Insomnia - Working on Insomnia

Transferring Files

Insomnia will no longer support Direct File Transfers using SCP/SFTP protocols - Do not use File Transfer Clients such as FileZilla, CyberDuck, WinSCP, scp, sftp, etc... Instead, please use Globus. Globus offers a lot of features that direct file transfer does not such as auto recovery if your transfer was interrupted. This is particular useful when transferring huge amount of files. Also, Globus handles large amount of data transfer much better and faster. See Globus documentation below.

Globus Connect

Globus is a utility (technically, SaaS, or Software as a Service) which among others allows file transfer between personal computers and HPC clusters. It is particularly useful for fast and reliable transfer of very large files, as well as a large number of small files.

To transfer data to/from the HPC clusters, request a Globus account. Email globus@columbia.edu with any questions.

Globus moves data between "endpoints". An endpoint is a unique name representing a Globus resource like a computer or a cluster, typically in the following format: <globus-username>#<machine name>. The endpoints for the resources you'll be using for transferring data need to be added to your account.

Before connecting, you will need to create your own endpoint on the machine from which or to which you will be transferring data to and from Insomnia. In order to to this, you'll need to download and run 'Globus Connect Personal' as described in:

https://www.globus.org/globus-connect-personal

Choose between Mac, Linux, or Windows, and follow the instructions for the download.

Once you run the downloaded software, you will be able to, via the online interface, enter the two endpoints of your transfer, specify the paths of the files/directories on the source and destination systems, and launch the transfer. Once it starts, it will take place in the background and you do not need to supervise it or even be logged in. 

Globus is a fairly sophisticated system which allows you also to work via Command Line Interface and programming API, and has other useful features. For details, please visit the globusonline.org site.

Globus Guest Collection

Globus allows you to securely share folders through guest collections, letting collaborators access data without needing direct access to your storage system. You control permissions (read/write) and roles, but sharing is only available on subscription-enabled endpoints. Only folders (not individual files) can be shared, and you may need to enable sharing or adjust settings if the Share option is unavailable.

You can find instructions on Globus' documentation:

https://docs.globus.org/guides/tutorials/manage-files/share-files/

Copying files from Ginsburg

Users that have an account on the Ginsburg cluster may access Ginsburg's storage system (/burg) by navigating to the /burg directory on the Insomnia login nodes.

Note that /burg are accessible on Insomnia's compute nodes.

Managing Jobs

To view all jobs on the system, use the squeue command.

To view information about a particular job, use scontrol.

To cancel a job, use scancel.

To view fair share information, use share.

Other useful commands 

Here's a partial list of useful Slurm commands.

Each command on both systems is naturally replete with flags and optional arguments which customize its functionality. For reference on Slurm. please refer to:

Slurm reference

Using Groups for Collaborative Research

Researchers will often wish to share access to a set of directories and files with a group of users. One mechanism that can be used to accomplish this is Unix groups. Habanero users can create and modify groups without assistance from HPC support by using the group command on Cunix.

To use the group command log in to cunix.columbia.edu. The group command is not available on Habanero itself.

To create a new group:

To view group members and owners:

To add a user to a group:

To remove a user from a group:

Group owners can add and remove owners and users. To add a group owner:

To remove an owner:

Note that existing user sessions will not be affected by changes in group membership. If a user is added or removed from a group they will have to log out and log back in to Insomnia. Note also that in some cases group changes can take up to an hour to propagate to Insomnia.

There are many ways to view your group membership. One way is to use the groups command.

Once a group has been created and users have been added, group members can use the chgrp and chmod commands to set group ownership and permissions on files and directories to values appropriate for sharing. For more information see the manual pages for the two commands.