From shou at ceh.ac.uk Wed Feb 13 11:03:11 2008 From: shou at ceh.ac.uk (Stewart Houten) Date: Wed, 13 Feb 2008 16:03:11 +0000 Subject: [Bio-Linux] Bio-Linux Security Update Message-ID: <20080213160311.GA29584@ivpcp068.nerc-oxford.ac.uk> Dear Bio-Linux user, Last weekend a security bug [1] was discovered in the Linux kernel which should affect all Bio-Linux users who have already upgraded to Etch. The bug has been fixed and a new kernel is now available. I would strongly recommend that all systems administrators upgrade their kernel and reboot their machines at the earliest convenience. To install the new kernel run (as root or sudo), apt-get update apt-get install linux-image-2.6-686 and then reboot. If you have any further questions please email the NEBC helpdesk - helpdesk at nebc.nox.ac.uk. Regards, Stewart -- Dr Stewart Houten, Bio-Linux Developer NEBC, CEH, Mansfield Road, Oxford, OX1 3SR http://nebc.nox.ac.uk/ [1] http://lists.debian.org/debian-security-announce/debian-security-announce-2008/msg00056.html From s.a.johns at sheffield.ac.uk Fri Feb 15 05:23:43 2008 From: s.a.johns at sheffield.ac.uk (Sarah Follett) Date: Fri, 15 Feb 2008 10:23:43 +0000 Subject: [Bio-Linux] Bio-Linux Security Update In-Reply-To: <20080213160311.GA29584@ivpcp068.nerc-oxford.ac.uk> References: <20080213160311.GA29584@ivpcp068.nerc-oxford.ac.uk> Message-ID: <1203071023.4522.3.camel@bio2.shef.ac.uk> Dear Stewart I have installed the update, as you suggested, but unfortunately now my computer won't boot up properly. If I allow it to automatically select Kernel 2.6.18-6-686 it gets so far and then stops at this; Begin:waiting for root file system... input:ImPS/2 Generic Wheel Mouse as /class/input/input2 I am able to boot up fully, as I have done now, if I manually select kernel 2.6.18-4-686. What should I do, or can you log in and sort it out? I am only here for 1 more week before I move to a new job, and I'd like to leave the machine in working order! Thanks Sarah On Wed, 2008-02-13 at 16:03 +0000, Stewart Houten wrote: > Dear Bio-Linux user, > > Last weekend a security bug [1] was discovered in the Linux kernel > which should affect all Bio-Linux users who have already upgraded to > Etch. The bug has been fixed and a new kernel is now available. I > would strongly recommend that all systems administrators upgrade their > kernel and reboot their machines at the earliest convenience. > > To install the new kernel run (as root or sudo), > > apt-get update > apt-get install linux-image-2.6-686 > > and then reboot. If you have any further questions please email the > NEBC helpdesk - helpdesk at nebc.nox.ac.uk. > > Regards, > Stewart > -- > Dr Stewart Houten, Bio-Linux Developer > NEBC, CEH, Mansfield Road, Oxford, OX1 3SR > http://nebc.nox.ac.uk/ > > [1] http://lists.debian.org/debian-security-announce/debian-security-announce-2008/msg00056.html > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux -- Dr Sarah Follett Department of Animal & Plant Sciences The University of Sheffield Alfred Denny Building Western Bank Sheffield S10 2TN Lab: 0114 222 0109 Office: 0114 222 0113 From a.shirras at lancaster.ac.uk Fri Feb 15 05:31:22 2008 From: a.shirras at lancaster.ac.uk (Shirras, Alan) Date: Fri, 15 Feb 2008 10:31:22 -0000 Subject: [Bio-Linux] Bio-Linux Security Update In-Reply-To: <1203071023.4522.3.camel@bio2.shef.ac.uk> References: <20080213160311.GA29584@ivpcp068.nerc-oxford.ac.uk> <1203071023.4522.3.camel@bio2.shef.ac.uk> Message-ID: <4F791AEA3320B046AE1CDAF84866FA2602967E64@exchange-be5.lancs.local> I have the same problem. Alan -----Original Message----- From: bio-linux-bounces at envgen.nerc-oxford.ac.uk [mailto:bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf Of Sarah Follett Sent: 15 February 2008 10:24 To: Bio-Linux help and discussion Subject: Re: [Bio-Linux] Bio-Linux Security Update Dear Stewart I have installed the update, as you suggested, but unfortunately now my computer won't boot up properly. If I allow it to automatically select Kernel 2.6.18-6-686 it gets so far and then stops at this; Begin:waiting for root file system... input:ImPS/2 Generic Wheel Mouse as /class/input/input2 I am able to boot up fully, as I have done now, if I manually select kernel 2.6.18-4-686. What should I do, or can you log in and sort it out? I am only here for 1 more week before I move to a new job, and I'd like to leave the machine in working order! Thanks Sarah On Wed, 2008-02-13 at 16:03 +0000, Stewart Houten wrote: > Dear Bio-Linux user, > > Last weekend a security bug [1] was discovered in the Linux kernel > which should affect all Bio-Linux users who have already upgraded to > Etch. The bug has been fixed and a new kernel is now available. I > would strongly recommend that all systems administrators upgrade their > kernel and reboot their machines at the earliest convenience. > > To install the new kernel run (as root or sudo), > > apt-get update > apt-get install linux-image-2.6-686 > > and then reboot. If you have any further questions please email the > NEBC helpdesk - helpdesk at nebc.nox.ac.uk. > > Regards, > Stewart > -- > Dr Stewart Houten, Bio-Linux Developer NEBC, CEH, Mansfield Road, > Oxford, OX1 3SR http://nebc.nox.ac.uk/ > > [1] > http://lists.debian.org/debian-security-announce/debian-security-annou > nce-2008/msg00056.html > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux -- Dr Sarah Follett Department of Animal & Plant Sciences The University of Sheffield Alfred Denny Building Western Bank Sheffield S10 2TN Lab: 0114 222 0109 Office: 0114 222 0113 _______________________________________________ Bio-Linux mailing list Bio-Linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From shou at ceh.ac.uk Fri Feb 15 05:59:11 2008 From: shou at ceh.ac.uk (Stewart Houten) Date: Fri, 15 Feb 2008 10:59:11 +0000 Subject: [Bio-Linux] Bio-Linux Security Update In-Reply-To: <1203071023.4522.3.camel@bio2.shef.ac.uk> References: <20080213160311.GA29584@ivpcp068.nerc-oxford.ac.uk> <1203071023.4522.3.camel@bio2.shef.ac.uk> Message-ID: <20080215105911.GA31848@ivpcp068.nerc-oxford.ac.uk> Hi Sarah and all on Bio-Linux, It appears the grub menu file has an error in and you seem to be the second person this has happened to so I am forwarding this reply to the list. When you install the new kernel the grub boot stanzas are regenerated using the default parameters at the head of the grub menu file. It seems the default is root device is declared as /dev/hda1, which is correct if you have a machine with IDE drives (ie. Dell 650) but not for SATA (Dell 670/490). If you have a Dell 670/490 then your machine has SATA drives (sda, not hda) and this will affect you. If you are unsure whether your machine has SATA disks run the command 'df' and look for /dev/sdaX. To fix this issue edit the file (as root/sudo) /boot/grub/menu.lst and modify the line that begins # kopt=root=/dev/hda1 ... to read "sda1" instead of "hda1". Then save the file and run update-grub Then reboot. I would recommend doing this before upgrading the kernel if possible but this case (Sarah) you need to boot the machine before doing any of the above. To do this, reboot the machine and at the blue Grub screen press 'e' to edit the highlighted line, then arrow-down to the line beginning "kernel /boot/vmlinuz..." and press 'e' again to edit. Scroll back along the line and edit the "root=/dev/hda1" part to read "root=/dev/sda1". Then press Enter to exit and then 'b' to boot the kernel with new line. One the machine boots you will still need to edit the grub menu file as described in the first half of this email. Apologies to all those that this has affected. If you have any further queries about this please reply to helpdesk at nebc.nox.ac.uk. Regards, Stewart -- Dr Stewart Houten, Bio-Linux Developer NEBC, CEH, Mansfield Road, Oxford, OX1 3SR http://nebc.nox.ac.uk/ From R.Van-Aerle at exeter.ac.uk Fri Feb 15 06:05:13 2008 From: R.Van-Aerle at exeter.ac.uk (Van-Aerle, Ronny) Date: Fri, 15 Feb 2008 11:05:13 -0000 Subject: [Bio-Linux] Bio-Linux Security Update References: <20080213160311.GA29584@ivpcp068.nerc-oxford.ac.uk> Message-ID: Dear Stewart, Just to let you know that I have updated my machine too and that I have no problems rebooting, etc. I read some messages from people who did have problems... Best wishes, Ronny -------------------------------------------------- Dr. Ronny van Aerle NERC Research Fellow University of Exeter Hatherly Laboratories Prince of Wales Road Exeter, EX4 4PS, United Kingdom Tel. +44 (0)1392 263455 Fax. +44 (0)1392 263700 -----Original Message----- From: bio-linux-bounces at envgen.nerc-oxford.ac.uk on behalf of Stewart Houten Sent: Wed 13/02/2008 16:03 To: bio-linux at envgen.nerc-oxford.ac.uk Subject: [Bio-Linux] Bio-Linux Security Update Dear Bio-Linux user, Last weekend a security bug [1] was discovered in the Linux kernel which should affect all Bio-Linux users who have already upgraded to Etch. The bug has been fixed and a new kernel is now available. I would strongly recommend that all systems administrators upgrade their kernel and reboot their machines at the earliest convenience. To install the new kernel run (as root or sudo), apt-get update apt-get install linux-image-2.6-686 and then reboot. If you have any further questions please email the NEBC helpdesk - helpdesk at nebc.nox.ac.uk. Regards, Stewart -- Dr Stewart Houten, Bio-Linux Developer NEBC, CEH, Mansfield Road, Oxford, OX1 3SR http://nebc.nox.ac.uk/ [1] http://lists.debian.org/debian-security-announce/debian-security-announce-2008/msg00056.html _______________________________________________ Bio-Linux mailing list Bio-Linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 3494 bytes Desc: not available URL: From sujai.kumar at ed.ac.uk Fri Feb 15 06:08:26 2008 From: sujai.kumar at ed.ac.uk (Sujai Kumar) Date: Fri, 15 Feb 2008 11:08:26 +0000 Subject: [Bio-Linux] Bio-Linux Security Update In-Reply-To: <20080215105911.GA31848@ivpcp068.nerc-oxford.ac.uk> References: <20080213160311.GA29584@ivpcp068.nerc-oxford.ac.uk> <1203071023.4522.3.camel@bio2.shef.ac.uk> <20080215105911.GA31848@ivpcp068.nerc-oxford.ac.uk> Message-ID: Dear Stewart Thanks for these instructions, but the problem happened on both a Dell Precision 650 and a Dell Poweredge 600SC (both with IDE drives). I haven't tried your fix yet (though as I said, I was able to get it to boot up by picking the earlier kernel on the Grub screen at startup time) because /dev/hda1 does seem to be the right option for these systems. - Sujai On Fri, Feb 15, 2008 at 10:59 AM, Stewart Houten wrote: > Hi Sarah and all on Bio-Linux, > > It appears the grub menu file has an error in and you seem to be the > second person this has happened to so I am forwarding this reply to > the list. > > When you install the new kernel the grub boot stanzas are regenerated > using the default parameters at the head of the grub menu file. It > seems the default is root device is declared as /dev/hda1, which is > correct if you have a machine with IDE drives (ie. Dell 650) but not > for SATA (Dell 670/490). > > If you have a Dell 670/490 then your machine has SATA drives (sda, not > hda) and this will affect you. If you are unsure whether your machine > has SATA disks run the command 'df' and look for /dev/sdaX. > > To fix this issue edit the file (as root/sudo) /boot/grub/menu.lst and > modify the line that begins > > # kopt=root=/dev/hda1 ... > > to read "sda1" instead of "hda1". Then save the file and run > > update-grub > > Then reboot. > > I would recommend doing this before upgrading the kernel if possible > but this case (Sarah) you need to boot the machine before doing any of > the above. To do this, reboot the machine and at the blue Grub screen > press 'e' to edit the highlighted line, then arrow-down to the line > beginning "kernel /boot/vmlinuz..." and press 'e' again to edit. > Scroll back along the line and edit the "root=/dev/hda1" part to read > "root=/dev/sda1". Then press Enter to exit and then 'b' to boot the > kernel with new line. > > One the machine boots you will still need to edit the grub menu file > as described in the first half of this email. > > Apologies to all those that this has affected. > > If you have any further queries about this please reply to > > helpdesk at nebc.nox.ac.uk. > > Regards, > Stewart > -- > Dr Stewart Houten, Bio-Linux Developer > NEBC, CEH, Mansfield Road, Oxford, OX1 3SR > http://nebc.nox.ac.uk/ > > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > > -- Sujai Kumar Bioinformatics The Ashworth Laboratories King's Buildings Campus University of Edinburgh EH9 3JT, UK +44 131 650 7403 (O) From a.shirras at lancaster.ac.uk Fri Feb 15 06:10:48 2008 From: a.shirras at lancaster.ac.uk (Shirras, Alan) Date: Fri, 15 Feb 2008 11:10:48 -0000 Subject: [Bio-Linux] Bio-Linux Security Update In-Reply-To: <20080215105911.GA31848@ivpcp068.nerc-oxford.ac.uk> References: <20080213160311.GA29584@ivpcp068.nerc-oxford.ac.uk><1203071023.4522.3.camel@bio2.shef.ac.uk> <20080215105911.GA31848@ivpcp068.nerc-oxford.ac.uk> Message-ID: <4F791AEA3320B046AE1CDAF84866FA2602967E65@exchange-be5.lancs.local> I have a 650 with IDE drives and I still encountered the restart problem. Alan -----Original Message----- From: bio-linux-bounces at envgen.nerc-oxford.ac.uk [mailto:bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf Of Stewart Houten Sent: 15 February 2008 10:59 To: Bio-Linux help and discussion Subject: Re: [Bio-Linux] Bio-Linux Security Update Hi Sarah and all on Bio-Linux, It appears the grub menu file has an error in and you seem to be the second person this has happened to so I am forwarding this reply to the list. When you install the new kernel the grub boot stanzas are regenerated using the default parameters at the head of the grub menu file. It seems the default is root device is declared as /dev/hda1, which is correct if you have a machine with IDE drives (ie. Dell 650) but not for SATA (Dell 670/490). If you have a Dell 670/490 then your machine has SATA drives (sda, not hda) and this will affect you. If you are unsure whether your machine has SATA disks run the command 'df' and look for /dev/sdaX. To fix this issue edit the file (as root/sudo) /boot/grub/menu.lst and modify the line that begins # kopt=root=/dev/hda1 ... to read "sda1" instead of "hda1". Then save the file and run update-grub Then reboot. I would recommend doing this before upgrading the kernel if possible but this case (Sarah) you need to boot the machine before doing any of the above. To do this, reboot the machine and at the blue Grub screen press 'e' to edit the highlighted line, then arrow-down to the line beginning "kernel /boot/vmlinuz..." and press 'e' again to edit. Scroll back along the line and edit the "root=/dev/hda1" part to read "root=/dev/sda1". Then press Enter to exit and then 'b' to boot the kernel with new line. One the machine boots you will still need to edit the grub menu file as described in the first half of this email. Apologies to all those that this has affected. If you have any further queries about this please reply to helpdesk at nebc.nox.ac.uk. Regards, Stewart -- Dr Stewart Houten, Bio-Linux Developer NEBC, CEH, Mansfield Road, Oxford, OX1 3SR http://nebc.nox.ac.uk/ _______________________________________________ Bio-Linux mailing list Bio-Linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From btiwari at ceh.ac.uk Fri Feb 15 06:40:01 2008 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Fri, 15 Feb 2008 11:40:01 +0000 Subject: [Bio-Linux] Please hold off on Bio-Linux Security Update if you have not already started it Message-ID: Dear all, As you will have noticed from recent emails, the Bio-Linux security update is causing some problems. Stewart sent out a fix this morning that will work on many machines (e.g. most or all 670's), but will not work on all (e.g. 650's and perhaps a few 670's). Unfortunately, we are still in the process of tracking down the cause of some of the issues. Given the situation, it might be best not to undertake the upgrade right now if you have not already done so. Hopefully we'll have solutions to the issues people are seeing later in the day. We will keep you posted. regards, Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* From shou at ceh.ac.uk Fri Feb 15 10:56:38 2008 From: shou at ceh.ac.uk (Stewart Houten) Date: Fri, 15 Feb 2008 15:56:38 +0000 Subject: [Bio-Linux] Bio-Linux Security Update - solution Message-ID: <20080215155638.GA2049@ivpcp068.nerc-oxford.ac.uk> Dear All, Apologies for the inconvenience of this. I seem to have got to the bottom of this issue and have some updated instructions for upgrading which should get around each of the problems posted here today. I have tested the following instructions on machines at the NEBC and am happy that they will work. However, as I am upgrading our key server this weekend the NEBC helpdesk and mailing lists will be off-line until Monday, so it would be prudent if only those that have already ran into problems attempt this until next week. * 1 Edit the file /etc/initramfs-tools/initramfs.conf and change the line MODULES=list to MODULES=most * 2 Check the "kopt" entry in /boot/grub/menu.lst (See previous email) If you have Dell 670/490 (with SATA disks) it should read "/dev/sda1", and for Dell 650s (with IDE disks) it should read "/dev/hda1". Modify this accordingly if necessary. * 3a THEN, upgrade your kernel (if you've already done this go to 3b.) apt-get update apt-get dist-upgrade which should install the new kernel, but if the linux-image-2.6.18-6-686 package is "kept back" you can install it explicitly with apt-get install linux-image-2.6.18-6-686 * 3b If you have already installed the kernel and ran into problems follow steps 1 and 2, then run dpkg-reconfigure linux-image-2.6.18-6-686 * 4. Reboot. Regards, Stewart -- Dr Stewart Houten, Bio-Linux Developer NEBC, CEH, Mansfield Road, Oxford, OX1 3SR http://nebc.nox.ac.uk/ From s.a.johns at sheffield.ac.uk Fri Feb 15 11:23:40 2008 From: s.a.johns at sheffield.ac.uk (Sarah Follett) Date: Fri, 15 Feb 2008 16:23:40 +0000 Subject: [Bio-Linux] Bio-Linux Security Update - solution In-Reply-To: <20080215155638.GA2049@ivpcp068.nerc-oxford.ac.uk> References: <20080215155638.GA2049@ivpcp068.nerc-oxford.ac.uk> Message-ID: <1203092620.4833.0.camel@bio2.shef.ac.uk> That seems to have done the trick, thanks Stewart! Sarah. On Fri, 2008-02-15 at 15:56 +0000, Stewart Houten wrote: > > * 1 Edit the file /etc/initramfs-tools/initramfs.conf and change the line > > MODULES=list > to > MODULES=most > > * 2 Check the "kopt" entry in /boot/grub/menu.lst (See previous email) > > If you have Dell 670/490 (with SATA disks) it should read "/dev/sda1", > and for Dell 650s (with IDE disks) it should read "/dev/hda1". Modify > this accordingly if necessary. > * 3b If you have already installed the kernel and ran into problems > follow steps 1 and 2, then run > > dpkg-reconfigure linux-image-2.6.18-6-686 > > * 4. Reboot. > > > Regards, > Stewart > -- > Dr Stewart Houten, Bio-Linux Developer > NEBC, CEH, Mansfield Road, Oxford, OX1 3SR > http://nebc.nox.ac.uk/ > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux -- Dr Sarah Follett Department of Animal & Plant Sciences The University of Sheffield Alfred Denny Building Western Bank Sheffield S10 2TN Lab: 0114 222 0109 Office: 0114 222 0113