Thanks, Nicholas :D I mainly posted this problem with a solution here for reference to other Debian users ;)
Yes, my processing memory requirements (typically ~30GB) are borderline to my current physical memory limit (~32GB), and as my images sometimes are a little bigger, this can push it into swapping, which indeed is not ideal.. I am modifying my code to batch this procedure to lower the gargantuan memory requirements of my image registration task, but in the meantime, for processes with large memory requirements that may occasionally need to swap, I found this kernel tuning at least allows the process to complete. Cheers! Steve. On Fri, 28 Jan 2022 at 23:56, Nicholas Geovanis <nickgeova...@gmail.com> wrote: > > > On Fri, Jan 28, 2022, 4:33 AM Steven J. West <stevenjonw...@gmail.com> > wrote: > >> Dear all, >> >> TL;DR/summary: >> >> - Tuning vm.watermark_boost_factor to 0 (disable) on Debian >> significantly improves performance on memory-intensive tasks that utilise >> SWAP space, by stopping preemptive kswapd freeing of memory, and >> subsequent page thrashing. >> - I suggest that Debian should tune vm-watermark_boost_fact=0 by >> default to prevent this problem >> >> I'm not a Debian maintainer, but this has got to be the best problem > report I ever saw :-) > > But for years I have adopted the philosophy at home which is demanded in > every data center I've worked in: If your Linux system is swapping, you > have configured it wrong. In the server farms there is no swapping. You > make sure you have enough RAM to prevent swapping. EOS. > > > I have recently installed Debian 11 on a HP Z8 G4 Workstation (Z3Z16AV) - >> 32GB RAM, installed with ~120GB SWAP on a 2TB solid state drive (specs at >> end of this message). >> >> I have been running some compute-intensive image processing tasks (CPU- >> and memory- intensive), which has on occasion had to dip into SWAP space, >> depending on image sizes (the processing I am running is image registration >> using elastix/transformix). >> >> I had benchmarked the code on my Ubuntu laptop (similar spec) without any >> problems, but when running on Debian, whenever SWAP was needed, the system >> processing significantly slowed down/essentially froze. >> >> After much debugging, I have traced this to the vm.watermark_boost_factor >> kernel parameter: >> >> Comparing the Ubuntu and Debian kernel parameters using sudo sysctl -a >> showed two key differences in virtual memory (vm) management parameters. >> >> - Ubuntu: >> - vm.swappiness=60 >> - vm.watermark_boost_factor=0 >> - Debian: >> - vm.swappiness=10 >> - vm.watermark_boost_factor=150 >> >> >> I identified what these two parameters control: >> >> >> - vm.swappiness : a parameter used to calculate the swap tendency ( >> https://access.redhat.com/solutions/103833) >> - vm.watermark_boost_factor : controls the level of reclaim when >> memory is being fragmented.. A boost factor of 0 will disable the >> feature. ( >> >> https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/8/html/8.4_release_notes/kernel_parameters_changes >> ) >> >> >> I changed swappiness and then watermark_boost_factor sequentially, to >> see whether tuning these parameters to match my Ubuntu system prevented the >> system from freezing under my memory-intensive task. >> >> >> - sudo sysctl vm.swappiness=60 on my Debian system did not prevent >> the freezing behaviour. >> - sudo sysctl vm.watermark_boost_factor=0 (disabling it) on my Debian >> system prevented the freezing behaviour. >> >> >> I then set these permanently by adding the following to /etc/sysctl.conf >> >> vm.swappiness=60 >> vm.watermark_boost_factor=0 >> >> >> Further searching revealed this Ubuntu bug report: >> >> https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1861359 >> >> swap storms kills interactive use >> With this key entry: >> >> Sultan Alsawaf (kerneltoast) wrote on 2020-03-27: #56 >> >> This problem is caused by an upstream memory management feature called >> watermark boosting. Normally, when a memory allocation fails and falls back >> to the page allocator, the page allocator will wake up kswapd to free up >> pages in order to make the memory allocation succeed. kswapd tries to free >> memory until it reaches a minimum amount of memory for each memory zone >> called the high watermark. >> >> What watermark boosting does is try to preemptively fire up kswapd to >> free memory when there hasn't been an allocation failure. It does this by >> increasing kswapd's high watermark goal and then firing up kswapd. The >> reason why this causes freezes is because, with the increased high >> watermark goal, kswapd will steal memory from processes that need it in >> order to make forward progress. These processes will, in turn, try to >> allocate memory again, which will cause kswapd to steal necessary pages >> from those processes again, in a positive feedback loop known as page >> thrashing. When page thrashing occurs, your system is essentially >> livelocked until the necessary forward progress can be made to stop >> processes from trying to continuously allocate memory and trigger kswapd to >> steal it back. >> >> This problem already occurs with kswapd *without* watermark boosting, but >> it's usually only encountered on machines with a small amount of memory >> and/or a slow CPU. Watermark boosting just makes the existing problem worse >> enough to notice on higher spec'd machines. >> >> To fix the issue in this bug, watermark boosting can be disabled with the >> following: >> # echo 0 > /proc/sys/vm/watermark_boost_factor >> >> There's really no harm in doing so, because watermark boosting is an >> inherently broken feature... >> >> >> So essentially, disabling watermark_boost_factor ensures effective >> swapping and reduces page thrashing. >> >> *I therefore suggest that Debian should >> tune vm.watermark_boost_factor=0 by default.* >> >> Cheers, >> >> Steve. >> >> >> Below are some more detailed specs of my Debian machine for reference: >> >> >> $ uname -a >> Linux panseer 5.10.0-11-amd64 #1 SMP Debian 5.10.92-1 (2022-01-18) x86_64 >> GNU/Linux >> >> >> $ lscpu >> Architecture: x86_64 >> CPU op-mode(s): 32-bit, 64-bit >> Byte Order: Little Endian >> Address sizes: 46 bits physical, 48 bits virtual >> CPU(s): 20 >> On-line CPU(s) list: 0-19 >> Thread(s) per core: 2 >> Core(s) per socket: 10 >> Socket(s): 1 >> NUMA node(s): 1 >> Vendor ID: GenuineIntel >> CPU family: 6 >> Model: 85 >> Model name: Intel(R) Xeon(R) Silver 4210R CPU @ >> 2.40GHz >> Stepping: 7 >> CPU MHz: 2511.149 >> CPU max MHz: 3200.0000 >> CPU min MHz: 1000.0000 >> BogoMIPS: 4800.00 >> Virtualization: VT-x >> L1d cache: 320 KiB >> L1i cache: 320 KiB >> L2 cache: 10 MiB >> L3 cache: 13.8 MiB >> NUMA node0 CPU(s): 0-19 >> Vulnerability Itlb multihit: KVM: Mitigation: VMX disabled >> Vulnerability L1tf: Not affected >> Vulnerability Mds: Not affected >> Vulnerability Meltdown: Not affected >> Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass >> disabled via prctl and seccomp >> Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and >> __user pointer sanitization >> Vulnerability Spectre v2: Mitigation; Enhanced IBRS, IBPB >> conditional, RSB filling >> Vulnerability Srbds: Not affected >> Vulnerability Tsx async abort: Mitigation; TSX disabled >> Flags: fpu vme de pse tsc msr pae mce cx8 apic >> sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm >> pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon >> pebs bts rep_good nopl xtopology >> nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx >> est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic mov >> be popcnt tsc_deadline_timer aes xsave >> avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 >> invpcid_single intel_ppin ssbd mba ibrs ibpb stibp ibrs_enhanced tp >> r_shadow vnmi flexpriority ept vpid >> ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm mpx rdt_a >> avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd a >> vx512bw avx512vl xsaveopt xsavec xgetbv1 >> xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat >> pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke avx512_ >> vnni md_clear flush_l1d arch_capabilities >> >> >> $ free -h >> total used free shared buff/cache >> available >> Mem: 31Gi 3.6Gi 24Gi 160Mi 3.2Gi >> 26Gi >> Swap: 119Gi 242Mi 118Gi >> >> >> >> >> Steven J. West >> BSc DPhil FRMS >> _________________________________ >> International Brain Lab Histology Research Fellow >> Sainsbury Wellcome Centre for Neural Circuits and Behaviour >> University College London >> 25 Howland St, Fitzrovia, London W1T 4JG >> +44 (0) 203 108 8197 >> steven.w...@internationalbrainlab.org >> https://www.internationalbrainlab.com/ >> https://www.sainsburywellcome.org/ >> >> >>
