R SIG Fedora - Jan 2016 - 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.duncan at gmail.com] 
Sent: Friday, January 08, 2016 8:13 PM
To: Wittner, Ben, Ph.D.; r-help at 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.utf8        LC_COLLATE=en_US.utf8
>   [5] LC_MONETARY=en_US.utf8    LC_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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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

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 at kagoshima ~]$ cat /etc/redhat-release
CentOS Linux release 7.2.1511 (Core) 
[bwittner at kagoshima ~]$ rpm -q centos-release
centos-release-7-2.1511.el7.centos.2.10.x86_64
[bwittner at 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 df000000 (32-bit, non-prefetchable) [size=16M]
        Memory at c0000000 (64-bit, prefetchable) [size=256M]
        Memory at dc000000 (64-bit, non-prefetchable) [size=32M]
        I/O ports at dc00 [size=128]
        Expansion ROM at defe0000 [disabled] [size=128K]
        Capabilities: <access denied>
        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:v000012D2d*sv*sd*bc03sc*i*
alias:          pci:v000010DEd*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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