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[SOLVED] Apps freezing for several seconds in stretch

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Faroe
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Joined: 2013-06-04 19:26

[SOLVED] Apps freezing for several seconds in stretch

#1 Post by Faroe »

Hello!

There's a problem that has been occurring in my Debian testing system for about two months now. Some apps such as Mirage, Thunar and Audacity tend to freeze occasionally. The freeze usually lasts for about 5 to 10 seconds, during which time the frozen window won't refresh or respond to mouse or keyboard input.

One test case that seems to reproduce the problem rather predictably goes like this:
1. Open some directory in Thunar that contains a lot of image files, like more than 100.
2. Open one of the images in Mirage.
3. Launch Gimp and open some image there. It doesn't have to be from the same directory.
4. Start browsing the images in Mirage by stepping forward one image at a time (pressing the down arrow key).
5. At some point, Mirage freezes, and wakes up after five to ten seconds. Any further keypresses get buffered, so that when the freeze is over, Mirage jumps forward several images.

I haven't been able to verify if Gimp always becomes similarly unresponsive at the same time as Mirage, but I've seen it happen at least on some occasions. When Gimp is not running, Mirage seems to work without any problem.

The issue is much worse in Audacity, where the freezing is more frequent and is not affected by Gimp. One symptom in Audacity is that the playback of four track audio stops suddenly and resumes a couple of seconds later with the tracks playing out of sync. However, I have no idea if this is even caused by the same problem.

My system:
- OS: dual booting Debian stretch (Linux 4.9.0-2-amd64) and Windows 7 Professional
- CPU: Intel Core i5-6400 2.70GHz
- GPU: Asus GeForce GTX750Ti 2GB (running the proprietary nvidia driver)
- RAM: Kingston 8GB 2400MHz DDR4
- Motherboard: ASUS H170M-PLUS LGA1151
- Hard drives: one 250GB SSD + one 250GB HDD

Now, I know I need to narrow this down, but I don't really know where to look. Things I have tried:
1. If I run Mirage and Gimp from a terminal, neither of them output any error messages when the freeze occurs.
2. I thought there might be something wrong with my WM or DE (Xfce), so I installed jwm and tried Mirage + Gimp there. The same freeze happened.
3. It seemed that the problem had first appeared after the Linux kernel was upgraded from 4.8.0 to 4.9.0 in late January, so I booted 4.8.0, but that made no difference either. I haven't tried any earlier kernel version, because I'm fairly certain that at least Audacity worked perfectly in early January, when running the 4.8.0 kernel.

There must be some log somewhere that I could look at, but I don't know where. I've tried `journalctl -b --no-pager`, `dmesg` and even `dbus-monitor --session`, but nothing comes up. I have also installed mcelog and it is running as a daemon, but `/var/log/mcelog` stays empty. There's nothing in `/var/log/Xorg.0.log` or `~/.xsession-errors` either.

I'm worried this could be a hardware issue. I have seen Thunar sometimes freeze in a similar fashion when navigating to another directory, but this is very difficult to reproduce. I bought the PC in early 2016 and it used to run both Debian and Windows flawlessly for a year. I've got an SSD and and an HDD, and they both contain ext4 partitions as well as NTFS partitions. Debian's root and Windows are on the SSD; my /home is on the HDD. I have run `fsck` on the ext4 partitions and checked the NTFS partitions using ScanDisk (or whatever it's called) from Windows, and found no errors.

There's also a strange crashing problem in Windows 7 that I think may have started happening around the same time the first of these freezes occurred in Debian. Windows just reboots the machine without warning, out of the blue, when I'm not even running any particularly demanding software. This has happened maybe four or five times. Debian never completely crashes on me, so I'm not sure this is related. Anyway, I think I should run memtest86+ as my next step.

Is there anything else I could do to locate the source of the freezes? Please let me know what other information I could provide. I'm sorry this post is rather long, but I didn't want to sound like "Debian keeps freezing. Please help me fix it."

Thank you for your help and patience!
Last edited by Faroe on 2017-06-02 17:47, edited 1 time in total.

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pylkko
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Re: Apps freezing for several seconds in stretch

#2 Post by pylkko »

Just to be sure, you could do a memtest. You could also try and see if some hard stressing (like with package stress or other similar) causes these freezes. Also, smart test. What i/o-scheduler are you using?

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phenest
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Re: Apps freezing for several seconds in stretch

#3 Post by phenest »

Is it overheating? Check CPU and GPU temperatures.
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Faroe
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Re: Apps freezing for several seconds in stretch

#4 Post by Faroe »

pylkko wrote:What i/o-scheduler are you using?
I wouldn't have been able to answer that, but I investigated a bit. The commands `cat /sys/block/sda/queue/scheduler` and `cat /sys/block/sdb/queue/scheduler` both give this output:

Code: Select all

noop deadline [cfq]
Is this what you meant? I assume these are the defaults. I wasn't even aware of different I/O schedulers until today. Thanks for the tip!

My SSD is /dev/sda and the HDD is /dev/sdb. Should I be using a different scheduler with either or both, and if so, how would I do that?

I launched memtest86+ 5.01 and pressed F2 to use multi-threaded mode. It froze completely after 90 seconds and I had to reboot. Then I restarted it in fail-safe mode and kept it running for three hours, during which time it went through two and a half passes and found no errors. I'm going to leave it running overnight to get a better picture.
phenest wrote:Is it overheating? Check CPU and GPU temperatures.
At the moment I don't seem to have any means of checking those in Debian, but I'll experiment a little with the lm-sensors, hddtemp and xfce4-sensors-plugin packages and report back later. Thank you!

Faroe
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Re: Apps freezing for several seconds in stretch

#5 Post by Faroe »

A quick update. So far this doesn't seem to be a case of faulty memory or overheating.

1. I left memtest86+ running for 14 hours (no multi-thread mode or fail-safe mode). It went through ten passes and found no errors.
2. According to psensor, the temperature of all four CPU cores stays between ~16°C and ~20°C while Mirage is running and even when it freezes. The CPU's "physical" sensor reports 25°C (+/-1).
3. psensor and nvidia-settings both report a steady 29-30°C GPU temperature before and during a freeze.
4. I performed the "short" self-test on both the SSD and the HDD via GSmartControl and no errors were found. The "extended" test would take 2 hours on the SSD and 90 minutes on the HDD, so I'll try them later.

I haven't tried changing the I/O scheduler yet. Is it always a good idea to use "deadline" with an SSD, as suggested in the Debian Wiki (https://wiki.debian.org/SSDOptimization ... -Scheduler)? Are there any caveats? Shouldn't it be the default?

One thing I only found out about today is the "discard/TRIM" problem that many SSD's seem to suffer from. I'll have to look into it to see if that could be relevant here.

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phenest
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Re: Apps freezing for several seconds in stretch

#6 Post by phenest »

Faroe wrote:2. According to psensor, the temperature of all four CPU cores stays between ~16°C and ~20°C
This seems rather cool. What CPU cooler are you using? Liquid cooling? I would've expected a temperature twice that.
Faroe wrote:One thing I only found out about today is the "discard/TRIM" problem that many SSD's seem to suffer from. I'll have to look into it to see if that could be relevant here.
I doubt it's relevant. If the program has loaded into memory and then freezes, then it's not the hard drive. If the hard drive was at fault or something like TRIM/discard was an issue, then I would expect the whole OS to be struggling.
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pylkko
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Re: Apps freezing for several seconds in stretch

#7 Post by pylkko »

Yeah, the only reason I thought about I/O-scheduler related issues was because you were saying that you were loading massive amounts of images or something from a traditional HDD, so I thought that perhaps the I/O load is "blocking". With simple schedulers that do not prioritize workloads it is possible that there is contention for available I/O bandwidth from other applications. Also maybe you could have been using one of the newer experiemntal ones or something But you are using CFQ. The Debian wiki, by the way, states that one should use Low-Latency I/O-Scheduler for SSD drives because:
https://wiki.debian.org/SSDOptimization#Low-Latency_IO-Scheduler wrote:The default I/O scheduler queues data to minimize seeks on HDDs, which is not necessary for SSDs. Thus, use the "deadline" scheduler that just ensures bulk transactions won't slow down small transactions
Since you have fairly extensively tested the RAM, the drive, the CPU is not overheating (although those numbers look suspicious to me too, standard room temp is 22 °C. cpu temp should no be less than that in normal setups), there are no log errors, it is starting to seem like there might be some software problem. Either bugs in testing of some kind or perhaps you have some kind of configuration problem. One thing that comes to mind at this moment is if you disabled swap entirely or made swappiness zero and then had some memory leaking process that could lead to "out of RAM". But then again this is happening on Windows also. On that information alone I would have suspected RAM or a bad sector in some part of the disk that holds Windows system files. It might be that the SSD is going bad, or perhaps it is not tolerating some powersave property. Is this a SATA drive? SSD's can just one day die without any preceding smart warnings.

Faroe
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Re: Apps freezing for several seconds in stretch

#8 Post by Faroe »

phenest wrote:
Faroe wrote:2. According to psensor, the temperature of all four CPU cores stays between ~16°C and ~20°C
This seems rather cool. What CPU cooler are you using? Liquid cooling? I would've expected a temperature twice that.
No liquid, but instead a Cooler Master Hyper 212 EVO fan. Some cores do momentarily peak at 30-35°C when launching programs such as Gimp, but they cool down again right after. Mind you, I haven't really watched the temperatures while putting the machine under a heavy load. I guess I should try out the stress and stress-ng packages.

Some new observations:
1. I changed the I/O scheduler of the SSD to "deadline" but that didn't stop the freezing.
2. I copied a total of ~560 photos from a DVD to two partitions on my HDD (one ext4, the other NTFS) using Thunar. The copy operation itself went smoothly, but Thunar became unresponsive immediately after that and stayed frozen for at least ten seconds. This kind of thing has happened a several times during the past two months. I thought it worth mentioning in case it helps locate a possible cause of the problem.
3. I did some image manipulation work in Gimp and it kept freezing every couple of minutes, for about five seconds at a time. I wasn't looking at the temperatures at the time, but I checked the graphs in psensor later and it seemed like the CPU had stayed between 20°C and 30°C.
4. I ran the extensive self-tests on both hard drives in GSmartControl and there were no errors. There was a warning that the Samsung SSD didn't report the correct checksum for the self-test log, but apparently that's nothing to worry about.
pylkko wrote:Is this a SATA drive?
Yes. Here is a snippet of the output from smartctl regarding the SSD:

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=== START OF INFORMATION SECTION ===
Model Family:     Samsung based SSDs
Device Model:     Samsung SSD 850 EVO 250GB
Serial Number:    S21PNXCG956720H
LU WWN Device Id: 5 002538 d4059bf26
Firmware Version: EMT01B6Q
User Capacity:    250,059,350,016 bytes [250 GB]
Sector Size:      512 bytes logical/physical
Rotation Rate:    Solid State Device
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   ACS-2, ATA8-ACS T13/1699-D revision 4c
SATA Version is:  SATA 3.1, 6.0 Gb/s (current: 6.0 Gb/s)
Local Time is:    Mon Apr 17 14:41:03 2017 EEST
SMART support is: Available - device has SMART capability.
SMART support is: Enabled
For what it's worth, this is what it says about the HDD. I don't know why no SATA version is reported.

Code: Select all

=== START OF INFORMATION SECTION ===
Model Family:     Western Digital Caviar SE Serial ATA
Device Model:     WDC WD2500JS-55NCB1
Serial Number:    WD-WCANK7837050
Firmware Version: 10.02E01
User Capacity:    250,059,350,016 bytes [250 GB]
Sector Size:      512 bytes logical/physical
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   ATA/ATAPI-7 (minor revision not indicated)
Local Time is:    Mon Apr 17 14:39:55 2017 EEST
SMART support is: Available - device has SMART capability.
SMART support is: Enabled
pylkko wrote:it is starting to seem like there might be some software problem.
I hope so too. I'd hate to have to start replacing my hardware, especially considering it's not very old yet. I wonder what the problematic software could be, however. A probable cause would seem to be some library that all these apps depend on, or more likely, somewhere higher up the dependency chain.

For a while it seemed like all programs affected by this were GTK+ 2 apps (Mirage, Gimp, Audacity, Thunar, Libreoffice), and that most often more than one would freeze simultaneously, while GTK+ 3 programs (Xfce4 Terminal, Psensor, Galculator) would keep running without problems. However, there's Firefox, which I think also depends on GTK+ 2 and has been running nicely even while those other apps freeze. On top of that, even Psensor froze up on me for a short while today.

One thing I haven't tried yet is running `fstrim` manually. At this point I don't know if any trimming of my SSD has ever taken place. Doesn't Windows take care of that? I'll have to study `fstrim` some more to determine if it's even safe.

Thanks for all your help so far. The quest continues.

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phenest
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Re: Apps freezing for several seconds in stretch

#9 Post by phenest »

Before you wear out your SSD doing extensive tests, you need to stand back and look at this objectively.

To start with, what are your start up and shutdown times like? If they are "normal", that is no freezing/pausing, then I don't think your SSD's nor the filing system is at fault. No amount of tweaking in that area is going to fix it if it's not the entire system that has issues.

I think you need to make a list of "affected" programs and look for common factors. Are all programs affected? Is it only ones with high CPU usage? Or high RAM usage? Or high hard drive usage? Or a combination?
Faroe wrote:
phenest wrote:
Faroe wrote:2. According to psensor, the temperature of all four CPU cores stays between ~16°C and ~20°C
This seems rather cool. What CPU cooler are you using? Liquid cooling? I would've expected a temperature twice that.
No liquid, but instead a Cooler Master Hyper 212 EVO fan. Some cores do momentarily peak at 30-35°C when launching programs such as Gimp, but they cool down again right after. Mind you, I haven't really watched the temperatures while putting the machine under a heavy load. I guess I should try out the stress and stress-ng packages.
Those temperatures still seem too cool. What temperatures does the BIOS report? I wouldn't stress test the CPU in case those reported temperatures are wrong. When was the last time the thermal paste was changed?
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acewiza
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Re: Apps freezing for several seconds in stretch

#10 Post by acewiza »

Try using a FM other than Thunar and see what happens.
Nobody would ever ask questions If everyone possessed encyclopedic knowledge of the man pages.

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phenest
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Re: Apps freezing for several seconds in stretch

#11 Post by phenest »

I just noticed you dual boot with Windows 7. Does that still work ok? Install CoreTemp in Windows and compare CPU temperatures. Do some similar work in Windows to see if that freezes. Do tests to compare Windows with Debian. That way you can eliminate a lot of hardware, or find a common factor.
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acewiza
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Re: Apps freezing for several seconds in stretch

#12 Post by acewiza »

phenest wrote:I just noticed you dual boot with Windows 7. Does that still work ok? Install CoreTemp in Windows and compare CPU temperatures. Do some similar work in Windows to see if that freezes. Do tests to compare Windows with Debian. That way you can eliminate a lot of hardware, or find a common factor.
Rather than wasting time playing with temperature experiments, the guilty piece of software might be discovered by a simple process of elimination. Thunar is well-know for freeze issues.
Nobody would ever ask questions If everyone possessed encyclopedic knowledge of the man pages.

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phenest
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Re: Apps freezing for several seconds in stretch

#13 Post by phenest »

Except that it's not just Thunar. The OP said GIMP did it, amongst others. It doesn't hurt to check hardware too. We'll leave it to the OP to decide.
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Re: Apps freezing for several seconds in stretch

#14 Post by pylkko »

the OP said it occurs in Windows also

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Re: Apps freezing for several seconds in stretch

#15 Post by phenest »

That eliminates a software problem.
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Faroe
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Re: Apps freezing for several seconds in stretch

#16 Post by Faroe »

acewiza wrote:Thunar is well-know for freeze issues.
Oh, indeed, I'd had my share of headaches caused by Thunar before this freezing problem appeared. I'm glad Thunar 1.6.11 doesn't crash every time I rename a file, like 1.6.10 would. Anyway, Thunar has a feature set that I'm happy with and I don't think it can be blamed for the freezing. It happens even when Thunar is not running in daemon mode in the background.
pylkko wrote:the OP said it occurs in Windows also
The symptoms in Windows 7 are much more troubling: the entire system just reboots itself without any obvious reason. However, I have no idea if those crashes are related to the freezes in Debian. In other words, they could very well be. I think they began occurring around the same time, but for all I know, it could simply be a case of Windows crashing because it is Windows.
phenest wrote:What temperatures does the BIOS report?
The ASUS UEFI BIOS Utility reports CPU temperatures between 25°C and 27°C, which corresponds to the value of the CPU's "Physical id 0" sensor as reported by `sensors` when no resource-hungry software is running. The BIOS utility doesn't monitor the temperature of individual CPU cores.
phenest wrote:When was the last time the thermal paste was changed?
I'm fairly sure it's never been changed. The machine was assembled less than sixteen months ago and I haven't touched the stuff.

Thanks for all the support. I'll try to assemble a list of software that suffers from the freezes and look for a pattern. I probably won't have time to come back to this until next weekend, but please let me know if there's anything else I should look into.

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Re: Apps freezing for several seconds in stretch

#17 Post by Bulkley »

Freezes are very often hardware related as posters above hinted at. A failing video card can drive you nuts. Software that overloads a video card or memory can do it.

Top of the list should be software that does not agree with the assigned OS, in this case Stretch.

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Re: Apps freezing for several seconds in stretch

#18 Post by pylkko »

phenest wrote:That eliminates a software problem.
Almost, I'd say, but not entirely. Since there are settings and configurations that can cause hardware to misbehave or even brake (for example some SSD's don't tolerate SATA Active Link Power Management, or you can do firmware updates from software that would cause hardware to misbehave in many OS's etc.). Also, the problem might only appear to be the same in the two OS's but actually be distinct problems.

OP also said that drive is using SATA 3.1, so there should be no periodic system freezes from frequent TRIM (is asynchronous after 3.1).

Faroe, are you using "discard"?

After you said that you got these freezes using images, I immediately thought if this problem might be worse with say audio. But now I reread your post and see that you do say in it that multichannel audio in Audacity is really behaving in odd ways. Are the audio files that you are editing on the HDD or the SSD? Audacity, I believe, uses a temp folder on the system disk, so that would be on the SSD.

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Re: Apps freezing for several seconds in stretch

#19 Post by dasein »

I may be giving a long-winded +1 to Bulkley here, I can't quite tell.

It's way too early to be making a list and checking it twice to find out which software is naughty and nice when hardware hasn't been ruled out (or anywhere close to it). If I've read the seemingly contradictory posts of the OP correctly...

1) Everything was running fine for over a year, Linux ran great. Windows ran great. All was sunshine and puppies.

2) Two different OSes are currently exhibiting problems simultaneously on the same rig. The symptoms are admittedly markedly different, which makes it impossible to determine the extent to which these issues are related. But as a purely statistical matter, Cosmic Coincidence is the least likely explanation for cross-OS borkage.

3) Interacting bugs within specific applications is also a very unlikely explanation. If it were the applications themselves, some percentage of the other folks who use those same apps would be reporting similar issues. I haven't done a Web search for similar symptoms with other distros (that's the OP's job after all), but at least as far as Debian goes, his experience seems to be unique.

4) The "stress" conditions reported by the OP don't strike me as particularly stressful for a multi-core rig with 8GB of RAM.

5) The OP doesn't say whether s/he's fully updated on Stretch, which, given the timing, is absolutely crucial. Eight weeks ago corresponds roughly to when Stretch would be at its buggiest-of-all-time.

6) Am I the only one who wants to see this OP's sources.list? Because I most certainly do.

Diagnostic/remedial steps that I haven't seen suggested...

1) Update Stretch and repro the problem

2) Repro the problem using another distro--say, Fedora (live medium is fine)

3) Repro the problem using a different set of initial "stressors" (say, 20 tabs open in Firefox)

There are still plenty of untried diagnostic steps (isolating RAM slots, running with only one drive active, ensuring that memtest is updated to the latest version). But they are all less likely to be informative than these initial steps.

Faroe
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Re: Apps freezing for several seconds in stretch

#20 Post by Faroe »

pylkko wrote:Faroe, are you using "discard"?
No, I'm not. I assume you're referring to the mount option, which doesn't appear in my /etc/fstab. Also `findmnt -O discard` gives no output but `findmnt -O nodiscard` does. Is that the correct way to check this?
pylkko wrote:But now I reread your post and see that you do say in it that multichannel audio in Audacity is really behaving in odd ways. Are the audio files that you are editing on the HDD or the SSD?
The files are on the HDD. I should point out that the out-of-sync error I described happens quite rarely. More often Audacity freezes in the same way as Mirage, i.e. during playback (even if there are only two tracks and one is muted), it stops refreshing the window for several seconds, while the audio keeps playing as usual.
dasein wrote:4) The "stress" conditions reported by the OP don't strike me as particularly stressful for a multi-core rig with 8GB of RAM.
I'm sorry if I haven't been very clear. The conditions I've reported are not "stress" conditions, just ordinary everyday tasks. I haven't tried to run any actual stress tests yet.
dasein wrote:5) The OP doesn't say whether s/he's fully updated on Stretch, which, given the timing, is absolutely crucial.
I believe I am. The system automatically updates the package cache daily and notifies me if there are upgradable packages. These days there are several almost every day.

If I run `sudo apt-get update` and `sudo apt-get upgrade` manually, the latter says:

Code: Select all

0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
dasein wrote:6) Am I the only one who wants to see this OP's sources.list? Because I most certainly do.
I'm glad you asked. I wouldn't be at all surprised if the file was somehow messed up.

Code: Select all

#

# deb cdrom:[Debian GNU/Linux 8.3.0 _Jessie_ - Official amd64 xfce-CD Binary-1 20160123-19:00]/ jessie main

deb http://httpredir.debian.org/debian/ stretch main non-free contrib
deb-src http://httpredir.debian.org/debian/ stretch main non-free contrib

deb http://security.debian.org/ stretch/updates main contrib non-free
deb-src http://security.debian.org/ stretch/updates main contrib non-free

# stretch-updates, previously known as 'volatile'
deb http://httpredir.debian.org/debian/ stretch-updates main contrib non-free
deb-src http://httpredir.debian.org/debian/ stretch-updates main contrib non-free

# jessie-backports, previously on backports.debian.org
#deb http://httpredir.debian.org/debian/ jessie-backports main contrib non-free
#deb-src http://httpredir.debian.org/debian/ jessie-backports main contrib non-free
It's basically inherited from jessie. I noticed only just now that the first pair of deb/deb-src lines contains "main non-free contrib" while in the rest of them, the order of the components is "main contrib non-free". That inconsistency must have been there for years. I changed the order of the first lines to match the others and ran `sudo apt-get update` and `sudo apt-get upgrade` again, but the ordering doesn't seem to make a difference. Not that I expected any.

My /etc/apt/sources.list.d/ is empty.
dasein wrote:2) Repro the problem using another distro--say, Fedora (live medium is fine)
I guess I should do just that, once I have a little more spare time.

Thanks for all the feedback, again.

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