Avogadro crashes X on ubuntu 14 under vnc

General Discussion
1

This is driving me crazy, and maybe someone has seen it. I have tried
everything. I have a new ubuntu 14 machine and I built everthing with
no errors, and avogadro runs fine on the console and ssh -X , but when
I try to run it under vnc it always crashes the X server. I have tried
every xserver I could find and every version of xstartup I could find.
The whole vnc client crashes when I try just avogadro.

After a crash the vnc log file shows:

Thu Apr 16 23:46:04 2015
Connections: accepted: 0.0.0.0::51330
SConnection: Client needs protocol version 3.8
SConnection: Client requests security type VncAuth(2)
VNCSConnST: Server default pixel format depth 16 (16bpp) little-endian rgb565
VNCSConnST: Client pixel format depth 16 (16bpp) little-endian rgb565
XIO: fatal IO error 11 (Resource temporarily unavailable) on X server ":16"
after 172 requests (172 known processed) with 0 events remaining.

If I run avogadro -h under vnc I see (and it does not crash the server):

avogadro -h
Xlib: extension “XInputExtension” missing on display “:16”.
"Avogadro version: 1.1.1 Git: 5e4d1f7
LibAvogadro version: 1.1.1 Git: 5e4d1f7"
Locale: "en_GB"
Translation successfully loaded.
Usage: avogadro [options] [files]

Avogadro - Advanced Molecular Editor (version 1.1.1)

Options:
-h, --help Show help options (this)
-v, --version Show version information

So there are too symptoms–the XIO crash and the
Xlib: extension “XInputExtension” missing on display “:16”.

Neither of these happen on the console or a regular sh -X session.

I really need to get this working under vnc, so if anyone has any
ideas or experience with this I would greatly appreciate it!

Thank you!

Sincerely,

Ron

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

2

It runs fine under nomachine, but the enterprise version of nomachine
needed to have virtual desktops is very expensive. Thanks,

Ron

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3

On Thu, Apr 16, 2015 at 11:56 PM, Cohen, Ronald
rcohen@carnegiescience.edu wrote:

This is driving me crazy, and maybe someone has seen it. I have tried
everything. I have a new ubuntu 14 machine and I built everthing with
no errors, and avogadro runs fine on the console and ssh -X , but when
I try to run it under vnc it always crashes the X server. I have tried
every xserver I could find and every version of xstartup I could find.
The whole vnc client crashes when I try just avogadro.

After a crash the vnc log file shows:

Thu Apr 16 23:46:04 2015
Connections: accepted: 0.0.0.0::51330
SConnection: Client needs protocol version 3.8
SConnection: Client requests security type VncAuth(2)
VNCSConnST: Server default pixel format depth 16 (16bpp) little-endian rgb565
VNCSConnST: Client pixel format depth 16 (16bpp) little-endian rgb565
XIO: fatal IO error 11 (Resource temporarily unavailable) on X server “:16”
after 172 requests (172 known processed) with 0 events remaining.

If I run avogadro -h under vnc I see (and it does not crash the server):

avogadro -h
Xlib: extension “XInputExtension” missing on display “:16”.
“Avogadro version: 1.1.1 Git: 5e4d1f7
LibAvogadro version: 1.1.1 Git: 5e4d1f7”
Locale: “en_GB”
Translation successfully loaded.
Usage: avogadro [options] [files]

Avogadro - Advanced Molecular Editor (version 1.1.1)

Options:
-h, --help Show help options (this)
-v, --version Show version information

So there are too symptoms–the XIO crash and the
Xlib: extension “XInputExtension” missing on display “:16”.

Neither of these happen on the console or a regular sh -X session.

I really need to get this working under vnc, so if anyone has any
ideas or experience with this I would greatly appreciate it!

Thank you!

Sincerely,

Ron

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

3

Hi Ron,

What VNC server/client are you trying to use? I have Ubuntu 14.04 and
could try to replicate, I would expect this to work with VNC, the
major complication is often getting a good OpenGL context but VNC
usually does rendering on the server-side and simplifies this.

Thanks,

Marcus

On Fri, Apr 17, 2015 at 9:19 AM, Cohen, Ronald
rcohen@carnegiescience.edu wrote:

It runs fine under nomachine, but the enterprise version of nomachine
needed to have virtual desktops is very expensive. Thanks,

Ron

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

On Thu, Apr 16, 2015 at 11:56 PM, Cohen, Ronald
rcohen@carnegiescience.edu wrote:

This is driving me crazy, and maybe someone has seen it. I have tried
everything. I have a new ubuntu 14 machine and I built everthing with
no errors, and avogadro runs fine on the console and ssh -X , but when
I try to run it under vnc it always crashes the X server. I have tried
every xserver I could find and every version of xstartup I could find.
The whole vnc client crashes when I try just avogadro.

After a crash the vnc log file shows:

Thu Apr 16 23:46:04 2015
Connections: accepted: 0.0.0.0::51330
SConnection: Client needs protocol version 3.8
SConnection: Client requests security type VncAuth(2)
VNCSConnST: Server default pixel format depth 16 (16bpp) little-endian rgb565
VNCSConnST: Client pixel format depth 16 (16bpp) little-endian rgb565
XIO: fatal IO error 11 (Resource temporarily unavailable) on X server “:16”
after 172 requests (172 known processed) with 0 events remaining.

If I run avogadro -h under vnc I see (and it does not crash the server):

avogadro -h
Xlib: extension “XInputExtension” missing on display “:16”.
“Avogadro version: 1.1.1 Git: 5e4d1f7
LibAvogadro version: 1.1.1 Git: 5e4d1f7”
Locale: “en_GB”
Translation successfully loaded.
Usage: avogadro [options] [files]

Avogadro - Advanced Molecular Editor (version 1.1.1)

Options:
-h, --help Show help options (this)
-v, --version Show version information

So there are too symptoms–the XIO crash and the
Xlib: extension “XInputExtension” missing on display “:16”.

Neither of these happen on the console or a regular sh -X session.

I really need to get this working under vnc, so if anyone has any
ideas or experience with this I would greatly appreciate it!

Thank you!

Sincerely,

Ron

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF

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4

I have tried everything, but mainly vnc4server and tightvncserver as
servers, and jollysfastvnc as the client. Note however it seems that X
server crashes, not just VNC and not the client. Even with a bug it
seems only the program should crash, not everything. I found it works
fine with NX (nomachine), but that is expensive. It is completely
reproducible–it never works under regular vnc. Ron

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3

On Mon, Apr 20, 2015 at 3:49 PM, Marcus D. Hanwell
marcus.hanwell@kitware.com wrote:

Hi Ron,

What VNC server/client are you trying to use? I have Ubuntu 14.04 and
could try to replicate, I would expect this to work with VNC, the
major complication is often getting a good OpenGL context but VNC
usually does rendering on the server-side and simplifies this.

Thanks,

Marcus

On Fri, Apr 17, 2015 at 9:19 AM, Cohen, Ronald
rcohen@carnegiescience.edu wrote:

It runs fine under nomachine, but the enterprise version of nomachine
needed to have virtual desktops is very expensive. Thanks,

Ron

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

On Thu, Apr 16, 2015 at 11:56 PM, Cohen, Ronald
rcohen@carnegiescience.edu wrote:

This is driving me crazy, and maybe someone has seen it. I have tried
everything. I have a new ubuntu 14 machine and I built everthing with
no errors, and avogadro runs fine on the console and ssh -X , but when
I try to run it under vnc it always crashes the X server. I have tried
every xserver I could find and every version of xstartup I could find.
The whole vnc client crashes when I try just avogadro.

After a crash the vnc log file shows:

Thu Apr 16 23:46:04 2015
Connections: accepted: 0.0.0.0::51330
SConnection: Client needs protocol version 3.8
SConnection: Client requests security type VncAuth(2)
VNCSConnST: Server default pixel format depth 16 (16bpp) little-endian rgb565
VNCSConnST: Client pixel format depth 16 (16bpp) little-endian rgb565
XIO: fatal IO error 11 (Resource temporarily unavailable) on X server “:16”
after 172 requests (172 known processed) with 0 events remaining.

If I run avogadro -h under vnc I see (and it does not crash the server):

avogadro -h
Xlib: extension “XInputExtension” missing on display “:16”.
“Avogadro version: 1.1.1 Git: 5e4d1f7
LibAvogadro version: 1.1.1 Git: 5e4d1f7”
Locale: “en_GB”
Translation successfully loaded.
Usage: avogadro [options] [files]

Avogadro - Advanced Molecular Editor (version 1.1.1)

Options:
-h, --help Show help options (this)
-v, --version Show version information

So there are too symptoms–the XIO crash and the
Xlib: extension “XInputExtension” missing on display “:16”.

Neither of these happen on the console or a regular sh -X session.

I really need to get this working under vnc, so if anyone has any
ideas or experience with this I would greatly appreciate it!

Thank you!

Sincerely,

Ron

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF

Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options

BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF

Avogadro-Discuss mailing list
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avogadro-discuss List Signup and Options