@mluypaert Thanks for the details.
Do you know whether the problem reproduces with any bowtie2 example that I could run for myself? I'm not familiar w/ it. Apparently there's a workaround for it, if you're willing to test: to disable NUMA balancing. This _might_ impact performance on some memory-intensive workloads that use memory on multiple NUMA nodes. If you previously used kernel versions 3.13.0-156 to 3.13.0-158 there should be no performance impact, as NUMA balancing was disabled in those versions to workaround a regression on 3.13.0-155. It was re-enabled by default on 3.13.0-159. You can disable NUMA balancing on a running system with this command: $ sudo sysctl -w kernel.numa_balancing=0 And then make the change persistent across reboots with this command: $ echo 'kernel.numa_balancing = 0' | sudo tee /etc/sysctl.d/99-numa- balancing.conf If you'd like to try that, please let us know how it goes in a few months maybe? :-) Thanks for your response anyway. cheers, Mauricio -- You received this bug notification because you are a member of Kernel Packages, which is subscribed to linux in Ubuntu. https://bugs.launchpad.net/bugs/1813018 Title: Kernel Oops - unable to handle kernel paging request; RIP is at wait_migrate_huge_page+0x51/0x70 Status in linux package in Ubuntu: Confirmed Bug description: Kernel oops occurs randomly every now and then, seemingly when running memory-intensive processes (so far, it happened to me when using bowtie2 or STAR). Running Ubuntu 14.04 LTS on AWS EC2 instances (m4.* and c4.* family classes). After the error occurs, the server stays accessible through SSH, but the commands w, htop, ps (and maybe others) seem to hang, while commands like ls, cd, top and others keep working. Whatever process was running and (probably) caused the crash seems to go into a sleeping mode. Rebooting (sudo reboot) makes the instance refuse all connections (more than an hour after initiating the reboot). Stopping the (AWS EC2) instance and starting again makes the instance function normally again. Restarting the task that was running when the instance crashed on the newly (re)started instance usually works with no more problems. --- AlsaDevices: total 0 crw-rw---- 1 root audio 116, 1 Jan 23 12:49 seq crw-rw---- 1 root audio 116, 33 Jan 23 12:49 timer AplayDevices: Error: [Errno 2] No such file or directory ApportVersion: 2.14.1-0ubuntu3.29 Architecture: amd64 ArecordDevices: Error: [Errno 2] No such file or directory AudioDevicesInUse: Error: command ['fuser', '-v', '/dev/snd/seq', '/dev/snd/timer'] failed with exit code 1: CRDA: Error: [Errno 2] No such file or directory DistroRelease: Ubuntu 14.04 Ec2AMI: ami-4473183b Ec2AMIManifest: (unknown) Ec2AvailabilityZone: us-east-1c Ec2InstanceType: m4.16xlarge Ec2Kernel: unavailable Ec2Ramdisk: unavailable IwConfig: Error: [Errno 2] No such file or directory Lsusb: Error: command ['lsusb'] failed with exit code 1: unable to initialize libusb: -99 MachineType: Xen HVM domU Package: linux (not installed) PciMultimedia: ProcEnviron: TERM=xterm PATH=(custom, no user) XDG_RUNTIME_DIR=<set> LANG=en_US.UTF-8 SHELL=/bin/bash ProcFB: ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.13.0-164-generic root=UUID=d4f2aafc-946a-4514-930d-4c45e676f198 ro console=tty1 console=ttyS0 ProcVersionSignature: Ubuntu 3.13.0-164.214-generic 3.13.11-ckt39 RelatedPackageVersions: linux-restricted-modules-3.13.0-164-generic N/A linux-backports-modules-3.13.0-164-generic N/A linux-firmware N/A RfKill: Error: [Errno 2] No such file or directory Tags: trusty ec2-images Uname: Linux 3.13.0-164-generic x86_64 UpgradeStatus: No upgrade log present (probably fresh install) UserGroups: sudo WifiSyslog: _MarkForUpload: True dmi.bios.date: 08/24/2006 dmi.bios.vendor: Xen dmi.bios.version: 4.2.amazon dmi.chassis.type: 1 dmi.chassis.vendor: Xen dmi.modalias: dmi:bvnXen:bvr4.2.amazon:bd08/24/2006:svnXen:pnHVMdomU:pvr4.2.amazon:cvnXen:ct1:cvr: dmi.product.name: HVM domU dmi.product.version: 4.2.amazon dmi.sys.vendor: Xen To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1813018/+subscriptions -- Mailing list: https://launchpad.net/~kernel-packages Post to : kernel-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~kernel-packages More help : https://help.launchpad.net/ListHelp
