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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 02:18:50
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---------------------------------------- > 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... |
