Insomnia - Working on Insomnia

Transferring Files

You can  use SCP (secure copy protocol) to transfer data and other program files between your local machine and Insomnia. Unix/Linux and Cygwin users can use the scp command, Windows users can use WinSCP, and Mac users can use SCP from the built-in Terminal just like Linux, or the free (for Education) program, Fetch.

Rsync is available too, though here we will cover scp.

For large file transfers we recommend the use of Globus, documented below.

This is how you would transfer "MyDataFile" to your home directory on the cluster using scp from a Mac or Linux command line.

$ scp MyDataFile <UNI>@insomnia.rcs.columbia.edu:~/

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, submit our request form to join Columbia's Globus subscription group (you will need to log in first - new users should select Columbia University from the drop-down). 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.

Copying files from Ginsburg or Terremoto

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.

Terremoto users can access their storage system (/moto) by navigating to /moto on the Insomnia login nodes.

Note that neither /burg nor /moto are accessible on Insomnia's compute nodes.

Managing Jobs

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

$ squeue

To view information about a particular job, use scontrol.

$ scontrol show job [job ID]

To cancel a job, use scancel.

$ scancel [job ID]

To view fair share information, use sshare.

$ sshare

Other useful commands 

Here's a partial list of useful Slurm commands.

sbatch       # submit a job

sinfo       # list of partitions/queues on the cluster

scontrol show job <jobID>      # see status of running job

sacct -j <jobID>      # see status of completed job

scontrol show node <nodeName>      # information about a node

sshare      # information about fair share

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:

$ group -c <GROUP_NAME>

To view group members and owners:

$ group -i <GROUP_NAME>

To add a user to a group:

$ group -m <GROUP_NAME> <UNI>

To remove a user from a group:

$ group -M <GROUP_NAME> <UNI>

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

$ group -o <GROUP_NAME> <UNI>

To remove an owner:

$ group -O <GROUP_NAME>

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.

$ groups
user burglab

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.

$ man chgrp
$ man chmod