Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7
Ugh.
Below I declared victory, but today I learned that the NVIDIA driver has a
problem the nouveau driver did not have. Namely, when using the NVIDIA driver,
if I plot a lot of stuff in the RGL window and then using the mouse expand the
RGL window, R usually crashes.
One work-around seems to be to
1) close all RGL windows, if there are any
2) call rgl.clear() to create an RGL window
3) re-size that window using your mouse
4) do your plotting
-Original Message-
From: R-SIG-Fedora [mailto:r-sig-fedora-boun...@r-project.org] On Behalf Of
Wittner, Ben, Ph.D.
Sent: Monday, January 11, 2016 5:14 PM
To: Tom Callaway; r-sig-fedora@r-project.org
Cc: Duncan Murdoch
Subject: Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's
visible in the RGL device window on CentOS 7
Tom,
Bingo!
I followed the instructions in the link below, which allowed me to install the
nvidia driver, which fixed the original problem with rgl.snapshot.
Thanks very much for all your help.
I guess I'll file a bug in the CentOS Bug Tracker so that the nouveau driver
might get fixed. I'll also post to R-help so someone with the same problem who
only searches R-help and not this SIG will see the solution.
-Ben
-Original Message-
From: Tom Callaway [mailto:tcall...@redhat.com]
Sent: Monday, January 11, 2016 4:10 PM
To: Wittner, Ben, Ph.D.; r-sig-fedora@r-project.org
Cc: Duncan Murdoch
Subject: Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's
visible in the RGL device window on CentOS 7
I have not tried it personally, but these instructions seem correct:
http://www.dedoimedo.com/computers/centos-7-nvidia.html
Basically, edit the grub2 cmdline to include the extra option:
rdblacklist=nouveau
hth,
~tom
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Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7
Tom,
I thought about filing a bug report with Nouveau, but it seems that working
directly with Nouveau is well beyond my capabilities.
I have no idea how to do most of the stuff Nouveau says to do in their
troubleshooting page. And for the small minority of things that I think I might
be able to figure out, each one would take me hours of reading and
experimentation and begging for help. I'm not an OS guy.
And also, I don't think I can afford to be frequently installing and
uninstalling drivers because I need my machine to be stable for my real work.
Nouveau's bug reporting page says "If you are using packages from your
distribution and are unable/unwilling to test the latest versions of all the
pieces of nouveau, send the bug reports to your distribution and not directly
to us." So I thought I should submit the bug report to CentOS.
I'm hoping that it will be relatively easy for someone at CentOS to reproduce
the bug and then take it from there, probably working with Nouveau.
-Ben
-Original Message-
From: Tom Callaway [mailto:tcall...@redhat.com]
> I guess I'll file a bug in the CentOS Bug Tracker so that the nouveau driver
> might get fixed. I'll also post to R-help so someone with the same problem
> who only searches R-help and not this SIG will see the solution.
Awesome. If you have the cycles, I'm sure the CentOS people would appreciate it
if you ran through the nouveau troubleshooting first:
http://nouveau.freedesktop.org/wiki/Bugs/
You might consider also filing a bug with the Nouveau upstream, as the CentOS
people may not be experts with that driver, but the upstream certainly will be.
Keep in mind that they may want you to test the latest version of the driver
first.
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Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7
On 01/11/2016 05:13 PM, Wittner, Ben, Ph.D. wrote: > I followed the instructions in the link below, which allowed me to install > the nvidia driver, which fixed the original problem with rgl.snapshot. > > Thanks very much for all your help. > > I guess I'll file a bug in the CentOS Bug Tracker so that the nouveau driver > might get fixed. I'll also post to R-help so someone with the same problem > who only searches R-help and not this SIG will see the solution. Awesome. If you have the cycles, I'm sure the CentOS people would appreciate it if you ran through the nouveau troubleshooting first: http://nouveau.freedesktop.org/wiki/Bugs/ You might consider also filing a bug with the Nouveau upstream, as the CentOS people may not be experts with that driver, but the upstream certainly will be. Keep in mind that they may want you to test the latest version of the driver first. Glad we got it working for you though. :) ~tom == Red Hat ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7
Tom,
Bingo!
I followed the instructions in the link below, which allowed me to install the
nvidia driver, which fixed the original problem with rgl.snapshot.
Thanks very much for all your help.
I guess I'll file a bug in the CentOS Bug Tracker so that the nouveau driver
might get fixed. I'll also post to R-help so someone with the same problem who
only searches R-help and not this SIG will see the solution.
-Ben
-Original Message-
From: Tom Callaway [mailto:tcall...@redhat.com]
Sent: Monday, January 11, 2016 4:10 PM
To: Wittner, Ben, Ph.D.; r-sig-fedora@r-project.org
Cc: Duncan Murdoch
Subject: Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's
visible in the RGL device window on CentOS 7
I have not tried it personally, but these instructions seem correct:
http://www.dedoimedo.com/computers/centos-7-nvidia.html
Basically, edit the grub2 cmdline to include the extra option:
rdblacklist=nouveau
hth,
~tom
==
Red Hat
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Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7
On 01/11/2016 03:52 PM, Wittner, Ben, Ph.D. wrote: > I started trying to do this, but I'm stuck. > I started with > http://us.download.nvidia.com/XFree86/Linux-x86_64/340.96/README/installdriver.html > , which led me to > http://us.download.nvidia.com/XFree86/Linux-x86_64/340.96/README/commonproblems.html#nouveau > . I created /etc/modprobe.d/disable-nouveau.conf as instructed then > rebooted, but the nvidia installer found the nouveau driver running anyway, > so it wrote two more .conf files (one in /usr/lib/modproe.d and the other in > /etc/modeprobe.d) and then halted. I rebooted and tried the installer again, > but again it noticed the nouveau driver running. > I suspect this is because the initial ramdisk image contains Nouveau because, > even though I've done systemctl set-default multi-user.target, during boot I > still see something that looks like a graphical screen display for a while > before it drops back to a text mode to display the login prompt. > So, following the instructions, I tried to rebuild the initial ramdisk image. > The nvidia documentation does not say how to do that, so I Googled and found > https://wiki.centos.org/TipsAndTricks/CreateNewInitrd , which unfortunately > gives instructions only for CentOS 5 and CentOS 6, but not CentOS 7. I'm > afraid to do the wrong thing, so I'm stuck. > Any suggestions would be appreciated. > \ I have not tried it personally, but these instructions seem correct: http://www.dedoimedo.com/computers/centos-7-nvidia.html Basically, edit the grub2 cmdline to include the extra option: rdblacklist=nouveau hth, ~tom == Red Hat ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7
Tom,
> Okay. I do "official" package builds of R for RHEL/CentOS as part of the EPEL
> repository:
> https://fedoraproject.org/wiki/EPEL
> If its not painful for you to do so, testing my packages vs yours just to
> rule out misconfiguration in R would be
> helpful. I don't think this is likely, but I'm being thorough.
I've now tried the EPEL version of R and it still has the problem.
> Okay. Nouveau is _not_ the NVIDIA driver, that's the open source driver
> provided by the Linux kernel.
> It is possible this is a bug in nouveau.
> You may want to try to install the NVIDIA driver and see if it resolves your
> issue:
> http://www.nvidia.com/object/unix.html
I started trying to do this, but I'm stuck.
I started with
http://us.download.nvidia.com/XFree86/Linux-x86_64/340.96/README/installdriver.html
, which led me to
http://us.download.nvidia.com/XFree86/Linux-x86_64/340.96/README/commonproblems.html#nouveau
. I created /etc/modprobe.d/disable-nouveau.conf as instructed then rebooted,
but the nvidia installer found the nouveau driver running anyway, so it wrote
two more .conf files (one in /usr/lib/modproe.d and the other in
/etc/modeprobe.d) and then halted. I rebooted and tried the installer again,
but again it noticed the nouveau driver running.
I suspect this is because the initial ramdisk image contains Nouveau because,
even though I've done systemctl set-default multi-user.target, during boot I
still see something that looks like a graphical screen display for a while
before it drops back to a text mode to display the login prompt.
So, following the instructions, I tried to rebuild the initial ramdisk image.
The nvidia documentation does not say how to do that, so I Googled and found
https://wiki.centos.org/TipsAndTricks/CreateNewInitrd , which unfortunately
gives instructions only for CentOS 5 and CentOS 6, but not CentOS 7. I'm afraid
to do the wrong thing, so I'm stuck.
Any suggestions would be appreciated.
Thanks.
-Ben
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Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7
On 01/11/2016 01:24 PM, Wittner, Ben, Ph.D. wrote: > Dear Tom, Thank you very much for thinking about this. Please see my replies > below. -Ben > >> Are you using the EPEL R 3.2.3 builds? > > I'm not sure what the question means, but I'm pretty sure the answer is no. I > know I built the versions of R I used from source code (i.e., ./configure > followed by make). Okay. I do "official" package builds of R for RHEL/CentOS as part of the EPEL repository: https://fedoraproject.org/wiki/EPEL If its not painful for you to do so, testing my packages vs yours just to rule out misconfiguration in R would be helpful. I don't think this is likely, but I'm being thorough. >> What version of the NVIDIA driver are you using? > > Since the output of lspci above said "Kernel driver in use: nouveau", I > executed the command modinfo nouveau, getting the following output: Okay. Nouveau is _not_ the NVIDIA driver, that's the open source driver provided by the Linux kernel. It is possible this is a bug in nouveau. You may want to try to install the NVIDIA driver and see if it resolves your issue: http://www.nvidia.com/object/unix.html ~tom == Red Hat ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7
Dear Tom, Thank you very much for thinking about this. Please see my replies
below. -Ben
> Are you using the EPEL R 3.2.3 builds?
I'm not sure what the question means, but I'm pretty sure the answer is no. I
know I built the versions of R I used from source code (i.e., ./configure
followed by make).
> What version of Centos 7? 7.2?
[bwittner@kagoshima ~]$ cat /etc/redhat-release
CentOS Linux release 7.2.1511 (Core)
[bwittner@kagoshima ~]$ rpm -q centos-release
centos-release-7-2.1511.el7.centos.2.10.x86_64
[bwittner@kagoshima ~]$ uname -rmi
3.10.0-327.3.1.el7.x86_64 x86_64 x86_64
> Is the NVIDIA driver in play?
I think so. When I execute the command lspci -v, the only block that has
mention of VGA is the following:
07:00.0 VGA compatible controller: NVIDIA Corporation G84GL [Quadro FX 370]
(rev a1) (prog-if 00 [VGA controller])
Subsystem: NVIDIA Corporation Device 0491
Flags: bus master, fast devsel, latency 0, IRQ 42
Memory at df00 (32-bit, non-prefetchable) [size=16M]
Memory at c000 (64-bit, prefetchable) [size=256M]
Memory at dc00 (64-bit, non-prefetchable) [size=32M]
I/O ports at dc00 [size=128]
Expansion ROM at defe [disabled] [size=128K]
Capabilities:
Kernel driver in use: nouveau
> What version of the NVIDIA driver are you using?
Since the output of lspci above said "Kernel driver in use: nouveau", I
executed the command modinfo nouveau, getting the following output:
filename:
/lib/modules/3.10.0-327.3.1.el7.x86_64/kernel/drivers/gpu/drm/nouveau/nouveau.ko
license:GPL and additional rights
description:nVidia Riva/TNT/GeForce/Quadro/Tesla
author: Nouveau Project
rhelversion:7.2
srcversion: C131306B4DEC7AB88BC647D
alias: pci:v12D2d*sv*sd*bc03sc*i*
alias: pci:v10DEd*sv*sd*bc03sc*i*
depends:drm,drm_kms_helper,ttm,mxm-wmi,i2c-core,wmi,video,i2c-algo-bit
intree: Y
vermagic: 3.10.0-327.3.1.el7.x86_64 SMP mod_unload modversions
signer: CentOS Linux kernel signing key
sig_key:3D:4E:71:B0:42:9A:39:8B:8B:78:3B:6F:8B:ED:3B:AF:09:9E:E9:A7
sig_hashalgo: sha256
parm: tv_norm:Default TV norm.
Supported: PAL, PAL-M, PAL-N, PAL-Nc, NTSC-M, NTSC-J,
hd480i, hd480p, hd576i, hd576p, hd720p, hd1080i.
Default: PAL
*NOTE* Ignored for cards with external TV encoders. (charp)
parm: vram_pushbuf:Create DMA push buffers in VRAM (int)
parm: nofbaccel:Disable fbcon acceleration (int)
parm: tv_disable:Disable TV-out detection (int)
parm: ignorelid:Ignore ACPI lid status (int)
parm: duallink:Allow dual-link TMDS (default: enabled) (int)
parm: pstate:enable sysfs pstate file, which will be moved in the
future (int)
parm: config:option string to pass to driver core (charp)
parm: debug:debug string to pass to driver core (charp)
parm: noaccel:disable kernel/abi16 acceleration (int)
parm: modeset:enable driver (default: auto, 0 = disabled, 1 =
enabled, 2 = headless) (int)
parm: runpm:disable (0), force enable (1), optimus only default (-1)
(int)
parm: agpmode:AGP mode (0 to disable AGP) (int)
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Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7
On 01/11/2016 10:55 AM, Wittner, Ben, Ph.D. wrote: > Dear R-SIG-Fedora, > > I'm finding that on CentOS 7, rgl.snapshot (a function in the R package rgl, > which provides an R interface to the OpenGL 3-d graphics library) only > captures a small portion what's visible in the RGL device window. This does > not happen with the same R and rgl versions on CentOS 5.3 (see details below). > > The maintainer of rgl, Duncan Murdoch, responded (see below) that the rgl > code has not changed in a long time, so it's likely, although not certain, > that the problem lies with CentOS 7. > > I know very little about graphics, but it seems to me from looking at the rgl > source code that the fundamental work of rgl.snapshot is done by calls to > glReadBuffer, glPixelStorei, and glReadPixels, which seem to be functions in > the OpenGL library. > > Can anyone take a look at this or advise me on how to proceed? Are you using the EPEL R 3.2.3 builds? What version of Centos 7? 7.2? Is the NVIDIA driver in play? What version of the NVIDIA driver are you using? ~tom == Red Hat ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
[R-sig-Fedora] rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7
Dear R-SIG-Fedora,
I'm finding that on CentOS 7, rgl.snapshot (a function in the R package rgl,
which provides an R interface to the OpenGL 3-d graphics library) only captures
a small portion what's visible in the RGL device window. This does not happen
with the same R and rgl versions on CentOS 5.3 (see details below).
The maintainer of rgl, Duncan Murdoch, responded (see below) that the rgl code
has not changed in a long time, so it's likely, although not certain, that the
problem lies with CentOS 7.
I know very little about graphics, but it seems to me from looking at the rgl
source code that the fundamental work of rgl.snapshot is done by calls to
glReadBuffer, glPixelStorei, and glReadPixels, which seem to be functions in
the OpenGL library.
Can anyone take a look at this or advise me on how to proceed?
Thanks very much in advance.
-Ben
-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Friday, January 08, 2016 8:13 PM
To: Wittner, Ben, Ph.D.; r-h...@r-project.org
Subject: Re: [R] rgl.snapshot only captures a small portion what's visible in
the RGL device window on CentOS 7
On 08/01/2016 4:13 PM, Wittner, Ben, Ph.D. wrote:
> Hello,
>
> As an example, I ran the following code:
>
> library("rgl")
> example(plot3d)
> rgl.snapshot("test.png")
>
> The full plot is visible in the window titled RGL device 1 [Focus],
> but only a small portion of the upper left part of the plot is visible
> in test.png (see attached test.png, if the list server attaches it.
> Otherwise, email me if you like and I'll send it directly to you.)
>
> The output of sessionInfo() is as follows:
>
> R version 3.2.3 (2015-12-10)
> Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7
> (Core)
>
> locale:
> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
> [3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8
> [5] LC_MONETARY=en_US.utf8LC_MESSAGES=en_US.utf8
> [7] LC_PAPER=en_US.utf8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] rgl_0.95.1441
>
> loaded via a namespace (and not attached):
> [1] tools_3.2.3
>
> In addition to the CentOS 7 machine, I have a CentOS 5.3 machine, which has R
> 3.0.2 and rgl 0.93.996. I tried the code above on it and it captured the full
> window in the output of rgl.snapshot (i.e., it worked properly).
>
> To see whether the difference could be attributed to the CentOS version or
> the R/rgl version, I put R 3.0.2 with rgl 0.93.996 on the CentOS 7 machine
> and ran the code above. As with the earlier CentOS 7 run, only a small
> portion of the plot was visible in the output of rgl.snapshot. So it seems
> the difference is due to a difference in the CentOS versions and not the
> R/rgl versions.
>
> Thanks in advance for any help.
>
I think you'll need to contact CentOS about this. That code hasn't changed in
rgl in a long time. It's possible that rgl is wrong, but I'd need more
information from them to convince me.
Duncan Murdoch
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