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RFC2324
Jun 7, 2012

Http 418


zerofunk posted:

From what I can tell, you do still need to install them for OpenCL support. That was why I installed them. Otherwise I think you’re right and I was using everything just fine for a few months without them.

Huh, thats an oversight.

Have you checked to make sure its not loading both? Might have to blacklist the stock one

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zerofunk
Apr 24, 2004


No, mostly because I'm not really sure how to figure that out to be honest I was trying to look at dmesg earlier and ended up kind of stuck because nothing was showing from previous system starts. I just learned about journalctl though, so I now have what looks to be the issue.

amdgpu 0000:25:00.0: Direct firmware load for amdgpu/vega10_gpu_info.bin failed with error -2
amdgpu 0000:25:00.0: amdgpu: Failed to load gpu_info firmware "amdgpu/vega10_gpu_info.bin"
amdgpu 0000:25:00.0: amdgpu: Fatal error during GPU init
[drm] amdgpu: finishing device.
BUG: kernel NULL pointer dereference, address: 0000000000000044

Looking at the logs from when it works... I don't see anything referencing a firmware load - definitely no error. The lines leading up to that point look a little different though. Some of the same things are in both, some aren't.

I'll try uninstalling it tomorrow and see what kind of impact that has.

Bobulus
Jan 28, 2007



Hi, dumb question time. I'm a biologist who only has a passing knowledge of linux due to messing with red-hat and ubuntu on my home PC two decades ago.



I've been running a data-intensive analysis for two days straight now, but now I'm wondering if the system is throttling it in some way. Am I reading this right? Top says that while the iqtree process is requesting 100% of the CPU resources, for the system, 90% of the CPU resources are idle?

The system is adminned by someone who knows even less than me, so it wouldn't surprise me if we've configured something wrong.

robostac
Sep 23, 2009


Your application is probably single threaded so it's using 100% of one core but there are multiple cores available and most of them are idle.

If you press '1' while top is running it should show you idle/usage stats for each core instead of an overall percentage.

RFC2324
Jun 7, 2012

Http 418


Bobulus posted:

Hi, dumb question time. I'm a biologist who only has a passing knowledge of linux due to messing with red-hat and ubuntu on my home PC two decades ago.



I've been running a data-intensive analysis for two days straight now, but now I'm wondering if the system is throttling it in some way. Am I reading this right? Top says that while the iqtree process is requesting 100% of the CPU resources, for the system, 90% of the CPU resources are idle?

The system is adminned by someone who knows even less than me, so it wouldn't surprise me if we've configured something wrong.

Usage numbers in linux can be weird. I highly suggest installing htop, which will give you a much better idea of whats actually being used.

Unless you went all customization happy on the OS, it shouldn't be throttling anything down, that isn't stock behavior. If you did go customization happy, stop that, the defaults are usually sane.

Bobulus
Jan 28, 2007



robostac posted:

Your application is probably single threaded so it's using 100% of one core but there are multiple cores available and most of them are idle.

If you press '1' while top is running it should show you idle/usage stats for each core instead of an overall percentage.

Yeah, that looks to be the problem:



One CPU maxed out, the rest just sitting there. The weird thing is that the application is set to use all 12 cores.

Documentation posted:

--nthreads
number of threads to use; specifying the value ‘auto’ will cause the number of available CPU cores on your system, if determinable, to be used

Default: 1

command posted:

--nthreads 12


The command itself is running inside a shell environment. I don't know much about that, other than it uses docker. Now I'm wondering if something about the shell is set wrong, such that it only has 'access' to one core? I'm just guessing since I don't know much about modern linux?

RFC2324
Jun 7, 2012

Http 418


Bobulus posted:

Yeah, that looks to be the problem:



One CPU maxed out, the rest just sitting there. The weird thing is that the application is set to use all 12 cores.




The command itself is running inside a shell environment. I don't know much about that, other than it uses docker. Now I'm wondering if something about the shell is set wrong, such that it only has 'access' to one core? I'm just guessing since I don't know much about modern linux?

Might check docker config.

minato
Jun 7, 2004

cutty cain't hang, say 7-up.

Taco Defender

"--cpu-quote=X" when running docker will cap the number of CPUs you can use, but that's not the only way CPUs can be constrained.

Before checking that, I'd suggest checking to see if there are actually 12 threads running. If you do a "ps -eLf" (as root) then it'll show all processes, and I think there should be a line per-thread. If you don't see 12 (almost identical) lines then your "-nthreads 12" directive isn't working.

BaseballPCHiker
Jan 16, 2006



Anyone here use Mint 20? Is it worth the upgrade to over Mint 19? I just built a new home PC and was wondering if it was worth the hassle to reinstall over 19 that I had laying around already on a usb drive.

D. Ebdrup
Mar 13, 2009



From the man-page, it looks like starting top with -H or pressing H when using top interactively will aggregate all the threads, just like it does on FreeBSD.

Computer viking
May 30, 2011
Now with less breakage.

Also, nothing spends all its time doing parallel work - it may just be in a single-threaded phase right now.

D. Ebdrup
Mar 13, 2009



Computer viking posted:

Also, nothing spends all its time doing parallel work - it may just be in a single-threaded phase right now.
The load averages prove its been running with a single thread for at least the past 30 minutes, and more importantly iqtree is a piece of data analysis software for evolutionary geonomics, so I would assume it does a lot of data crunching and therefore would be as parallelized as possible by default, as finding out how many hardware threads are available on any Unix-like is extremely easy.

Unless something isn't parallelizable, there's little reason not to do it on any modern OS with all the locking primitives available - and it turns out that many of the things we thought were unparallelizable simply aren't; case in point, in the past video encoding used to be thought impossible whereas nowadays h264 can be parallelized.

The bigger issue often is fetching data into main storage from external storage (ie. from disk to memory) or any of the numerous uninterruptable wait states that is denoted by D process state, but top on Linux doesn't seem to show the process state, for reasons which must've made sense to its developers but don't make any sense to me.

It's further complicated by the fact that some (not all, and they aren't very well-documented if at all) of those uninterruptable wait states also affect load averages on Linux but not any other Unix-like, so you can't even use them and need to resort to either a tracing framework or mpstat which isn't in the base system of any distribution.

Severing
Aug 26, 2017



I've been hearing for a while that an AMD gpu is the way to go and I had a chance to pick up an 5700XT fairly cheap recently to replace a 1070. Things aren't always better though, even though I am getting much better FPS in games.

For example, in Eve Online things are pretty fine. Much better FPS as you would expect from a better card.

In Elder Scrolls Online though I keep getting lots of hitching. I've messed with every setting, messed with an addons that lets you tweak settings such as max FPS, potato moded it you name it and nothing fixes it. It was pretty smooth on the 1070 (none of this hitching) and on Windows the game is perfect. Same monitor too, a 144Hz 1440p monitor that supports Activesync (which is enabled) and is certified by Nvidia too (its an Asus TUF VG27A).

I saw some advice, which was to add the following to my xorg.conf.d as it apparently enables variable refresh. This did not help however. I've also made sure the monitor is runnning at 144Hz in GNOME's display config as well and tried it both under Wayland and Xorg.

code:
Section "Device"
  Identifier "AMD"
  Driver "amdgpu"
  Option "TearFree" "1"
  Option "VariableRefresh" "true"
EndSection

Any ideas what else I could tweak to resolve the hitching?

Computer viking
May 30, 2011
Now with less breakage.

Oh yeah, that historical load really doesn't show many signs of life.

I'm otherwise familiar with the ... shape of the problem - one of the things I do for a living is helping our researchers run (and write) bioinformatics code. They have large data sets, so I grab any obvious opportunities to parallelize to save time - the big constraint tends to be RAM, things head into the hundreds of GB uncomfortably fast.

(Also on FreeBSD, incidentally. It makes a perfectly pleasant analysis server, except for the sporadic tool and R package that has never been tested on a non-linux. My personal favourite thing is hardcoding /bin/make and using gmake syntax.)

FunkyAl
Mar 28, 2010

Your vitals soar.


Alright I'm getting into linux for the first time, I installed a partition but can't seeem to get it to boot windows. When I boot it gives me the option of linux or windows at /dev/sda1, but my windows is located in /dev/sda2. How can I get into that?

Volguus
Mar 3, 2009


FunkyAl posted:

Alright I'm getting into linux for the first time, I installed a partition but can't seeem to get it to boot windows. When I boot it gives me the option of linux or windows at /dev/sda1, but my windows is located in /dev/sda2. How can I get into that?

If you select that option (windows at /dev/sda1), what happens?

FunkyAl
Mar 28, 2010

Your vitals soar.


Volguus posted:

If you select that option (windows at /dev/sda1), what happens?

The screen goes black and then returns me to the same grub(?) screen. Also on mine it says on/dev/sda1

Volguus
Mar 3, 2009


FunkyAl posted:

The screen goes black and then returns me to the same grub(?) screen. Also on mine it says on/dev/sda1

You can edit (temporarily) the grub entry by pressing e while in the menu. Fiddle with the partition it's trying to load. Once you get it working make it permanent in linux.

FunkyAl
Mar 28, 2010

Your vitals soar.


What command should I give it? I tried a generic "boot" command but it said it needed a kernel. I am also new at this and mostly illiterate.

FunkyAl
Mar 28, 2010

Your vitals soar.


Ayy I fixed it I just ran the boot repair! Otherwise, what are the fun things to do in linux.

D. Ebdrup
Mar 13, 2009



Run... Gentoo?

KozmoNaut
Apr 23, 2008

Happiness is a warm
Turbo Plasma Rifle


Grimey Drawer

Computer stuff, mostly.

FunkyAl
Mar 28, 2010

Your vitals soar.


Can i build a wisecracking computer butler in "lisp"

E: or change what the "start" bar is like

D. Ebdrup
Mar 13, 2009



With enough effort, probably.

Antigravitas
Dec 8, 2019

Outside Context Problem


You can install `sl` and have a fun surprise when you typo `ls`.

For something unique, does your desktop environment ship wobbly windows? They are extremely cool.

namlosh
Feb 11, 2014

I blew up


Ha, that’s funny...

Whatever happened to all of those bitchin’ desktop replacements/enhancements? Like Beryl and Compiz?

Those literally got me into learning Linux. Having your desktop be a cube that you could spin while playing a different 1080p movie on each side back in the day was a real eye opener that maybe I wasn’t getting the best performance from Windows.

I still use mainly windows, but I have a few Linux servers around the network doing various things.

Thx flashy desktops!

mystes
May 31, 2006



namlosh posted:

Ha, that’s funny...

Whatever happened to all of those bitchin’ desktop replacements/enhancements? Like Beryl and Compiz?

Those literally got me into learning Linux. Having your desktop be a cube that you could spin while playing a different 1080p movie on each side back in the day was a real eye opener that maybe I wasn’t getting the best performance from Windows.

I still use mainly windows, but I have a few Linux servers around the network doing various things.

Thx flashy desktops!
Compositors still exist obviously but those effects are dumb.

Antigravitas
Dec 8, 2019

Outside Context Problem


mystes posted:

Compositors still exist obviously but those effects are dumb.



namlosh posted:

Whatever happened to all of those bitchin’ desktop replacements/enhancements? Like Beryl and Compiz?


KDE Plasma is still carrying those effects. Using wobbly windows to put a very subtle effect on moving windows actually looks pretty neat.

You can configure effects pretty thoroughly:

D. Ebdrup
Mar 13, 2009



Holy poo poo, compiz fusion.
I remember writing a guide on how to do that for FreeBSD, when compiz was a brand new thing.

namlosh
Feb 11, 2014

I blew up


Yassssssss

Seriously, those got me into trying Linux. People posted their desktops on YouTube... it was like a major thing, then it wasn’t lol.

Gonna see if I can find a live CD I can boot so I can do that again just for fun... any recommendations?

Antigravitas
Dec 8, 2019

Outside Context Problem


KDE Neon is basically KDE's showcase distro. They have a live image.

namlosh
Feb 11, 2014

I blew up


Antigravitas posted:

KDE Neon is basically KDE's showcase distro. They have a live image.

Perfect, thank you

D. Ebdrup
Mar 13, 2009



In case wayland is a thing anyone's interested in, there's a 3D compositor based on wlroots, inspired by compiz - and it as well as its plugins also available on FreeBSD.

NihilCredo
Jun 6, 2011

iram omni possibili modo preme:
plus una illa te diffamabit, quam multæ virtutes commendabunt



D. Ebdrup posted:

In case wayland is a thing anyone's interested in, there's a 3D compositor based on wlroots, inspired by compiz - and it as well as its plugins also available on FreeBSD.

Do any of the more popular compositors / desktop environments support something like this tiling plugin?

(Tiling WMs not included, of course - tiling windows is something I find occasionally useful but do not want to always have active)

I really like the way this Wayfire implementation looks, it seems better than Windows's:

https://www.youtube.com/watch?v=SKfhPsA8TxU

namlosh
Feb 11, 2014

I blew up


Yessssss, straight into my veins:

cube plugin

CaptainSarcastic
Jul 6, 2013

HAIL SATAN


I love my wobbly windows.

As just a basic quality-of-life thing I find just dimming inactive windows is the most valuable, and I'm amazed that Microsoft hasn't stolen it for Windows. I was searching the other day and couldn't even find a program to bring that behavior into Windows that wasn't years out of date.

Antigravitas
Dec 8, 2019

Outside Context Problem


There are a ton of QoL features Windows is really slow to adopt. It took 3rd party programs to get more than one task bar. Setting a window to always be on top, despite being supported by the window manager, was something individual programs had to implement. Multi-desktops were also a really late addition and adding additional buttons to the window decoration is hacky as hell.

Have they finally managed to add tabs to the file explorer?

Kassad
Nov 11, 2005

It's about time.


It drives me nuts that file extensions still aren't visible by default on Windows 10.

mystes
May 31, 2006



NihilCredo posted:

Do any of the more popular compositors / desktop environments support something like this tiling plugin?

(Tiling WMs not included, of course - tiling windows is something I find occasionally useful but do not want to always have active)

I really like the way this Wayfire implementation looks, it seems better than Windows's:

https://www.youtube.com/watch?v=SKfhPsA8TxU
https://github.com/paperwm/PaperWM and https://github.com/lingtjien/Grid-Tiling-Kwin but I haven't tried either and I'm not sure the former can be toggled on and off easily. They also look like the might be jankier (more like using one of the tiling programs for windows) than an actual tiling wm.

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KozmoNaut
Apr 23, 2008

Happiness is a warm
Turbo Plasma Rifle


Grimey Drawer

Antigravitas posted:

KDE Neon is basically KDE's showcase distro. They have a live image.

It's based on the latest Ubuntu LTS release, so PPAs and various other Ubuntu-related stuff works on it too.

I've been using it as my desktop distro for a while now, it has generally been a good experience, KDE is a wonderful desktop. I've since installed openSUSE Leap on my HTPC/server and my laptop, and I'll probably migrate the desktop at some point as well. KDE Neon is a rolling release distro, so there are tons of new updates pretty much every day, which gets a little tiring. Also I don't like how Ubuntu is going all-in on Snaps for software packaging now, it sucks so bad.

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