Changes between Version 1 and Version 2 of Archer2/PPTransfer


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Timestamp:
07/01/21 13:23:44 (3 months ago)
Author:
grenville
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  • Archer2/PPTransfer

    v1 v2  
    33last updated 16 December 2020 
    44 
    5 The `pptransfer` task used to run on the ARCHER Data Transfer Node (dtn02) which we no longer have access to. The instructions show how to modify a suite to run the `pptransfer` task on the ARCHER2 login nodes and push the data across to JASMIN from ARCHER2 `/work` disk.   
     5The `pptransfer` task used to run on the ARCHER Data Transfer Node (dtn02) which we no longer have access to. These instructions show how to modify a suite to run the `pptransfer` task on the ARCHER2 login nodes and push the data across to JASMIN from ARCHER2 `/work` disk.   
    66 
    77'''Note 1:''' 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. 
     
    99'''Note 2:''' 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. 
    1010 
     11'''Note 3:''' We anticipate that the full ARCHER2 system will have `serial` nodes in which case the cylc configuration will be closer to the current ARCHER set up, but until then, we need to use the login nodes. In what follows, references to `HPC_SERIAL` remain in anticipation of the full system and are harmless. 
     12 
    1113== Suite Changes == 
     14 
     15Note, see u-bs251-archer2 for a complete working postproc and pptransfer example suite. 
    1216 
    1317In the rose suite editor go to ''"postproc -> Post processing - common settings"'': 
     
    1923    * Set `remote_host` to '''hpxfer1.jasmin.ac.uk''' \\ (If you do not have access to `hpxfer1.jasmin.ac.uk` use either `xfer1.jasmin.ac.uk` or `xfer2.jasmin.ac.uk` instead.) 
    2024 
    21 In the `~/roses/<SUITEID>/site/archer.rc` file edit the section `[[PPTRANSFER_RESOURCE]]`: 
     25Ideally you will have ARCHER2 specific file, `~/roses/<SUITEID>/site/archer2.rc`  
    2226 
    23  * Replace the  line `host = dtn02.rdf.ac.uk` with `host = login.archer.ac.uk` 
     27 * Replace the line `host = dtn02.rdf.ac.uk` with `host = login.archer.ac.uk` 
    2428 
    25  * Add the line `inherit = HPC_SERIAL` directly above the line beginning `pre-script =` 
     29Ideally, `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): 
    2630 
    27  * Add these 2 lines:  
    28    {{{ 
    29    [[[job]]] 
    30        execution time limit = PT12H 
    31     }}} 
     31{{{ 
     32    [[POSTPROC_RESOURCE]] 
     33        inherit = HPC_SERIAL 
     34        pre-script = """module restore /work/y07/shared/umshared/modulefiles/postproc/2020.12.11 
     35                        module list 2>&1 
     36                        ulimit -s unlimited 
     37                     """ 
     38   
    3239 
    33 The section should now look something like the following (Remember it may not be identical due to suite differences) : 
    34 {{{ 
    3540    [[PPTRANSFER_RESOURCE]] 
    36         inherit = HPC_SERIAL 
    37         pre-script = """module load anaconda""" 
    38         [[[remote]]] 
    39             host = login.archer.ac.uk 
     41        inherit = POSTPROC_RESOURCE 
    4042        [[[job]]] 
    41             execution time limit = PT12H 
    42         [[[environment]]] 
    43             UMDIR = ~um 
    44             PLATFORM = linux 
     43            batch system = background 
    4544}}} 
     45 
    4646 
    4747== Setup required on ARCHER == 
    4848 
    49 You now need to setup `ssh-agent` on both ARCHER post-processing nodes (espp1 & espp2) to be able to login to `hpxfer1.jasmin.ac.uk`. 
     49You now need to setup `ssh-agent` on ARCHER2 login nodes to be able to login to `hpxfer1.jasmin.ac.uk`. 
    5050 
    51 1. Login to ARCHER (Note: this needs to be from somewhere other than PUMA) 
     511. Login to ARCHER2 (Note: this needs to be from somewhere other than PUMA) 
    5252 
    53 2. From ARCHER login node login to '''espp1''' (You will be prompted for your ARCHER password only) 
    54  
    55 3. Add the following lines to your `~/.bashrc` or `~/.profile` (May also be `~/.bash_profile`): 
     532. Add the following lines to your `~/.bash_profile`: 
    5654{{{ 
    57 # ssh-agent setup on pp nodes 
    58 if [[ `hostname` = esPP00* ]] 
    59 then 
     55# ssh-agent setup on login nodes 
    6056  . ~/.ssh/ssh-setup 
    61 fi 
    6257}}} 
    6358 
    64593. Copy the `~/.ssh/ssh-setup` script. 
    6560{{{ 
    66 $ cp /work/y07/y07/umshared/um-training/ssh-setup ~/.ssh 
     61$ cp /work/y07/umshared/umshared/um-training/ssh-setup ~/.ssh 
    6762}}} 
    6863 
     
    7772}}} 
    7873 
    79  Where `<jasmin_username>` is your JASMIN username and `<jasmin_key>` is the name of you ssh-key. 
     74 Where `<jasmin_username>` is your JASMIN username and `<jasmin_key>` is the name of your ssh-key. 
    8075 
    8176 '''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. 
    8277 
    83 6. Logout of espp1 and then log back in again to start up your ssh-agent. 
     786. Logout and then log back in again to start up your ssh-agent. 
    8479 
    85807. 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. 
     
    87828. 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. 
    8883 
    89 9. Start up ssh-agent on the other post-processing node. Login to '''espp2''' to start up ssh-agent. 
    90  
    91 10. Run `ssh-add ~/.ssh/<jasmin_key>` where <jasmin_key> is the name of your JASMIN ssh-key 
    92  
    93 11. Again you should now be able to login to the JASMIN transfer node without being prompted for passphrase/password. 
    9484 
    9585== Updating a Running Suite ==