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Virtual Memory Under Linux

Why does hydrus keep crashing under Linux when it has lots of virtual memory?

Symptoms

Hydrus crashes without a crash log
Standard error reads Killed
System logs say OOMKiller
Programs appear to havevery high virtual memory utilization despite low real memory.

tl;dr :: The fix

Add the followng line to the end of /etc/sysctl.conf. You will need admin, so use

sudo nano /etc/sysctl.conf or sudo gedit /etc/sysctl.conf

vm.min_free_kbytes=1153434
vm.overcommit_memory=1

Check that you have (enough) swap space or you might still run out of memory.

sudo swapon --show

If you need swap

sudo fallocate -l 16G /swapfile #make 16GiB of swap
sudo chmod 600 /swapfile
sudo mkswap /swapfile

Add to /etc/fstab so your swap is mounted on reboot

/swapfile swap swap defaults 0 0

You may add as many swapfiles as you like, and should add a new swapfile before you delete an old one if you plan to do so, as unmounting a swapfile will evict its contents back in to real memory. You may also wish to use a swapfile type that uses compression, this saves you some disk space for a little bit of a performance hit, but also significantly saves on mostly empty memory.

Reboot for all changes to take effect, or use sysctl to set vm variables.

Details

Linux's memory allocator is lazy and does not perform opportunistic reclaim. This means that the system will continue to give your process memory from the real and virtual memory pool(swap) until there is none left.

Linux will only cleanup if the available total real and virtual memory falls below the watermark as defined in the system control configuration file /etc/sysctl.conf. The watermark's name is vm.min_free_kbytes, it is the number of kilobytes the system keeps in reserve, and therefore the maximum amount of memory the system can allocate in one go before needing to reclaim memory it gave eariler but which is no longer in use.

The default value is vm.min_free_kbytes=65536, which means 66MiB (megabytes).

If for a given request the amount of memory asked to be allocated is under vm.min_free_kbytes, but this would result in an ammount of total free memory less than vm.min_free_kbytes then the OS will clean up memory to service the request.

If vm.min_free_kbytes is less than the ammount requested and there is no virtual memory left, then the system is officially unable to service the request and will lauch the OOMKiller (Out of Memory Killer) to free memory by kiling memory glut processes.

Increase the vm.min_free_kbytes value to prevent this scenario.

The OOM Killer

The OOM kill decides which program to kill to reclaim memory, since hydrus loves memory it is usually picked first, even if another program asking for memory caused the OOM condition. Setting the minimum free kilobytes higher will avoid the running of the OOMkiller which is always preferable, and almost always preventable.

Memory Overcommmit

We mentioned that Linux will keep giving out memory, but actually it's possible for Linux to launch the OOM killer if it just feel like our program is aking for too much memory too quickly. Since hydrus is a heavyweight scientific processing package we need to turn this feature off. To turn it off change the value of vm.overcommit_memory which defaults to 2.

Set vm.overcommit_memory=1 this prevents the OS from using a heuristic and it will just always give memory to anyone who asks for it.

What about swappiness?

Swapiness is a setting you might have seen, but it only determines Linux's desire to spend a little bit of time moving memory you haven't touched in a while out of real memory and into virtual memory, it will not prevent the OOM condition it just determines how much time to use for moving things into swap.

Why does my Linux system studder or become unresponsive when hydrus has been running a while?

You are running out of pages because Linux releases I/O buffer pages only when a file is closed. Thus the OS is waiting for you to hit the watermark(as described in "why is hydrus crashing") to start freeing pages, which causes the chug. When contents is written from memory to disk the page is retained so that if you reread that part of the disk the OS does not need to access disk it just pulls it from the much faster memory. This is usually a good thing, but Hydrus does not close database files so it eats up pages over time. This is really good for hydrus but sucks for the responsiveness of other apps, and will cause hydrus to consume pages after doing a lengthy operation in anticipation of needing them again, even when it is thereafter idle. You need to set vm.dirtytime_expire_seconds to a lower value.

vm.dirtytime_expire_seconds When a lazytime inode is constantly having its pages dirtied, the inode with an updated timestamp will never get chance to be written out. And, if the only thing that has happened on the file system is a dirtytime inode caused by an atime update, a worker will be scheduled to make sure that inode eventually gets pushed out to disk. This tunable is used to define when dirty inode is old enough to be eligible for writeback by the kernel flusher threads. And, it is also used as the interval to wakeup dirtytime writeback thread.

On many distros this happens only once every 12 hours, try setting it close to every one hour or 2. This will cause the OS to drop pages that were written over 1-2 hours ago. Returning them to the free store for use by other programs.

https://www.kernel.org/doc/Documentation/sysctl/vm.txt

Why does everything become clunky for a bit if I have tuned all of the above settings?

The kernel launches a process called kswapd to swap and reclaim memory pages, its behaviour is goverened by the following two values

vm.vfs_cache_pressure The tendancy for the kernel to reclaim I/O cache for files and directories. Default=100, set to 110 to bias the kernel into reclaiming I/O pages over keeping them at a "fair rate" compared to other pages. Hydrus tends to write a lot of files and then ignore them for a long time, so its a good idea to prefer freeing pages for infrequent I/O. Note: Increasing vfs_cache_pressure significantly beyond 100 may have negative performance impact. Reclaim code needs to take various locks to find freeable directory and inode objects. With vfs_cache_pressure=1000, it will look for ten times more freeable objects than there are.
watermark_scale_factor This factor controls the aggressiveness of kswapd. It defines the amount of memory left in a node/system before kswapd is woken up and how much memory needs to be free before kswapd goes back to sleep. The unit is in fractions of 10,000. The default value of 10 means the distances between watermarks are 0.1% of the available memory in the node/system. The maximum value is 1000, or 10% of memory. A high rate of threads entering direct reclaim (allocstall) or kswapd going to sleep prematurely (kswapd_low_wmark_hit_quickly) can indicate that the number of free pages kswapd maintains for latency reasons is too small for the allocation bursts occurring in the system. This knob can then be used to tune kswapd aggressiveness accordingly.

I like to keep watermark_scale_factor at 70 (70/10,000)=0.7%, so kswapd will run until at least 0.7% of system memory has been reclaimed. i.e. If 32GiB (real and virt) of memory, it will try to keep at least 0.224 GiB immediately available.