Description of problem: yum update is choking the OS at the moment. Version-Release number of selected component (if applicable): 3.2.28-5.fc14 (64 bit) How reproducible: Every time. Bug seems to have been introduced in the last week or two. Steps to Reproduce: 1. Run yum update to download daily set of packages. (Delta rebuild functionality enabled.) Actual results: 2. Whilst yum is running, other applications and screen redraws have become extremely sluggish. Monitoring with top shows that yum is using the CPU intensively. At times, even top will stop responding. Expected results: yum should not be a resource hog. Other applications' performance and screen refresh speeds should not be affected by the fact that this utility is running. Additional info: Changing the nice value seemed to help a little but I will need to experiment some more with that.
> Bug seems to have been introduced in the last week or two. yum hasn't changed since Fed-14 GA. > Monitoring with top shows that yum is using the CPU intensively. Do you know what yum is doing at these times? What does "yum -v" say in the time output?
could you dump out the list of pkgs which have changed since you started noticing the issue?
James, There were only three packages to download today and performance seemed better as a result: ********************************** Running Transaction Updating : libimobiledevice-1.0.4-1.fc14.x86_64 1/6 Updating : libxml++-2.33.1-1.fc14.x86_64 2/6 Updating : directfb-1.4.11-1.fc14.i686 3/6 Cleanup : libimobiledevice-1.0.3-1.fc14.x86_64 4/6 Cleanup : libxml++-2.32.0-1.fc14.x86_64 5/6 Cleanup : directfb-1.4.3-1.fc14.i686 6/6 VerifyTransaction time: 34.998 Transaction time: 59.494 ********************************** I am not sure if the verification time should be more than 50% of the transaction time, though. It did seem to pause at that point for quite a while. Seth, how do I dump out that list of packages? Is it with an RPM command?
Is this system a clean install or an upgrade from earlier systems? If you run: rm -f /var/lib/rpm/__db* rpm --rebuilddb does performance improve? Finally, look in /var/log/yum.log and you should be able to get a list of updates/installs since a specific date
Seth, thanks for that. 1. No, I used preupgrade to move from F13 to F14. I was running F14 during its beta phase, so there might be some legacy junk on there. 2. I just ran these commands. I will have to wait until more packages are available for yum update to pick. (I haven't run yum install very frequently recently to make a valid comparison with that.) 3. I have attached the yum log for the last few weeks.
Created attachment 463598 [details] yum log from Nov 11 onwards.
FWIW - a few other packages have changed outside of yum: 1. I have been running the Firefox nightly builds for a while. 2. I also removed OO.org and installed the beta of LibreOffice but that was definitely after I started having the yum performance issues.
VerifyTransaction time does seem high ... but that should be _all_ I/O (so while I could see it affecting interactive performance ... it shouldn't show up in top). Not sure what to suggest, maybe make sure your FS for /var is working fine ... and that you aren't running out of memory or something. There are a bunch of I/O improvements in the latest upstream (in rawhide, and my rawhide rebuild repo.) which you could try, if you want ... but I have no idea why it would be maxing out the CPU (and I doubt there are any upstream changes to reduce CPU usage, significantly).
Thanks for looking into this. Here are this morning's results. It was choking up the machine at the verification stage again: ***************** Running Transaction Updating : gvnc-0.4.2-3.fc14.x86_64 1/18 Updating : gtk-vnc-0.4.2-3.fc14.x86_64 2/18 Updating : gtk-vnc-python-0.4.2-3.fc14.x86_64 3/18 Updating : telepathy-logger-0.1.7-1.fc14.x86_64 4/18 Updating : gthumb-2.12.1-1.fc14.x86_64 5/18 Updating : sysvinit-tools-2.87-6.dsf.fc14.x86_64 6/18 Updating : libicu-4.4.1-6.fc14.x86_64 7/18 Updating : directfb-1.4.11-2.fc14.i686 8/18 Updating : 1:autocorr-en-3.3.0-17.2.fc14.noarch 9/18 Cleanup : gtk-vnc-python-0.4.2-1.fc14.x86_64 10/18 Cleanup : gtk-vnc-0.4.2-1.fc14.x86_64 11/18 Cleanup : gvnc-0.4.2-1.fc14.x86_64 12/18 Cleanup : telepathy-logger-0.1.5-1.fc14.x86_64 13/18 Cleanup : gthumb-2.12.0-1.fc14.x86_64 14/18 Cleanup : sysvinit-tools-2.87-5.dsf.fc14.x86_64 15/18 Cleanup : libicu-4.4.1-5.fc14.x86_64 16/18 Cleanup : directfb-1.4.11-1.fc14.i686 17/18 Cleanup : 1:autocorr-en-3.3.0-15.2.fc14.noarch 18/18 VerifyTransaction time: 170.791 Transaction time: 334.233 ******************** I'll grab the new yum from Rawhide as you suggest and try it out.
As suggested, I upgraded to yum 3.2.28-14.fc15 from Rawhide. The verification time was much improved: ***************************** Running Transaction Updating : 3:koffice-kdchart-2.2.2-4.fc14.1.x86_64 1/94 Updating : 3:koffice-libs-2.2.2-4.fc14.1.x86_64 2/94 Updating : 3:koffice-core-2.2.2-4.fc14.1.x86_64 3/94 Updating : 3:koffice-kexi-2.2.2-4.fc14.1.x86_64 4/94 Updating : 3:koffice-kexi-libs-2.2.2-4.fc14.1.x86_64 5/94 Updating : 3:koffice-filters-2.2.2-4.fc14.1.x86_64 6/94 Updating : 3:koffice-krita-libs-2.2.2-4.fc14.1.x86_64 7/94 Updating : 3:koffice-krita-2.2.2-4.fc14.1.x86_64 8/94 Updating : 3:koffice-kplato-2.2.2-4.fc14.1.x86_64 9/94 Updating : 3:koffice-kplato-libs-2.2.2-4.fc14.1.x86_64 10/94 Updating : 3:koffice-kpresenter-libs-2.2.2-4.fc14.1.x86_64 11/94 Updating : 3:koffice-kpresenter-2.2.2-4.fc14.1.x86_64 12/94 Updating : 3:koffice-karbon-2.2.2-4.fc14.1.x86_64 13/94 Updating : 3:koffice-karbon-libs-2.2.2-4.fc14.1.x86_64 14/94 Updating : 3:koffice-kchart-2.2.2-4.fc14.1.x86_64 15/94 Updating : 3:koffice-kchart-libs-2.2.2-4.fc14.1.x86_64 16/94 Updating : 3:koffice-kformula-libs-2.2.2-4.fc14.1.x86_64 17/94 Updating : 3:koffice-kformula-2.2.2-4.fc14.1.x86_64 18/94 Updating : 3:koffice-kword-2.2.2-4.fc14.1.x86_64 19/94 Updating : 3:koffice-kword-libs-2.2.2-4.fc14.1.x86_64 20/94 Updating : usermode-1.106.1-1.fc14.1.x86_64 21/94 Updating : 3:koffice-kspread-2.2.2-4.fc14.1.x86_64 22/94 Updating : compiz-0.8.6-6.fc14.x86_64 23/94 Updating : libass-0.9.11-1.fc14.1.x86_64 24/94 Updating : celt-0.8.1-1.fc14.1.x86_64 25/94 Updating : wxBase-2.8.11-3.fc14.x86_64 26/94 Updating : wxGTK-2.8.11-3.fc14.x86_64 27/94 Updating : gstreamer-plugins-bad-free-0.10.20-3.fc14.1.x86_64 28/94 Updating : compiz-gnome-0.8.6-6.fc14.x86_64 29/94 Updating : usermode-gtk-1.106.1-1.fc14.1.x86_64 30/94 Updating : setuptool-1.19.11-1.fc14.1.x86_64 31/94 Updating : 3:koffice-kexi-driver-pgsql-2.2.2-4.fc14.1.x86_64 32/94 Updating : 3:koffice-kexi-driver-mysql-2.2.2-4.fc14.1.x86_64 33/94 Updating : folks-0.1.16-1.fc14.1.x86_64 34/94 Updating : 5:mutt-1.5.21-1.fc14.1.x86_64 35/94 Updating : pycryptopp-0.5.25-1.fc14.1.x86_64 36/94 Updating : sudo-1.7.4p4-4.fc14.x86_64 37/94 Updating : clutter-1.2.14-1.fc14.1.x86_64 38/94 Updating : compiz-0.8.6-6.fc14.i686 39/94 Updating : scribus-doc-1.3.9-1.fc14.noarch 40/94 Updating : scribus-1.3.9-1.fc14.x86_64 41/94 Updating : 3:koffice-suite-2.2.2-4.fc14.1.x86_64 42/94 Updating : 3:koffice-devel-2.2.2-4.fc14.1.x86_64 43/94 Updating : 3:koffice-kdchart-devel-2.2.2-4.fc14.1.x86_64 44/94 Updating : 3:koffice-debuginfo-2.2.2-4.fc14.1.x86_64 45/94 Updating : python-crypto-2.3-2.fc14.1.x86_64 46/94 Updating : clutter-debuginfo-1.2.14-1.fc14.1.x86_64 47/94 Cleanup : 3:koffice-kexi-driver-mysql-2.2.2-4.fc14.x86_64 48/94 Cleanup : 3:koffice-kexi-driver-pgsql-2.2.2-4.fc14.x86_64 49/94 Cleanup : gstreamer-plugins-bad-free-0.10.20-3.fc14.x86_64 50/94 Cleanup : scribus-doc-1.3.8-1.fc14.noarch 51/94 Cleanup : scribus-1.3.8-1.fc14.x86_64 52/94 Cleanup : wxGTK-2.8.11-2.fc14.x86_64 53/94 Cleanup : setuptool-1.19.11-1.fc14.x86_64 54/94 Cleanup : usermode-gtk-1.106.1-1.fc14.x86_64 55/94 Cleanup : compiz-gnome-0.8.6-3.fc14.x86_64 56/94 Cleanup : compiz-0.8.6-3.fc14 57/94 Cleanup : usermode-1.106.1-1.fc14.x86_64 58/94 Cleanup : wxBase-2.8.11-2.fc14.x86_64 59/94 Cleanup : libass-0.9.11-1.fc14.x86_64 60/94 Cleanup : celt-0.8.1-1.fc14.x86_64 61/94 Cleanup : folks-0.1.16-1.fc14.x86_64 62/94 Cleanup : 5:mutt-1.5.21-1.fc14.x86_64 63/94 Cleanup : pycryptopp-0.5.25-1.fc14.x86_64 64/94 Cleanup : sudo-1.7.4p4-3.fc14.x86_64 65/94 Cleanup : clutter-1.2.14-1.fc14.x86_64 66/94 Cleanup : 3:koffice-suite-2.2.2-4.fc14.x86_64 67/94 Cleanup : 3:koffice-krita-libs-2.2.2-4.fc14.x86_64 68/94 Cleanup : 3:koffice-krita-2.2.2-4.fc14.x86_64 69/94 Cleanup : 3:koffice-kword-2.2.2-4.fc14.x86_64 70/94 Cleanup : 3:koffice-kword-libs-2.2.2-4.fc14.x86_64 71/94 Cleanup : 3:koffice-kpresenter-libs-2.2.2-4.fc14.x86_64 72/94 Cleanup : 3:koffice-kpresenter-2.2.2-4.fc14.x86_64 73/94 Cleanup : 3:koffice-karbon-2.2.2-4.fc14.x86_64 74/94 Cleanup : 3:koffice-karbon-libs-2.2.2-4.fc14.x86_64 75/94 Cleanup : 3:koffice-kchart-2.2.2-4.fc14.x86_64 76/94 Cleanup : 3:koffice-kchart-libs-2.2.2-4.fc14.x86_64 77/94 Cleanup : 3:koffice-kformula-libs-2.2.2-4.fc14.x86_64 78/94 Cleanup : 3:koffice-kformula-2.2.2-4.fc14.x86_64 79/94 Cleanup : 3:koffice-kplato-2.2.2-4.fc14.x86_64 80/94 Cleanup : 3:koffice-kplato-libs-2.2.2-4.fc14.x86_64 81/94 Cleanup : 3:koffice-devel-2.2.2-4.fc14.x86_64 82/94 Cleanup : 3:koffice-kexi-2.2.2-4.fc14.x86_64 83/94 Cleanup : 3:koffice-kexi-libs-2.2.2-4.fc14.x86_64 84/94 Cleanup : 3:koffice-filters-2.2.2-4.fc14.x86_64 85/94 Cleanup : 3:koffice-kspread-2.2.2-4.fc14.x86_64 86/94 Cleanup : 3:koffice-core-2.2.2-4.fc14.x86_64 87/94 Cleanup : 3:koffice-libs-2.2.2-4.fc14.x86_64 88/94 Cleanup : 3:koffice-kdchart-devel-2.2.2-4.fc14.x86_64 89/94 Cleanup : 3:koffice-kdchart-2.2.2-4.fc14.x86_64 90/94 Cleanup : compiz-0.8.6-3.fc14 91/94 Cleanup : 3:koffice-debuginfo-2.2.2-4.fc14.x86_64 92/94 Cleanup : python-crypto-2.3-2.fc14.x86_64 93/94 Cleanup : clutter-debuginfo-1.2.14-1.fc14.x86_64 94/94 VerifyTransaction time: 10.447 Transaction time: 514.403 **************************
I just ran it again and it is definitely much better now: ************************** Running Transaction Updating : krb5-debuginfo-1.8.2-7.fc14.x86_64 1/2 Cleanup : krb5-debuginfo-1.8.2-6.fc14.x86_64 2/2 VerifyTransaction time: 2.692 Transaction time: 20.561 **************************
Should this be closed now?
I guess, given it went away ... but I'm still not sure how it can be using so much CPU at that point though (or what we did to fix it ... maybe the hardlink code, but who knows). David, I don't suppose you are/were using btrfs?
No, just standard ext4.
FWIW, #566514 had a small benchmark script attached, measuring the time to complete an install/removal, yum vs. rpm. Ran it just now on an F16 system, on a dual AMD Opteron 2.2GHz. Yum is still twice as slow than rpm: $ ./bench-yum.sh telnet-0.17-51.fc16.i686.rpm 3.4.3 Installed: rpm-4.9.1.2-6.fc16.i686 at 2012-03-12 03:49 Built : Fedora Project at 2012-03-07 11:29 Committed: Panu Matilainen <pmatilai> at 2012-03-07 Installed: yum-3.4.3-23.fc16.noarch at 2012-04-08 17:43 Built : Fedora Project at 2012-03-16 19:11 Committed: James Antill <james at fedoraproject.org> at 2012-03-16 -------------------------------------------- Test 1: installation using plain rpm: rpm -i telnet-0.17-51.fc16.i686.rpm Elapsed time: 7.80 s -------------------------------------------- Test 2: removal using plain rpm: rpm -e telnet Elapsed time: 5.92 s -------------------------------------------- Test 3: installation using yum (takes longer b/c rpmdb changed outside of yum): yum -q --disableplugin=* --disablerepo=* -y --nogpg install telnet-0.17-51.fc16.i686.rpm Elapsed time: 18.22 s -------------------------------------------- Test 4: removal using yum: yum -q --disableplugin=* --disablerepo=* -y remove telnet Elapsed time: 14.33 s -------------------------------------------- Test 5: again installation using yum: yum -q --disableplugin=* --disablerepo=* -y --nogpg install telnet-0.17-51.fc16.i686.rpm Elapsed time: 13.27 s -------------------------------------------- Test 6: again removal using yum: yum -q --disableplugin=* --disablerepo=* -y remove telnet Elapsed time: 13.91 s $ mount | grep ext4 /dev/sda1 on / type ext4 (rw,nodev,noatime,seclabel,user_xattr,barrier=1,data=ordered)
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