Uppsala Multidisciplinary Center for Advanced Computational Science

Grus user guide

0. PREREQUISITES

In order to  access the grus delivery service you need to have an UPPMAX account. You also need to have accepted the SNIC common user agreement in SUPR.

In addition, you need to be a member of a delivery project (these are called deliveryNNNNN where N represent a digit). SUPR will tell you if you are a member and the account page should list the account on the resource grus (this can also be useful to verify your username).


1. Set up 2 factor authentication

Follow the instuctions in Setting up two factor authetication.

Note that this is a second factor specific for UPPMAX. You may have set up two factor authentication for other sites (e.g. SUPR), but you can not use codes from that second factor for authenticating to UPPMAX.


2. Login

Note that grus only supports connections with sftp. If you connect with regular ssh you will be disconnected directly after authentication.

The user name you will use is your ordinary UPPMAX user name followed by a dash (-) followed by the project ID of the project you want to work on (e.g.
username-projectname).

One of the security measures on Grus is that all projects are kept separate, so you will have to tell Grus which project's folder you want to connect to.

As password you use your normal UPPMAX password directly followed by
the six digits from the second factor application from step 1 (these should change every thirty second, enter whatever is currently on display).

Ex. if your password is "VerySecret" and the second factor code is 123 456 you would type VerySecret123456 as the password in this step.

If the passwords have been entered correctly you should now be connected and you will see the files belonging to this project.

The easy way:

The easiest way to get your data is to start a graphical Filezilla window, either on your own computer or on the login node of the cluster you want to transfer your data to, and handle all the transfers through that (see Filezilla user guide). If you want to start it on a login node, this is done by connecting to the login node with Xforwarding enabled (the ability to transfer graphics over ssh). Just add a -Y to your ordinary ssh command you type when connecting to uppmax. This requires you to have some kind of Xserver installed on your own computer to be able to take care of the graphics that will be sent. If you have a Mac you can install XQuartz and Windows users can use MobaXterm.

$ ssh -Y <username>@<cluster>.uppmax.uu.se
ex.
$ ssh -Y myuser@milou.uppmax.uu.se

Once this is done, you start Filezilla by simply typing

$ filezilla

on the login node. This will open a graphical Filezilla window and you can start transferring the files. The server you want to tell Filezilla to connect to is (hint: you will want to open File - Site Manager, or ctrl+s, and add a new site, and then connect to it):

Host: grus.uppmax.uu.se
Port: 22
Protocol: SFTP
Logon Type: Ask for password
User name: <username>-<projid>
ex.
myuser-delivery999999
Password (you will be asked when connecting): uppmax password+2nd factor
ex.
VerySecret123456

Once connected you should see the files on Grus on the right hand side of the Filezilla windows and the files on the computer you are running Filezilla on on the left side. You can now drag and drop file either way to upload and download files.

The other (hard) way:

The other way to transfer files involve running SFTP on the command line and type all the commands yourself. This is only recommended for advanced users and only if Xforwarding for some reason is unavailable. You start off by connecting to Grus using the sftp program.

$ sftp <username>-<projid>@grus.uppmax.uu.se
Ex.
$ sftp myuser-delivery999999@grus.uppmax.uu.se

As password you use your normal UPPMAX password directly followed by
the six digits from the second factor application from step 1.

Ex. if your password is "VerySecret" and the second factor code is 123 456 you would type VerySecret123456 as the password in this step.

Once connected you will have to type the sftp commands to upload/download files. Have a look at the Basic SFTP commands guide to get started with it.