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"Stephen P. Molnar" 09-12-2012 04:20 PM

Missing Files Prevent Installation/Execution of Applications
 
I am in the midst of changing distributions for reasons that aren't really
germane to this note.

I have installed Debian-6.0.5-amd64 on my Dell Inspiron Laptop in VM
VirtualBox 4.1.22. I am having problems installing/running two applications:
MGLTools-1.5.4-Linux-86_64-install and PyRx-Linux-x68-Install (both are
available from www.scripps.edu).

MGLTools installs without any problems,but when I try to run I get:

computation@debian:~/Applications/MGLTools-1.5.4/bin$ ./adt
setting PYTHONHOME environment
Run AutoDockTools from
/home/computation/Applications/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools

Welcome to Python Molecule Viewer!
Visit http://mgltools.scripps.edu/documentation to read latest documentation.

Resource file used to customize PMV:
/home/computation/.mgltools/1.5.4/Pmv/_pmvrc
opengl extension GL_EXT_packed_depth_stencil is not present
X Error of failed request: BadDrawable (invalid Pixmap or Window parameter)
Major opcode of failed request: 14 (X_GetGeometry)
Resource id in failed request: 0x6200032
Serial number of failed request: 4436
Current serial number in output stream: 4436

The PyRx instalation process gives me:

computation@debian:~/Applications$ ./PyRx-0.9-Linux-x86-Install
invalid command name "bind"
while executing
"::unknown bind Text <Tab>"
("uplevel" body line 1)
invoked from within
"uplevel 1 $next $args"
(procedure "::obj::Unknown" line 3)
invoked from within
"bind Text <Tab>"
(procedure "::InstallJammer::InitializeGui" line 19)
invoked from within
"::InstallJammer::InitializeGui "
(procedure "::InstallJammer::InitInstall" line 63)
invoked from within
"::InstallJammer::InitInstall"
(file "/installkitvfs/main.tcl" line 38527)

I think that I know enough to realize that there are missing libraries.
However, while I have been a linux user for a number of years now, I am not an
OS type of individual and have no idea what I need to install to get these
applications to run on Debian.

Any assistance will be appreciated.

Thanks in advance.
--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
Foundation for Chemistry Stochastic and Multivariant
www.FoundationForChemistry.com
(614)312-7528 (c) Skype: smolnar1


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lee 09-12-2012 06:17 PM

Missing Files Prevent Installation/Execution of Applications
 
"Stephen P. Molnar" <s.molnar@sbcglobal.net> writes:

> opengl extension GL_EXT_packed_depth_stencil is not present

This makes me think that you need another driver for the graphics card
which supports the required extension.


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"Stephen P. Molnar" 09-12-2012 07:47 PM

Missing Files Prevent Installation/Execution of Applications
 
On Wednesday 12 September 2012 14:17:45 lee wrote:
> "Stephen P. Molnar" <s.molnar@sbcglobal.net> writes:
> > opengl extension GL_EXT_packed_depth_stencil is not present
>
> This makes me think that you need another driver for the graphics card
> which supports the required extension.

OK, that makes sense, except which one(s)?

My laptop has:

Adapter Type Intel(R) HD Graphics Family, Intel Corporation compatible
Driver Version 8.15.10.2455
Installed Drivers
igdumd64.dll,igd10umd64.dll,igd10umd64.dll,igdumdx 32,igd10umd32,igd10umd32

which are, of course, for MS Win 7. Now, please keep in mind that I know
absolutely nothing about hardware! Will installing additional drivers mess up
the system?

--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
Foundation for Chemistry Stochastic and Multivariant
www.FoundationForChemistry.com
(614)312-7528 (c) Skype: smolnar1


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Andrei POPESCU 09-12-2012 08:52 PM

Missing Files Prevent Installation/Execution of Applications
 
On Mi, 12 sep 12, 15:47:10, Stephen P. Molnar wrote:
>
> which are, of course, for MS Win 7. Now, please keep in mind that I know
> absolutely nothing about hardware! Will installing additional drivers mess up
> the system?

Make sure you have the guest additions installed.

Kind regards,
Andrei
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"Stephen P. Molnar" 09-12-2012 10:45 PM

Missing Files Prevent Installation/Execution of Applications
 
On Wednesday 12 September 2012 16:52:06 Andrei POPESCU wrote:
> On Mi, 12 sep 12, 15:47:10, Stephen P. Molnar wrote:
> > which are, of course, for MS Win 7. Now, please keep in mind that I know
> > absolutely nothing about hardware! Will installing additional drivers
> > mess up the system?
>
> Make sure you have the guest additions installed.
>
> Kind regards,
> Andrei
Thank you for your note. Indeed, I do have the guest additions installed.
--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
Foundation for Chemistry Stochastic and Multivariant
www.FoundationForChemistry.com
(614)312-7528 (c) Skype: smolnar1


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Ralf Mardorf 09-12-2012 11:04 PM

Missing Files Prevent Installation/Execution of Applications
 
On Wed, 2012-09-12 at 18:45 -0400, Stephen P. Molnar wrote:
> On Wednesday 12 September 2012 16:52:06 Andrei POPESCU wrote:
> > Make sure you have the guest additions installed.
> Thank you for your note. Indeed, I do have the guest additions installed.

You've got VirtualBox 4.1.22, the current version installed. Do the
guest additions fit to this version? Perhaps you started with an older
version of VBox, upgraded VBox, but not the guest additions.
Does the extension pack fit to this version? Maybe the extension pack
has got no impact to the trouble, I don't know.


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"Stephen P. Molnar" 09-13-2012 12:28 AM

Missing Files Prevent Installation/Execution of Applications
 
On Wednesday 12 September 2012 19:04:55 Ralf Mardorf wrote:
> On Wed, 2012-09-12 at 18:45 -0400, Stephen P. Molnar wrote:
> > On Wednesday 12 September 2012 16:52:06 Andrei POPESCU wrote:
> > > Make sure you have the guest additions installed.
> >
> > Thank you for your note. Indeed, I do have the guest additions
> > installed.
>
> You've got VirtualBox 4.1.22, the current version installed. Do the
> guest additions fit to this version? Perhaps you started with an older
> version of VBox, upgraded VBox, but not the guest additions.
> Does the extension pack fit to this version? Maybe the extension pack
> has got no impact to the trouble, I don't know.

The entire VirtualBox installation, including the guest additions are up to
date. I'm afraid that I don't see what this has to do with missing libraries.

--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
Foundation for Chemistry Stochastic and Multivariant
www.FoundationForChemistry.com
(614)312-7528 (c) Skype: smolnar1


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lee 09-13-2012 03:15 AM

Missing Files Prevent Installation/Execution of Applications
 
"Stephen P. Molnar" <s.molnar@sbcglobal.net> writes:

> On Wednesday 12 September 2012 14:17:45 lee wrote:
>> "Stephen P. Molnar" <s.molnar@sbcglobal.net> writes:
>> > opengl extension GL_EXT_packed_depth_stencil is not present
>>
>> This makes me think that you need another driver for the graphics card
>> which supports the required extension.
>
> OK, that makes sense, except which one(s)?
>
> My laptop has:
>
> Adapter Type Intel(R) HD Graphics Family, Intel Corporation compatible
> Driver Version 8.15.10.2455
> Installed Drivers
> igdumd64.dll,igd10umd64.dll,igd10umd64.dll,igdumdx 32,igd10umd32,igd10umd32
>
> which are, of course, for MS Win 7. Now, please keep in mind that I know
> absolutely nothing about hardware! Will installing additional drivers mess up
> the system?

Unfortunately, my understanding of how the graphics stuff works with VMs
is very incomplete. I just haven't used them much, especially not on
windoze. I've seen VirtualBox on windoze once, used to run more windoze
in it ... so I'm clueless :(

As a shot into the dark, I would guess that a driver for a physically
present graphics card would need to be able to actually access the
graphics card to be able to fully make use of its features. I don't
know to what extend that is possible from inside a VM --- I sure
wouldn't like it if I was running a VM and suddenly something running in
the VM would access the physically present graphics card and mess up my
X session ...

I'm interested in finding out how this works with VMs, though, since I
currently plan to set one up ...


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Camaleón 09-13-2012 02:10 PM

Missing Files Prevent Installation/Execution of Applications
 
On Wed, 12 Sep 2012 12:20:14 -0400, Stephen P. Molnar wrote:

(...)

> MGLTools installs without any problems,but when I try to run I get:

(...)

> GL_EXT_packed_depth_stencil is not present

(...)

What's the emulated graphic card?

Anyway, VirtualBox VGA 3D capabilities are rather limited and the
application you are trying to run seems to make an extensive usage of the
VGA capabilities.

Are you sure VirtualBox is listed as supported scennario for this
software?

> The PyRx instalation process gives me:
>
> computation@debian:~/Applications$ ./PyRx-0.9-Linux-x86-Install invalid
> command name "bind"

(...)

Check if these forum thread posts help:

http://mgl.scripps.edu/forum/viewtopic.php?f=25&t=1066

Greetings,

--
Camaleón


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"Stephen P. Molnar" 09-13-2012 05:42 PM

Missing Files Prevent Installation/Execution of Applications
 
On Thursday 13 September 2012 10:10:58 Camaleón wrote:
> On Wed, 12 Sep 2012 12:20:14 -0400, Stephen P. Molnar wrote:
>
> (...)
>
> > MGLTools installs without any problems,but when I try to run I get:
> (...)
>
> > GL_EXT_packed_depth_stencil is not present
>
> (...)
>
> What's the emulated graphic card?
>
> Anyway, VirtualBox VGA 3D capabilities are rather limited and the
> application you are trying to run seems to make an extensive usage of the
> VGA capabilities.
>
> Are you sure VirtualBox is listed as supported scennario for this
> software?
>
> > The PyRx instalation process gives me:
> >
> > computation@debian:~/Applications$ ./PyRx-0.9-Linux-x86-Install invalid
> > command name "bind"
>
> (...)
>
> Check if these forum thread posts help:
>
> http://mgl.scripps.edu/forum/viewtopic.php?f=25&t=1066
>
> Greetings,

Thanks for your note.

As a matter of fact, these are not 3D applications. I've run both on other
linux OS's.

Google turned out to be my friend and I installed the 32 bit libraries with
apt-get install ia32-libs ia32-libs-gtk. Having accomplished that I installed
PyRx successfully and it now runs on my 64 bit Debian system.

Unfortunately, the problem with MGLTools still exists:

computation@debian:~/Applications/MGLTools-1.5.4/bin$ ./adt
setting PYTHONHOME environment
Run AutoDockTools from
/home/computation/Applications/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools
Resource file used to customize PMV:
/home/computation/.mgltools/1.5.4/Pmv/_pmvrc
opengl extension GL_EXT_packed_depth_stencil is not present
X Error of failed request: BadDrawable (invalid Pixmap or Window parameter)
Major opcode of failed request: 14 (X_GetGeometry)
Resource id in failed request: 0x5e00032
Serial number of failed request: 4435

There is obviously something missing.
--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
Foundation for Chemistry Stochastic and Multivariant
www.FoundationForChemistry.com
(614)312-7528 (c) Skype: smolnar1


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