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lpsw
Posts: 305
Joined: Thu Jun 25, 2015 4:45 pm
Location: USA

Re: Zip keeps running out of memory

Tue Aug 03, 2021 2:59 pm

Have you reenabled swap?
Self-education is, I firmly believe, the only kind of education there is - Isaac Asimov

kcajminer2312
Posts: 303
Joined: Sun Jan 31, 2021 12:37 pm

Re: Zip keeps running out of memory

Tue Aug 03, 2021 3:02 pm

lpsw wrote:
Tue Aug 03, 2021 2:59 pm
Have you reenabled swap?
yes 0% in use

usage dropped less than 30% just by lowering the size

still more than it should be for 0%
Last edited by kcajminer2312 on Tue Aug 03, 2021 3:07 pm, edited 1 time in total.

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timkehres
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Re: Zip keeps running out of memory

Tue Aug 03, 2021 3:06 pm

kcajminer2312 wrote:
Tue Aug 03, 2021 2:57 pm
lpsw wrote:
Tue Aug 03, 2021 2:55 pm
Reenable swap.
Monitor swap via top or vmstat.
Adjust Reduce the size of the swapfile accordingly.
I am using conky and i have no swap in use
The suggestions above about monitoring your memory usage are right on the point. Depending on how you use your system it is not hard to run out of memory. We had problems with the 8GB boards combined with a minimal swapfile on a regular basis. In addition to top (or htop) and vmstat another great monitoring tool is glances.

If you find that you're running out of virtual memory (at which point the computer will most likely hang) adding swap is the only option. You can do file based swap or if you have a high performance microSD card with some extra space, you might consider using gparted to carve out a native swap partition and use that.

-- Tim

kcajminer2312
Posts: 303
Joined: Sun Jan 31, 2021 12:37 pm

Re: Zip keeps running out of memory

Tue Aug 03, 2021 3:08 pm

timkehres wrote:
Tue Aug 03, 2021 3:06 pm
kcajminer2312 wrote:
Tue Aug 03, 2021 2:57 pm
lpsw wrote:
Tue Aug 03, 2021 2:55 pm
Reenable swap.
Monitor swap via top or vmstat.
Adjust Reduce the size of the swapfile accordingly.
I am using conky and i have no swap in use
The suggestions above about monitoring your memory usage are right on the point. Depending on how you use your system it is not hard to run out of memory. We had problems with the 8GB boards combined with a minimal swapfile on a regular basis. In addition to top (or htop) and vmstat another great monitoring tool is glances.

If you find that you're running out of virtual memory (at which point the computer will most likely hang) adding swap is the only option. You can do file based swap or if you have a high performance microSD card with some extra space, you might consider using gparted to carve out a native swap partition and use that.

-- Tim
I can see I am only using around 500 MB RAM with no virtual

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lpsw
Posts: 305
Joined: Thu Jun 25, 2015 4:45 pm
Location: USA

Re: Zip keeps running out of memory

Tue Aug 03, 2021 3:11 pm

kcajminer2312 wrote:
Tue Aug 03, 2021 3:02 pm
lpsw wrote:
Tue Aug 03, 2021 2:59 pm
Have you reenabled swap?
still more than it should be for 0%
I'll mention this one one time:

The "swap" in kswapd is a bit misleading. It does more than just swap modified pages to the swap file. It main task is to keep the memory management system operating efficiently.
Self-education is, I firmly believe, the only kind of education there is - Isaac Asimov

kcajminer2312
Posts: 303
Joined: Sun Jan 31, 2021 12:37 pm

Re: Zip keeps running out of memory

Tue Aug 03, 2021 3:18 pm

lpsw wrote:
Tue Aug 03, 2021 3:11 pm
kcajminer2312 wrote:
Tue Aug 03, 2021 3:02 pm
lpsw wrote:
Tue Aug 03, 2021 2:59 pm
Have you reenabled swap?
still more than it should be for 0%
I'll mention this one one time:

The "swap" in kswapd is a bit misleading. It does more than just swap modified pages to the swap file. It main task is to keep the memory management system operating efficiently.
It shouldn't spike at 150% usgae

You would understand it more if you looked at my screen shot

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lpsw
Posts: 305
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Location: USA

Re: Zip keeps running out of memory

Tue Aug 03, 2021 3:24 pm

I looked at your screen shot.
Clearly I'm not much help to you so I'll stop trying.
Self-education is, I firmly believe, the only kind of education there is - Isaac Asimov

kcajminer2312
Posts: 303
Joined: Sun Jan 31, 2021 12:37 pm

Re: Zip keeps running out of memory

Tue Aug 03, 2021 3:27 pm

lpsw wrote:
Tue Aug 03, 2021 3:24 pm
I looked at your screen shot.
Clearly I'm not much help to you so I'll stop trying.
60-100% of kswapd0 is not normal
rsync is causing the spikes in usgae for kswapd0

bjtheone
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Location: The Frozen North (AKA Canada)

Re: Zip keeps running out of memory

Tue Aug 03, 2021 4:46 pm

Could you post the entire backup process and exactly how you run it (command line, cron, etc). Also detail what you are backing up and approximately how large it is.

I use rsync nightly, via cron, in what I think is a similar fashion to make a "synced" backup of my home account and have zero performance issues.

kcajminer2312
Posts: 303
Joined: Sun Jan 31, 2021 12:37 pm

Re: Zip keeps running out of memory

Tue Aug 03, 2021 4:50 pm

bjtheone wrote:
Tue Aug 03, 2021 4:46 pm
Could you post the entire backup process and exactly how you run it (command line, cron, etc). Also detail what you are backing up and approximately how large it is.

I use rsync nightly, via cron, in what I think is a similar fashion to make a "synced" backup of my home account and have zero performance issues.
sudo apt -y update
sudo apt -y full-upgrade
sudo apt -y dist-upgrade
sudo apt -y autoremove
mkdir -p /media/pi/BACKUP/TMP/pi/media/pi/COX-SERVER
sudo chmod -R 777 /media/pi/BACKUP/TMP/pi/

sudo rsync -avAXEWSlHhr --delete /boot /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /etc /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete --exclude '.wine' /home /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /root /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /var /media/pi/BACKUP/TMP/pi/
sudo cp -ruv /backup.sh /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /media/pi/COX-SERVER /media/pi/BACKUP/TMP/pi/media/pi/
sudo rsync -avAXEWSlHhr --delete /media/pi/COX-SERVER /media/pi/BACKUP/TMP/pi/media/pi/
now="$(date +'%Y.%m.%d.zip')"
dpkg -l > /media/pi/BACKUP/TMP/pi/installedPackages
cd /media/pi/BACKUP/TMP/pi/
sudo chmod -R 777 /media/pi/BACKUP/TMP/pi/
sudo zip -r /media/pi/BACKUP/Backup/$now ./*

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lpsw
Posts: 305
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Location: USA

Re: Zip keeps running out of memory

Tue Aug 03, 2021 5:10 pm

Self-education is, I firmly believe, the only kind of education there is - Isaac Asimov

bls
Posts: 1690
Joined: Mon Oct 22, 2018 11:25 pm
Location: Seattle, WA

Re: Zip keeps running out of memory

Tue Aug 03, 2021 5:27 pm

kcajminer2312 wrote:
Tue Aug 03, 2021 4:50 pm
bjtheone wrote:
Tue Aug 03, 2021 4:46 pm
Could you post the entire backup process and exactly how you run it (command line, cron, etc). Also detail what you are backing up and approximately how large it is.

I use rsync nightly, via cron, in what I think is a similar fashion to make a "synced" backup of my home account and have zero performance issues.
sudo apt -y update
sudo apt -y full-upgrade
sudo apt -y dist-upgrade
sudo apt -y autoremove
mkdir -p /media/pi/BACKUP/TMP/pi/media/pi/COX-SERVER
sudo chmod -R 777 /media/pi/BACKUP/TMP/pi/

sudo rsync -avAXEWSlHhr --delete /boot /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /etc /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete --exclude '.wine' /home /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /root /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /var /media/pi/BACKUP/TMP/pi/
sudo cp -ruv /backup.sh /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /media/pi/COX-SERVER /media/pi/BACKUP/TMP/pi/media/pi/
sudo rsync -avAXEWSlHhr --delete /media/pi/COX-SERVER /media/pi/BACKUP/TMP/pi/media/pi/
now="$(date +'%Y.%m.%d.zip')"
dpkg -l > /media/pi/BACKUP/TMP/pi/installedPackages
cd /media/pi/BACKUP/TMP/pi/
sudo chmod -R 777 /media/pi/BACKUP/TMP/pi/
sudo zip -r /media/pi/BACKUP/Backup/$now ./*
This is a very curious script. Besides the huge opportunity for typos in directory names (how many times in /media/pi/BACKUP/... there? Could define it once with a variable and eliminate the possiblity of future errors), I have a few other questions:
  • You say it runs out of memory. Where? Have you put in debug outputs to sort this out?
  • You create .../COX-SERVER up at the top, and then back it up, not once, but twice. Is there a reason for that?
  • You change the file protections on every single file you backup. Won't that make recovery a bit difficult?
  • You're very brave to be doing your apt update/upgrade in a script, which presumably you run non-interactively
  • Do you change the protections to 777 twice just to make sure that they actually all get changed? :)
  • You do realize that by changing the protections to 777 some of your rsync switches are redundant or useless? (-A, -X, -E, for instance)
Pi tools:
Quickly and easily build customized-just-for-you SSDs/SD Cards: https://github.com/gitbls/sdm
Easily run and manage your network's DHCP/DNS servers on a Pi: https://github.com/gitbls/ndm
Easy and secure strongSwan VPN installer/manager: https://github.com/gitbls/pistrong
Lightweight Virtual VNC Config: https://github.com/gitbls/RPiVNCHowTo

kcajminer2312
Posts: 303
Joined: Sun Jan 31, 2021 12:37 pm

Re: Zip keeps running out of memory

Tue Aug 03, 2021 5:39 pm

bls wrote:
Tue Aug 03, 2021 5:27 pm
kcajminer2312 wrote:
Tue Aug 03, 2021 4:50 pm
bjtheone wrote:
Tue Aug 03, 2021 4:46 pm
Could you post the entire backup process and exactly how you run it (command line, cron, etc). Also detail what you are backing up and approximately how large it is.

I use rsync nightly, via cron, in what I think is a similar fashion to make a "synced" backup of my home account and have zero performance issues.
sudo apt -y update
sudo apt -y full-upgrade
sudo apt -y dist-upgrade
sudo apt -y autoremove
mkdir -p /media/pi/BACKUP/TMP/pi/media/pi/COX-SERVER
sudo chmod -R 777 /media/pi/BACKUP/TMP/pi/

sudo rsync -avAXEWSlHhr --delete /boot /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /etc /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete --exclude '.wine' /home /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /root /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /var /media/pi/BACKUP/TMP/pi/
sudo cp -ruv /backup.sh /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /media/pi/COX-SERVER /media/pi/BACKUP/TMP/pi/media/pi/
sudo rsync -avAXEWSlHhr --delete /media/pi/COX-SERVER /media/pi/BACKUP/TMP/pi/media/pi/
now="$(date +'%Y.%m.%d.zip')"
dpkg -l > /media/pi/BACKUP/TMP/pi/installedPackages
cd /media/pi/BACKUP/TMP/pi/
sudo chmod -R 777 /media/pi/BACKUP/TMP/pi/
sudo zip -r /media/pi/BACKUP/Backup/$now ./*
This is a very curious script. Besides the huge opportunity for typos in directory names (how many times in /media/pi/BACKUP/... there? Could define it once with a variable and eliminate the possiblity of future errors), I have a few other questions:
  • You say it runs out of memory. Where? Have you put in debug outputs to sort this out?
  • You create .../COX-SERVER up at the top, and then back it up, not once, but twice. Is there a reason for that?
  • You change the file protections on every single file you backup. Won't that make recovery a bit difficult?
  • You're very brave to be doing your apt update/upgrade in a script, which presumably you run non-interactively
  • Do you change the protections to 777 twice just to make sure that they actually all get changed? :)
  • You do realize that by changing the protections to 777 some of your rsync switches are redundant or useless? (-A, -X, -E, for instance)
I dont know where it runs out of memory
/COX-SERVER is another drive in the system, at some point it wasn't being created by rsync
I allow everyone access to the backup before the zip, so zip has access to all the files
that apt has never failed
thats after the data has been writen, before the zip

bls
Posts: 1690
Joined: Mon Oct 22, 2018 11:25 pm
Location: Seattle, WA

Re: Zip keeps running out of memory

Tue Aug 03, 2021 5:41 pm

kcajminer2312 wrote:
Tue Aug 03, 2021 5:39 pm

I dont know where it runs out of memory
/COX-SERVER is another drive in the system, at some point it wasn't being created by rsync
I allow everyone access to the backup before the zip, so zip has access to all the files
that apt has never failed
thats after the data has been writen, before the zip
Perhaps you should do some debugging of the zip command to see where it's dying.

A couple of thoughts...Have the zip output redirected to a file (not in the backup tree of course) so you can see where it's dying. Do a directory of the whole tree that you're zipping up to help you see how far through the tree it gets.
Pi tools:
Quickly and easily build customized-just-for-you SSDs/SD Cards: https://github.com/gitbls/sdm
Easily run and manage your network's DHCP/DNS servers on a Pi: https://github.com/gitbls/ndm
Easy and secure strongSwan VPN installer/manager: https://github.com/gitbls/pistrong
Lightweight Virtual VNC Config: https://github.com/gitbls/RPiVNCHowTo

kcajminer2312
Posts: 303
Joined: Sun Jan 31, 2021 12:37 pm

Re: Zip keeps running out of memory

Tue Aug 03, 2021 5:56 pm

bls wrote:
Tue Aug 03, 2021 5:41 pm
kcajminer2312 wrote:
Tue Aug 03, 2021 5:39 pm

I dont know where it runs out of memory
/COX-SERVER is another drive in the system, at some point it wasn't being created by rsync
I allow everyone access to the backup before the zip, so zip has access to all the files
that apt has never failed
thats after the data has been writen, before the zip
Perhaps you should do some debugging of the zip command to see where it's dying.

A couple of thoughts...Have the zip output redirected to a file (not in the backup tree of course) so you can see where it's dying. Do a directory of the whole tree that you're zipping up to help you see how far through the tree it gets.
its the rsync at the minute because i removed everything in /media/pi/BACKUP/TMP/pi when it was running out of memory
so now its doing a full backup

kcajminer2312
Posts: 303
Joined: Sun Jan 31, 2021 12:37 pm

Re: Zip keeps running out of memory

Tue Aug 03, 2021 6:53 pm

the copying of the files into RAM must be causing the system to hang and kswapd0 to get confused or something

kcajminer2312
Posts: 303
Joined: Sun Jan 31, 2021 12:37 pm

Re: Zip keeps running out of memory

Tue Aug 03, 2021 9:50 pm

my pi keeps signing me out
is it because its running out of memory

pidd
Posts: 2527
Joined: Fri May 29, 2020 8:29 pm
Location: Wirral, UK
Contact: Website

Re: Zip keeps running out of memory

Wed Aug 04, 2021 12:12 am

Nothing to do with your zip problem but ..... you appear to be deleting backups as soon as you create them.

eg

Code: Select all

sudo rsync -avAXEWSlHhr --delete /boot /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /etc /media/pi/BACKUP/TMP/pi/
The first line will write all of /boot to /media/pi/BACKUP/TMP/pi/

But then the second line will delete all of that content because it is syncing with /etc which presumably doesn't contain the same files as /boot.

bls
Posts: 1690
Joined: Mon Oct 22, 2018 11:25 pm
Location: Seattle, WA

Re: Zip keeps running out of memory

Wed Aug 04, 2021 12:22 am

pidd wrote:
Wed Aug 04, 2021 12:12 am
Nothing to do with your zip problem but ..... you appear to be deleting backups as soon as you create them.

eg

Code: Select all

sudo rsync -avAXEWSlHhr --delete /boot /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /etc /media/pi/BACKUP/TMP/pi/
The first line will write all of /boot to /media/pi/BACKUP/TMP/pi/

But then the second line will delete all of that content because it is syncing with /etc which presumably doesn't contain the same files as /boot.
Not sure I agree @pidd.

Note that he didn't have the trailing slash on "--delete /boot" and /etc. If he did, you'd be correct, but in this case, rsync creates /media/pi/BACKUP/TMP/pi/etc and ..../boot. And they are different, so no deletes would happen.

I'd suggest trimming this script down to a single line, and get that working. Then, add another line. etc etc. It would take less time to sort out where the problem is than the current approach.

And, @OP, please be a bit more positive in your posts here. You seem to be quick to point to specific behaviors you're seeing (and to me it reads a bit negative), rather than searching for the root cause, which you'll find by doing some debugging as I suggested above.

Nobody has the same configuration as you do, and likely nobody's going to debug your scripts for you.

My $.02. Not trying to insult anyone, just trying to help you get this solved.
Pi tools:
Quickly and easily build customized-just-for-you SSDs/SD Cards: https://github.com/gitbls/sdm
Easily run and manage your network's DHCP/DNS servers on a Pi: https://github.com/gitbls/ndm
Easy and secure strongSwan VPN installer/manager: https://github.com/gitbls/pistrong
Lightweight Virtual VNC Config: https://github.com/gitbls/RPiVNCHowTo

pidd
Posts: 2527
Joined: Fri May 29, 2020 8:29 pm
Location: Wirral, UK
Contact: Website

Re: Zip keeps running out of memory

Wed Aug 04, 2021 12:57 am

As a start to tidying things up - and keeping it to your style ....

Noting that everything is sudo'd, there will be no permission problems (if its run as root's cron there is no need to sudo anyway)

apt dist-upgrade doesn't exist (I think), even if it did it is the same as full-upgrade

Rsync's -W and -S are probably mutually exclusive (I've not checked), -a includes -r -l etc

I'm not sure about the quotes around the now variable assignment, I've removed them, this might have been your zip problem?

This comes with no warranty :lol:

Code: Select all

sudo apt -y update
sudo apt -y full-upgrade
sudo apt -y autoremove

sudo rsync -avSHh --delete /boot/ /media/pi/BACKUP/TMP/pi/boot/
sudo rsync -avSHh --delete /etc/ /media/pi/BACKUP/TMP/pi/etc/
sudo rsync -avSHh --delete --exclude '.wine' /home/ /media/pi/BACKUP/TMP/pi/home/
sudo rsync -avSHh --delete /root/ /media/pi/BACKUP/TMP/pi/root/
sudo rsync -avSHh --delete /var/ /media/pi/BACKUP/TMP/pi/var/
sudo rsync -avSHh --delete /media/pi/COX-SERVER/ /media/pi/BACKUP/TMP/pi/media/pi/COX-SERVER/

sudo cp -ruv /backup.sh /media/pi/BACKUP/TMP/pi/
sudo dpkg -l > /media/pi/BACKUP/TMP/pi/installedPackages

now=$(date +'%Y.%m.%d.zip')
sudo zip -r /media/pi/BACKUP/Backup/$now /media/pi/BACKUP/TMP/pi/
Last edited by pidd on Wed Aug 04, 2021 1:07 am, edited 2 times in total.

pidd
Posts: 2527
Joined: Fri May 29, 2020 8:29 pm
Location: Wirral, UK
Contact: Website

Re: Zip keeps running out of memory

Wed Aug 04, 2021 1:04 am

bls wrote:
Wed Aug 04, 2021 12:22 am
pidd wrote:
Wed Aug 04, 2021 12:12 am
Nothing to do with your zip problem but ..... you appear to be deleting backups as soon as you create them.

eg

Code: Select all

sudo rsync -avAXEWSlHhr --delete /boot /media/pi/BACKUP/TMP/pi/
sudo rsync -avAXEWSlHhr --delete /etc /media/pi/BACKUP/TMP/pi/
The first line will write all of /boot to /media/pi/BACKUP/TMP/pi/

But then the second line will delete all of that content because it is syncing with /etc which presumably doesn't contain the same files as /boot.
Not sure I agree @pidd.

Note that he didn't have the trailing slash on "--delete /boot" and /etc. If he did, you'd be correct, but in this case, rsync creates /media/pi/BACKUP/TMP/pi/etc and ..../boot. And they are different, so no deletes would happen.
You could be right - I use single line Rsync's with includes and so don't come across that issue.

Edit:

amended my suggested script to a belt and braces approach

kcajminer2312
Posts: 303
Joined: Sun Jan 31, 2021 12:37 pm

Re: Zip keeps running out of memory

Wed Aug 04, 2021 9:36 am

right this is a reply to all that I have just read.

dist-upgrade updates the OS, I dont think full-upgrade does that

--delete should delete files that only exist on the destination

the problem is still kswapd0

after changing the swapiness to 50 swap is filling before RAM

is there a way to repair all packages including the kernel without reinstalling

My 4 GB pi is being used like a 500MB so there is a problem

User avatar
rpdom
Posts: 19058
Joined: Sun May 06, 2012 5:17 am
Location: Chelmsford, Essex, UK

Re: Zip keeps running out of memory

Wed Aug 04, 2021 10:00 am

kcajminer2312 wrote:
Wed Aug 04, 2021 9:36 am
dist-upgrade updates the OS, I dont think full-upgrade does that
dist-upgrade and full upgrade are just different names for the same thing.
after changing the swapiness to 50 swap is filling before RAM
Idle processes will be swapped out to free up RAM for other things. The higher the value of swappiness, the sooner they get swapped out.
is there a way to repair all packages including the kernel without reinstalling
Why do you think packages may need repair?

What does "free -h" show when your system is having problems?
Unreadable squiggle

kcajminer2312
Posts: 303
Joined: Sun Jan 31, 2021 12:37 pm

Re: Zip keeps running out of memory

Wed Aug 04, 2021 10:02 am

rpdom wrote:
Wed Aug 04, 2021 10:00 am
kcajminer2312 wrote:
Wed Aug 04, 2021 9:36 am
dist-upgrade updates the OS, I dont think full-upgrade does that
dist-upgrade and full upgrade are just different names for the same thing.
after changing the swapiness to 50 swap is filling before RAM
Idle processes will be swapped out to free up RAM for other things. The higher the value of swappiness, the sooner they get swapped out.
is there a way to repair all packages including the kernel without reinstalling
Why do you think packages may need repair?

What does "free -h" show when your system is having problems?
the system has crashed because kswapd0 seems to think the pi only has 500MB

kcajminer2312
Posts: 303
Joined: Sun Jan 31, 2021 12:37 pm

Re: Zip keeps running out of memory

Wed Aug 04, 2021 10:02 am

kcajminer2312 wrote:
Wed Aug 04, 2021 10:02 am
rpdom wrote:
Wed Aug 04, 2021 10:00 am
kcajminer2312 wrote:
Wed Aug 04, 2021 9:36 am
dist-upgrade updates the OS, I dont think full-upgrade does that
dist-upgrade and full upgrade are just different names for the same thing.
after changing the swapiness to 50 swap is filling before RAM
Idle processes will be swapped out to free up RAM for other things. The higher the value of swappiness, the sooner they get swapped out.
is there a way to repair all packages including the kernel without reinstalling
Why do you think packages may need repair?

What does "free -h" show when your system is having problems?
the system is hanging because kswapd0 seems to think the pi only has 500MB
I will get free -h as soon as possible
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