[ensembl-dev] Ensembl VM questions

Andrew Yates ayates at ebi.ac.uk
Thu Aug 27 11:01:00 BST 2015


Hi G,

We've recently been experimenting with automating our VM builds and this has brought up an interesting issue when we have multiple Ensembl virtual machine appliances imported into the same VirtualBox infrastructure. This manifested itself as us being unable to SSH onto the running machine. A quick solution is:

sudo rm /etc/udev/rules.d/70-persistent-net.rules
sudo mkdir /etc/udev/rules.d/70-persistent-net.rules

The problem is that Ubuntu remembers what MAC address it was assigned and writes this to the persistent rules file. VirtualBox, when it imports an appliance, will attempt to assign the VM the MAC address it was packaged with but will also check for MAC address collisions. When there is a collision VirtualBox assigns a new MAC address to the new appliance. Ubuntu is now confused and refuses to interface with the external network.

Replacing the persistent rules file with a directory prevents Ubuntu from remembering as it's not possible to write a line to directory :).

There's more information available from https://github.com/mitchellh/packer/issues/866 <https://github.com/mitchellh/packer/issues/866> and you can see a shell script version of this solution with Chef's bento project at https://github.com/chef/bento/blob/master/scripts/ubuntu/networking.sh <https://github.com/chef/bento/blob/master/scripts/ubuntu/networking.sh>.

We are going to put this step into our VM deployment SOP to make sure the problem doesn't arise again

Hope this helps,

Andy

> On 27 Aug 2015, at 09:06, mag <mr6 at ebi.ac.uk> wrote:
> 
> Hi G,
> 
> I just tested the latest VM on my Mac, downloading a fresh copy, and had no connectivity issue.
> Do you get any error messages?
> 
> I can resize the window, but the block inside does not change, we will look into how to fix this for next release.
> 
> As for GRCh37, you simply need to replace the default 3306 port to 3337 to connect to the 81 release of GRCh37 databases.
> 
> 
> Regards,
> Magali
> 
> On 26/08/2015 20:27, Genomeo Dev wrote:
>> Dear all,
>> 
>> I am using a MAC and I have the following questions:
>> 
>> - When loading the latest ensembl VM 81 into virtual box, it does not seem to be able to connect to the network and also the session can not be resized to fit the monitor. I do not have such issues with VM 75 for example.
>> - If I want to use grch37 in the latest VM (81), what is the latest folder ensembl-api-folder to use?
>> 
>> Thanks,
>> 
>> -- 
>> G.
>> 
>> 
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