[Bio-linux-dev] iPlant Atmosphere
Tim Booth
tbooth at ceh.ac.uk
Thu Apr 23 11:09:36 EDT 2015
Hi Tony,
Thanks for the info. I'd certainly hope that there was no problem
running upgrade8.sh on any existing 14.04 system (VM or otherwise) but
it's nice to have confirmation it works in iPlant Atmosphere.
With our system that runs on VCloud Director (VMWare ESX) I'm able to
have a Bio-Linux base image where you can dynamically change the disk
size on deployment and the root partition ends up being that size, but
it took a good bit of hacking to achieve that. Unless you start with
everything on LVM then shunting /usr, /var and /home on to larger
partitions is inevitably what you end up doing.
> Do you know anyone else using iPlant Atmosphere (based on OpenStack)?
Nope.
Maybe try the cloudbiolinux list?
Cheers,
TIM
On Thu, 2015-04-23 at 15:33 +0100, Tony Travis wrote:
> Hi, Tim.
>
> I've created a Bio-Linux 8 instance on iPlant Atmosphere:
>
> https://atmo.iplantcollaborative.org
>
> ID396a5744-87c2-4d3f-ad40-75134482f5ee
>
> I worked around a problem of insufficient space on their default 10GB VM
> system volume by mounting /usr on a 20GB partition of an attached volume
> instead (I've asked them about getting a 20GB system volume):
>
> > # login to instance
> > ajt at beluga:~$ ssh ajtravis at 128.196.64.133
> >
> > # list available block devices
> > ajtravis at vm64-133:~$ lsblk
> > NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
> > vda 253:0 0 9.4G 0 disk /
> > vdb 253:16 0 60G 0 disk
> > vdc 253:32 0 120G 0 disk
> >
> > # partition attached volume /dev/vdc
> > parted /dev/vdc
> > unit MiB
> > mklabel msdos
> > mkpart primary 1 20GB
> > mkpart primary 20GB -0
> >
> > lsblk
> > NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
> > vda 253:0 0 9.4G 0 disk /
> > vdb 253:16 0 60G 0 disk
> > vdc 253:32 0 120G 0 disk
> > ├─vdc1 253:33 0 18.6G 0 part /usr
> > └─vdc2 253:34 0 101.4G 0 part
> >
> >
> > # create filesystems
> > mkfs -t ext4 /dev/vdc1
> > mkfs -t ext4 /dev/vdc2
> >
> > # move /usr onto attached volume
> > mount /dev/vdc1 /mnt
> > rsync -axHP /usr/ /mnt/
> > mv -i /usr /usr.old
> > mkdir /usr
> > mount /dev/vdc1 /usr
> >
> > # update /etc/fstab
> > vim /etc/fstab
> > ...
> > /dev/sda1 / ext3 defaults 0 0
> > /dev/vdc1 /usr ext4 defaults 0 0
> > ...
> >
> > # reboot to make sure /usr on attached volume is available at boot
> > reboot -f
> >
> > # login again and do Bio-Linux 8 upgrade
> > wget -q http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh
> >
>
> This is the disk usage after installation:
>
> > ajtravis at vm64-133:~$ df -hT -t ext3 -t ext4
> > Filesystem Type Size Used Avail Use% Mounted on
> > /dev/vda ext3 9.3G 3.8G 5.1G 43% /
> > /dev/vdc1 ext4 19G 8.9G 8.6G 52% /usr
>
> I can access my Bio-Linux 8 instance via "x2go", which is my preferred
> method, but I can't get their web-browser RealVNC client to connect: It
> complains that their licence has expired ;-)
>
> I going to use this Bio-Linux 8 instance to try out iPlant Atmosphere
> with a view to maybe using it for teaching a Bio-Linux course at UoA.
>
> Do you know anyone else using iPlant Atmosphere (based on OpenStack)?
>
> Bye,
>
> Tony.
>
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
>
>
>
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
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--
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://environmentalomics.org/bio-linux
+44 1491 69 2297
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