RE: [PyMOL] PyMol segmentation fault while starting from external python program

[Warren D. <wa...@de...>]

Dmitriy,

I spent a few minutes yesterday trying to track down the seg. fault -- =
there are at least three issues here...

One appears to be a race condition inside of Tcl/Tk-to-Python call =
interface, which is most apparent on multi-cpu systems, and for which I =
have no solution yet other than disabling the external GUI altogether.

The second is a blunder on my part in the CmdReady function in =
layer4/Cmd.c:

static PyObject *CmdReady(PyObject *dummy, PyObject *args)=20
{
return(APIResultCode(TempPyMOLGlobals->Ready));
}

should be

static PyObject *CmdReady(PyObject *dummy, PyObject *args)=20
{
   if(TempPyMOLGlobals) {
      return(APIResultCode(TempPyMOLGlobals->Ready));
   } else {
      return(APIResultCode(0));
   }
}

since TempPyMOLGlobals can't be derefrenced until it exists. =20

The third issue appears to be a Python initialization issue that also =
only rears its ugly head on SMP machines:

finish_launching() in modules/pymol/__init__.py needs to be updated as =
follows:

    def finish_launching():
        e=3Dthreading.Event()
        while not hasattr(__main__,'pymol'):
            e.wait(0.01)
        while not _cmd.ready():
            e.wait(0.01)
        while not hasattr(__main__.pymol,'xray'):
            e.wait(0.01)

in order to allow time for the xray module to initialize before loading =
structures.

These changes have been committed to CVS.

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: Dmitriy Igor Bryndin [mailto:bry...@ms...]=20
> Sent: Tuesday, October 11, 2005 5:06 AM
> To: Warren DeLano
> Cc: pym...@li...
> Subject: Re: [PyMOL] PyMol segmentation fault while starting=20
> from external python program
>=20
> Warren=20
>=20
> It seems like PyMol should have time to load after  import=20
> pymol and before anything else can be done with it.
> If I=B4ll do
>  ------------------------------
> pymol_argv =3D ['pymol', '-qx']
> import pymol
> # let`s give pymol some time to load
> for a in range(1000000):
> 	b=3D0=20
>=20
> pymol.finish_launching()=20
>=20
> from pymol import cmd=20
>=20
> cmd.load("$HOME/pept.pdb")
> cmd.show("sticks")
>  ------------------------------
> everything is fine. It loads and shows the picture.
> =B4for a in range(100)=B4  for example will produce segmentation =
fault.=20
>=20
> As far as I understand =B4pymol.finish_launching()=B4 is meant to=20
> produce such delay. Correct me if I=B4m wrong. But this call=20
> produce segm fault by itself without a waiting cycle.=20
>=20
> Can you recommend some workaround for this problem? This=20
> stupid cycle may work on my machine, but may not work on a=20
> faster one. Is there any way to find out that PyMol window=20
> had loaded?=20
>=20
> Thanks
>  Dmitriy Bryndin=20
>=20
> =20
>=20
> =20
>=20
> =20
>=20
>=20
> Warren DeLano writes:=20
>=20
> > Dmitriy,
> >=20
> > Due to problem with multithreading (especially with the Tcl/Tk=20
> > external GUI), we haven't been able to get the "import=20
> pymol" approach to work in
> > a stable robust manner across different OSes and environments.  =20
> >=20
> > So sight now, as per comments in=20
> "modules/pymol/__init__.py", the only=20
> > supported way to launch PyMOL is to run the __init__.py script on=20
> > startup.
> >=20
> > %python modules/pymol/__init__.py
> >=20
> > Hoever, if you disable the external GUI, then you might be=20
> able to get=20
> > "import pymol" to work...
> >=20
> > pymol_argv =3D ['pymol', '-qx']
> > import pymol
> > pymol.finish_launching()
> >=20
> > from pymol import cmd
> >=20
> > cmd.load(...etc.=20
> >=20
> >=20
> > Cheers,
> > Warren
> >=20
> >=20
> > --
> > Warren L. DeLano, Ph.D.                    =20
> > Principal Scientist
> >=20
> > . DeLano Scientific LLC =20
> > . 400 Oyster Point Blvd., Suite 213          =20
> > . South San Francisco, CA 94080 USA  =20
> > . Biz:(650)-872-0942  Tech:(650)-872-0834    =20
> > . Fax:(650)-872-0273  Cell:(650)-346-1154
> > . mailto:wa...@de...     =20
> >  =20
> >=20
> >> -----Original Message-----
> >> From: pym...@li...
> >> [mailto:pym...@li...] On Behalf=20
> Of Dmitriy=20
> >> Igor Bryndin
> >> Sent: Monday, October 10, 2005 2:33 PM
> >> To: pym...@li...
> >> Subject: [PyMOL] PyMol segmentation fault while starting from=20
> >> external python program
> >>=20
> >> Launching PyMol form external python script will produce=20
> >> segmaentation fault.
> >> For example starting "launch.py" from "/pymol/examples/launching"
> >>  ----------------------------------------------
> >> $ python launch.py
> >> zsh: segmentation fault  python launch.py
> >>  ----------------------------------------------
> >> Crashes without even showing PyMol windows. =20
> >>=20
> >> Tried it on Fedora Core 1, Fedora Core 4, Mandriva 2005. The same=20
> >> story.
> >> Different pythons and compiling different versions of=20
> PyMol does not=20
> >> change anything.
> >>=20
> >> It will launch PyMol windows if there is only
> >>    import pymol
> >> line. =20
> >>=20
> >> Adding
> >>    pymol.finish_launching()
> >> or
> >>    from pymol import cmd
> >>    cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
> >> will produce segmentation fault. With no windows shown. =20
> >>=20
> >> The same time if I'll try to debug step by step, let's say,=20
> >> "launch_demo.py"
> >> (from "/pymol/examples/launching")
> >>  -------------------------------
> >> pymol.finish_launching()
> >> from pymol import cmd
> >> cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
> >> cmd.show("sticks")
> >>  -------------------------------
> >> using IDLE. Everything will work. It starts windows, loads a file,=20
> >> changes to sticks...
> >> Running it "python launch_demo.py" will wait for a second=20
> and return=20
> >> segmentation fault.
> >>=20
> >> If someone knows what's going on, please help me. =20
> >>=20
> >>  Thanks
> >>    Dmitriy Bryndin
> >>=20
> >> =20
> >>=20
> >> =20
> >>=20
> >> -------------------------------------------------------
> >> This SF.Net email is sponsored by:
> >> Power Architecture Resource Center: Free content, downloads,=20
> >> discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> PyM...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>=20
> >> =20
> >>=20
> >>=20
> >=20
> =20
>=20
>=20
>=20
>=20
>=20
>=20