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Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.
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From: Mike M. <mar...@ho...> - 2012-10-05 14:25:13
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---------------------------------------- > From: jas...@sc... > Date: Fri, 5 Oct 2012 09:08:44 -0500 > Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb. > To: mar...@ho... > CC: li...@co...; pym...@li... > > Mike, > > Many distros have PyMOL already in their package management system. > Have you tried that first? > no, I think I tried to download from sourceforge first. > I suggest downloading the latest code, v1.5.0.4, from the open-source > project page, if you want to build by hand. > see comments in my last post, I think that is what I did. Although autoreconf may not have helped anything. > To build, you need Python 2.7 or later and the process is very simple: > > sudo python setup.py install > sudo python setup2.py install > that was what created the first version I ran, it seemed fine until I tried to display a test pdb then it hung in 100 cpu on one core. > Then, follow the directions for copying "pymol" to /usr/local/bin or > wherever you want. > > If your machine does have shader issues and they don't automatically > disable, please let us know. You do not need a license to run the > open-source version. If the splash screen says that, I need to change > that. I don't really recall what the first version said, I think it was hypothetical as in "may need license" etc. The version from "./configure" had a whole bunch of problems- simple syntax errors like missing comma to no link to the ccealignmodule but once I kluged around the CGO problems I think I was on my own :) Anyway it seems fine now, although attempting to use "fit" on my 2 molecules gave a non-intuitive result I think the one was so mangled that it had problems aligning them. > > I routinely build on Ubuntu without problems. Just make sure the > python you build with is the same that you run with. > > Cheers, > > -- Jason > > > On Thu, Oct 4, 2012 at 9:18 PM, Mike Marchywka <mar...@ho...> wrote: > > > > > > > > ---------------------------------------- > >> CC: pym...@li... > >> From: li...@co... > >> Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb. > >> Date: Thu, 4 Oct 2012 22:03:59 -0400 > >> To: mar...@ho... > >> > >> You don't need a license for the open source version. > >> > >> If you provided details on what OS/distribution you are building on, people may try to replicate and understand why the python version hung. In my experience, using setup.py generally worked out of the box. > > > > Well, I thought there may be a dev list or something for the most of this stuff but in any case I'm on Ubuntu > > but that probably was not a big factor for some of the issues I ran into I just wanted to display > > 2 molecules side by side and could not get jmol or gdis to work right away and someone suggested > > this. ( fwiw, I have my own molecule viewer that IIRC I wrote to learn glut on cygwin but > > I imagine that would be an even bigger chore to port LOL). > > > > If I can reconstruct, I apparently started with pymol-v1.5.0.1.tar and I think at some point I ran > > autoreconf -l thinking I could go the "configure" route but then did python setup.py build and > > install in separeate steps., This seemed to work but attempts to display the test pdb > > files never displayed anything, I could not get any more menu's and one core was running > > at 100 percent until I killed it. > > > > Going the confugre route, I think the first problem was with a bunch of undefined CGO things. > > but you can see the changes below. The EXT thing was spurious probably as there was a missing -lGLEW > > and I had to relink. This is obviously a raw dump of things that I tried along with stuff that ultimately > > worked but fwiw. > > > > > > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name "*.h" > > ./layer0/os_gl.h > > ./contrib/uiuc/plugins/include/molfile_plugin.h > > ./generated/include/ShaderText.h > > ./config.h > > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name "*.c" > > ./layer0/ShaderText.c > > ./layer0/ShaderMgr.c > > ./layer3/Executive.c > > ./generated/src/ShaderText.c > > ./layer2/ObjectVolume.c > > ./layer1/CGO.c > > ./layer1/Scene.c > > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ > > > > > > > > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm `find -mtime -2 -name "*.c" ` > > ./layer0/ShaderMgr.c:97: FeedbackAdd(G, " mjm forcing glew ok Shaders available.\n"); > > ./layer0/ShaderMgr.c:98:// this should work but turn off for now mjm > > ./layer0/ShaderMgr.c-99-// if (GLEW_VERSION_2_0) > > ./layer0/ShaderMgr.c-100- if (1) > > -- > > ./layer3/Executive.c:76:// mjm > > ./layer3/Executive.c-77-#include"modules/cealign/src/ce_types.h" > > ./layer3/Executive.c-78-/* Externals for CEAlign */ > > -- > > ./layer1/Scene.c:2910://mjm > > ./layer1/Scene.c-2911- 1.0F, 1.0F, 0.1F, 1.f > > ./layer1/Scene.c-2912- }; > > -- > > ./layer1/Scene.c:10000: //mjm > > ./layer1/Scene.c-10001-//glBlitFramebufferEXT (0, 0, I->offscreen_width / 2, I->offscreen_height, > > ./layer1/Scene.c-10002- glBlitFramebuffer (0, 0, I->offscreen_width / 2, I->offscreen_height, > > -- > > ./layer1/Scene.c:10007://mjm > > ./layer1/Scene.c-10008- glBlitFramebuffer (I->offscreen_width / 2, 0, I->offscreen_width, I->offscreen_height, > > ./layer1/Scene.c-10009- //glBlitFramebufferEXT (I->offscreen_width / 2, 0, I->offscreen_width, I->offscreen_height, > > -- > > ./layer1/Scene.c:10016: //mjm > > ./layer1/Scene.c-10017- //glBlitFramebufferEXT (0, 0, I->offscreen_width, I->offscreen_height, > > ./layer1/Scene.c-10018- glBlitFramebuffer (0, 0, I->offscreen_width, I->offscreen_height, > > -- > > ./layer1/Scene.c:10024: //mjm > > ./layer1/Scene.c-10025-// glBlitFramebufferEXT (0, 0, I->offscreen_width, I->offscreen_height, > > ./layer1/Scene.c-10026- glBlitFramebuffer (0, 0, I->offscreen_width, I->offscreen_height, > > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ > > > > > > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm `find -mtime -2 -name "*.h" ` > > ./layer0/os_gl.h:6:// mjm > > ./layer0/os_gl.h-7-//#if defined(_PYMOL_IOS) || defined(ANDROID) > > ./layer0/os_gl.h-8-#if 1 > > ./layer0/os_gl.h:9:// mjm > > ./layer0/os_gl.h-10-// #define _PYMOL_PURE_OPENGL_ES > > ./layer0/os_gl.h-11-#define _PYMOL_CGO_DRAWARRAYS > > -- > > ./contrib/uiuc/plugins/include/molfile_plugin.h:249:// mjm - these are in the games lass LOL > > ./contrib/uiuc/plugins/include/molfile_plugin.h-250-int have_esp; > > ./contrib/uiuc/plugins/include/molfile_plugin.h-251-int have_npa; > > -- > > ./contrib/uiuc/plugins/include/molfile_plugin.h:312:// mjm > > ./contrib/uiuc/plugins/include/molfile_plugin.h-313-int multiplicity; > > ./contrib/uiuc/plugins/include/molfile_plugin.h-314-int * esp_charges; > > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ > > > > > > > > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ cat relink > > gcc --verbose -shared -fPIC -DPIC -Wl,--no-as-needed -Wl,--whole-archive contrib/uiuc/plugins/molfile_plugin/src/.libs/libmolfile_plugin0.a modules/cealign/src/ccealignmodule.o ov/src/.libs/libov.a layer0/.libs/liblayer0.a layer1/.libs/liblayer1.a layer2/.libs/liblayer2.a layer3/.libs/liblayer3.a layer4/.libs/liblayer4.a layer5/.libs/liblayer5.a -Wl,--no-whole-archive -L/usr/lib/x86_64-linux-gnu -Wl,--whole-archive -lGLEW -lGL -lGLU /usr/lib/x86_64-linux-gnu/libfreetype.so -lz -lpng -lglut -Wl,--no-whole-archive -ldl -O2 -Wl,-soname -Wl,libpymol.so.0 -o .libs/libpymol.so.0.0.0 > > #gcc -shared -fPIC -DPIC -Wl,--whole-archive contrib/uiuc/plugins/molfile_plugin/src/.libs/libmolfile_plugin0.a ov/src/.libs/libov.a layer0/.libs/liblayer0.a layer1/.libs/liblayer1.a layer2/.libs/liblayer2.a layer3/.libs/liblayer3.a layer4/.libs/liblayer4.a layer5/.libs/liblayer5.a -Wl,--no-whole-archive -L/usr/lib/x86_64-linux-gnu -lGL -lGLU /usr/lib/x86_64-linux-gnu/libfreetype.so -lz -lpng -lglut -ldl -O2 -Wl,-soname -Wl,libpymol.so.0 -o .libs/libpymol.so.0.0.0 > > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ > > > > > > > > > > > >> > >> -David > >> > >> On Oct 4, 2012, at 9:22 PM, Mike Marchywka <mar...@ho...> wrote: > >> > >> > > >> > > >> > > >> > fwiw, I never figured out why the out-of-the-box build hung using the python approach > >> > but I went through the "./cogifure, make make install route" > >> > and did get the test molecules to display. However, I ran into lots of problems with the ShaderMgr and > >> > ccealignmodule and then finally the link was missing -lGLEW. > >> > > >> > In any case it looks like I am all set but I thought the download would come closer to working right > >> > away. > >> > > >> > And the xyz files I wanted to display do appear to come up just great. > >> > > >> > So do I need a license for the open source version? > >> > Thanks. > >> > > >> > > >> > > >> > note new address > >> > Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. > >> > formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency > >> > > >> > > >> > > >> > ---------------------------------------- > >> >> From: mar...@ho... > >> >> To: pym...@li... > >> >> Date: Thu, 4 Oct 2012 15:43:53 -0400 > >> >> Subject: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb. > >> >> > >> >> > >> >> > >> >> > >> >> Is there some common reason for this? > >> >> CPU on one core stays at 100 percent and no more menu's come up. > >> >> > >> >> The larger window says at the bottom that the version is supposed to be licensed > >> >> but I just pulled it down from sourceforge and not sure that this version needs a key > >> >> to work. > >> >> > >> >> Thanks. > >> >> > >> >> > >> >> note new address > >> >> Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. > >> >> formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency > >> >> > >> >> > >> >> ------------------------------------------------------------------------------ > >> >> Don't let slow site performance ruin your business. Deploy New Relic APM > >> >> Deploy New Relic app performance management and know exactly > >> >> what is happening inside your Ruby, Python, PHP, Java, and .NET app > >> >> Try New Relic at no cost today and get our sweet Data Nerd shirt too! > >> >> http://p.sf.net/sfu/newrelic-dev2dev > >> >> _______________________________________________ > >> >> PyMOL-users mailing list (PyM...@li...) > >> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> >> Archives: http://www.mail-archive.com/pym...@li... > >> > > >> > ------------------------------------------------------------------------------ > >> > Don't let slow site performance ruin your business. Deploy New Relic APM > >> > Deploy New Relic app performance management and know exactly > >> > what is happening inside your Ruby, Python, PHP, Java, and .NET app > >> > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > >> > http://p.sf.net/sfu/newrelic-dev2dev > >> > _______________________________________________ > >> > PyMOL-users mailing list (PyM...@li...) > >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > Archives: http://www.mail-archive.com/pym...@li... > > > > ------------------------------------------------------------------------------ > > Don't let slow site performance ruin your business. Deploy New Relic APM > > Deploy New Relic app performance management and know exactly > > what is happening inside your Ruby, Python, PHP, Java, and .NET app > > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > > http://p.sf.net/sfu/newrelic-dev2dev > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrödinger, Inc. > > (e) Jas...@sc... > (o) +1 (603) 374-7120 |
