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  • getting started
    • get started with jasmin
    • generate ssh key pair
    • get jasmin portal account
    • get login account
    • beginners training workshop
    • how to contact us about jasmin issues
    • jasmin status
    • jasmin training accounts
    • tips for new users
    • how to login
    • multiple account types
    • present ssh key
    • reconfirm email address
    • reset jasmin account password
    • ssh auth
    • storage
    • understanding new jasmin storage
    • update a jasmin account
  • interactive computing
    • interactive computing overview
    • check network details
    • login servers
    • login problems
    • graphical linux desktop access using nx
    • sci servers
    • tenancy sci analysis vms
    • transfer servers
    • jasmin notebooks service
    • jasmin notebooks service with gpus
    • creating a virtual environment in the notebooks service
    • project specific servers
    • dask gateway
    • access from vscode
  • batch computing
    • lotus overview
    • slurm scheduler overview
    • slurm queues
    • lotus cluster specification
    • how to monitor slurm jobs
    • how to submit a job
    • how to submit an mpi parallel job
    • example job 2 calc md5s
    • orchid gpu cluster
    • slurm status
    • slurm quick reference
  • software on jasmin
    • software overview
    • quickstart software envs
    • python virtual environments
    • additional software
    • community software esmvaltool
    • community software checksit
    • compiling and linking
    • conda environments and python virtual environments
    • conda removal
    • creating and using miniforge environments
    • idl
    • jasmin sci software environment
    • jasmin software faqs
    • jaspy envs
    • matplotlib
    • nag library
    • name dispersion model
    • geocat replaces ncl
    • postgres databases on request
    • running python on jasmin
    • running r on jasmin
    • rocky9 migration 2024
    • share software envs
  • data transfer
    • data transfer overview
    • data transfer tools
    • globus transfers with jasmin
    • bbcp
    • ftp and lftp
    • globus command line interface
    • globus connect personal
    • gridftp ssh auth
    • rclone
    • rsync scp sftp
    • scheduling automating transfers
    • transfers from archer2
  • short term project storage
    • apply for access to a gws
    • elastic tape command line interface hints
    • faqs storage
    • gws etiquette
    • gws scanner ui
    • gws scanner
    • gws alert system
    • install xfc client
    • xfc
    • introduction to group workspaces
    • jdma
    • managing a gws
    • secondary copy using elastic tape
    • share gws data on jasmin
    • share gws data via http
    • using the jasmin object store
    • configuring cors for object storage
  • long term archive storage
    • ceda archive
  • mass
    • external access to mass faq
    • how to apply for mass access
    • moose the mass client user guide
    • setting up your jasmin account for access to mass
  • for cloud tenants
    • introduction to the jasmin cloud
    • jasmin cloud portal
    • cluster as a service
    • cluster as a service kubernetes
    • cluster as a service identity manager
    • cluster as a service slurm
    • cluster as a service pangeo
    • cluster as a service shared storage
    • adding and removing ssh keys from an external cloud vm
    • provisioning tenancy sci vm managed cloud
    • sysadmin guidance external cloud
    • best practice
  • workflow management
    • rose cylc on jasmin
    • using cron
  • uncategorized
    • mobaxterm
    • requesting resources
    • processing requests for resources
    • acknowledging jasmin
    • approving requests for access
    • working with many linux groups
    • jasmin conditions of use
  1.   Getting Started
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tips-for-new-users

 

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Tips for new users

On this page
“Sci” machines usage guidelines   LOTUS usage guidelines   Xfer servers guidelines   How to report an issue  

These tips for new users are based on users’ queries encountered by our helpdesk. They are not exhaustive but may help solve some initial problems and set out best practice.

  • Sci machines
  • LOTUS
  • Xfer servers
  • How to report an issue

“Sci” machines usage guidelines  

  1. Check the current load and number of users on the sci machines, as shown by the login servers, to select a less-used sci machine. The available Sci machines and their specifications are listed in the table of this help page
  2. The sci machines are not for running large, long-running tasks, or scripts that spawn multiple child processes. The batch processing cluster LOTUS is available for heavier processing. The sci machines are for development, testing, and light interactive use. Overloading these with processing seriously impairs performance for interactive use by others.
  3. Do not write to the temporary partition /tmpon sci machines. Use your home directory, a scratch volume or a Group Workspace . Any temporary data files can reside in a subdirectory of your group workspace instead of /tmp. To do this, please add the following lines (or similar) to your $HOME/.bashrc file:
export TMPDIR=/group_workspaces/jasmin/<your_project>/<your_username>/tmp
## create the directory if needed
[ -d $TMPDIR ] || mkdir -p $TMPDIR
  1. If a process hangs, do not simply close the terminal window. Please contact the helpdesk and alert the team so that the process can be shut down. Otherwise hung processes build up and contribute to machine overloading.
  2. Do not “hog” IDL development licenses. A limited number of these are available for development and compilation of IDL code which should then be run on LOTUS using IDL runtime licenses, of which there are many more.
  3. Do not use sci machines for data transfer: xfer hosts are provided for this purpose.

LOTUS usage guidelines  

  1. Do not use IDL development licences on LOTUS. There are many runtime licenses available, but the development licenses are for interactive use on the sci machines, where IDL code can be compiled, then run on LOTUS using a runtime license.
  2. Beware of inadvertently filling up /tmp on LOTUS nodes. This can take nodes out of action (perhaps for other users who still have jobs running on the same node) if /tmp fills up. Design your code to clean up as it goes along, and use environment variables to control where your applications write temporary data, ideally to storage which is not specific to a LOTUS node. If your job crashes, check which nodes were involved and clean up after yourself.
  3. Do not store data in scratch areas for long periods of time. Move data away to group workspaces once your processing has finished.

Xfer servers guidelines  

  1. Do not run a large number (>16) of rsync or scp transfer processes in parallel.
  2. Do not run processing on xfer servers: they are provided for data transfer only
  3. For heavy/high-performance data transfers, use Globus or one of the hpxfer servers.

How to report an issue  

When you do experience an issue, please;

  1. Make it clear whether you are simply advising the helpdesk of a general issue (which will be noted, but not necessarily investigated for a specific response), or
  2. Provide FULL and SPECIFIC details of your problem so that it can be investigated. JASMIN is a complex infrastructure with many hundreds of hosts and storage volumes, so reporting that “JASMIN” or “Storage” is slow, is not sufficient.
  3. If you are experiencing difficulties accessing a particular storage volume from a particular sci machine, please state:
    • the full path to the data you are trying to access:
    • the full hostname of the machine (but please try the same access from at least one other machine to help establish whether it’s related to the machine or the storage)
    • the date and time of the issue (for matching up with system reports/log files. Using the date and time of the email is not sufficient: please be specific in your report)
  4. Be patient: sometimes, queries will take longer to resolve if they are complex or if relevant staff are not available.
  5. Some issues will only be resolved by strategic improvements which are planned as part of phased upgrades to JASMIN accompanied by capital procurements followed by integration work, all carried out by the same, small team.
Last updated on 2024-09-05 as part of:  replacing refs using old syntax & tidied some other links (f03769a9c)
On this page:
“Sci” machines usage guidelines   LOTUS usage guidelines   Xfer servers guidelines   How to report an issue  
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