----------------------------------------
> CC: pymol-users@lists.sourceforge.net
> From: li...@cowsandmilk.net
> 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: marchy...@hotmail.com
>
> 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 <marchy...@hotmail.com> 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: marchy...@hotmail.com
> >> To: pymol-users@lists.sourceforge.net
> >> 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!
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> >> _______________________________________________
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> >
> > ------------------------------------------------------------------------------
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