Page tree
Skip to end of metadata
Go to start of metadata

Transferring Files


You must use SCP (secure copy protocol) to transfer data and other program files between your local machine and Ginsburg. Unix/Linux and Cygwin users can use the scp command, Windows users can use WinSCP, and Mac users can use Fugu. For large file transfers we recommend the use of Globus, documented below.


Please use the server motion.rcs.columbia.edu when transferring files. 


For example, this is how you would transfer "MyDataFile" to the cluster using scp from the command line.


$ scp MyDataFile <UNI>@motion.rcs.columbia.edu:<DESTINATION_PATH>


If you specify no path after the colon, the file will end up in your home directory (no check for the existence of its older version is performed in this case).


Globus Connect (Under Construction)


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.


In order to avail yourself of Globus, you must first create an account (including your user name and password) by going to https://www.globus.org/signup. 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.


Ginsburg's Globus endpoint has not been activated yet.

Once it is available we will share information here on how to connect to it.


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 Ginsburg. 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 Habanero or Terremoto


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

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


Note that neither /rigel nor /moto are accessible on Ginsburg'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.eduThe 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 Ginsburg. Note also that in some cases group changes can take up to an hour to propagate to Ginsburg.


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
  • No labels