Mailman 3 September 2014 - yt-users

ProfilePlot in YT-3.0
by John Regan 28 Sep '14

28 Sep '14

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

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Re: [yt-users] yt-users Digest, Vol 79, Issue 37
by Brandon Bozek 26 Sep '14

26 Sep '14

Thanks! That was the hint I needed. I am on a cluster that loads modules to have access to various packages and I had the module for python loaded. Unloading it, caused it to move forward. thanks for the quick help everyone! On Fri, Sep 26, 2014 at 5:34 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: yt-users Digest, Vol 79, Issue 35 (Nathan Goldbaum) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 26 Sep 2014 14:33:53 -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] yt-users Digest, Vol 79, Issue 35 > Message-ID: > <CAJXewO= > MeHbEEEXptVmH6jKDYkp+KNuJsHreqNbt1weyLJccKQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hmm, I guess it's possible that building yt's python failed, and later in > the install script it is trying to install mercurial using the system > python. > > Would you mind uploading the full install log somewhere? Dropbox and > google drive are useful for sharing big files like this over e-mail. > > -Nathan > > On Fri, Sep 26, 2014 at 2:29 PM, Brandon Bozek <brandon.bozek(a)gmail.com> > wrote: > > > Thanks for the series of replies. > > > > I ran "bash install_script.sh" to start the install. I am able to create > > file/directory in the directory I am in. The install script creates > > ./yt-x86_64/ and downloads a bunch of files before hitting this hiccup. > > > > > > On Fri, Sep 26, 2014 at 5:21 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. install error on large cluster (Brandon Bozek) > >> 2. Re: install error on large cluster (Nathan Goldbaum) > >> 3. Re: install error on large cluster (Chris Malone) > >> 4. Re: install error on large cluster (Nathan Goldbaum) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Fri, 26 Sep 2014 17:03:58 -0400 > >> From: Brandon Bozek <brandon.bozek(a)gmail.com> > >> To: yt-users(a)lists.spacepope.org > >> Subject: [yt-users] install error on large cluster > >> Message-ID: > >> <CADMUOqetC_YKk6TAiW+YKxSqbm5edmdx7s_t= > >> xS6z+3q4v5W4A(a)mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> Hello All, > >> > >> I am trying to install yt on a cluster at my institution and I ran the > >> install script for the stable version and got this error: "error: could > >> not > >> create '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > >> Read-only file system". > >> > >> The last few lines are copied below. Please let me know if I should send > >> anything else. > >> > >> Thanks! > >> Brandon > >> > >> creating build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/coal-folder.png -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/style-gitweb.css -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/background.png -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/style-coal.css -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/hglogo.png -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/style-paper.css -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/style.css -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/excanvas.js -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/coal-file.png -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/hgicon.png -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/mercurial.js -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/feed-icon-14x14.png -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/style-monoblue.css -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> running build_scripts > >> > >> creating build/scripts-2.7 > >> > >> copying and adjusting hg -> build/scripts-2.7 > >> > >> changing mode of build/scripts-2.7/hg from 644 to 755 > >> > >> running install > >> > >> running build > >> > >> running build_mo > >> > >> running build_ext > >> > >> running build_py > >> > >> running build_scripts > >> > >> running install_lib > >> > >> creating /usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial > >> > >> error: could not create > >> '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > Read-only > >> file system > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: < > >> > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >> > > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Fri, 26 Sep 2014 14:07:04 -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] install error on large cluster > >> Message-ID: > >> < > >> CAJXewOmmu0Oux1FaTFndS4jT_ede0waH3_VdtzeHgKFuELr-oA(a)mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> Hi Brandon, > >> > >> How did you invoke the install script? > >> > >> -Nathan > >> > >> On Fri, Sep 26, 2014 at 2:03 PM, Brandon Bozek <brandon.bozek(a)gmail.com > > > >> wrote: > >> > >> > Hello All, > >> > > >> > I am trying to install yt on a cluster at my institution and I ran the > >> > install script for the stable version and got this error: "error: > could > >> not > >> > create > '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > >> > Read-only file system". > >> > > >> > The last few lines are copied below. Please let me know if I should > send > >> > anything else. > >> > > >> > Thanks! > >> > Brandon > >> > > >> > creating build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/coal-folder.png -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/style-gitweb.css -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/background.png -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/style-coal.css -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/hglogo.png -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/style-paper.css -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/style.css -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/excanvas.js -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/coal-file.png -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/hgicon.png -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/mercurial.js -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/feed-icon-14x14.png -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/style-monoblue.css -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > running build_scripts > >> > > >> > creating build/scripts-2.7 > >> > > >> > copying and adjusting hg -> build/scripts-2.7 > >> > > >> > changing mode of build/scripts-2.7/hg from 644 to 755 > >> > > >> > running install > >> > > >> > running build > >> > > >> > running build_mo > >> > > >> > running build_ext > >> > > >> > running build_py > >> > > >> > running build_scripts > >> > > >> > running install_lib > >> > > >> > creating /usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial > >> > > >> > error: could not create > >> > '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > >> Read-only > >> > file system > >> > > >> > _______________________________________________ > >> > 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: 3 > >> Date: Fri, 26 Sep 2014 15:18:26 -0600 > >> From: Chris Malone <chris.m.malone(a)gmail.com> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] install error on large cluster > >> Message-ID: > >> < > >> CAED6uLZnaSBn0z_9T4yzMd1PzQRrT3jUyRU+eWK6tqT3i7XC6A(a)mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> Hi Brandon, > >> > >> The 'Read-only file system' part makes me think the issue isn't related > to > >> the yt build. Usually that message happens when the filesystem detected > >> an > >> error and the OS remounts the file system in read-only mode. Are there > >> any > >> other issues on the FS? Are you able to manually create a > file/directory > >> on that FS? > >> > >> Chris > >> > >> On Fri, Sep 26, 2014 at 3:03 PM, Brandon Bozek <brandon.bozek(a)gmail.com > > > >> wrote: > >> > >> > Hello All, > >> > > >> > I am trying to install yt on a cluster at my institution and I ran the > >> > install script for the stable version and got this error: "error: > could > >> not > >> > create > '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > >> > Read-only file system". > >> > > >> > The last few lines are copied below. Please let me know if I should > send > >> > anything else. > >> > > >> > Thanks! > >> > Brandon > >> > > >> > creating build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/coal-folder.png -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/style-gitweb.css -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/background.png -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/style-coal.css -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/hglogo.png -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/style-paper.css -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/style.css -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/excanvas.js -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/coal-file.png -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/hgicon.png -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/mercurial.js -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/feed-icon-14x14.png -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > copying mercurial/templates/static/style-monoblue.css -> > >> > build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > > >> > running build_scripts > >> > > >> > creating build/scripts-2.7 > >> > > >> > copying and adjusting hg -> build/scripts-2.7 > >> > > >> > changing mode of build/scripts-2.7/hg from 644 to 755 > >> > > >> > running install > >> > > >> > running build > >> > > >> > running build_mo > >> > > >> > running build_ext > >> > > >> > running build_py > >> > > >> > running build_scripts > >> > > >> > running install_lib > >> > > >> > creating /usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial > >> > > >> > error: could not create > >> > '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > >> Read-only > >> > file system > >> > > >> > _______________________________________________ > >> > 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: 4 > >> Date: Fri, 26 Sep 2014 14:20:58 -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 error on large cluster > >> Message-ID: > >> < > >> CAJXewOm4JzsXUGPhDpQ6CfnM1XNkMTR5xDemLx14hivKWy_dPA(a)mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> On Fri, Sep 26, 2014 at 2:18 PM, Chris Malone <chris.m.malone(a)gmail.com > > > >> wrote: > >> > >> > Hi Brandon, > >> > > >> > The 'Read-only file system' part makes me think the issue isn't > related > >> to > >> > the yt build. Usually that message happens when the filesystem > >> detected an > >> > error and the OS remounts the file system in read-only mode. Are > there > >> any > >> > other issues on the FS? Are you able to manually create a > >> file/directory > >> > on that FS? > >> > > >> > >> Note that mercurial is being installed into /usr/local, which should > never > >> happen using the install script. That's why I asked how the install > >> script > >> was being invoked. > >> > >> > >> > > >> > Chris > >> > > >> > On Fri, Sep 26, 2014 at 3:03 PM, Brandon Bozek < > brandon.bozek(a)gmail.com > >> > > >> > wrote: > >> > > >> >> Hello All, > >> >> > >> >> I am trying to install yt on a cluster at my institution and I ran > the > >> >> install script for the stable version and got this error: "error: > >> could not > >> >> create > '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > >> >> Read-only file system". > >> >> > >> >> The last few lines are copied below. Please let me know if I should > >> send > >> >> anything else. > >> >> > >> >> Thanks! > >> >> Brandon > >> >> > >> >> creating build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/coal-folder.png -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/style-gitweb.css -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/background.png -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/style-coal.css -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/hglogo.png -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/style-paper.css -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/style.css -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/excanvas.js -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/coal-file.png -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/hgicon.png -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/mercurial.js -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/feed-icon-14x14.png -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> copying mercurial/templates/static/style-monoblue.css -> > >> >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> >> > >> >> running build_scripts > >> >> > >> >> creating build/scripts-2.7 > >> >> > >> >> copying and adjusting hg -> build/scripts-2.7 > >> >> > >> >> changing mode of build/scripts-2.7/hg from 644 to 755 > >> >> > >> >> running install > >> >> > >> >> running build > >> >> > >> >> running build_mo > >> >> > >> >> running build_ext > >> >> > >> >> running build_py > >> >> > >> >> running build_scripts > >> >> > >> >> running install_lib > >> >> > >> >> creating > /usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial > >> >> > >> >> error: could not create > >> >> '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > >> Read-only > >> >> file system > >> >> > >> >> _______________________________________________ > >> >> 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 > >> > > >> > > >> -------------- 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 35 > >> **************************************** > >> > > > > > > _______________________________________________ > > 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 37 > **************************************** >

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Re: [yt-users] yt-users Digest, Vol 79, Issue 35
by Brandon Bozek 26 Sep '14

26 Sep '14

Thanks for the series of replies. I ran "bash install_script.sh" to start the install. I am able to create file/directory in the directory I am in. The install script creates ./yt-x86_64/ and downloads a bunch of files before hitting this hiccup. On Fri, Sep 26, 2014 at 5:21 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. install error on large cluster (Brandon Bozek) > 2. Re: install error on large cluster (Nathan Goldbaum) > 3. Re: install error on large cluster (Chris Malone) > 4. Re: install error on large cluster (Nathan Goldbaum) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 26 Sep 2014 17:03:58 -0400 > From: Brandon Bozek <brandon.bozek(a)gmail.com> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] install error on large cluster > Message-ID: > <CADMUOqetC_YKk6TAiW+YKxSqbm5edmdx7s_t= > xS6z+3q4v5W4A(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello All, > > I am trying to install yt on a cluster at my institution and I ran the > install script for the stable version and got this error: "error: could not > create '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > Read-only file system". > > The last few lines are copied below. Please let me know if I should send > anything else. > > Thanks! > Brandon > > creating build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/coal-folder.png -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/style-gitweb.css -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/background.png -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/style-coal.css -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/hglogo.png -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/style-paper.css -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/style.css -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/excanvas.js -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/coal-file.png -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/hgicon.png -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/mercurial.js -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/feed-icon-14x14.png -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > copying mercurial/templates/static/style-monoblue.css -> > build/lib.linux-x86_64-2.7/mercurial/templates/static > > running build_scripts > > creating build/scripts-2.7 > > copying and adjusting hg -> build/scripts-2.7 > > changing mode of build/scripts-2.7/hg from 644 to 755 > > running install > > running build > > running build_mo > > running build_ext > > running build_py > > running build_scripts > > running install_lib > > creating /usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial > > error: could not create > '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': Read-only > file system > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Fri, 26 Sep 2014 14:07:04 -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] install error on large cluster > Message-ID: > < > CAJXewOmmu0Oux1FaTFndS4jT_ede0waH3_VdtzeHgKFuELr-oA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Brandon, > > How did you invoke the install script? > > -Nathan > > On Fri, Sep 26, 2014 at 2:03 PM, Brandon Bozek <brandon.bozek(a)gmail.com> > wrote: > > > Hello All, > > > > I am trying to install yt on a cluster at my institution and I ran the > > install script for the stable version and got this error: "error: could > not > > create '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > > Read-only file system". > > > > The last few lines are copied below. Please let me know if I should send > > anything else. > > > > Thanks! > > Brandon > > > > creating build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/coal-folder.png -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/style-gitweb.css -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/background.png -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/style-coal.css -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/hglogo.png -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/style-paper.css -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/style.css -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/excanvas.js -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/coal-file.png -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/hgicon.png -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/mercurial.js -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/feed-icon-14x14.png -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/style-monoblue.css -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > running build_scripts > > > > creating build/scripts-2.7 > > > > copying and adjusting hg -> build/scripts-2.7 > > > > changing mode of build/scripts-2.7/hg from 644 to 755 > > > > running install > > > > running build > > > > running build_mo > > > > running build_ext > > > > running build_py > > > > running build_scripts > > > > running install_lib > > > > creating /usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial > > > > error: could not create > > '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > Read-only > > file system > > > > _______________________________________________ > > 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: 3 > Date: Fri, 26 Sep 2014 15:18:26 -0600 > From: Chris Malone <chris.m.malone(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] install error on large cluster > Message-ID: > < > CAED6uLZnaSBn0z_9T4yzMd1PzQRrT3jUyRU+eWK6tqT3i7XC6A(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Brandon, > > The 'Read-only file system' part makes me think the issue isn't related to > the yt build. Usually that message happens when the filesystem detected an > error and the OS remounts the file system in read-only mode. Are there any > other issues on the FS? Are you able to manually create a file/directory > on that FS? > > Chris > > On Fri, Sep 26, 2014 at 3:03 PM, Brandon Bozek <brandon.bozek(a)gmail.com> > wrote: > > > Hello All, > > > > I am trying to install yt on a cluster at my institution and I ran the > > install script for the stable version and got this error: "error: could > not > > create '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > > Read-only file system". > > > > The last few lines are copied below. Please let me know if I should send > > anything else. > > > > Thanks! > > Brandon > > > > creating build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/coal-folder.png -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/style-gitweb.css -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/background.png -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/style-coal.css -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/hglogo.png -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/style-paper.css -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/style.css -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/excanvas.js -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/coal-file.png -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/hgicon.png -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/mercurial.js -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/feed-icon-14x14.png -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > copying mercurial/templates/static/style-monoblue.css -> > > build/lib.linux-x86_64-2.7/mercurial/templates/static > > > > running build_scripts > > > > creating build/scripts-2.7 > > > > copying and adjusting hg -> build/scripts-2.7 > > > > changing mode of build/scripts-2.7/hg from 644 to 755 > > > > running install > > > > running build > > > > running build_mo > > > > running build_ext > > > > running build_py > > > > running build_scripts > > > > running install_lib > > > > creating /usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial > > > > error: could not create > > '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > Read-only > > file system > > > > _______________________________________________ > > 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: 4 > Date: Fri, 26 Sep 2014 14:20:58 -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 error on large cluster > Message-ID: > < > CAJXewOm4JzsXUGPhDpQ6CfnM1XNkMTR5xDemLx14hivKWy_dPA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Fri, Sep 26, 2014 at 2:18 PM, Chris Malone <chris.m.malone(a)gmail.com> > wrote: > > > Hi Brandon, > > > > The 'Read-only file system' part makes me think the issue isn't related > to > > the yt build. Usually that message happens when the filesystem detected > an > > error and the OS remounts the file system in read-only mode. Are there > any > > other issues on the FS? Are you able to manually create a file/directory > > on that FS? > > > > Note that mercurial is being installed into /usr/local, which should never > happen using the install script. That's why I asked how the install script > was being invoked. > > > > > > Chris > > > > On Fri, Sep 26, 2014 at 3:03 PM, Brandon Bozek <brandon.bozek(a)gmail.com> > > wrote: > > > >> Hello All, > >> > >> I am trying to install yt on a cluster at my institution and I ran the > >> install script for the stable version and got this error: "error: could > not > >> create '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > >> Read-only file system". > >> > >> The last few lines are copied below. Please let me know if I should send > >> anything else. > >> > >> Thanks! > >> Brandon > >> > >> creating build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/coal-folder.png -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/style-gitweb.css -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/background.png -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/style-coal.css -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/hglogo.png -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/style-paper.css -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/style.css -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/excanvas.js -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/coal-file.png -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/hgicon.png -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/mercurial.js -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/feed-icon-14x14.png -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> copying mercurial/templates/static/style-monoblue.css -> > >> build/lib.linux-x86_64-2.7/mercurial/templates/static > >> > >> running build_scripts > >> > >> creating build/scripts-2.7 > >> > >> copying and adjusting hg -> build/scripts-2.7 > >> > >> changing mode of build/scripts-2.7/hg from 644 to 755 > >> > >> running install > >> > >> running build > >> > >> running build_mo > >> > >> running build_ext > >> > >> running build_py > >> > >> running build_scripts > >> > >> running install_lib > >> > >> creating /usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial > >> > >> error: could not create > >> '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': > Read-only > >> file system > >> > >> _______________________________________________ > >> 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 > > > > > -------------- 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 35 > **************************************** >

2 1

install error on large cluster
by Brandon Bozek 26 Sep '14

26 Sep '14

Hello All, I am trying to install yt on a cluster at my institution and I ran the install script for the stable version and got this error: "error: could not create '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': Read-only file system". The last few lines are copied below. Please let me know if I should send anything else. Thanks! Brandon creating build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/coal-folder.png -> build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/style-gitweb.css -> build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/background.png -> build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/style-coal.css -> build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/hglogo.png -> build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/style-paper.css -> build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/style.css -> build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/excanvas.js -> build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/coal-file.png -> build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/hgicon.png -> build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/mercurial.js -> build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/feed-icon-14x14.png -> build/lib.linux-x86_64-2.7/mercurial/templates/static copying mercurial/templates/static/style-monoblue.css -> build/lib.linux-x86_64-2.7/mercurial/templates/static running build_scripts creating build/scripts-2.7 copying and adjusting hg -> build/scripts-2.7 changing mode of build/scripts-2.7/hg from 644 to 755 running install running build running build_mo running build_ext running build_py running build_scripts running install_lib creating /usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial error: could not create '/usr/local/python/2.7.3/lib/python2.7/site-packages/mercurial': Read-only file system

3 4

quick question
by Daniel Whalen 26 Sep '14

26 Sep '14

I am trying to use yt to visualize 3D spherical coordinate data sets created with the ZEUS-MP code. I know yt can directly read in such data, but are there any issues when the grid is ratioed in the radial coordinate (ie, logarithmically spaced zones in radius). Thanks! Dan Whalen

3 6

Setting Units
by John Regan 26 Sep '14

26 Sep '14

Hi All, I'm having a little trouble with Units in YT-3.0. I want to calculate the rates for some collisional dissociations as used in Enzo. The rates are fits so the dimensions are not going to be as required and YT doesn't like that! An example script showing the problem is shown below: ##################################################### import yt from yt.utilities.physical_constants import kboltz import numpy as np def _k7(field, data): #H + e -> HM + gamma Tergs = data["Temperature"]*kboltz TeV = Tergs.convert_to_units('eV') krate = 6.77e-15*np.power(TeV, 0.8779) return krate #cm^3 s^-1 yt.add_field(("gas", "k7rate"), units="cm**3/s", function=_k7) Filename = "....../RD0000/RD0000" ds = yt.load(Filename) sp = ds.sphere('max', (100, 'kpc')) print sp["k7rate"] ####################################################### The script fails with the error: yt.utilities.exceptions.YTUnitConversionError: Unit dimensionalities do not match. Tried to convert between eV**(8779/10000) (dim (length)**(8779/5000)*(mass)**(8779/10000)/(time)**(8779/5000)) and cm**3/s (dim (length)**3/(time)). which makes sense because the _k7() function is just a fit based on temperature. Is there a way to "set" the units of k7 to be cm^3 s^-1? Cheers, John

5 7

Installation problem
by Lei Yang 26 Sep '14

26 Sep '14

Dear yt-users, I was trying to install yt using pip on my mac, but I got an error massage “ValueError: got unexpected compilation option: language”, and "Command python setup.py egg_info failed with error code 1 in /private/var/folders/t0/7w97r14x7z3cm9kf1s9jq0mh0000gn/T/pip_build_leiyang/yt “. I have no idea what’s going on there. Would you please give me some tips to figure this out? Thanks so much!!! Lei

2 1

yt isocontour flux
by Lile Wang 24 Sep '14

24 Sep '14

Hi All, I just got the problem when I am trying to calculate the flux crossing an isocontour flux. The minimized example looks like this (data dumps are generated by Enzo): >>> ds = load( 'DD0501/data0501' ) >>> dd = ds.all_data() >>> flux = dd.calculate_isocontour_flux( 'density', 1e-, 'x-velocity', 'y-velocity', 'z-velocity', 'density' ) Then I got the exception: --------------------------------------------------------------------------- [8/936] AttributeError Traceback (most recent call last) /u/lilew/Apps/yt-x86_64/src/yt-hg/scripts/iyt in <module>() ----> 1 flux = sp.calculate_isocontour_flux( 'density', rho, 'velocity_x', 'velocity_y', 'velocity_z', 'density' ) /u/lilew/Apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in calculate_isocontour_flux(self, field, value, field_x, field_y, field_z, fluxing_field) 1077 """ 1078 flux = 0.0 -> 1079 for g in self._get_grid_objs(): 1080 flux += self._calculate_flux_in_grid(g, field, value, 1081 field_x, field_y, field_z, fluxing_field) /u/lilew/Apps/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.pyc in _get_grid_objs(self) 1042 if self._distributed: 1043 return ParallelObjectIterator(self, True, attr='_grids') -> 1044 return ObjectIterator(self, True, attr='_grids') 1045 1046 def get_dependencies(self, fields): /u/lilew/Apps/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.pyc in __init__(self, pobj, just_list, attr) 123 gs = getattr(pobj, attr) 124 else: --> 125 gs = getattr(pobj._data_source, attr) 126 if len(gs) == 0: 127 raise YTNoDataInObjectError(pobj) AttributeError: 'YTSphere' object has no attribute '_data_source' --------------------------------------------------------------------------------------------------------------- Could you please help me find out what is wrong? Any ideas are appreciated. Thanks! Cheers, Lile Wang

2 1

yt isocontour flux
by Lile Wang 22 Sep '14

22 Sep '14

Hi All, I just got the problem when I am trying to calculate the flux crossing an isocontour flux. The minimized example looks like this (data dumps are generated by Enzo): >>> ds = load( ‘DD0501/data0501’ ) >>> dd = ds.all_data() >>> flux = dd.calculate_isocontour_flux( 'density', 1e-, ‘x-velocity’, ‘y-velocity’, ‘z-velocity’, ‘density’ ) Then I got the exception: --------------------------------------------------------------------------- [8/936] AttributeError Traceback (most recent call last) /u/lilew/Apps/yt-x86_64/src/yt-hg/scripts/iyt in <module>() ----> 1 flux = sp.calculate_isocontour_flux( 'density', rho, 'velocity_x', 'velocity_y', 'velocity_z', 'density' ) /u/lilew/Apps/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in calculate_isocontour_flux(self, field, value, field_x, field_y, field_z, fluxing_field) 1077 """ 1078 flux = 0.0 -> 1079 for g in self._get_grid_objs(): 1080 flux += self._calculate_flux_in_grid(g, field, value, 1081 field_x, field_y, field_z, fluxing_field) /u/lilew/Apps/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.pyc in _get_grid_objs(self) 1042 if self._distributed: 1043 return ParallelObjectIterator(self, True, attr='_grids') -> 1044 return ObjectIterator(self, True, attr='_grids') 1045 1046 def get_dependencies(self, fields): /u/lilew/Apps/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.pyc in __init__(self, pobj, just_list, attr) 123 gs = getattr(pobj, attr) 124 else: --> 125 gs = getattr(pobj._data_source, attr) 126 if len(gs) == 0: 127 raise YTNoDataInObjectError(pobj) AttributeError: 'YTSphere' object has no attribute '_data_source' ————————————————————————————————————— Could you please help me find out what is wrong? Any ideas are appreciated. Thanks! Cheers, Lile Wang

1 0

Installation on Windows
by Matthew Past 22 Sep '14

22 Sep '14

Hello, I am new to yt, and trying to install it on my Windows 7 PC for a research project I am going to be working on. I have miniconda installed, but I have no idea where to go from there. I am also relatively new to python as well. Any help would be appreciated. Thanks, Matt

2 1