NCAS Computational Modelling Services

Data Transfer from ARCHER2 to JASMIN

Configuring PPTransfer

The now-recommended method for transferring data between ARCHER2 and JASMIN is using GridFTP using certificate authentication. This allows data transfers to run on the ARCHER2 serial nodes using certificate-based authentication rather than SSH. Certificates are valid for up to a month from initiation and can be easily extended/regenerated for longer running simulations.

These instructions show how to setup your GridFTP certificate and modify a suite to run the pptransfer task on the ARCHER2 serial nodes to push the data across to JASMIN from ARCHER2 /work disk.

Note: Instructions cannot cover all possible suite setup combinations so you may need to adjust them accordingly. For example, tasks may be named slightly differently or inherit differently.

Obtaining a JASMIN short-lived credential

A fuller explanation of the process is given in the document Data Transfer Tools: GridFTP (certificate-based authentication)

  • Login to ARCHER2.

  • Change directory to your ARCHER2 work directory - /work/n02/n02/USERNAME.

  • [First Time Only] “Bootstrap trust” to setup your local certificate store with those needed to interact with the JASMIN server.
    $ $UMDIR/bin/onlineca-get-trustroots-wget.sh -U https://slcs.jasmin.ac.uk/trustroots/ -b
    Bootstrapping Short-Lived Credential Service root of trust.
    Trust roots have been installed in /home/n02/n02/USERNAME/.globus/certificates.
    
  • Obtain a short-term credential (this must be called cred.jasmin) using your JASMIN accounts portal username USERNAME.
    $ $UMDIR/bin/onlineca-get-cert-wget.sh -U https://slcs.jasmin.ac.uk/certificate/ -l USERNAME -o ./cred.jasmin
    

    When prompted for a passphrase, this is the password associated with your JASMIN account portal account (NOT your SSH passphrase)

  • Change the permissions on the newly-created cred.jasmin file so that it is only readable by you.

    $ chmod 600 cred.jasmin

This credential is valid, by default, for 30days. You can see the validity period by inspecting the certificate using the following command:

$ openssl x509 -in cred.jasmin -noout -startdate -enddate
notBefore=Mar 11 17:32:59 2022 GMT
notAfter=Apr 10 17:32:59 2022 GMT

This means you can use this certificate for the following 30days, after which you will need to repeat this step to obtain a new one.

Suite Changes

Note, see u-be303/archer2 for a complete working postproc and pptransfer example suite.

In the rose suite editor go to “postproc -> Post processing - common settings”:

  • In panel “Archer Archiving” change archive_root_path to be a directory on the /work disk
    For example; /work/n02/n02/<username>/archive where <username> is your ARCHER2 username.
    This will be a temporary area to stage your data before transfer to JASMIN.

  • In panel “JASMIN Transfer”:

    • Set transfer_type to Push
    • Set remote_host to gridftp1.jasmin.ac.uk
    • Set gridftp to true

Ideally you will have an ARCHER2 specific cylc .rc file, ~/roses/<SUITEID>/site/archer2.rc

Ideally, archer2.rc will include sections [[POSTPROC_RESOURCE]] and [[PPTRANSFER_RESOURCE]] (that may not be precisely the case, but what follows should guide you to configure your suite):

Make your suite look like this:

    [[POSTPROC_RESOURCE]]
        inherit = HPC_SERIAL
        pre-script = """module load postproc
                        module list 2>&1
                        ulimit -s unlimited
                     """
                     
    [[PPTRANSFER_RESOURCE]]
        inherit = POSTPROC_RESOURCE

If there is no [[POSTPROC_RESOURCE]] section, make [[PPTRANSFER_RESOURCE]] look like this:

    [[PPTRANSFER_RESOURCE]]
        inherit = HPC_SERIAL
        pre-script = """module load postproc
                        module list 2>&1
                        ulimit -s unlimited
                     """