Hi @mluypaert, Do you still hit this problem?
Would you be able to provide steps of how you run bowtie2/star that reproudces the problem? And/or be able to try a workaround that might prevent it from happening? Thank you, 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
