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Prerequisites

Step 1: Create an ssh key#

To be able to graphically connect to a node, you need to create a ssh key first, without passphrase to avoid having to type it each time. The following procedure has to be done **once and for all** only the first time you want to use a graphic tool.

On the machine you want to log from, here maestro.pasteur.fr, do:

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[login@maestro ~]$ ssh-keygen

If you don't already have a ssh keys for other machines,

  1. keep the default name of the files that will contain the private and public keys:  ~/.ssh/id_rsa and  ~/.ssh/id_rsa.pub  respectively.
  2. then press  Enter  until you get the prompt again (no passphrase).

Check with command

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[login@maestro ~]$ ls -l ~/.ssh

that the newly created files have permissions

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-rw-------

Given that your home is accessible on every node of the cluster, you just have to copy and paste the content of the newly created .pub file at the end of the file  ~/.ssh/authorized_keys

If you have kept the default name, the command should look like

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[login@maestro ~]$ cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys

Check permissions of the authorized_keys file with command:

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[login@maestro ~]$ ls -l ~/.ssh/authorized_keys

It should be

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-rw------

If it's not the case, change permissions using chmod command:

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[login@maestro ~]$ chmod 600 ~/.ssh/authorized_keys

Please, use command

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[login@maestro ~]$ ls -ld  ~/.ssh

check that your .ssh directory also has permissions

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drwx--S---

If not, change them by typing:

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[login@maestro ~]$ chmod 700 ~/.ssh

Step 2: the way to connect depends on where your computer is#

maestro.pasteur.fr is NOT accessible from outside.

  • If you are outside the Pasteur Paris campus:
  • first use the VPN (links for download available on the page) so that your computer will be put in  the dedicated Pasteur subnetwork,
  • then connect to maestro.pasteur.fr as explained in Step 3
  • If you are  inside  the Pasteur Paris campus, connect directly to maestro.pasteur.fr as explained in Step 3

Reminder: X-forwarding (graphical display) is blocked by the ssh.pasteur.fr  gateway.

Step 3: check/install a X server on your machine and log on maestro.pasteur.fr#

Mac OS X and Linux users#

Prerequisite for Mac OS X user#

  1. ensure that XQuartz is installed, up-to-date and that you have closed the Mac session and reopened one at least once after installation/update
  2. if your Mac hasn't been "pasteurized",  prefer XQuartz Terminal to Apple Terminal.

Connection through ssh#

Then connect to the submit node maestro.pasteur.fr :

  1. open a terminal window and type
  2. if you are on a Mac

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ssh -Y <yourlogin>@maestro.pasteur.fr
  1. if you are on a Linux machine

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ssh -X <yourlogin>@maestro.pasteur.fr
  1. if the following lines appear, type yes

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hostname:~ login$  ssh -Y login@maestro.pasteur.fr
The authenticity of host 'maestro.pasteur.fr (192.168.148.50)' can't be established.
ECDSA key fingerprint is SHA256:dL7fa6chcQzbOcC/64vKHLMK9z4J8IcP/DHPZWWdsCw.
Are you sure you want to continue connecting (yes/no)?
  1. type your password

Windows users#

PuTTY users:

  1. check Enable X11 forwarding  box under Connections-> SSH -> X11  in the Category Panel
  2. install an X Server such as Xming to have the graphical display

  3. once done

    1. click on PuTTY icon
  5. fill the Host Name field with maestro.pasteur.fr and port with 22
  6. ensure that SSH is selected for Connection Type
  7. click Open
  8. type your login
  9. type your password

Non PuTTY users:

  1. install a combined X Server and ssh client such as  MobaXTerm
  2. proceed in a terminal window like the Max OS X and Linux users (see above)

Step 4: submit your first graphical jobs with --x11 option in your srun#

To test that the graphic forwarding works, once connected to maestro with X11 Forwarding enabled, you can try to submit xeyes , a pair of eyes that seems to follow the mouse moves. For that, don't forget the --x11  option to your srun command

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login@maestro ~ $  srun  --x11 xeyes

If a window with such pair of eyes appears, it works as expected.

Note that:

  • If you forget the --x11, you will have an error message of the type

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Error: Can't open display: localhost:18.0
srun: error: maestro-<number>: task 0: Exited with exit code 1
  • if you forget to connect with graphic forwarding (through ssh -X  from a Linux or ssh -Y  from a Mac), you will have this kind of error message

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srun: error: No DISPLAY variable set, cannot setup x11 forwarding.

Now check with a real program.

For example, let's say that you want to use CLC Genomics WB. First you have to load it in your environment:

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login@maestro ~ $  module av clc
--------------------------------- /opt/gensoft/modules -------------------------------
clc-assembly-cell/5.1.0(default)  CLCGenomicsWorkbench/11.0.1  CLCGenomicsWorkbench/20.0.4(default)
login@maestro ~ $ module load CLCGenomicsWorkbench/20.0.4

before submitting them with --x11 option (and in the correct partition to get a license):

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login@maestro ~ $  srun --x11 -p clcgwb clcgenomicswb20

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