BeGenDiv has three compute servers (nile, lagaoa and yangtze) that are hosted at the FU Computer Science department.
ssh username@andorra.imp.fu-berlin.defrom there login to nile/lagoa/yangtze:
ssh nile
ssh
can be configured to tunnel through andorra automatically. Create an ssh
config file at ~/.ssh/config
containing the following:
Host allegro User username HostName allegro ProxyCommand ssh username@andorra.imp.fu-berlin.de nc %h %p 2> /dev/null Host nile User username HostName nile ProxyCommand ssh username@andorra.imp.fu-berlin.de nc %h %p 2> /dev/null Host lagoa User username HostName lagoa ProxyCommand ssh username@andorra.imp.fu-berlin.de nc %h %p 2> /dev/null Host yangtze User username HostName yangtze ProxyCommand ssh username@andorra.imp.fu-berlin.de nc %h %p 2> /dev/null Host curta User username HostName curta.zedat.fu-berlin.de ProxyCommand ssh username@andorra.imp.fu-berlin.de nc %h %p 2> /dev/null
The home directory is the general IMP home directory, that is shared across all IMP computers. It has a quota (maximum disc usage) of 7813 MB.
The local discs (20TB) are mounted at /srv/public. They have the following folder structure on them: Your analysis input and output files should go into your users folder underusers
. Software can be made available for all users under software
. Tools that were downloaded as binary are in the bin
folder. Tools that were compiled are in the src
folder. Data files (like databases or genomes) can be found in the data
folder.
There is a miniconda installation set up under: /srv/public/shared/software/miniconda3. In the base folder there is software set up that needs to be generally used. You can activate the base environment using: "source /srv/public/shared/software/miniconda3/bin/activate" Specific project environments should be created in the user directory for each specific project.
You can use the "who" command to check which users are currently logged in to the server.
You can then write messages directly to users e.g.:write mdriller pts/0
this will open up a "chat" with the user mdriller and all the messages you type now will be send directly to the user. You can quit the chat using ctrl+c.
Additionally you can write messages to all users e.g. for annoucements using the wall command e.g.:wall "Hello there will be a server restart today so please all log out before 2pm"
F2
.bashrc
file to change the language to English:
export LANG=en_US.UTF-8