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 GB RAM
  • 4 CPUs, 160 threads
  • 20 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

configure ssh tunnel

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: folder structure on nile/lagoa/yangtze

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

  1. ask your friendly colleagues at BeGenDiv
  2. 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:
  1. start htop
  2. press F2
  3. press the right arrow key once
  4. press the delete ("Entf" on German keyboard) key
  5. press the right arrow key once
  6. 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

Comments

 
Topic attachments
I Attachment ActionSorted ascending Size Date Who Comment
nile_struc.pngpng nile_struc.png manage 28.0 K 12 Jun 2018 - 08:37 FelixHeeger folder structure on nile and lagoa
Topic revision: r6 - 22 Feb 2019, mdriller
 
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