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  •   Auto

    • Data transfer

     

    Transfers from ARCHER2

    Transfers from ARCHER2

     

    bbcp

    Data transfer tool bbcp

     

    ftp and lftp

    Data Transfer Tools: ftp and lftp

     

    Globus Connect Personal

    Globus Connect Personal

     

    rclone

    A "Swiss army knife" tool for data transfers

     

    Data Transfer Tools

    Data Transfer Tools

     

    Scheduling/Automating Transfers

    Scheduling/Automating Transfers

     

    GridFTP (SSH authentication)

    Data Transfer Tools: GridFTP (SSH authentication)

     

    Data transfer overview

    Overview of data transfer

     

    Globus Command-Line Interface

    Data Transfer Tools: Using the Globus Command-Line Interface

     

    Globus transfers with JASMIN

    Globus transfers with JASMIN

     

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    Data Transfer Tool: GridFTP (certificate-based authentication)

    Follow us

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    Data transfer

     

    Transfers from ARCHER2

    Transfers from ARCHER2

     

    bbcp

    Data transfer tool bbcp

     

    ftp and lftp

    Data Transfer Tools: ftp and lftp

     

    Globus Connect Personal

    Globus Connect Personal

     

    rclone

    A "Swiss army knife" tool for data transfers

     

    Data Transfer Tools

    Data Transfer Tools

     

    GridFTP (SSH authentication)

    Data Transfer Tools: GridFTP (SSH authentication)

     

    Data transfer overview

    Overview of data transfer

     

    Globus Command-Line Interface

    Data Transfer Tools: Using the Globus Command-Line Interface

     

    Globus transfers with JASMIN

    Globus transfers with JASMIN

     

    GridFTP (certificate-based authentication)

    Data Transfer Tool: GridFTP (certificate-based authentication)

     

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    Access to certain high-performance data transfer methods

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    \ No newline at end of file diff --git a/docs/data-transfer/index.xml b/docs/data-transfer/index.xml index ce8fa259f..7d64a10cf 100644 --- a/docs/data-transfer/index.xml +++ b/docs/data-transfer/index.xml @@ -3,10 +3,10 @@ The choice of available tools / routes Example of how to use the currently-recom What is bbcp?   bbcp is a simple command-line tool which can use your SSH connection to transfer data in and out of JASMIN efficiently.ftp and lftphttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/ftp-and-lftp/Mon, 22 Aug 2022 15:56:09 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/ftp-and-lftp/This article provides information about FTP (File Transfer Protocol) as a data transfer tool. In particular: what is FTP? where and how can I use FTP on JASMIN?Globus Connect Personalhttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/globus-connect-personal/Tue, 25 Jan 2022 11:19:40 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/globus-connect-personal/This article describes: how to create your own Globus endpoint using Globus Connect Personal This would enable you to transfer files to/from another Globus Endpoint using any of the Globus Online transfer tools (Web app, CLI or [Python SDK](https://globus-sdk- python.rclonehttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/rclone/Thu, 20 Jan 2022 10:22:59 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/rclone/This article provides information about the rclone data transfer tool. In particular: -what is rclone? installing rclone for yourself on JASMIN.Data Transfer Toolshttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/data-transfer-tools/Wed, 19 Jan 2022 12:25:45 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/data-transfer-tools/This article lists the data transfer tools available on JASMIN and provides links to articles that describe them in more detail.Scheduling/Automating Transfershttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/scheduling-automating-transfers/Wed, 07 Jul 2021 14:35:42 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/scheduling-automating-transfers/This article explains how to schedule or automate data transfers. It covers: -Scheduling download tasks using cron and LOTUS Using Globus for transfer automation [TODO] Overview   In many cases it can be useful to fetch data from an external source for processing/analysis on JASMIN on a regular basis, for example “every Monday at 11:00 fetch all last week’s data”.GridFTP (SSH authentication)https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/gridftp-ssh-auth/Wed, 16 Jun 2021 17:41:08 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/gridftp-ssh-auth/This article describes how to transfer data using GridFTP with SSH authentication. +what is rclone? installing rclone for yourself on JASMIN.Data Transfer Toolshttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/data-transfer-tools/Wed, 19 Jan 2022 12:25:45 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/data-transfer-tools/This article lists the data transfer tools available on JASMIN and provides links to articles that describe them in more detail.GridFTP (SSH authentication)https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/gridftp-ssh-auth/Wed, 16 Jun 2021 17:41:08 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/gridftp-ssh-auth/This article describes how to transfer data using GridFTP with SSH authentication.   The globus-url-copy command used here should not be confused with the Globus online data transfer service.Data transfer overviewhttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/data-transfer-overview/Wed, 16 Jun 2021 17:39:34 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/data-transfer-overview/This article introduces the topic of data transfer to/from JASMIN. Introduction to Data Transfer on JASMIN   As a JASMIN user you are very likely to be involved in data transfer.Globus Command-Line Interfacehttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/globus-command-line-interface/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/globus-command-line-interface/  Updated for new JASMIN Default Collection (replaces previous JASMIN Globus Endpoint) This article describes how to transfer data using the Globus Command Line Interface.Globus transfers with JASMINhttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/globus-transfers-with-jasmin/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/globus-transfers-with-jasmin/This article describes how to do data transfers using JASMIN’s new Globus endpoint (now called a collection ), based on the most recent version of Globus Connect Server.GridFTP (certificate-based authentication)https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/gridftp-cert-based-auth/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/gridftp-cert-based-auth/This article describes how to transfer data using gridftp with certificate- based authentication.   The globus-url-copy command used here should not be confused with the Globus online data transfer service.hpxfer access rolehttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/hpxfer-access-role/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/hpxfer-access-role/This article explains about access to high-performance data transfer services. -Applying for access   Some data transfer services are hosted in the JASMIN Data Transfer Zone for increased performance.JASMIN external connectionshttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/jasmin-external-connections/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/jasmin-external-connections/NOTE [January 2021] This article is now out of date. Some terminology, names and components are no longer current. A newer version will be posted here in due course.rsync, scp, sftphttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/rsync-scp-sftp/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/rsync-scp-sftp/This article tells you about some of the basic transfer tools available for use with JASMIN that work over an SSH connection: \ No newline at end of file +Applying for access   Some data transfer services are hosted in the JASMIN Data Transfer Zone for increased performance.JASMIN external connectionshttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/jasmin-external-connections/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/jasmin-external-connections/NOTE [January 2021] This article is now out of date. Some terminology, names and components are no longer current. A newer version will be posted here in due course.rsync, scp, sftphttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/rsync-scp-sftp/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/rsync-scp-sftp/This article tells you about some of the basic transfer tools available for use with JASMIN that work over an SSH connection:Scheduling/Automating Transfershttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/scheduling-automating-transfers/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/scheduling-automating-transfers/This article explains how to schedule or automate data transfers. It covers: +Scheduling download tasks using cron and LOTUS Using Globus for transfer automation Overview   In many cases it can be useful to fetch data from an external source for processing/analysis on JASMIN on a regular basis, for example “every Monday at 11:00 fetch all last week’s data”. \ No newline at end of file diff --git a/docs/data-transfer/jasmin-external-connections/index.html b/docs/data-transfer/jasmin-external-connections/index.html index 4791c7487..083c2e722 100644 --- a/docs/data-transfer/jasmin-external-connections/index.html +++ b/docs/data-transfer/jasmin-external-connections/index.html @@ -76,4 +76,4 @@  
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  •   Auto

    • Data transfer

     

    hpxfer access role

    Access to certain high-performance data transfer methods

     

    JASMIN external connections

    JASMIN external connections

     

    rsync, scp, sftp

    Data Transfer Tools: rsync, scp, sftp

    Follow us

    Social media & development

      +
    filezilla
     

     

    Scheduling/Automating Transfers

    Scheduling/Automating Transfers

    Follow us

    Social media & development

         
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    Docs

    Scheduling/Automating Transfers

     

    Share via

    Scheduling/Automating Transfers

     

    This article explains how to schedule or automate data transfers. It covers:

    • Scheduling download tasks using cron and LOTUS
    • Using Globus for transfer automation [TODO]

    Overview  

    In many cases it can be useful to fetch data from an external source for +

    Link copied to clipboard

    Scheduling/Automating Transfers

     

    This article explains how to schedule or automate data transfers. It covers:

    Overview  

    In many cases it can be useful to fetch data from an external source for processing/analysis on JASMIN on a regular basis, for example “every Monday at 11:00 fetch all last week’s data”. It can also be helpful to distribute the task downloading of some large datasets, or simply to be able rely on data @@ -26,29 +26,34 @@ periodic analysis.

    Using Globus for transfer automation  

    It is easy to automate transfers using Globus. This method has the advantage that you do not need to remain connected or logged in to any JASMIN server for the automated transfers -to take place on your behalf, and is more efficient and reliable than the other methods described below.

    Some introductory information about how to do this is available in this article +to take place on your behalf, and the transfer itself can be more efficient than other methods described below.

    Some introductory information about how to do this is available in this article Using the Globus command-line interface (with more to follow) but please also refer to the comprehensive Globus documentation and their automation examples. You can choose whether to schedule/automate tasks via the Globus web interface, command-line interface, or use their Globus SDK to build -Python code that uses this functionality.

    Scheduling download tasks using cron and LOTUS  

    While the cron server is provided for scheduling -tasks, it should not be used for the work of executing those tasks itself. -So we need a way for a task to be invoked from cron but executed where there -is lots of processing resource (i.e. LOTUS).

    In the examples below, we use the test queue (or partition, as queues are +Python code that uses this functionality.

    Scheduling download tasks using cron and LOTUS  

    While the cron server cron.jasmin.ac.uk is provided for scheduling +general tasks, it should not be used for the work of executing those tasks itself, and not for transfer tasks.

    xfer3 - transfer machine with cron  

    The transfer server xfer3.jasmin.ac.uk is also provided with cron, and should be used where +a task is primarily a transfer rather than a processing task and needs the functionality +of a transfer server. For access to xfer3 you will need the +xfer-sp access role  +. +Please refer to the above cron guidance for best practice advice.

    invoking LOTUS from cron to carry out multiple download tasks  

    Sometimes we need a tasks to be invoked from cron but executed where there +are lots of nodes to parallelise the tasks (i.e. the LOTUS cluster). In this case, we DO need to use the cron +server rather than xfer3, since we need to be able to talk to LOTUS (xfer3 can’t do that, as a transfer server).

    This will only work where the download can happen over HTTP(S), so depends on how the remote data is made available.

    We need it to:

    In the examples below, we use the test queue (or partition, as queues are known in SLURM). You can use this for testing, but once you know roughly how long your download(s) should take, you should choose an appropriate queue so that the jobs can be scheduled in a fair way alongside other users’ jobs.

    1. Single download script  

    The simple script below is used to download a single file from an external -source via HTTP using wget:

    #!/bin/bash 
-#SBATCH --partition=test
-#SBATCH -o %j.out 
-#SBATCH -e %j.err
-#SBATCH --time=00:30
-
-# executable 
-wget -q -O 1MB_${SLURM_JOBID}.zip http://speedtest.tele2.net/1MB.zip
-

    In this example, the file is labelled with the id of the job which downloaded +source via HTTP using wget. It initially uses the test partition (queue), but +once you had tested it, you would need to use a more appropriate queue.

    #!/bin/bash 
+#SBATCH --partition=test
+#SBATCH -o %j.out 
+#SBATCH -e %j.err
+#SBATCH --time=00:30
+
+# executable 
+wget -q -O 1MB_${SLURM_JOBID}.zip http://speedtest.tele2.net/1MB.zip

    In this example, the file is labelled with the id of the job which downloaded it, e.g. 1MB_61117380.zip

    The same could be also achieved using curl, or using a Python script making use of (for example) the requests library.

    A note about transfer tools: since we are delegating the actual download task to a LOTUS node, we are restricted to transfer tools already installed on @@ -58,13 +63,10 @@ cluster, so you may be limited to downloading via HTTP(S), FTP, or via tools available via libraries in the Python environment such (which you do have access to and can easily customise to install additional libraries using -virtual environments).

    Download tools installed on LOTUS nodes include:

    In our simple example above, we can subit this script to LOTUS from the -command line with

    sbatch test_download.sh
-

    This could be invoked on a regular basis by adding a crontab entry like this

    30 * * * * sbatch /home/users/username/test_download.sh
-

    However it would be safer to wrap this in a crontamer command like this to +virtual environments).

    Due to networking limitations, LOTUS nodes cannot perform downloads using SSH-based methods, i.e. scp/rsync/sftp.

    Download tools installed on LOTUS nodes include:

    In our simple example above, we can subit this script to LOTUS from the +command line with

    sbatch test_download.sh

    This could be invoked on a regular basis by adding a crontab entry like this

    30 * * * * sbatch /home/users/username/test_download.sh

    However it would be safer to wrap this in a crontamer command like this to ensure one instance of the task had finished before the next started: (see -Using cron for details)

    30 * * * * crontamer -t 2h 'sbatch /home/users/username/test_download.sh'
-

    2. Multi-node downloads  

    We could expand this example to download multiple items, perhaps 1 directory +Using cron for details)

    30 * * * * crontamer -t 2h 'sbatch /home/users/username/test_download.sh'

    2. Multi-node downloads  

    We could expand this example to download multiple items, perhaps 1 directory of data for each day of a month, and have 1 element of a job array handle the downloading of each day’s data.

    A few words of warning: Distributing download tasks as shown below can cause unintended side-effects. Here, we’re submitting an array of 10 download @@ -79,19 +81,18 @@ not cause a problem. A limit of 10 jobs would be a sensible maximum, for one user.

    We’ll simulate this here by downloading the same external file to 10 different output files, but you could adapt this concept for your own purposes depending -on the layout of the source and destination data.

    #!/bin/bash 
-#SBATCH --partition=test
-#SBATCH -o %A_%a.out
-#SBATCH -e %A_%a.err
-#SBATCH --time=00:30
-#SBATCH --array=1-10
-#SBATCH --time=00:30
-
-# executable 
-wget -q -O 1MB_${SLURM_ARRAY_TASK_ID}.zip http://speedtest.tele2.net/1MB.zip
-
-echo "script completed"
-

    In this (perhaps contrived) example, we’re setting up an array of 10 elements +on the layout of the source and destination data.

    #!/bin/bash 
+#SBATCH --partition=test
+#SBATCH -o %A_%a.out
+#SBATCH -e %A_%a.err
+#SBATCH --time=00:30
+#SBATCH --array=1-10
+#SBATCH --time=00:30
+
+# executable 
+wget -q -O 1MB_${SLURM_ARRAY_TASK_ID}.zip http://speedtest.tele2.net/1MB.zip
+
+echo "script completed"

    In this (perhaps contrived) example, we’re setting up an array of 10 elements and using the SLURM_ARRAY_TASK_ID environment variable to name the output files (otherwise they’d all be the same). In a real-world example you could apply your own logic to divide up files or directories matching certain @@ -99,10 +100,10 @@ in (1).

    Some tools provide functionality for mirroring or synchronising directories, i.e. only downloading those files in a directory which are new have been added since the last time a task was run. These can be useful to avoid repeated -downloads of the same data.

    Last updated: February 9, 2024 -• content updates (b9c07b51)
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      +downloads of the same data.

    Last updated: February 12, 2024 +• content updates (8eb086be)
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    Docs

    Creating a virtual environment in the jasmin notebooks service

     

    notebook
     
    notebook
     
    Share via

    Creating a virtual environment in the notebooks service

     

    Creating a virtual environment is useful to allow a discrete set of extra +

    Link copied to clipboard

    Creating a virtual environment in the notebooks service

     

    Creating a virtual environment is useful to allow a discrete set of extra packages to be installed to meet specific requirements. This allows a user to run multiple environments with different dependencies without conflicts.

    There are a number of ways to create a virtual environment to use with the notebook service. This document outlines the most common and reccomended @@ -78,11 +78,11 @@ packages = ['pyjokes'] sp.check_call([sys.executable, '-m', 'pip', 'install'] + packages)

    Can I use conda instead of a virtual environment?  

    Yes, no problem.

    To create a conda environment, sinply run the following at the JASMIN -Notebooks shell:

    conda create --name name-insert-here ipykernel

    Install any packages you which to use in the environment:

    conda install --name name-insert-here pyjokes

    Make the notebook service recognise your environment as a kernel:

    conda run --name name-insert-here python -m ipykernel install --user --name name-insert-here

    Can get rid of old kernels from the notebook service?  

    Yes.

    To list the names of kernels you have installed, run the following at the +Notebooks shell:

    conda create --name name-insert-here ipykernel

    Install any packages you which to use in the environment:

    conda install --name name-insert-here pyjokes

    Make the notebook service recognise your environment as a kernel:

    conda run --name name-insert-here python -m ipykernel install --user --name name-insert-here

    Can I get rid of my old kernels from the notebook service?  

    Yes.

    To list the names of kernels you have installed, run the following at the JASMIN notebook’s shell:

    jupyter kernelspec list

    To remove one of them, run:

    jupyter kernelspec uninstall insert-name-here
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    \ No newline at end of file diff --git a/index.xml b/index.xml index 24d764139..84830bd0f 100644 --- a/index.xml +++ b/index.xml @@ -45,8 +45,7 @@ how a GWS Manager can organise for some directories within a GWS to be shared wi Overview of the &ldquo;jasmin-sci&rdquo; software environment Activating and deactivating the &ldquo;jasmin-sci&rdquo; environment Using the &ldquo;jasmin-sci&rdquo; environment with Jaspy Overview of the &ldquo;jasmin-sci&rdquo; software environment &nbsp; The jasmin-sci software environment is intended as a supplement to Jaspy and contains extra software packages for use with scientific data analysis which, for various reasons, are not provided as part of Jaspy itself.Running python on JASMINhttps://jellyfish-app-u7lat.ondigitalocean.app/docs/software-on-jasmin/running-python-on-jasmin/Tue, 16 Nov 2021 09:40:35 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/software-on-jasmin/running-python-on-jasmin/On the JASMIN analysis machines and on Lotus, we support Python2.7 and Python3.7 through Jaspy. When you log in, the default version of Python is 2.Secondary copy using Elastic Tapehttps://jellyfish-app-u7lat.ondigitalocean.app/docs/short-term-project-storage/secondary-copy-using-elastic-tape/Tue, 16 Nov 2021 09:00:38 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/short-term-project-storage/secondary-copy-using-elastic-tape/Introduction &nbsp; Elastic Tape is a system developed for use with JASMIN Group Workspaces (GWSs), enabling the Group Workspace Manager to:Processing requests for resourceshttps://jellyfish-app-u7lat.ondigitalocean.app/docs/uncategorized/processing-requests-for-resources/Mon, 08 Nov 2021 14:24:58 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/uncategorized/processing-requests-for-resources/This article is for consortium managers and explains: The overall process and role of consortium manager How to process a request for new resources for a service, submitted by a project How to process a request for additional resources on an existing project&rsquo;s service Introduction &nbsp; Please make sure you have read the article &ldquo;Requesting resources&rdquo; to understand how the process works from the requester&rsquo;s point of view.How to apply for MASS accesshttps://jellyfish-app-u7lat.ondigitalocean.app/docs/mass/how-to-apply-for-mass-access/Tue, 07 Sep 2021 12:33:03 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/mass/how-to-apply-for-mass-access/Introduction &nbsp; To access data held in the Met Office MASS archive, you will need: -a sponsor access to the mass-cli1 client machine a MASS account Your sponsor will need to be a Senior Met Office Scientist with whom you are working on a collaborative research project.Scheduling/Automating Transfershttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/scheduling-automating-transfers/Wed, 07 Jul 2021 14:35:42 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/scheduling-automating-transfers/This article explains how to schedule or automate data transfers. It covers: -Scheduling download tasks using cron and LOTUS Using Globus for transfer automation [TODO] Overview &nbsp; In many cases it can be useful to fetch data from an external source for processing/analysis on JASMIN on a regular basis, for example &ldquo;every Monday at 11:00 fetch all last week&rsquo;s data&rdquo;.GridFTP (SSH authentication)https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/gridftp-ssh-auth/Wed, 16 Jun 2021 17:41:08 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/gridftp-ssh-auth/This article describes how to transfer data using GridFTP with SSH authentication. +a sponsor access to the mass-cli1 client machine a MASS account Your sponsor will need to be a Senior Met Office Scientist with whom you are working on a collaborative research project.GridFTP (SSH authentication)https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/gridftp-ssh-auth/Wed, 16 Jun 2021 17:41:08 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/gridftp-ssh-auth/This article describes how to transfer data using GridFTP with SSH authentication. &nbsp; The globus-url-copy command used here should not be confused with the Globus online data transfer service.Data transfer overviewhttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/data-transfer-overview/Wed, 16 Jun 2021 17:39:34 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/data-transfer-overview/This article introduces the topic of data transfer to/from JASMIN. Introduction to Data Transfer on JASMIN &nbsp; As a JASMIN user you are very likely to be involved in data transfer.Using Matplotlib for visualisation on JASMINhttps://jellyfish-app-u7lat.ondigitalocean.app/docs/software-on-jasmin/matplotlib/Fri, 14 May 2021 11:59:35 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/software-on-jasmin/matplotlib/This article provides a basic example of using Matplotlib on JASMIN to generate a plot. It also gives an important tip that may stop your code failing when run on the LOTUS cluster.Additional software packages (under: /apps/jasmin/)https://jellyfish-app-u7lat.ondigitalocean.app/docs/software-on-jasmin/additional-software/Fri, 14 May 2021 11:58:38 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/software-on-jasmin/additional-software/This article provides details of additional packages that exist under the /apps/jasmin/ directory which is available on all scientific analysis servers and on the LOTUS batch cluster on JASMIN.Transfer Cache (XFC)https://jellyfish-app-u7lat.ondigitalocean.app/docs/short-term-project-storage/xfc/Thu, 22 Apr 2021 14:59:13 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/short-term-project-storage/xfc/What is the XFC? &nbsp; The Transfer Cache (XFC) provides a large area of temporary storage for users of JASMIN to store large files and / or a large volume of files on a short-term basis.Install XFC clienthttps://jellyfish-app-u7lat.ondigitalocean.app/docs/short-term-project-storage/install-xfc-client/Thu, 22 Apr 2021 14:48:38 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/short-term-project-storage/install-xfc-client/XFC client install &nbsp; In order to initiate and manage your usage of the XFC (transfer cache) service, you need to use the XFC client.Met Office NAME Modelhttps://jellyfish-app-u7lat.ondigitalocean.app/docs/software-on-jasmin/name-dispersion-model/Tue, 20 Apr 2021 08:45:40 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/software-on-jasmin/name-dispersion-model/This article provides links to information about running the Met Office atmospheric dispersion model, NAME, on JASMIN. The NAME atmospheric dispersion model &nbsp; The Met Office&rsquo;s Numerical Atmospheric-dispersion Modelling Environment (NAME) https://www.SLURM statushttps://jellyfish-app-u7lat.ondigitalocean.app/docs/batch-computing/slurm-status/Mon, 08 Mar 2021 15:47:16 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/batch-computing/slurm-status/TODO: UPDATE THE URL @@ -63,6 +62,7 @@ What is a software environment? &nbsp; A software environment is typically a how to transfer data using the Globus Command Line Interface.Globus transfers with JASMINhttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/globus-transfers-with-jasmin/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/globus-transfers-with-jasmin/This article describes how to do data transfers using JASMIN&rsquo;s new Globus endpoint (now called a collection ), based on the most recent version of Globus Connect Server.GridFTP (certificate-based authentication)https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/gridftp-cert-based-auth/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/gridftp-cert-based-auth/This article describes how to transfer data using gridftp with certificate- based authentication. &nbsp; The globus-url-copy command used here should not be confused with the Globus online data transfer service.GWS Scannerhttps://jellyfish-app-u7lat.ondigitalocean.app/docs/short-term-project-storage/gws-scanner/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/short-term-project-storage/gws-scanner/Introduction &nbsp; This article explains about the process that runs in the background scanning all group workspaces to gather basic information about usage, which are fed into a database to be made available to users via the GWS Scanner User Interface.hpxfer access rolehttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/hpxfer-access-role/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/hpxfer-access-role/This article explains about access to high-performance data transfer services. Applying for access &nbsp; Some data transfer services are hosted in the JASMIN Data Transfer Zone for increased performance.JASMIN external connectionshttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/jasmin-external-connections/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/jasmin-external-connections/NOTE [January 2021] This article is now out of date. Some terminology, names and components are no longer current. A newer version will be posted here in due course.JASMIN Notebooks Servicehttps://jellyfish-app-u7lat.ondigitalocean.app/docs/interactive-computing/jasmin-notebooks-service/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/interactive-computing/jasmin-notebooks-service/The JASMIN Notebooks Service provides access to Jupyter Notebooks in the web browser. -What is a Jupyter Notebook? &nbsp; A Jupyter Notebook is an interactive document containing live code and visualisations that can be viewed and modified in a web browser.rsync, scp, sftphttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/rsync-scp-sftp/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/rsync-scp-sftp/This article tells you about some of the basic transfer tools available for use with JASMIN that work over an SSH connection:Slurm queueshttps://jellyfish-app-u7lat.ondigitalocean.app/docs/batch-computing/slurm-queues/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/batch-computing/slurm-queues/This article introduces the Slurm scheduler queues/partitions for batch job submissions to the LOTUS and ORCHID clusters. +What is a Jupyter Notebook? &nbsp; A Jupyter Notebook is an interactive document containing live code and visualisations that can be viewed and modified in a web browser.rsync, scp, sftphttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/rsync-scp-sftp/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/rsync-scp-sftp/This article tells you about some of the basic transfer tools available for use with JASMIN that work over an SSH connection:Scheduling/Automating Transfershttps://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/scheduling-automating-transfers/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/data-transfer/scheduling-automating-transfers/This article explains how to schedule or automate data transfers. It covers: +Scheduling download tasks using cron and LOTUS Using Globus for transfer automation Overview &nbsp; In many cases it can be useful to fetch data from an external source for processing/analysis on JASMIN on a regular basis, for example &ldquo;every Monday at 11:00 fetch all last week&rsquo;s data&rdquo;.Slurm queueshttps://jellyfish-app-u7lat.ondigitalocean.app/docs/batch-computing/slurm-queues/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/batch-computing/slurm-queues/This article introduces the Slurm scheduler queues/partitions for batch job submissions to the LOTUS and ORCHID clusters. Queue names &nbsp; The Slurm queues in the LOTUS cluster are:Using the JASMIN Object Storehttps://jellyfish-app-u7lat.ondigitalocean.app/docs/short-term-project-storage/using-the-jasmin-object-store/Mon, 01 Jan 0001 00:00:00 +0000https://jellyfish-app-u7lat.ondigitalocean.app/docs/short-term-project-storage/using-the-jasmin-object-store/This article describes how to use the JASMIN high-performance object storage. What is object storage? &nbsp; An object store is a data storage system that manages data as objects referenced by a globally unique identifier, with attached metadata. \ No newline at end of file diff --git a/js/main.bundle.min.d81bc1047107f00af7e79bd736cf5cb47a277a0439e6aa138a2c9345d700e82a.js b/js/main.bundle.min.b7e7e0d18bc5eb51141801267a5f0c4190fc2269b412a4dedf224afa399181d8.js similarity index 99% rename from js/main.bundle.min.d81bc1047107f00af7e79bd736cf5cb47a277a0439e6aa138a2c9345d700e82a.js rename to js/main.bundle.min.b7e7e0d18bc5eb51141801267a5f0c4190fc2269b412a4dedf224afa399181d8.js index 926c2c967..e54d9a6b0 100644 --- a/js/main.bundle.min.d81bc1047107f00af7e79bd736cf5cb47a277a0439e6aa138a2c9345d700e82a.js +++ b/js/main.bundle.min.b7e7e0d18bc5eb51141801267a5f0c4190fc2269b412a4dedf224afa399181d8.js @@ -359,7 +359,7 @@ import sys import subprocess as sp packages = ['pyjokes'] sp.check_call( To create a conda environment, sinply run the following at the JASMIN Notebooks shell: conda create --name name-insert-here ipykernel Install any packages you which to use in the environment: conda install --name name-insert-here pyjokes Make the notebook service recognise your environment as a kernel: -conda run --name name-insert-here python -m ipykernel install --user --name name-insert-here Can get rid of old kernels from the notebook service?   Yes. +conda run --name name-insert-here python -m ipykernel install --user --name name-insert-here Can I get rid of my old kernels from the notebook service?   Yes. To list the names of kernels you have installed, run the following at the JASMIN notebook’s shell: jupyter kernelspec list To remove one of them, run: jupyter kernelspec uninstall insert-name-here `}).add({id:24,tag:"en",href:"/docs/software-on-jasmin/creating-and-using-miniconda-environments/",title:"Creating and using miniconda environments",description:"Creating and using miniconda environments",content:`On JASMIN, we provide a wide range of packages via the Jaspy environment (which is itself a Conda environment). This page gives detail on how to create and use your own personal Conda environments via the miniconda installer, as an alternative to the use of Jaspy. @@ -1475,23 +1475,28 @@ R --version Here are commands to do a simple plot to a file, which you can use t png("myplot.png") x <- c(1,2,3,4) y <- x*x plot(x,y) dev.off() (You could use the “display” command on JASMIN to view the output file.) Here is a minimal example of using the “library” command to load one of the many add-on libraries that have been installed to supplement the core R distribution. It uses the “prettyunits” package to convert a number of bytes to human-readable format. [username@sci3.jasmin.ac.uk ~]$ module load jasr [username@sci3.jasmin.ac.uk ~]$ R --quiet > library(prettyunits) > pretty_bytes(12345678) [1] "12.35 MB" > `}).add({id:95,tag:"en",href:"/docs/data-transfer/scheduling-automating-transfers/",title:"Scheduling/Automating Transfers",description:"Scheduling/Automating Transfers",content:`This article explains how to schedule or automate data transfers. It covers: -Scheduling download tasks using cron and LOTUS Using Globus for transfer automation [TODO] Overview   In many cases it can be useful to fetch data from an external source for processing/analysis on JASMIN on a regular basis, for example “every Monday at 11:00 fetch all last week’s data”. It can also be helpful to distribute the task downloading of some large datasets, or simply to be able rely on data being pulled in from some external source to an accumulating dataset used for periodic analysis. -Using Globus for transfer automation   It is easy to automate transfers using Globus. This method has the advantage that you do not need to remain connected or logged in to any JASMIN server for the automated transfers to take place on your behalf, and is more efficient and reliable than the other methods described below. +Scheduling download tasks using cron and LOTUS Using Globus for transfer automation Overview   In many cases it can be useful to fetch data from an external source for processing/analysis on JASMIN on a regular basis, for example “every Monday at 11:00 fetch all last week’s data”. It can also be helpful to distribute the task downloading of some large datasets, or simply to be able rely on data being pulled in from some external source to an accumulating dataset used for periodic analysis. +Using Globus for transfer automation   It is easy to automate transfers using Globus. This method has the advantage that you do not need to remain connected or logged in to any JASMIN server for the automated transfers to take place on your behalf, and the transfer itself can be more efficient than other methods described below. Some introductory information about how to do this is available in this article Using the Globus command-line interface (with more to follow) but please also refer to the comprehensive Globus documentation and their automation examples. You can choose whether to schedule/automate tasks via the Globus web interface, command-line interface, or use their Globus SDK to build Python code that uses this functionality. -Scheduling download tasks using cron and LOTUS   While the cron server is provided for scheduling tasks, it should not be used for the work of executing those tasks itself. So we need a way for a task to be invoked from cron but executed where there is lots of processing resource (i.e. LOTUS). -In the examples below, we use the test queue (or partition, as queues are known in SLURM). You can use this for testing, but once you know roughly how long your download(s) should take, you should choose an appropriate queue so that the jobs can be scheduled in a fair way alongside other users’ jobs. -1. Single download script   The simple script below is used to download a single file from an external source via HTTP using wget: -#!/bin/bash #SBATCH --partition=test #SBATCH -o %j.out #SBATCH -e %j.err #SBATCH --time=00:30 # executable wget -q -O 1MB_$SLURM_JOBID.zip http://speedtest.tele2.net/1MB.zip In this example, the file is labelled with the id of the job which downloaded it, e.g. 1MB_61117380.zip +Scheduling download tasks using cron and LOTUS   While the cron server cron.jasmin.ac.uk is provided for scheduling general tasks, it should not be used for the work of executing those tasks itself, and not for transfer tasks. +xfer3 - transfer machine with cron   The transfer server xfer3.jasmin.ac.uk is also provided with cron, and should be used where a task is primarily a transfer rather than a processing task and needs the functionality of a transfer server. For access to xfer3 you will need the xfer-sp access role  . Please refer to the above cron guidance for best practice advice. +invoking LOTUS from cron to carry out multiple download tasks   Sometimes we need a tasks to be invoked from cron but executed where there are lots of nodes to parallelise the tasks (i.e. the LOTUS cluster). In this case, we DO need to use the cron server rather than xfer3, since we need to be able to talk to LOTUS (xfer3 can’t do that, as a transfer server). +This will only work where the download can happen over HTTP(S), so depends on how the remote data is made available. +We need it to: +invoke a job submission script at regular intervals have that script initiate downloads using LOTUS nodes In the examples below, we use the test queue (or partition, as queues are known in SLURM). You can use this for testing, but once you know roughly how long your download(s) should take, you should choose an appropriate queue so that the jobs can be scheduled in a fair way alongside other users’ jobs. +1. Single download script   The simple script below is used to download a single file from an external source via HTTP using wget. It initially uses the test partition (queue), but once you had tested it, you would need to use a more appropriate queue. +#!/bin/bash #SBATCH --partition=test #SBATCH -o %j.out #SBATCH -e %j.err #SBATCH --time=00:30 # executable wget -q -O 1MB_$SLURM_JOBID.zip http://speedtest.tele2.net/1MB.zipIn this example, the file is labelled with the id of the job which downloaded it, e.g. 1MB_61117380.zip The same could be also achieved using curl, or using a Python script making use of (for example) the requests library. A note about transfer tools: since we are delegating the actual download task to a LOTUS node, we are restricted to transfer tools already installed on those nodes or available in the user’s path at a location cross-mounted with nodes in the LOTUS cluster (see Table 1 in Access to Storage), such as $HOME or a group workspace. It is not possible for the JASMIN team to install specialist data transfer tools across the whole cluster, so you may be limited to downloading via HTTP(S), FTP, or via tools available via libraries in the Python environment such (which you do have access to and can easily customise to install additional libraries using virtual environments). +Due to networking limitations, LOTUS nodes cannot perform downloads using SSH-based methods, i.e. scp/rsync/sftp. Download tools installed on LOTUS nodes include: wget curl ftp (but not lftp) In our simple example above, we can subit this script to LOTUS from the command line with sbatch test_download.sh This could be invoked on a regular basis by adding a crontab entry like this -30 * * * * sbatch /home/users/username/test_download.sh However it would be safer to wrap this in a crontamer command like this to ensure one instance of the task had finished before the next started: (see Using cron for details) -30 * * * * crontamer -t 2h 'sbatch /home/users/username/test_download.sh' 2. Multi-node downloads   We could expand this example to download multiple items, perhaps 1 directory of data for each day of a month, and have 1 element of a job array handle the downloading of each day’s data. +30 * * * * sbatch /home/users/username/test_download.shHowever it would be safer to wrap this in a crontamer command like this to ensure one instance of the task had finished before the next started: (see Using cron for details) +30 * * * * crontamer -t 2h 'sbatch /home/users/username/test_download.sh' 2. Multi-node downloads   We could expand this example to download multiple items, perhaps 1 directory of data for each day of a month, and have 1 element of a job array handle the downloading of each day’s data. A few words of warning: Distributing download tasks as shown below can cause unintended side-effects. Here, we’re submitting an array of 10 download jobs, each initiating a request for a 1MB file which may well happen simultaneously. So we need to be confident that the systems and networks at either end can cope with that. It would be all too easy to submit a task to download several thousand large data files and cause problems for other users of JASMIN (and other users on its host institution’s network), or indeed at the other end. Taken to the extreme, this could appear over the network as a Distributed Denial-of-Service (DDoS) attack. As with all LOTUS tasks: start small, test, and increase to sensible scales when you are confident it will not cause a problem. A limit of 10 jobs would be a sensible maximum, for one user. We’ll simulate this here by downloading the same external file to 10 different output files, but you could adapt this concept for your own purposes depending on the layout of the source and destination data. -#!/bin/bash #SBATCH --partition=test #SBATCH -o %A_%a.out #SBATCH -e %A_%a.err #SBATCH --time=00:30 #SBATCH --array=1-10 #SBATCH --time=00:30 # executable wget -q -O 1MB_$SLURM_ARRAY_TASK_ID.zip http://speedtest.tele2.net/1MB.zip echo "script completed" In this (perhaps contrived) example, we’re setting up an array of 10 elements and using the SLURM_ARRAY_TASK_ID environment variable to name the output files (otherwise they’d all be the same). In a real-world example you could apply your own logic to divide up files or directories matching certain patterns to become elements of a job array. +#!/bin/bash #SBATCH --partition=test #SBATCH -o %A_%a.out #SBATCH -e %A_%a.err #SBATCH --time=00:30 #SBATCH --array=1-10 #SBATCH --time=00:30 # executable wget -q -O 1MB_$SLURM_ARRAY_TASK_ID.zip http://speedtest.tele2.net/1MB.zip echo "script completed"In this (perhaps contrived) example, we’re setting up an array of 10 elements and using the SLURM_ARRAY_TASK_ID environment variable to name the output files (otherwise they’d all be the same). In a real-world example you could apply your own logic to divide up files or directories matching certain patterns to become elements of a job array. The script could then be scheduled to be invoked at regular intervals as shown in (1). Some tools provide functionality for mirroring or synchronising directories, i.e. only downloading those files in a directory which are new have been added since the last time a task was run. These can be useful to avoid repeated downloads of the same data. `}).add({id:96,tag:"en",href:"/docs/interactive-computing/sci-servers/",title:"Scientific analysis servers",description:"Scientific analysis servers",content:` Intro   Once you have logged on to one of the login servers you can then ssh to a scientific analysis (sci) server to do your work. The sci servers are not directly accessible outside the firewall of RAL (JASMIN’s host instution) so most users will need to access them via a login server. diff --git a/sitemap.xml b/sitemap.xml index c10ab1a48..b9ab4526e 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1 +1 @@ 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