[Bio-linux-dev] iPlant Atmosphere

[Tony Travis]

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.