wiki:Archer/Transition2020/PPTransfer

Version 10 (modified by ros, 10 months ago) (diff)

Configuring pptransfer app and UM suite to pull data on /work from JASMIN

The pptransfer task used to run on the ARCHER Data Transfer Node (dtn02) which we no longer have access to from February 19th. The instructions below modify a suite to run the pptransfer task on the JASMIN transfer nodes and pull the data across from ARCHER /work disk.

In the rose suite editor go to "postproc → Post processing - common settings"’’:

  • In panel "Archer Archiving" change archive_root_path to be a directory in your $DATADIR on /work disk (e.g. /work/n02/n02/<username>/archive). This will be a temporary area to stage your data before transfer to JASMIN.
  • In panel "JASMIN Transfer" change transfer_type to Pull and remote_host to login.archer.ac.uk

In the ~/roses/<SUITEID>/site/archer.rc file edit the section [[PPTRANSFER_RESOURCE]]:

  • Remove the line pre-script = "module load anaconda"'
  • Replace the line host = dtn02.rdf.ac.uk with host = jasmin-xfer2.ceda.ac.uk

You now need to setup ssh-agent to be able to login to jasmin-xfer2.ceda.ac.uk and from there to login.archer.ac.uk.

Setup required on PUMA and JASMIN

PUMA:

These instructions assume you already have an ssh-agent running on PUMA which you would already have needed in order to run a UM suite on ARCHER.

  • Log on to PUMA.
  • Make sure you have a copy of your JASMIN ssh-key in your ~/.ssh directory. This is the key you generated when you applied for access to JASMIN. The remainder of the instructions assume it is called id_dsa_jasmin please replace this with the name of your key as appropriate.
  • Setup ~/.ssh/config file to login to the jasmin-xfer node. For example:
    Host jasmin-xfer2.ceda.ac.uk
    Hostname jasmin-xfer2.ceda.ac.uk
    User <jasmin-username>
    IdentityFile ~/.ssh/id_dsa_jasmin
    ForwardAgent no
    

Replace <jasmin-username> with your JASMIN username.

  • Run ssh-add ~/.ssh/id_dsa_jasmin to attach the key to your existing ssh-agent.

JASMIN:

  1. Log on to JASMIN: ssh jasmin-xfer2ceda.ac.uk
  1. Setup PATH to Rose, Cylc and FCM:
  • In your ~/.bash_profile add the following:
    if [[ `hostname` = "jasmin-cylc.ceda.ac.uk" ]]; then
      # Rose/cylc on jasmin-cylc
      export PATH=/apps/contrib/metomi/bin:$PATH
    else
      # Rose/cylc on jasmin-xfer
      export PATH=/home/users/rshatcher/software/bin:$PATH 
    fi
    
  1. Setup ssh-agent to access ARCHER Login Nodes:
  • Copy the private key you use on PUMA to access ARCHER over to JASMIN. This will be something like ~/.ssh/id_dsa.
    scp <puma-username>@puma.nerc.ac.uk:~/.ssh/id_dsa ~/.ssh
    
  • Copy the ssh-agent start up script:
    cp ~rshatcher/setup ~/.ssh
    
  • In your ~/.bashrc add the following to start up ssh-agent:
    if [[ `hostname` = "jasmin-xfer2.ceda.ac.uk" ]] ; then
      # ssh-agent setup for transfer app
      . ~/.ssh/setup
    fi
    
  • In your ~/.ssh/config add the following lines:
    Host login.archer.ac.uk
      Hostname login.archer.ac.uk
      User <archer-username>
    

Replacing <archer-username with your ARCHER username.

  • Log out of jasmin-xfer2 and back in again.
  • Run ssh-add. You will be prompted for your passphrase.

Check that you can now ssh to ARCHER without prompt for password/passphrase by running:

ssh login.archer.ac.uk

Loading the changes into the suite

Instructions differ depending in if you are modifying an already running suite or new suite.

Already running suite

  • Run rose suite-run --reload
  • Load the build of the pptransfer scripts on JASMIN into the suite
cylc insert <SUITEID> fcm_make_pptransfer.<CYCLEPOINT>
cylc insert <SUITEID> fcm_male2_pptransfer.<CYCLEPOINT>

where <SUITEID>is the name of the suite and <CYCLEPOINT> is the name of the cycle to insert into eg. 19890901T000Z

You should see 2 new tasks appear in the cylc GUI.

Right click on fcm_make_pptransfer and select Trigger Run (now). Once this has succeed do the same for fcm_make2_pptransfer.

New suite

Simply start the suite as normal: rose suite-run