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Data Management and Transfer for Mimir-II

All large data sets - i.e. the data you will be working with - should go to your personal Mimir directory:

/hpcdata/Mimir/<uname>

Here and in the following, <uname> refers to your user account / login name.

You can also transfer data into a shared directory if there are more than one users working with the same data:

/hpcdata/Mimir/shared/

All Mimir-II users share the same group HTC-Mimir, which have access to the shared directory. After transferring file(s) data into the shared folder you need to change the ownership and permission:

[..]$ chown -R <uname>:HTC-Mimir /hpcdata/Mimir/shared/data

followed by:

[..]$ chmod -R 771 /hpcdata/Mimir/shared/data

which makes the file(s) read-write-executable by anyone in the group HTC-Mimir.

note

Contact the system administrator if you need to securely share data between certain users.

caution

Elja is not a data storage device! There is a finite amount of disk space. As a courtesy to the other users of Elja please remove large data sets after they have been processed. Large data which is left untouched for TBD months will be deleted.

Transferring Data from Mimir-I to Mimir-II#

When your account is active and you have logged into Elja (which hosts Mimir-II) you can use scp to transfer files from Mimir-I. For individual files:

[..]$ scp -p <mimir1username>@mimir.cs.hi.is:/nfs/bigdata/../data /hpcdata/Mimir/<uname>/.

and for directories with multiple files add -r (recursive):

[..]$ scp -p -r <mimir1username>@mimir.cs.hi.is:/nfs/bigdata/../data/ /hpcdata/Mimir/<uname>/.

Transferring Local Data To-and-From Mimir-II#

On a unix system the commands are more or less the same as above, and happen in a shell/terminal on the local computer.

From local-to-Elja:

[..]$ scp -p -r localdata/ <uname>@elja.hi.is:/hpcdata/Mimir/<uname>/.

From Elja-to-local:

[..]$ scp -p -r <uname>@elja.hi.is:/hpcdata/Mimir/<uname>/data/ .

For Windows it is recommended to make use of FileZilla or Cyberduck. See the section on Connecting and SSH keys for instructions on how to set up the SFTP connection.

caution

ALL data management should happen in the users personal or shared Mimir folder! Do not try to store large files in your home folder /users/home/<uname>. The system administrator reserves the right to remove large files from the /users/home/<uname> directory, without notice.