wiki:Docs/PostProcessingAppArcher2Setup

Version 24 (modified by ros, 3 months ago) (diff)

Update for ARCHER2

ARCHER2 specific setup instructions for data transfer to JASMIN

Instructions depend on whether your suite has the PP Transfer option already available and also if this is your first time using the Transfer App.

To determine if your suite already has PP Transfer available search in the rose edit GUI for the variable PPTRANSFER. If PPTRANSFER variable is found then your suite is already setup with the Transfer app.

Determine which of the following scenarios you fall into and follow the instructions listed.

Scenario 1 - PP Transfer not already in the suite and you have never used the Transfer app before.

Scenario 2: PP Transfer already in suite and you have either never used the Transfer app before or it is configured for ARCHER.

Add PP Transfer task to a suite

Only follow these instructions if your suite doesn't already have the "PP Transfer" option available.

rose-suite.conf

  1. Add PPTRANSFER=true
  1. The PPTRANSFER variable will, by default, appear under "suite conf → jinja2". To tell Rose to place it with all the other suite control switches (e.g. "Build UM" & "Run Reconfiguration") usually found in a panel in the suite conf section under "Build and Run" or Tasks edit the meta/rose-meta.conf file to add in the metadata for the PPTRANSFER variable. Place it under the definition for POSTPROC. (This step is optional.)
    [jinja2:suite.rc=PPTRANSFER]
    compulsory=true
    description=Transfer files archived with PostProc to a remote machine
    help=
    ns=<panel_namespace>
    sort-key=runPostproc1
    title=PP Transfer
    type=boolean
    

Where <panel_namespace> is the same value as for the POSTPROC entry in this file; e.g. ns=Build and Run

suite.rc

Note: Depending on the suite setup you may find the appropriate sections to modify in the site/archer.rc file rather than the suite.rc.

  1. Add the build & run of pptransfer task into the cylc graph initial cycle. Add the line:
    {{ 'fcm_make_pptransfer => fcm_make2_pptransfer' + (' => pptransfer' if RUN else '') if PPTRANSFER else '' }}
    
    to the cylc graph for the initial cycle, indicated by [[[ R1 ]]]. For example: (insertion indicated by "⇐ Add line here")
        [[dependencies]]
            [[[ R1 ]]]
                graph = """
    {{ 'fcm_make_pp => fcm_make2_pp' + (' => postproc' if RUN else '') if POSTPROC else '' }}
    {{ 'fcm_make_pptransfer => fcm_make2_pptransfer' + (' => pptransfer' if RUN else '') if PPTRANSFER else '' }}    <== Add line here
    {{ 'fcm_make_ocean => fcm_make2_ocean' + (' => recon' if RECON else ' => coupled' if RUN else '') if BUILD_OCEAN else '' }}
    {{ 'fcm_make_um => fcm_make2_um' + (' => recon' if RECON else ' => coupled' if RUN else '') if BUILD_UM else '' }}
    {{ 'install_ancil => recon ' if RECON else ('install_ancil => coupled' if RUN else '')}}
    {{ 'recon' + (' => coupled' if RUN else '') if RECON else '' }}
    {{ 'clearout' + (' => coupled' if RUN else '') if CLEAROUT else '' }}
    """
    
  1. Add the pptransfer task into the graph for all subsequent cycles such that it runs after the postproc task and also waits for the previous pptransfer task to complete. As an example for a coupled suite (All added lines indicated with "⇐"):
            [[[ {{FMT}} ]]]
                graph = """
    {% if RUN %}
    coupled[-{{FMT}}] => coupled {{ '=> \\' if POSTPROC or HOUSEKEEP else '' }}
      {% if POSTPROC %}
    postproc {{ '=> \\' if PPTRANSFER or HOUSEKEEP else '' }}     <= "PPTRANSFER or" added here
      {% endif %}
      {% if PPTRANSFER %}                                         <=
    pptransfer {{ '=> \\' if HOUSEKEEP else '' }}                 <=
      {% endif %}                                                 <=
      {% if HOUSEKEEP %}
    housekeeping
      {% endif %}
      {% if POSTPROC %}
    postproc[-{{FMT}}] => postproc
      {% endif %}
      {% if PPTRANSFER %}                                         <=
    pptransfer[-{{FMT}}] => pptransfer                            <=
      {% endif %}                                                 <=
    {% endif %}
    """
    

Take care to ensure there is no trailing whitespace at the end of each added line.

  1. In the [[postproc]] task check that pre-script is set as follows:
        [[postproc]]
            inherit = ...
            pre-script = "module restore /work/y07/shared/umshared/modulefiles/postproc/2020.12.11; module list 2>&1; ulimit -s unlimited"
            ...
    
  1. At the end of the file add the pptransfer task definitions:
        [[PPTRANSFER]]
            inherit = HPC_SERIAL
            [[[job]]]
                batch system = background
            [[[environment]]]
                UMDIR=~um
    
        [[PPTRANSFER_BUILD]]
            [[[environment]]]
                ROSE_TASK_APP=fcm_make_pp
    
        [[fcm_make_pptransfer]]
            inherit = None, LINUX_UM, PPTRANSFER_BUILD
    
        [[fcm_make2_pptransfer]]
            inherit = None, PPTRANSFER, PPTRANSFER_BUILD
       
        [[pptransfer]]
            inherit = PPTRANSFER
            pre-script = "module load cray-python"
            [[[environment]]]
                CYCLEPERIOD = $( rose date $CYLC_TASK_CYCLE_POINT $CYLC_TASK_CYCLE_POINT --calendar {{CALENDAR}} --offset2 {{FMT}} -f y,m,d,h,M,s )
                ROSE_TASK_APP=postproc
                PLATFORM = linux
    

Note: LINUX_UM may be called something different (e.g EXTRACT_RESOURCE) depending on the suite.

Set up ssh-key to connect from ARCHER2 to JASMIN

This section setups up connection from ARCHER2 login node to JASMIN.

  1. Login to login.archer2.ac.uk (Note: this needs to be from somewhere other than PUMA)
  1. Add the following lines to your profile. This will be either ~/.profile or ~/.bash_profile. (Create one if it doesn't already exist):
    # ssh-agent setup
    . ~/.ssh/ssh-setup
    
  1. Copy the ~/.ssh/ssh-setup script.
    $ cp /work/y07/shared/umshared/um-training/ssh-setup ~/.ssh
    
  1. Copy the ssh-key you use to access JASMIN to ~/.ssh directory (e.g. id_rsa_jasmin).
  1. Add the following to your ~/.ssh/config file (create one if it doesn't already exist):
    Host hpxfer1.jasmin.ac.uk
    User <jasmin_username>
    IdentityFile ~/.ssh/<jasmin_key>
    ForwardAgent no
    

Where <jasmin_username> is your JASMIN username and <jasmin_key> is the name of you ssh-key.

Note: in order to use hpxfer1.jasmin.ac.uk you need to have requested access to the High Performance Data Transfer service via the JASMIN accounts portal.

  1. Logout of ARCHER2 and then log back in again to start up your ssh-agent.
  1. Run ssh-add ~/.ssh/<jasmin_key> where <jasmin_key> is the name of your JASMIN ssh-key E.g. id_rsa_jasmin. (This is the key you generated when you applied for access to JASMIN). Type in your passphrase when prompted to do so.
  1. You should now be able to login to the required JASMIN transfer node (either xfer[1-2].jasmin.ac.uk or the high performance node hpxfer1.jasmin.ac.uk) without being prompted for passphrase/password.