Remote Jupyter Kernel at CSCS

cscs-access.md

Configuration

Direct Access to Computing Systems

1. Get an Account and store your account name export CSCS_USER=unixname.

3. Configure direct access to the computing system. You can use the ssh_config template:

   $ cat >> ~/.ssh/config <<EOF
   
   Host ela.cscs.ch
    User $CSCS_USER
   
   Match host !ela.cscs.ch,*.cscs.ch
    ControlMaster auto
    ControlPath ~/.ssh/%r@%h:%p
    ControlPersist 1
    User $CSCS_USER
    ProxyCommand ssh -q -Y ela.cscs.ch -W %h:%p
   EOF
   

   NOTE: check that you don't have any conflicting rules in ~/.ssh/config.

4. Connect to the computing system (in following example use export CSCS_SYSTEM=daint.cscs.ch) using ssh $CSCS_SYSTEM.

Compute Node

0. Make sure you are connected to $CSCS_SYSTEM (check previous section).
1. Configure direct access to nodes without password:

   $ ssh-keygen
   $ cat .ssh/id_rsa.pub >> .ssh/authorized_keys

2. Start new compute node in interactive mode: srun -C gpu -J test -v -u bash -i and check the output of uname -a.
3. From new terminal start new SSH connection to $CSCS_SYSTEM and check the job:

   (local)$ ssh $CSCS_SYSTEM
   ($CSCS_SYSTEM)$ squeue -u $USER -l
   Tue May  9 07:43:20 2017
     JOBID PARTITION     NAME     USER    STATE       TIME TIME_LIMI  NODES NODELIST(REASON)
    123456    normal     test    $USER  RUNNING       0:15   1:00:00      1 nid00000
   
   ($CSCS_SYSTEM)$ export CSCS_NODE=nid00000  # the name in last column 
   ($CSCS_SYSTEM)$ ssh $CSCS_NODE
   ($CSCS_NODE)$ uname -a
   Linux nid00000 3.12.60-52.49.1_2.0-cray_ari_c #1 SMP Mon Nov 21 15:40:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

   Compare the output from step 2 and if they are equal the connection was successful. Now close this terminal.
4. Close the running srun command by pressing ctrc+c twice.

Things to know

• Storage is limited: https://user.cscs.ch/storage/file_systems/
• Pytorch https://user.cscs.ch/computing/data_science/pytorch/
• Tensorflow https://user.cscs.ch/computing/data_science/tensorflow/
• Virtualenv http://usertest.cscs.ch/tools/interactive/python/