Re: [PyMOL] Segmentation fault while starting Pymol in ubuntu 11

[lina]

On Tue, Oct 18, 2011 at 12:08 AM, Tao-wei Huang  wrote:
> Hi all,
>
> I have problems with starting pymol in ubuntu. When I started it from
> terminal, I just received the error message: Segmentation fault. I
> tried googling pymol segmentation fault, but I don't find effective
> information to fix this problem. If you have any idea or experience
> about this, please tell me. Thank you very much.

Last time I met segment fault when I updated some graphic-driver packages.

>
>
> Cheers,
> Tao
>
> --
> All the data continuously generated in your IT infrastructure contains a
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>

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Re: [PyMOL] Segmentation fault while starting Pymol in ubuntu 11

[Troels Emtekær Linnet]

What version do you have installed?

Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE 
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752



2011/10/17 Tao-wei Huang 

> Hi all,
>
> I have problems with starting pymol in ubuntu. When I started it from
> terminal, I just received the error message: Segmentation fault. I
> tried googling pymol segmentation fault, but I don't find effective
> information to fix this problem. If you have any idea or experience
> about this, please tell me. Thank you very much.
>
>
> Cheers,
> Tao
>
>
> --
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct___
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[PyMOL] Segmentation fault while starting Pymol in ubuntu 11

[Tao-wei Huang]

Hi all,

I have problems with starting pymol in ubuntu. When I started it from
terminal, I just received the error message: Segmentation fault. I
tried googling pymol segmentation fault, but I don't find effective
information to fix this problem. If you have any idea or experience
about this, please tell me. Thank you very much.


Cheers,
Tao

--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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Re: [PyMOL] how to activate pymol from remote server

[Alvin Oga]

hi masataka

> > >> how to activate pymol from remote server?
> > >> i.e. how to start pymol in [S] by scripting from [C]

assuming your laptop and remote-machine is X11 capable:

- you can use ip# 

or by name
- www.remote-machine.com  if your dns/hosts files is setup right

laptop# xhost +remote-machine

laptop# ssh -l loginName  remote-machine

login@remote-machine# export DISPLAY=laptop:0.0
login@remote-machine# xterm - see if it works
login@remote-machine# pymol

> > I wonder, if even in this case X-forwarding is needed.

yes .. many different ways to do that

> > | freeglut (pymol): failed to open display ''
> > | PyMOL: abrupt program termination.

the machine you intend to run pymol will need all
the supporting libraries ...

> > | $ gedit (one shell script).sh
> > | (gedit:3887): Gtk-WARNING **: cannot open display:

you need to define DISPLAY environment variables on
the remote machine and also allow it to export and display
on your (local) laptop
- some folks consider this "dangerous" but 
it does help to get work done ...  just be careful
( always use ssh ... NOT telnet or other un-encrypted sessions )

> > | $ grep X11Forwarding /etc/ssh/sshd_config
> > | X11Forwarding yes

that is NOT sufficient...

the environment variable DISPLAY must also be defined
explicitly or defined with ssh login command

have fun
alvin

--
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
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Re: [PyMOL] how to activate pymol from remote server

[Thomas Holder]

Hi Masataka,

> Sorry for lack of information, what all I'd like to do is:
> - Scripting in [C] (on Cygwin or telnet over Command Prompt etc.
> welcome), which includes login procedure to [S] by 'ssh -l (loginname)
> (hostname)'
> - pymol GUI open in [S]'s window (not in [C])

that was not clear before, I assumed the GUI should be opened on [C]. 
Then you do not need X-forwarding. Instead, on [S] there must be a 
running X from the same user and you need to know the DISPLAY variable 
there!

ssh -l loginname hostname
export DISPLAY=:0.0   # just as example!
pymol -qip  # this will listen for commands on the command line

Also check:
http://pymolwiki.org/index.php/Command_Line_Options
http://pymolwiki.org/index.php/Launching_From_a_Script

And yet to mention: Troels is right, it's not really a PyMOL issue. Try 
launching a simple program (like xclock) and if you are successful, then 
try the same with PyMOL.

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology

--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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Re: [PyMOL] how to activate pymol from remote server

[Troels Emtekær Linnet]

*This does not seem to be an issue of Pymol.*

If you can't open a display to any program, like "gedit", you are not doing
it right.

Get an open display to any program, and then try Pymol.
Here is a start to do it.
*http://x.cygwin.com/docs/ug/using-remote-apps.html*

You NEED to pass *-Y* to the ssh program.

ssh *-Y* -l (loginname) (hostname)


But please come back again, if have problems regarding Pymol.

If you only neeed Pymol scripting, and no display, you can check here:
http://www.pymolwiki.org/index.php/Launching_PyMOL#Running_PyMOL_in_batch_mode
"pymol -cq"


Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE 
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752



2011/10/17 grantaka36 

> Hi Thomas,
>
> I appreciate your advice very much, testing and cannot find green
> signal yet as [2]. For now, what I want to do is [1], so please give
> me, if any enough, advice or workaround.  If information might be
> inadequate, please contact me.
>
> [1]
> >> how to activate pymol from remote server?
> >> i.e. how to start pymol in [S] by scripting from [C]
>
> Sorry for lack of information, what all I'd like to do is:
> - Scripting in [C] (on Cygwin or telnet over Command Prompt etc.
> welcome), which includes login procedure to [S] by 'ssh -l (loginname)
> (hostname)'
> - pymol GUI open in [S]'s window (not in [C])
>
> I wonder, if even in this case X-forwarding is needed.
>
> [2]
> > do you have a X server running on Windows? It works for me with Cygwin
> with
> > installed X and GL libraries (but it's not very convenient because quite
> > slow).
> >
> > ssh -Y linuxserver
> > pymol
>
> Windows [C] didn't have X-server so I installed Xming 6.9.0.31 and
> kept running, 'pymol' returns:
> | freeglut (pymol): failed to open display ''
> | PyMOL: abrupt program termination.
>
> Another command returns:
> | $ gedit (one shell script).sh
> | (gedit:3887): Gtk-WARNING **: cannot open display:
> | (returned empty)
> | $
>
> | $ grep X11Forwarding /etc/ssh/sshd_config
> | X11Forwarding yes
> | $ grep X11DisplayOffset /etc/ssh/sshd_config
> | X11DisplayOffset 10
>
> So, I think X-forwarding setting done but not all of 'install X and GL
> libraries' might be intalled yet.
>
>
> Regards,
> Masataka
>
>
> 2011/10/15 Thomas Holder :
> > Hi Masataka,
> >
> > do you have a X server running on Windows? It works for me with Cygwin
> with
> > installed X and GL libraries (but it's not very convenient because quite
> > slow).
> >
> > ssh -Y linuxserver
> > pymol
> >
> > If pymol is set up on that linux server correct and runs there by just
> > typing "pymol", it should as well from an X-forwarded ssh connection. No
> > need to export variables. Don't use the -R and -display arguments.
> >
> > Cheers,
> >  Thomas
> >
> >
> > grantaka36 wrote, On 10/14/11 07:35:
> >>
> >> Dear list members,
> >>
> >> Would you please tell me the way, how to activate pymol from remote
> >> server? i.e. how to start pymol in [S] by scripting from [C]
> >>
> >> --
> >> - From Windows client [C], SSH2 logging in to the remote server [S]
> >> (Linux x64, Ubuntu 10)
> >> - [S]
> >> -- installed PyMOL 1.2 r2, PATH includes '/usr/bin/pymol' so only
> >> 'pymol' entering enable to activate pymol GUI
> >> -- 'python' returns
> >> -- Python 2.6.6 (r266:84292, Sep 15 2010, 16:22:56)
> >> -- [GCC 4.4.5] on linux2
> >> - [C]
> >> -- first trying the following:
> >> PYMOL_PATH=/usr/bin/pymol
> >> HOST_ID=`uname -n`
> >> pymol -R -display:${HOST_ID}:0.0
> >> -- returns:
> >> Traceback (most recent call last):
> >>  File "/usr/lib/python2.6/runpy.py", line 122, in _run_module_as_main
> >>"__main__", fname, loader, pkg_name)
> >>  File "/usr/lib/python2.6/runpy.py", line 34, in _run_code
> >>exec code in run_globals
> >>  File "/usr/lib/pymodules/python2.6/pymol/__init__.py", line 495, in
> >> 
> >>invocation.parse_args(pymol_argv)
> >>  File "/usr/lib/pymodules/python2.6/pymol/invocation.py", line 251,
> >> in parse_args
> >>options.stereo_mode = int(av.pop())
> >> IndexError: pop from empty list
> >> --
> >>
> >> By referring,
> >>
> >>
> http://www.pymolwiki.org/index.php/Launching_PyMOL#Launching_PyMOL_from_an_external_application
> >>>
> >>> If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined,
> >>> then you can launch PyMOL from an external Python program
> >>
> >> But I don't know which path to designate LD_LIBRARY_PATH and TCL_LIBRARY
> >>
> >>
> >> Regards,
> >> Masataka
> >
> > --
> > Thomas Holder
> > MPI for Developmental Biology
> > Spemannstr. 35
> > D-72076 Tübingen
> >
>
>
> --
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it.