From A.J.Pemberton at bham.ac.uk Thu Jul 15 05:12:54 2010 From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton) Date: Thu, 15 Jul 2010 10:12:54 +0100 Subject: [Bio-Linux] Problem booting installation DVD - biolinux 6 Message-ID: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> Dear biolinux users, I have encountered a problem installing biolinux 6 onto one of my 64-bit servers. The server has a built-in CDROM drive but no DVD drive. So I connected my USB DVD drive to the system so that I could install the software. The DVD boots initially but after loading the kernel, I get the following: Busybox v 1.13.3 (ubuntu 1:1.13.3-1ubuntu11). Built-in shell (ash) Enter help for a list of built-in commands (initramfs) Unable to find a live filesystem It looks as if after booting the kernel, it cannot find the DVD. Can anyone suggest a workaround or how to find the filesystem from the above prompt and set the install going? Regards, Tony Pemberton -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.travis at abdn.ac.uk Thu Jul 15 05:24:09 2010 From: a.travis at abdn.ac.uk (Tony Travis) Date: Thu, 15 Jul 2010 10:24:09 +0100 Subject: [Bio-Linux] Problem booting installation DVD - biolinux 6 In-Reply-To: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> References: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> Message-ID: <4C3ED3B9.5060607@abdn.ac.uk> On 15/07/10 10:12, Anthony Pemberton wrote: > Dear biolinux users, > > I have encountered a problem installing biolinux 6 onto one of my 64-bit > servers. The server has a built-in CDROM drive but no DVD drive. So I > connected my USB DVD drive to the system so that I could install the > software. The DVD boots initially but after loading the kernel, I get > the following: > > Busybox v 1.13.3 (ubuntu 1:1.13.3-1ubuntu11). Built-in shell (ash) Enter > help for a list of built-in commands > > (initramfs) Unable to find a live filesystem > > It looks as if after booting the kernel, it cannot find the DVD. Can > anyone suggest a workaround or how to find the filesystem from the above > prompt and set the install going? Hello, Tony. Is your server BIOS set to support 'legacy' USB devices? You could try booting from a USB-stick instead... Another possibility is to clone a Bio-Linux installation from another machine. I do this for our NBX (NuGO Black Box) servers - Very easy! I'm running Bio-Linux 6 on all our servers: Make sure to uninstall: network-manager This is not appropriate on a server and can cause network problems. HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt From A.J.Pemberton at bham.ac.uk Thu Jul 15 06:16:29 2010 From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton) Date: Thu, 15 Jul 2010 11:16:29 +0100 Subject: [Bio-Linux] Problem booting installation DVD - biolinux 6 In-Reply-To: <4C3ED3B9.5060607@abdn.ac.uk> References: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> <4C3ED3B9.5060607@abdn.ac.uk> Message-ID: <3A5B0BBDAF00724AB5F101556501023001F94CA550@LESMBX1.adf.bham.ac.uk> Hello Tony, Just checked - the BIOS is set for USB legacy support. I tried a 32bit ubuntu 8.04 live CD in the same drive (USB external) and this boots OK. So - is it the DVD filesystem that the kernel cannot read for some reason? If I can get hold of a USB key of sufficient capacity, I will give it a try, Regards, Tony Pemberton -----Original Message----- From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tony Travis Sent: 15 July 2010 10:24 To: bio-linux at nebclists.nerc.ac.uk Subject: Re: [Bio-Linux] Problem booting installation DVD - biolinux 6 On 15/07/10 10:12, Anthony Pemberton wrote: > Dear biolinux users, > > I have encountered a problem installing biolinux 6 onto one of my 64-bit > servers. The server has a built-in CDROM drive but no DVD drive. So I > connected my USB DVD drive to the system so that I could install the > software. The DVD boots initially but after loading the kernel, I get > the following: > > Busybox v 1.13.3 (ubuntu 1:1.13.3-1ubuntu11). Built-in shell (ash) Enter > help for a list of built-in commands > > (initramfs) Unable to find a live filesystem > > It looks as if after booting the kernel, it cannot find the DVD. Can > anyone suggest a workaround or how to find the filesystem from the above > prompt and set the install going? Hello, Tony. Is your server BIOS set to support 'legacy' USB devices? You could try booting from a USB-stick instead... Another possibility is to clone a Bio-Linux installation from another machine. I do this for our NBX (NuGO Black Box) servers - Very easy! I'm running Bio-Linux 6 on all our servers: Make sure to uninstall: network-manager This is not appropriate on a server and can cause network problems. HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From A.J.Pemberton at bham.ac.uk Fri Jul 16 05:07:17 2010 From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton) Date: Fri, 16 Jul 2010 10:07:17 +0100 Subject: [Bio-Linux] Problem booting installation DVD - biolinux 6 In-Reply-To: <4C3ED3B9.5060607@abdn.ac.uk> References: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> <4C3ED3B9.5060607@abdn.ac.uk> Message-ID: <3A5B0BBDAF00724AB5F101556501023001F94CA572@LESMBX1.adf.bham.ac.uk> Dear biolinux users, I am still having problems with the biolinux 6 install. I have tried booting the USB-stick and the problem is worse - no kernel boot. I have checked the BIOS settings - the USB legacy mode was enabled. I tested the stick on my 64-bit workstation and it works fine. I can boot to the live system on the workstation, but the server just hangs. Does anyone have any suggestions has to how I can proceed? What else can I try? Regards, Tony Pemberton -----Original Message----- From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tony Travis Sent: 15 July 2010 10:24 To: bio-linux at nebclists.nerc.ac.uk Subject: Re: [Bio-Linux] Problem booting installation DVD - biolinux 6 On 15/07/10 10:12, Anthony Pemberton wrote: > Dear biolinux users, > > I have encountered a problem installing biolinux 6 onto one of my 64-bit > servers. The server has a built-in CDROM drive but no DVD drive. So I > connected my USB DVD drive to the system so that I could install the > software. The DVD boots initially but after loading the kernel, I get > the following: > > Busybox v 1.13.3 (ubuntu 1:1.13.3-1ubuntu11). Built-in shell (ash) Enter > help for a list of built-in commands > > (initramfs) Unable to find a live filesystem > > It looks as if after booting the kernel, it cannot find the DVD. Can > anyone suggest a workaround or how to find the filesystem from the above > prompt and set the install going? Hello, Tony. Is your server BIOS set to support 'legacy' USB devices? You could try booting from a USB-stick instead... Another possibility is to clone a Bio-Linux installation from another machine. I do this for our NBX (NuGO Black Box) servers - Very easy! I'm running Bio-Linux 6 on all our servers: Make sure to uninstall: network-manager This is not appropriate on a server and can cause network problems. HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From a.travis at abdn.ac.uk Fri Jul 16 05:41:18 2010 From: a.travis at abdn.ac.uk (Tony Travis) Date: Fri, 16 Jul 2010 10:41:18 +0100 Subject: [Bio-Linux] Problem booting installation DVD - biolinux 6 In-Reply-To: <3A5B0BBDAF00724AB5F101556501023001F94CA572@LESMBX1.adf.bham.ac.uk> References: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> <4C3ED3B9.5060607@abdn.ac.uk> <3A5B0BBDAF00724AB5F101556501023001F94CA572@LESMBX1.adf.bham.ac.uk> Message-ID: <4C40293E.9000308@abdn.ac.uk> On 16/07/10 10:07, Anthony Pemberton wrote: > Dear biolinux users, > > I am still having problems with the biolinux 6 install. I have tried > booting the USB-stick and the problem is worse - no kernel boot. I > have checked the BIOS settings - the USB legacy mode was enabled. I > tested the stick on my 64-bit workstation and it works fine. I can > boot to the live system on the workstation, but the server just > hangs. > > Does anyone have any suggestions has to how I can proceed? What else > can I try? Hello, Tony. Here are some options: #1 Put your server system disk into another machine Install Bio-Linux 6 on the other machine Put the disk back into your server #2 Boot 64-bit Ubuntu 10.04 LTS from the Official CD rsync or dump/restore another instance of Bio-Linux 6 #3 Install 64-bit Ubuntu 10.04 LTS from the Official CD Configure APT for the Bio-Linux 6 repo's Install Bio-Linux 6 packages #4 Give up and install Windows 7 ;-) HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt From mgollery at unr.edu Fri Jul 16 10:55:01 2010 From: mgollery at unr.edu (Martin Gollery) Date: Fri, 16 Jul 2010 07:55:01 -0700 Subject: [Bio-Linux] Problem booting installation DVD - biolinux 6 In-Reply-To: <4C40293E.9000308@abdn.ac.uk> References: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> <4C3ED3B9.5060607@abdn.ac.uk> <3A5B0BBDAF00724AB5F101556501023001F94CA572@LESMBX1.adf.bham.ac.uk> <4C40293E.9000308@abdn.ac.uk> Message-ID: Or set up an instance on EC2, then you can run it from anywhere! On Fri, Jul 16, 2010 at 2:41 AM, Tony Travis wrote: > On 16/07/10 10:07, Anthony Pemberton wrote: >> >> Dear biolinux users, >> >> I am still having problems with the biolinux 6 install. I have tried >> booting the USB-stick and the problem is worse - no kernel boot. I >> have checked the BIOS settings - the USB legacy mode was enabled. I >> tested the stick on my 64-bit workstation and it works fine. I can >> boot to the live system on the workstation, but the server just >> hangs. >> >> Does anyone have any suggestions has to how I can proceed? What else >> can I try? > > Hello, Tony. > > Here are some options: > > #1 Put your server system disk into another machine > ? Install Bio-Linux 6 on the other machine > ? Put the disk back into your server > > #2 Boot 64-bit Ubuntu 10.04 LTS from the Official CD > ? rsync or dump/restore another instance of Bio-Linux 6 > > #3 Install 64-bit Ubuntu 10.04 LTS from the Official CD > ? Configure APT for the Bio-Linux 6 repo's > ? Install Bio-Linux 6 packages > > #4 Give up and install Windows 7 ;-) > > HTH, > > ?Tony. > -- > Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition > and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK > tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk > mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -- -- Martin Gollery Senior Bioinformatics Scientist Tahoe Informatics www.bioinformaticist.biz www.hiddenmarkovmodels.com From a.travis at abdn.ac.uk Fri Jul 16 11:41:48 2010 From: a.travis at abdn.ac.uk (Tony Travis) Date: Fri, 16 Jul 2010 16:41:48 +0100 Subject: [Bio-Linux] Problem booting installation DVD - biolinux 6 In-Reply-To: References: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> <4C3ED3B9.5060607@abdn.ac.uk> <3A5B0BBDAF00724AB5F101556501023001F94CA572@LESMBX1.adf.bham.ac.uk> <4C40293E.9000308@abdn.ac.uk> Message-ID: <4C407DBC.7020801@abdn.ac.uk> On 16/07/10 15:55, Martin Gollery wrote: > Or set up an instance on EC2, then you can run it from anywhere! Hello, Martin. Yes, in principle, and as long as you can afford to download your work because Amazon make their money by charging much more to retrieve data than they do to store it... Seriously, though, I'm setting up Eucalyptus at RINH to try out the AMI that Tim et al. are working on with the JVCI. I think 'private' clouds compatible with EC2/S3 etc. are the way forward. The economics of using AWS does make sense if you almost never use a computer, but the more you use a computer the less economic it is to rent a share of one from Amazon. Eucalyptus is well supported by Ubuntu server edition: http://www.ubuntu.com/partners/eucalyptus I'd be interested to hear from anyone else doing this sort of thing? Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt From mclange at ucdavis.edu Fri Jul 16 12:45:40 2010 From: mclange at ucdavis.edu (matthew lange) Date: Fri, 16 Jul 2010 09:45:40 -0700 Subject: [Bio-Linux] Problem booting installation DVD - biolinux 6 In-Reply-To: <4C407DBC.7020801@abdn.ac.uk> References: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> <4C3ED3B9.5060607@abdn.ac.uk> <3A5B0BBDAF00724AB5F101556501023001F94CA572@LESMBX1.adf.bham.ac.uk> <4C40293E.9000308@abdn.ac.uk> <4C407DBC.7020801@abdn.ac.uk> Message-ID: Yes, I am also getting started building my own private (15 server) cloudaho on Ubuntu too--looking forward to comparing notes and hearing/telling issues/finer-points as they arise. Cheers, matthew On Fri, Jul 16, 2010 at 8:41 AM, Tony Travis wrote: > On 16/07/10 15:55, Martin Gollery wrote: > >> Or set up an instance on EC2, then you can run it from anywhere! >> > > Hello, Martin. > > Yes, in principle, and as long as you can afford to download your work > because Amazon make their money by charging much more to retrieve data than > they do to store it... > > Seriously, though, I'm setting up Eucalyptus at RINH to try out the AMI > that Tim et al. are working on with the JVCI. I think 'private' clouds > compatible with EC2/S3 etc. are the way forward. The economics of using AWS > does make sense if you almost never use a computer, but the more you use a > computer the less economic it is to rent a share of one from Amazon. > > Eucalyptus is well supported by Ubuntu server edition: > > http://www.ubuntu.com/partners/eucalyptus > > I'd be interested to hear from anyone else doing this sort of thing? > > Bye, > > > Tony. > -- > Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition > and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK > tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk > mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -------------- next part -------------- An HTML attachment was scrubbed... URL: From A.J.Pemberton at bham.ac.uk Fri Jul 16 12:51:01 2010 From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton) Date: Fri, 16 Jul 2010 17:51:01 +0100 Subject: [Bio-Linux] Problem booting installation DVD - biolinux 6 In-Reply-To: <4C407DBC.7020801@abdn.ac.uk> References: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> <4C3ED3B9.5060607@abdn.ac.uk> <3A5B0BBDAF00724AB5F101556501023001F94CA572@LESMBX1.adf.bham.ac.uk> <4C40293E.9000308@abdn.ac.uk> <4C407DBC.7020801@abdn.ac.uk> Message-ID: <3A5B0BBDAF00724AB5F101556501023001F94CA58F@LESMBX1.adf.bham.ac.uk> Hi Tony and Martin, After a very tedious morning here in sunny Birmingham, I have managed the first step of option #3 from Tony's list. I now have Ubuntu 10.04 running on the server. To complete, do I just need to add the nebc repos to the sources file? I tried option #1, by taking the SATA disk from the server and putting it in our Dell Precision 360 workstation and booting from the USB stick and then trying to do an install. For some obscure reason, the installer would not recognize the server disk, despite fdisk -l showing the disk and its partitions in all their glory using the USB-live system. I could even mount the partitions and see the files on them! After checking the Dell BIOS and my handy-work inside the Dell a few times, I gave up on option #1 Regards, Tony P. -----Original Message----- From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tony Travis Sent: 16 July 2010 16:42 To: bio-linux at nebclists.nerc.ac.uk Subject: Re: [Bio-Linux] Problem booting installation DVD - biolinux 6 On 16/07/10 15:55, Martin Gollery wrote: > Or set up an instance on EC2, then you can run it from anywhere! Hello, Martin. Yes, in principle, and as long as you can afford to download your work because Amazon make their money by charging much more to retrieve data than they do to store it... Seriously, though, I'm setting up Eucalyptus at RINH to try out the AMI that Tim et al. are working on with the JVCI. I think 'private' clouds compatible with EC2/S3 etc. are the way forward. The economics of using AWS does make sense if you almost never use a computer, but the more you use a computer the less economic it is to rent a share of one from Amazon. Eucalyptus is well supported by Ubuntu server edition: http://www.ubuntu.com/partners/eucalyptus I'd be interested to hear from anyone else doing this sort of thing? Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From tbooth at ceh.ac.uk Fri Jul 16 12:08:27 2010 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 16 Jul 2010 17:08:27 +0100 Subject: [Bio-Linux] Problem booting installation DVD - biolinux 6 In-Reply-To: <4C407DBC.7020801@abdn.ac.uk> References: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> <4C3ED3B9.5060607@abdn.ac.uk> <3A5B0BBDAF00724AB5F101556501023001F94CA572@LESMBX1.adf.bham.ac.uk> <4C40293E.9000308@abdn.ac.uk> <4C407DBC.7020801@abdn.ac.uk> Message-ID: <1279296507.3284.622.camel@barsukas> More to the point, Martin, how do you get an EC2 instance to boot from a USB drive? To update this list about progress on Cloud Bio-Linux, I'm not officially funded to work on the project but I'm very excited by it and was recently at a CodeFest in Boston where I joined the main developers and we made a lot of progress. One thing that became clear is that the development needs to focus around the configuration management - ie. the script that takes a Vanilla Ubuntu and turns it into Bio-Linux - rather than just trying to make a static AMI image. We're using a system called Fabric to manage the configuration. The advantage of this approach is that one recipe will work for EC2, Eucalyptus, VMWare, Xen, or a regular old server - anything that's running a basic Ubuntu and has a net connection. You'll just need to run a couple of commands and the machine will grab the latest spec from the net and Bio-Linux-ify itself. Of course, we can and still will release pre-made AMIs - I see it as something akin to providing source and binaries for a piece of software. There is a developer list linked here: https://sourceforge.net/apps/mediawiki/jcvicloud/index.php But I'll keep this list posted on any major announcements. Cheers, TIM On Fri, 2010-07-16 at 16:41 +0100, Tony Travis wrote: > On 16/07/10 15:55, Martin Gollery wrote: > > Or set up an instance on EC2, then you can run it from anywhere! > > Hello, Martin. > > Yes, in principle, and as long as you can afford to download your work > because Amazon make their money by charging much more to retrieve data > than they do to store it... > > Seriously, though, I'm setting up Eucalyptus at RINH to try out the AMI > that Tim et al. are working on with the JVCI. I think 'private' clouds > compatible with EC2/S3 etc. are the way forward. The economics of using > AWS does make sense if you almost never use a computer, but the more you > use a computer the less economic it is to rent a share of one from Amazon. > > Eucalyptus is well supported by Ubuntu server edition: > > http://www.ubuntu.com/partners/eucalyptus > > I'd be interested to hear from anyone else doing this sort of thing? > > Bye, > > Tony. -- Tim Booth NERC Environmental Bioinformatics Centre at CEH Wallingford +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From tbooth at ceh.ac.uk Fri Jul 16 11:49:29 2010 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 16 Jul 2010 16:49:29 +0100 Subject: [Bio-Linux] Problem booting installation DVD - biolinux 6 In-Reply-To: <4C40293E.9000308@abdn.ac.uk> References: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> <4C3ED3B9.5060607@abdn.ac.uk> <3A5B0BBDAF00724AB5F101556501023001F94CA572@LESMBX1.adf.bham.ac.uk> <4C40293E.9000308@abdn.ac.uk> Message-ID: <1279295369.3284.603.camel@barsukas> Hi, Possibly the boot-USB-from-CD hack previously used by Tony T. would work here (http://www.pendrivelinux.com/usb-boot-cd-for-ubuntu-810/#more-680). However, this is quite a faff and I've no idea if it still works on Ubuntu 10.04. If you already have Linux on the server you can also bootstrap the kernel+initrd from your existing Grub on the hard drive, but this requires knowledge of Grub configuration. If it comes down to it I could talk you through it on the phone next week. Otherwise I'd second Tony's answer number 3 - install regular Ubuntu and then beef it up with our packages. I can send you a list of all packages on Bio-Linux plus a tarball of all the R libraries which gets you all the software. You'll still be missing quite a few customisations like the firewall setup, default user settings, desktop icons, database configuration but for a server machine these may not all be appropriate in any case. Let me know what you want to do. Cheers, TIM On Fri, 2010-07-16 at 10:41 +0100, Tony Travis wrote: > On 16/07/10 10:07, Anthony Pemberton wrote: > > Dear biolinux users, > > > > I am still having problems with the biolinux 6 install. I have tried > > booting the USB-stick and the problem is worse - no kernel boot. I > > have checked the BIOS settings - the USB legacy mode was enabled. I > > tested the stick on my 64-bit workstation and it works fine. I can > > boot to the live system on the workstation, but the server just > > hangs. > > > > Does anyone have any suggestions has to how I can proceed? What else > > can I try? > > Hello, Tony. > > Here are some options: > > #1 Put your server system disk into another machine > Install Bio-Linux 6 on the other machine > Put the disk back into your server > > #2 Boot 64-bit Ubuntu 10.04 LTS from the Official CD > rsync or dump/restore another instance of Bio-Linux 6 > > #3 Install 64-bit Ubuntu 10.04 LTS from the Official CD > Configure APT for the Bio-Linux 6 repo's > Install Bio-Linux 6 packages > > #4 Give up and install Windows 7 ;-) > > HTH, > > Tony. -- Tim Booth NERC Environmental Bioinformatics Centre at CEH Wallingford +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From a.travis at abdn.ac.uk Fri Jul 16 16:04:29 2010 From: a.travis at abdn.ac.uk (Tony Travis) Date: Fri, 16 Jul 2010 21:04:29 +0100 Subject: [Bio-Linux] Problem booting installation DVD - biolinux 6 In-Reply-To: <3A5B0BBDAF00724AB5F101556501023001F94CA58F@LESMBX1.adf.bham.ac.uk> References: <3A5B0BBDAF00724AB5F101556501023001F94CA54F@LESMBX1.adf.bham.ac.uk> <4C3ED3B9.5060607@abdn.ac.uk> <3A5B0BBDAF00724AB5F101556501023001F94CA572@LESMBX1.adf.bham.ac.uk> <4C40293E.9000308@abdn.ac.uk> <4C407DBC.7020801@abdn.ac.uk> <3A5B0BBDAF00724AB5F101556501023001F94CA58F@LESMBX1.adf.bham.ac.uk> Message-ID: <4C40BB4D.1060705@abdn.ac.uk> On 16/07/10 17:51, Anthony Pemberton wrote: > Hi Tony and Martin, > > After a very tedious morning here in sunny Birmingham, I have managed > the first step of option #3 from Tony's list. I now have Ubuntu 10.04 > running on the server. To complete, do I just need to add the nebc > repos to the sources file? Hello, Tony. If only it was that easy ;-) I would copy the /etc/apt folder from Bio-Linux 6 and use that if you want to be as compatible as possible. I've also got a little script I use to compare package lists (attached). To compare your server with the packages installed in Bio-Linux 6 use the list bio-linux-6.0.22.sel: dpkg-dsel localhost bio-linux-6.0.22.sel I use this script to track my deliberate and accidental changes to Bio-Linux, and to compare servers that other people have installed. Just in case it's not self-evident, the list is the output from: dpkg --get-selections > I tried option #1, by taking the SATA disk from the server and > putting it in our Dell Precision 360 workstation and booting from the > USB stick and then trying to do an install. For some obscure reason, > the installer would not recognize the server disk, despite fdisk -l > showing the disk and its partitions in all their glory using the > USB-live system. I could even mount the partitions and see the files > on them! After checking the Dell BIOS and my handy-work inside the > Dell a few times, I gave up on option #1 Well, there's been a lot of talk on the Beowulf list lately about Dell not supporting 'third-party' SATA drives in their servers... Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: dpkg-dsel URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: bio-linux-6.0.22.sel URL: