Install the Rockstar halo finder? >> >> INST_SCIPY=0 # Install scipy? >> >> >> >> >> >> After downloading and activating Xcode command line tools, I got the >> >> script to complete successfully. I activated it using the activate.csh >> >> script. >> >> >> >> However, when I then try to start yt, it pauses for 30 seconds or so, and >> >> then issues the response ?Abort?, with no further errors. I get the same >> >> response if I try to import yt into the python (running in the yt >> >> environment). Abort, and return to the command line. >> >> >> >> I have tried erasing the yt-x86_64 directory and reinstalling from >> >> scratch, with no change in behavior. I also examined the yt_install.log. >> >> I found a number of, presumably irrelevant, errors in the configuration >> >> tests, but also an error at the end of the long section on building Ipython >> >> (almost at the end of the script, just before readline assembly that looks >> >> possibly relevant: >> >> >> >> gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch` >> >> -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2 >> >> -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so >> >> funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so >> >> isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so >> >> callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so >> >> history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so >> >> tilde.so compat.so -lncurses >> >> Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn) >> >> Target: x86_64-apple-darwin13.3.0 >> >> Thread model: posix >> >> clang: error: invalid argument '-compatibility_version 6' only allowed >> >> with '-dynamiclib' >> >> clang: error: invalid argument '-compatibility_version 6' only allowed >> >> with '-dynamiclib' >> >> make[1]: *** [libreadline.6.2.dylib] Error 1 >> >> make: [shared] Error 2 (ignored) >> >> >> >> Any insight on how to proceed? >> >> >> >> Best, >> >> >> >> Mordecai >> >> >> >> >> >> -- >> >> Mordecai-Mark Mac Low Curator & Professor >> >> +1-212-496-3443 Department of Astrophysics >> >> +1-212-769-5007 (fax) American Museum of Natural History >> >> mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> yt-users mailing list >> >> yt-users(a)lists.spacepope.org >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> >> >> > -------------- next part -------------- >> > An HTML attachment was scrubbed... >> > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201…> >> > >> > ------------------------------ >> > >> > Message: 2 >> > Date: Sun, 28 Sep 2014 19:33:51 -0400 >> > From: Professor Maller <amaller(a)citytech.cuny.edu> >> > To: yt-users(a)lists.spacepope.org >> > Subject: Re: [yt-users] install failure >> > Message-ID: >> > <CACCSjdNPC0QVrxDooBEQ2W7Mp6KaBJxNJZ9eLvH6TG8WyD7m0Q(a)mail.gmail.com> >> > Content-Type: text/plain; charset="utf-8" >> > >> > Hi Mordecai, >> > >> > Depending on what you want to do with yt, if you need the latest build or >> > not, but I've had success on Mac with the anaconda distribution of python >> > which includes yt-3.0. https://store.continuum.io/cshop/anaconda/. >> > >> > >> > Ari >> > >> > >> > >> > On Sun, Sep 28, 2014 at 4:30 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. Re: ProfilePlot in YT-3.0 (Nathan Goldbaum) >> >> 2. install failure (Mordecai-Mark Mac Low) >> >> 3. Re: install failure (Peter Teuben) >> >> >> >> >> >> ---------------------------------------------------------------------- >> >> >> >> Message: 1 >> >> Date: Sun, 28 Sep 2014 12:14:04 -0700 >> >> From: Nathan Goldbaum <nathan12343(a)gmail.com> >> >> To: Discussion of the yt analysis package >> >> <yt-users(a)lists.spacepope.org> >> >> Subject: Re: [yt-users] ProfilePlot in YT-3.0 >> >> Message-ID: >> >> < >> >> CAJXewOkKaMPBE02RH_VY4rNTXgOobeJ02qOOZY5PRk332GGveg(a)mail.gmail.com> >> >> Content-Type: text/plain; charset="utf-8" >> >> >> >> On Sunday, September 28, 2014, John Regan <johnanthonyregan(a)gmail.com> >> >> wrote: >> >> >> >>> Hi Nathan, >> >>> >> >>> Thanks for that. I'll have a look at what helper functions would be >> >> useful >> >>> as I use the ProfilePlot routine and I can issue a PR then. I think it >> >>> would be worth updating the docs with info like you just sent me. >> >>> >> >> >> >> Again, please feel free to open a pull request. >> >> >> >> >> >>> >> >>> Cheers, >> >>> John >> >>> >> >>> On Sun, Sep 28, 2014 at 11:17 AM, Nathan Goldbaum <nathan12343(a)gmail.com >> >>> <javascript:_e(%7B%7D,'cvml','nathan12343(a)gmail.com');>> wrote: >> >>> >> >>>> Hi John, >> >>>> >> >>>> ProfilePlot is a wrapper around the Profile1D class, which calculates >> >> and >> >>>> stores the histograms. To access the underlying data you need to access >> >>>> the profile object via the profiles attribute of the ProfilePlot: >> >>>> >> >>>> import yt >> >>>> ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') >> >>>> plot = yt.ProfilePlot(ds.all_data(), 'radius', 'density') >> >>>> profile = plot.profiles[0] >> >>>> print profile.x_field, profile.x >> >>>> print profile.field_data.keys(), profile['density'] >> >>>> >> >>>> There are probably a number of ways that the current API can be improved >> >>>> to make it more straightforward to access this data. PRs along this >> >> front >> >>>> would be very welcome, I think. >> >>>> >> >>>> -Nathan >> >>>> >> >>>> On Sun, Sep 28, 2014 at 1:05 AM, John Regan <johnanthonyregan(a)gmail.com >> >>>> <javascript:_e(%7B%7D,'cvml','johnanthonyregan(a)gmail.com');>> wrote: >> >>>> >> >>>>> HI All, >> >>>>> >> >>>>> Is there an easy way to access the x_field and the y_fields in the >> >>>>> ProfilePlot function? >> >>>>> >> >>>>> So for example >> >>>>> >> >>>>> prof = ProfilePlot(sphere, "radius", "density") >> >>>>> >> >>>>> >> >>>>> print prof.x_field >> >>>>> print prof.y_field[0] >> >>>>> >> >>>>> I inserted a couple of hack functions into the ProfilePlot class to >> >>>>> return the x_field and the .items() tuple but there is probably a >> >> better >> >>>>> way? >> >>>>> >> >>>>> John >> >>>>> >> >>>>> _______________________________________________ >> >>>>> yt-users mailing list >> >>>>> yt-users(a)lists.spacepope.org >> >>>>> <javascript:_e(%7B%7D,'cvml','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 >> >>>> <javascript:_e(%7B%7D,'cvml','yt-users(a)lists.spacepope.org');> >> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >>>> >> >>>> >> >>> >> >> -------------- next part -------------- >> >> An HTML attachment was scrubbed... >> >> URL: < >> >> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… >> >>> >> >> >> >> ------------------------------ >> >> >> >> Message: 2 >> >> Date: Sun, 28 Sep 2014 15:36:55 -0400 >> >> From: Mordecai-Mark Mac Low <mordecai(a)amnh.org> >> >> To: <yt-users(a)lists.spacepope.org> >> >> Subject: [yt-users] install failure >> >> Message-ID: <C2FC80DA-9E95-476E-BB68-E5944D4597F3(a)amnh.org> >> >> Content-Type: text/plain; charset="windows-1252" >> >> >> >> Hi, I am having a fatal problem installing yt on my MacBook Pro running OS >> >> X v10.9.4. I am using the install script, with the options set as follows: >> >> >> >> >> >> # Here's where you put the HDF5 path if you like; otherwise it'll download >> >> it >> >> # and install it on its own >> >> #HDF5_DIR=/opt/local/lib >> >> >> >> # If you need to supply arguments to the NumPy or SciPy build, supply them >> >> here >> >> # This one turns on gfortran manually: >> >> #NUMPY_ARGS="--fcompiler=gnu95" >> >> # If you absolutely can't get the fortran to work, try this: >> >> #NUMPY_ARGS="--fcompiler=fake" >> >> >> >> INST_HG=0 # Install Mercurial or not? If hg is not already >> >> # installed, yt cannot be installed. >> >> INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with >> >> # the system zlib, which is compiled statically. >> >> # If need be, you can turn this off. >> >> INST_BZLIB=1 # On some systems, libbzip2 is missing. This can >> >> # lead to broken mercurial installations. >> >> INST_PNG=1 # Install a local libpng? Same things apply as with zlib. >> >> INST_FTYPE=1 # Install FreeType2 locally? >> >> INST_ENZO=0 # Clone a copy of Enzo? >> >> INST_SQLITE3=1 # Install a local version of SQLite3? >> >> INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without a >> >> # working TeX installation. >> >> INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings? >> >> INST_ROCKSTAR=1 # Install the Rockstar halo finder? >> >> INST_SCIPY=0 # Install scipy? >> >> >> >> >> >> After downloading and activating Xcode command line tools, I got the >> >> script to complete successfully. I activated it using the activate.csh >> >> script. >> >> >> >> However, when I then try to start yt, it pauses for 30 seconds or so, and >> >> then issues the response ?Abort?, with no further errors. I get the same >> >> response if I try to import yt into the python (running in the yt >> >> environment). Abort, and return to the command line. >> >> >> >> I have tried erasing the yt-x86_64 directory and reinstalling from >> >> scratch, with no change in behavior. I also examined the yt_install.log. >> >> I found a number of, presumably irrelevant, errors in the configuration >> >> tests, but also an error at the end of the long section on building Ipython >> >> (almost at the end of the script, just before readline assembly that looks >> >> possibly relevant: >> >> >> >> gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch` >> >> -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2 >> >> -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so >> >> funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so >> >> isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so >> >> callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so >> >> history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so >> >> tilde.so compat.so -lncurses >> >> Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn) >> >> Target: x86_64-apple-darwin13.3.0 >> >> Thread model: posix >> >> clang: error: invalid argument '-compatibility_version 6' only allowed >> >> with '-dynamiclib' >> >> clang: error: invalid argument '-compatibility_version 6' only allowed >> >> with '-dynamiclib' >> >> make[1]: *** [libreadline.6.2.dylib] Error 1 >> >> make: [shared] Error 2 (ignored) >> >> >> >> Any insight on how to proceed? >> >> >> >> Best, >> >> >> >> Mordecai >> >> >> >> >> >> -- >> >> Mordecai-Mark Mac Low Curator & Professor >> >> +1-212-496-3443 Department of Astrophysics >> >> +1-212-769-5007 (fax) American Museum of Natural History >> >> mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA >> >> >> >> >> >> >> >> >> >> -------------- next part -------------- >> >> An HTML attachment was scrubbed... >> >> URL: < >> >> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… >> >>> >> >> >> >> ------------------------------ >> >> >> >> Message: 3 >> >> Date: Sun, 28 Sep 2014 16:30:01 -0400 >> >> From: Peter Teuben <teuben(a)astro.umd.edu> >> >> To: yt-users(a)lists.spacepope.org >> >> Subject: Re: [yt-users] install failure >> >> Message-ID: <54286FC9.1010003(a)astro.umd.edu> >> >> Content-Type: text/plain; charset="windows-1252" >> >> >> >> >> >> just "abort" usually tells me it can't find enough memory while loading >> >> the executable. >> >> I assume you got plenty of that. >> >> >> >> On linux I would then use 'strace' to see if the kernel tells me more. >> >> And the ldd >> >> command to see what shared libs it might need. >> >> >> >> On a mac, there appears to be the dtruss command for strace. Me and Mac >> >> appear >> >> to be in a continues state of dislike, all I got was >> >> dtrace: failed to initialize dtrace: DTrace requires additional >> >> privileges >> >> so I'm sure somebody can tell me what that means (I don't have admin on >> >> that mac) >> >> >> >> peter >> >> >> >> >> >> On 09/28/2014 03:36 PM, Mordecai-Mark Mac Low wrote: >> >>> Hi, I am having a fatal problem installing yt on my MacBook Pro >> >>> running OS X v10.9.4. I am using the install script, with the options >> >>> set as follows: >> >>> >> >>> >> >>> # Here's where you put the HDF5 path if you like; otherwise it'll >> >>> download it >> >>> # and install it on its own >> >>> #HDF5_DIR=/opt/local/lib >> >>> >> >>> # If you need to supply arguments to the NumPy or SciPy build, supply >> >>> them here >> >>> # This one turns on gfortran manually: >> >>> #NUMPY_ARGS="--fcompiler=gnu95" >> >>> # If you absolutely can't get the fortran to work, try this: >> >>> #NUMPY_ARGS="--fcompiler=fake" >> >>> >> >>> INST_HG=0 # Install Mercurial or not? If hg is not already >> >>> # installed, yt cannot be installed. >> >>> INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with >> >>> # the system zlib, which is compiled statically. >> >>> # If need be, you can turn this off. >> >>> INST_BZLIB=1 # On some systems, libbzip2 is missing. This can >> >>> # lead to broken mercurial installations. >> >>> INST_PNG=1 # Install a local libpng? Same things apply as with >> >> zlib. >> >>> INST_FTYPE=1 # Install FreeType2 locally? >> >>> INST_ENZO=0 # Clone a copy of Enzo? >> >>> INST_SQLITE3=1 # Install a local version of SQLite3? >> >>> INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without >> >> a >> >>> # working TeX installation. >> >>> INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings? >> >>> INST_ROCKSTAR=1 # Install the Rockstar halo finder? >> >>> INST_SCIPY=0 # Install scipy? >> >>> >> >>> >> >>> After downloading and activating Xcode command line tools, I got the >> >>> script to complete successfully. I activated it using the activate.csh >> >>> script. >> >>> >> >>> However, when I then try to start yt, it pauses for 30 seconds or so, >> >>> and then issues the response ?Abort?, with no further errors. I get >> >>> the same response if I try to import yt into the python (running in >> >>> the yt environment). Abort, and return to the command line. >> >>> >> >>> I have tried erasing the yt-x86_64 directory and reinstalling from >> >>> scratch, with no change in behavior. I also examined the >> >>> yt_install.log. I found a number of, presumably irrelevant, errors in >> >>> the configuration tests, but also an error at the end of the long >> >>> section on building Ipython (almost at the end of the script, just >> >>> before readline assembly that looks possibly relevant: >> >>> >> >>> gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch` >> >>> -install_name /usr/local/lib/libreadline.6.2.dylib -current_version >> >>> 6.2 -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so >> >>> vi_mode.so funmap.so keymaps.so parens.so search.so rltty.so >> >>> complete.so bind.so isearch.so display.so signals.so util.so kill.so >> >>> undo.so macro.so input.so callback.so terminal.so text.so nls.so >> >>> misc.so xmalloc.so xfree.so history.so histexpand.so histfile.so >> >>> histsearch.so shell.so mbutil.so tilde.so compat.so -lncurses >> >>> Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn) >> >>> Target: x86_64-apple-darwin13.3.0 >> >>> Thread model: posix >> >>> clang: error: invalid argument '-compatibility_version 6' only >> >>> allowed with '-dynamiclib' >> >>> clang: error: invalid argument '-compatibility_version 6' only >> >>> allowed with '-dynamiclib' >> >>> make[1]: *** [libreadline.6.2.dylib] Error 1 >> >>> make: [shared] Error 2 (ignored) >> >>> >> >>> Any insight on how to proceed? >> >>> >> >>> Best, >> >>> >> >>> Mordecai >> >>> >> >>> >> >>> -- >> >>> Mordecai-Mark Mac Low Curator & Professor >> >>> +1-212-496-3443 Department of Astrophysics >> >>> +1-212-769-5007 (fax) American Museum of Natural History >> >>> mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> _______________________________________________ >> >>> yt-users mailing list >> >>> yt-users(a)lists.spacepope.org >> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> >> -------------- next part -------------- >> >> An HTML attachment was scrubbed... >> >> URL: < >> >> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… >> >>> >> >> >> >> ------------------------------ >> >> >> >> Subject: Digest Footer >> >> >> >> _______________________________________________ >> >> 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 79, Issue 40 >> >> **************************************** >> >> >> > -------------- next part -------------- >> > An HTML attachment was scrubbed... >> > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201…> >> > >> > ------------------------------ >> > >> > Subject: Digest Footer >> > >> > _______________________________________________ >> > 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 79, Issue 41 >> > **************************************** >> >> -- >> Mordecai-Mark Mac Low Curator & Professor >> +1-212-496-3443 Department of Astrophysics >> +1-212-769-5007 (fax) American Museum of Natural History >> mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA >> >> >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > > > -- > Mordecai-Mark Mac Low Curator & Professor > +1-212-496-3443 Department of Astrophysics > +1-212-769-5007 (fax) American Museum of Natural History > mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA > > > > > -- Mordecai-Mark Mac Low Curator & Professor +1-212-496-3443 Department of Astrophysics +1-212-769-5007 (fax) American Museum of Natural History mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA

3 2

Re: [yt-users] install failure
by Mordecai-Mark Mac Low 29 Sep '14

29 Sep '14

Begin forwarded message: > From: Peter Teuben <teuben(a)astro.umd.edu> > Subject: Re: dtruss to debug yt > Date: September 28, 2014 at 21:22:13 EDT > To: Mordecai-Mark Mac Low <mordecai(a)amnh.org> > > Hi Mordecai > > I don't see anything obviously wrong with this. Often it's one of the last read's > or open's that points to something odd. > > that's a long listing! 11k lines, of which almost 1/3 are just opening a file. > Almost 3700 files! What the heck, i thought. Actually, 2790 or so are just attempt > (i guess to check) and they are not present. So that still leaves the app with > about 900 files to open. Looks like about 100 of those are opening more than once, > kinda odd. Buy again, nothing obvious in terms of filling memory or something else. > > > Maybe that readline does some good, although I saw no reference to that in the > dtruss output. > > peter > > > > On 09/28/2014 08:43 PM, Mordecai-Mark Mac Low wrote: >> Dear Peter, >> >> Thanks for the suggestion of using dtruss. >> >> It turns out that it just needs to be run under su to do its work. However… although (or perhaps because) I got 1.3 Mb of output, I was unable to pull out a smoking gun about what was going wrong. I have posted the output to: >> >> https://dl.dropboxusercontent.com/u/31830722/dtruss-trace-yt.txt >> >> Do you see anything going obviously wrong? >> >> - Mordecai >> >> >> -- >> Mordecai-Mark Mac Low Curator & Professor >> +1-212-496-3443 Department of Astrophysics >> +1-212-769-5007 (fax) American Museum of Natural History >> mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA >> >> >> > -- Mordecai-Mark Mac Low Curator & Professor +1-212-496-3443 Department of Astrophysics +1-212-769-5007 (fax) American Museum of Natural History mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA

1 0

Re: [yt-users] install failure
by Mordecai-Mark Mac Low 29 Sep '14

29 Sep '14

Nathan, I’ve posted the full install log to https://dl.dropboxusercontent.com/u/31830722/yt_install.log It does look like ipython is trying to compile readline. I have the regular Mac Python installation, but would have to learn anaconda or canopy before using them for an installation, which I was hoping to avoid for the moment by using the install script. Best, Mordecai On Sep 28, 2014, at 19:33, yt-users-request(a)lists.spacepope.org wrote: > Message: 1 > Date: Sun, 28 Sep 2014 13:57:47 -0700 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] install failure > Message-ID: > <CAJXewO=G9M7V0deBGtU46s68kdKPVTqsmhEBxV+yG7-K=8HcgQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Mordecai, > > We've had some reports about incompatibilities with the install script on > OS X Mavericks recently, but I don't think this error has been reported > before. Unfortunately getting the install script to work portably in all > cases is a labor of love and sometimes errors like these crop up. > > Googling for your error returns this discussion on the readline mailing > list: https://lists.gnu.org/archive/html/bug-readline/2013-12/msg00002.html. > Apparently the version you're compiling needs to be patched to compile > cleanly on mavericks. I haven't checked whether the patch has made its way > into a readline release. > > I'm not sure what exactly is compiling readline (IPython maybe?), but > earlier in the install script we should have installed a pure-python > version of the readline library from pypi if we were unable to import it. > It would help to figure out what went wrong if you could upload the full > install log somewhere. > > Do you have a python environment setup on your laptop already? It's very > straightforward to install yt using anaconda, canopy, or a manually > configured python environment, bypassing all the bootstrapping that the > install script must do. Take a look at the following page in the > documentation: > > http://yt-project.org/doc/installing.html#installing-yt-using-anaconda > http://yt-project.org/doc/installing.html#installing-yt-using-pip-or-from-s… > > Hope that's helpful. > > -Nathan > > > On Sun, Sep 28, 2014 at 12:36 PM, Mordecai-Mark Mac Low <mordecai(a)amnh.org> > wrote: > >> Hi, I am having a fatal problem installing yt on my MacBook Pro running OS >> X v10.9.4. I am using the install script, with the options set as follows: >> >> >> # Here's where you put the HDF5 path if you like; otherwise it'll download >> it >> # and install it on its own >> #HDF5_DIR=/opt/local/lib >> >> # If you need to supply arguments to the NumPy or SciPy build, supply them >> here >> # This one turns on gfortran manually: >> #NUMPY_ARGS="--fcompiler=gnu95" >> # If you absolutely can't get the fortran to work, try this: >> #NUMPY_ARGS="--fcompiler=fake" >> >> INST_HG=0 # Install Mercurial or not? If hg is not already >> # installed, yt cannot be installed. >> INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with >> # the system zlib, which is compiled statically. >> # If need be, you can turn this off. >> INST_BZLIB=1 # On some systems, libbzip2 is missing. This can >> # lead to broken mercurial installations. >> INST_PNG=1 # Install a local libpng? Same things apply as with zlib. >> INST_FTYPE=1 # Install FreeType2 locally? >> INST_ENZO=0 # Clone a copy of Enzo? >> INST_SQLITE3=1 # Install a local version of SQLite3? >> INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without a >> # working TeX installation. >> INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings? >> INST_ROCKSTAR=1 # Install the Rockstar halo finder? >> INST_SCIPY=0 # Install scipy? >> >> >> After downloading and activating Xcode command line tools, I got the >> script to complete successfully. I activated it using the activate.csh >> script. >> >> However, when I then try to start yt, it pauses for 30 seconds or so, and >> then issues the response ?Abort?, with no further errors. I get the same >> response if I try to import yt into the python (running in the yt >> environment). Abort, and return to the command line. >> >> I have tried erasing the yt-x86_64 directory and reinstalling from >> scratch, with no change in behavior. I also examined the yt_install.log. >> I found a number of, presumably irrelevant, errors in the configuration >> tests, but also an error at the end of the long section on building Ipython >> (almost at the end of the script, just before readline assembly that looks >> possibly relevant: >> >> gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch` >> -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2 >> -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so >> funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so >> isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so >> callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so >> history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so >> tilde.so compat.so -lncurses >> Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn) >> Target: x86_64-apple-darwin13.3.0 >> Thread model: posix >> clang: error: invalid argument '-compatibility_version 6' only allowed >> with '-dynamiclib' >> clang: error: invalid argument '-compatibility_version 6' only allowed >> with '-dynamiclib' >> make[1]: *** [libreadline.6.2.dylib] Error 1 >> make: [shared] Error 2 (ignored) >> >> Any insight on how to proceed? >> >> Best, >> >> Mordecai >> >> >> -- >> Mordecai-Mark Mac Low Curator & Professor >> +1-212-496-3443 Department of Astrophysics >> +1-212-769-5007 (fax) American Museum of Natural History >> mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA >> >> >> >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >

2 1

Re: [yt-users] install failure
by Professor Maller 28 Sep '14

28 Sep '14

Hi Mordecai, Depending on what you want to do with yt, if you need the latest build or not, but I've had success on Mac with the anaconda distribution of python which includes yt-3.0. https://store.continuum.io/cshop/anaconda/. Ari On Sun, Sep 28, 2014 at 4:30 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. Re: ProfilePlot in YT-3.0 (Nathan Goldbaum) > 2. install failure (Mordecai-Mark Mac Low) > 3. Re: install failure (Peter Teuben) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 28 Sep 2014 12:14:04 -0700 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] ProfilePlot in YT-3.0 > Message-ID: > < > CAJXewOkKaMPBE02RH_VY4rNTXgOobeJ02qOOZY5PRk332GGveg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Sunday, September 28, 2014, John Regan <johnanthonyregan(a)gmail.com> > wrote: > > > Hi Nathan, > > > > Thanks for that. I'll have a look at what helper functions would be > useful > > as I use the ProfilePlot routine and I can issue a PR then. I think it > > would be worth updating the docs with info like you just sent me. > > > > Again, please feel free to open a pull request. > > > > > > Cheers, > > John > > > > On Sun, Sep 28, 2014 at 11:17 AM, Nathan Goldbaum <nathan12343(a)gmail.com > > <javascript:_e(%7B%7D,'cvml','nathan12343(a)gmail.com');>> wrote: > > > >> Hi John, > >> > >> ProfilePlot is a wrapper around the Profile1D class, which calculates > and > >> stores the histograms. To access the underlying data you need to access > >> the profile object via the profiles attribute of the ProfilePlot: > >> > >> import yt > >> ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') > >> plot = yt.ProfilePlot(ds.all_data(), 'radius', 'density') > >> profile = plot.profiles[0] > >> print profile.x_field, profile.x > >> print profile.field_data.keys(), profile['density'] > >> > >> There are probably a number of ways that the current API can be improved > >> to make it more straightforward to access this data. PRs along this > front > >> would be very welcome, I think. > >> > >> -Nathan > >> > >> On Sun, Sep 28, 2014 at 1:05 AM, John Regan <johnanthonyregan(a)gmail.com > >> <javascript:_e(%7B%7D,'cvml','johnanthonyregan(a)gmail.com');>> wrote: > >> > >>> HI All, > >>> > >>> Is there an easy way to access the x_field and the y_fields in the > >>> ProfilePlot function? > >>> > >>> So for example > >>> > >>> prof = ProfilePlot(sphere, "radius", "density") > >>> > >>> > >>> print prof.x_field > >>> print prof.y_field[0] > >>> > >>> I inserted a couple of hack functions into the ProfilePlot class to > >>> return the x_field and the .items() tuple but there is probably a > better > >>> way? > >>> > >>> John > >>> > >>> _______________________________________________ > >>> yt-users mailing list > >>> yt-users(a)lists.spacepope.org > >>> <javascript:_e(%7B%7D,'cvml','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 > >> <javascript:_e(%7B%7D,'cvml','yt-users(a)lists.spacepope.org');> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Sun, 28 Sep 2014 15:36:55 -0400 > From: Mordecai-Mark Mac Low <mordecai(a)amnh.org> > To: <yt-users(a)lists.spacepope.org> > Subject: [yt-users] install failure > Message-ID: <C2FC80DA-9E95-476E-BB68-E5944D4597F3(a)amnh.org> > Content-Type: text/plain; charset="windows-1252" > > Hi, I am having a fatal problem installing yt on my MacBook Pro running OS > X v10.9.4. I am using the install script, with the options set as follows: > > > # Here's where you put the HDF5 path if you like; otherwise it'll download > it > # and install it on its own > #HDF5_DIR=/opt/local/lib > > # If you need to supply arguments to the NumPy or SciPy build, supply them > here > # This one turns on gfortran manually: > #NUMPY_ARGS="--fcompiler=gnu95" > # If you absolutely can't get the fortran to work, try this: > #NUMPY_ARGS="--fcompiler=fake" > > INST_HG=0 # Install Mercurial or not? If hg is not already > # installed, yt cannot be installed. > INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with > # the system zlib, which is compiled statically. > # If need be, you can turn this off. > INST_BZLIB=1 # On some systems, libbzip2 is missing. This can > # lead to broken mercurial installations. > INST_PNG=1 # Install a local libpng? Same things apply as with zlib. > INST_FTYPE=1 # Install FreeType2 locally? > INST_ENZO=0 # Clone a copy of Enzo? > INST_SQLITE3=1 # Install a local version of SQLite3? > INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without a > # working TeX installation. > INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings? > INST_ROCKSTAR=1 # Install the Rockstar halo finder? > INST_SCIPY=0 # Install scipy? > > > After downloading and activating Xcode command line tools, I got the > script to complete successfully. I activated it using the activate.csh > script. > > However, when I then try to start yt, it pauses for 30 seconds or so, and > then issues the response ?Abort?, with no further errors. I get the same > response if I try to import yt into the python (running in the yt > environment). Abort, and return to the command line. > > I have tried erasing the yt-x86_64 directory and reinstalling from > scratch, with no change in behavior. I also examined the yt_install.log. > I found a number of, presumably irrelevant, errors in the configuration > tests, but also an error at the end of the long section on building Ipython > (almost at the end of the script, just before readline assembly that looks > possibly relevant: > > gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch` > -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2 > -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so > funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so > isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so > callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so > history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so > tilde.so compat.so -lncurses > Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn) > Target: x86_64-apple-darwin13.3.0 > Thread model: posix > clang: error: invalid argument '-compatibility_version 6' only allowed > with '-dynamiclib' > clang: error: invalid argument '-compatibility_version 6' only allowed > with '-dynamiclib' > make[1]: *** [libreadline.6.2.dylib] Error 1 > make: [shared] Error 2 (ignored) > > Any insight on how to proceed? > > Best, > > Mordecai > > > -- > Mordecai-Mark Mac Low Curator & Professor > +1-212-496-3443 Department of Astrophysics > +1-212-769-5007 (fax) American Museum of Natural History > mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 3 > Date: Sun, 28 Sep 2014 16:30:01 -0400 > From: Peter Teuben <teuben(a)astro.umd.edu> > To: yt-users(a)lists.spacepope.org > Subject: Re: [yt-users] install failure > Message-ID: <54286FC9.1010003(a)astro.umd.edu> > Content-Type: text/plain; charset="windows-1252" > > > just "abort" usually tells me it can't find enough memory while loading > the executable. > I assume you got plenty of that. > > On linux I would then use 'strace' to see if the kernel tells me more. > And the ldd > command to see what shared libs it might need. > > On a mac, there appears to be the dtruss command for strace. Me and Mac > appear > to be in a continues state of dislike, all I got was > dtrace: failed to initialize dtrace: DTrace requires additional > privileges > so I'm sure somebody can tell me what that means (I don't have admin on > that mac) > > peter > > > On 09/28/2014 03:36 PM, Mordecai-Mark Mac Low wrote: > > Hi, I am having a fatal problem installing yt on my MacBook Pro > > running OS X v10.9.4. I am using the install script, with the options > > set as follows: > > > > > > # Here's where you put the HDF5 path if you like; otherwise it'll > > download it > > # and install it on its own > > #HDF5_DIR=/opt/local/lib > > > > # If you need to supply arguments to the NumPy or SciPy build, supply > > them here > > # This one turns on gfortran manually: > > #NUMPY_ARGS="--fcompiler=gnu95" > > # If you absolutely can't get the fortran to work, try this: > > #NUMPY_ARGS="--fcompiler=fake" > > > > INST_HG=0 # Install Mercurial or not? If hg is not already > > # installed, yt cannot be installed. > > INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with > > # the system zlib, which is compiled statically. > > # If need be, you can turn this off. > > INST_BZLIB=1 # On some systems, libbzip2 is missing. This can > > # lead to broken mercurial installations. > > INST_PNG=1 # Install a local libpng? Same things apply as with > zlib. > > INST_FTYPE=1 # Install FreeType2 locally? > > INST_ENZO=0 # Clone a copy of Enzo? > > INST_SQLITE3=1 # Install a local version of SQLite3? > > INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without > a > > # working TeX installation. > > INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings? > > INST_ROCKSTAR=1 # Install the Rockstar halo finder? > > INST_SCIPY=0 # Install scipy? > > > > > > After downloading and activating Xcode command line tools, I got the > > script to complete successfully. I activated it using the activate.csh > > script. > > > > However, when I then try to start yt, it pauses for 30 seconds or so, > > and then issues the response ?Abort?, with no further errors. I get > > the same response if I try to import yt into the python (running in > > the yt environment). Abort, and return to the command line. > > > > I have tried erasing the yt-x86_64 directory and reinstalling from > > scratch, with no change in behavior. I also examined the > > yt_install.log. I found a number of, presumably irrelevant, errors in > > the configuration tests, but also an error at the end of the long > > section on building Ipython (almost at the end of the script, just > > before readline assembly that looks possibly relevant: > > > > gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch` > > -install_name /usr/local/lib/libreadline.6.2.dylib -current_version > > 6.2 -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so > > vi_mode.so funmap.so keymaps.so parens.so search.so rltty.so > > complete.so bind.so isearch.so display.so signals.so util.so kill.so > > undo.so macro.so input.so callback.so terminal.so text.so nls.so > > misc.so xmalloc.so xfree.so history.so histexpand.so histfile.so > > histsearch.so shell.so mbutil.so tilde.so compat.so -lncurses > > Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn) > > Target: x86_64-apple-darwin13.3.0 > > Thread model: posix > > clang: error: invalid argument '-compatibility_version 6' only > > allowed with '-dynamiclib' > > clang: error: invalid argument '-compatibility_version 6' only > > allowed with '-dynamiclib' > > make[1]: *** [libreadline.6.2.dylib] Error 1 > > make: [shared] Error 2 (ignored) > > > > Any insight on how to proceed? > > > > Best, > > > > Mordecai > > > > > > -- > > Mordecai-Mark Mac Low Curator & Professor > > +1-212-496-3443 Department of Astrophysics > > +1-212-769-5007 (fax) American Museum of Natural History > > mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA > > > > > > > > > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > 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 79, Issue 40 > **************************************** >

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install failure
by Mordecai-Mark Mac Low 28 Sep '14

28 Sep '14

Hi, I am having a fatal problem installing yt on my MacBook Pro running OS X v10.9.4. I am using the install script, with the options set as follows: # Here's where you put the HDF5 path if you like; otherwise it'll download it # and install it on its own #HDF5_DIR=/opt/local/lib # If you need to supply arguments to the NumPy or SciPy build, supply them here # This one turns on gfortran manually: #NUMPY_ARGS="--fcompiler=gnu95" # If you absolutely can't get the fortran to work, try this: #NUMPY_ARGS="--fcompiler=fake" INST_HG=0 # Install Mercurial or not? If hg is not already # installed, yt cannot be installed. INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with # the system zlib, which is compiled statically. # If need be, you can turn this off. INST_BZLIB=1 # On some systems, libbzip2 is missing. This can # lead to broken mercurial installations. INST_PNG=1 # Install a local libpng? Same things apply as with zlib. INST_FTYPE=1 # Install FreeType2 locally? INST_ENZO=0 # Clone a copy of Enzo? INST_SQLITE3=1 # Install a local version of SQLite3? INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without a # working TeX installation. INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings? INST_ROCKSTAR=1 # Install the Rockstar halo finder? INST_SCIPY=0 # Install scipy? After downloading and activating Xcode command line tools, I got the script to complete successfully. I activated it using the activate.csh script. However, when I then try to start yt, it pauses for 30 seconds or so, and then issues the response “Abort”, with no further errors. I get the same response if I try to import yt into the python (running in the yt environment). Abort, and return to the command line. I have tried erasing the yt-x86_64 directory and reinstalling from scratch, with no change in behavior. I also examined the yt_install.log. I found a number of, presumably irrelevant, errors in the configuration tests, but also an error at the end of the long section on building Ipython (almost at the end of the script, just before readline assembly that looks possibly relevant: gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch` -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2 -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so tilde.so compat.so -lncurses Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn) Target: x86_64-apple-darwin13.3.0 Thread model: posix clang: error: invalid argument '-compatibility_version 6' only allowed with '-dynamiclib' clang: error: invalid argument '-compatibility_version 6' only allowed with '-dynamiclib' make[1]: *** [libreadline.6.2.dylib] Error 1 make: [shared] Error 2 (ignored) Any insight on how to proceed? Best, Mordecai -- Mordecai-Mark Mac Low Curator & Professor +1-212-496-3443 Department of Astrophysics +1-212-769-5007 (fax) American Museum of Natural History mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA

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