[Bio-linux-dev] iPlant Atmosphere

[Tim Booth]

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.
> _______________________________________________
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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