Servers(nileAndLagoa)
BeGenDiv has three compute servers (nile, lagaoa and yangtze) that are hosted at the FU Computer Science department.
Hardware
nile
- 1.5 TB RAM
- 4 CPUs, 96 threads
- 20 TB hard disc space
lagoa
- 256 GB RAM
- 2 CPUs, 88 threads
- 20 TB hard disc space
yangtze
- 1.5 TB RAM
- 4 CPUs, 160 threads
- 40 TB hard disc space
Software
- Operating System nile/lagoa: Debian 4.9 (Jesse) [SMP Debian 4.9.88-1+deb9u1 (2018-05-07) x86_64 GNU/Linux]
- Operating System yangtze: Debian 4.19 (Buster) [SMP Debian 4.19.12-1 (2018-12-22) x86_64 GNU/Linux]
Connection
Connection needs to be tunneled through a FU login server (like lounge).
manual ssh login
login to lounge:
ssh username@lounge.imp.fu-berlin.de
from there login to nile/lagoa/yangtze:
ssh nile
ssh
can be configured to tunnel through lounge automatically. Create an
ssh
config file at
~/.ssh/config
containing the following:
Host allegro
User username
HostName allegro
ProxyCommand ssh username@lounge.imp.fu-berlin.de nc %h %p 2> /dev/null
Host nile
User username
HostName nile
ProxyCommand ssh username@lounge.imp.fu-berlin.de nc %h %p 2> /dev/null
Host lagoa
User username
HostName lagoa
ProxyCommand ssh username@lounge.imp.fu-berlin.de nc %h %p 2> /dev/null
Host yangtze
User username
HostName yangtze
ProxyCommand ssh username@lounge.imp.fu-berlin.de nc %h %p 2> /dev/null
File Structure
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 under
users
. 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.
Tips and Tricks
how to get help
- ask your friendly colleagues at BeGenDiv
- in case of hardware problems write to: staff@mi.fu-berlin.de
htop with many CPUs
If you want to use htop, but can not see the process list, because there are so many CPU bars, you can remove the CPU bars the following way:
- start htop
- press
F2
- press the right arrow key once
- press the delete ("Entf" on German keyboard) key
- press the right arrow key once
- press the delete key
changing language
Add the following to your
.bashrc
file to change the language to English:
export LANG=en_US.UTF-8