Uppsala Multidisciplinary Center for Advanced Computational Science

Bianca user guide

1. Set up 2 factor authentication

Follow the instuctions in Setting up two factor authetication.


2. Login

During the development phase, Bianca will only be accessible from another UPPMAX cluster. This might change once Bianca is in production.

The login procedure requires your to answer 2 separate password prompts. The first one logs you into the general Bianca login node (this is the step that requires 2 factor authentication), and the second one logs you into your projects private login node.

Start by connecting to the general Bianca login node. This step has to be done while being on one of the existing UPPMAX clusters (Rackham or Milou) login nodes, so make sure you are connected there before continuing.

The user name you will use is your ordinary UPPMAX user name, followed by the project ID of the project you want to work on. One of the security measures on Bianca is that all projects are kept separate on their own virtual clusters, so you will have to tell Bianca which project's cluster you want to connect to.

$ ssh -A <username>-<projid>@bianca.uppmax.uu.se
Ex.
$ ssh -A myname-sens2016999@bianca.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.

If the password is correct you will get a message about the login node being up and running. What happens now is that you are automatically redirected to login at your project's private login node. To be able to login there you will have to give your UPPMAX password once again, but without the 2 factor authentication code this time. If your password is "VerySecret" you would type in VerySecret as password in this step.

If the passwords have been entered correctly you should now be connected and you will see that the computer name at the start of the command line looks something like this:

[myuser@sens2016999-bianca ~]$

3. Transfer files to and from Bianca

Due to security, there is no internet access on Bianca so you can't download or upload files from the cluster. All files will be transferred through the wharf area of Bianca. The wharf has access to one of the folders in your project folder, but nothing else outside of it. The path to this folder once you are logged into your project's cluster will be

/proj/<projid>/nobackup/wharf/<username>/<username>-<projid>
Ex.
/proj/sens2016999/nobackup/wharf/myuser/myuser-sens2016999

There are two ways you can transfer files from the login node (Rackham or Milou) to Bianca.

The easy way:

The first and easiest is to start a graphical Filezilla window on the login node and handle all the transfers through that (see Filezilla user guide). 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: bianca-sftp.uppmax.uu.se
Port: 22
Protocol: SFTP
Logon Type: Ask for password
User name: <username>-<projid>
ex.
myuser-sens2016999
Password (you will be asked when connecting): uppmax password+2nd factor
ex.
VerySecret123456

Please note that in the wharf you only have access to upload your files to the directory that is named

<username>-<projid>
ex.
myuser-sens2016999

so you will want to go into that directory the first thing you do.

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 the wharf using the sftp program on one of the login nodes (Rackham or Milou).

$ sftp <username>-<projid>@bianca-sftp.uppmax.uu.se
Ex.
$ sftp myuser-sens2016999@bianca-sftp.uppmax.uu.se

Notice the different host name!

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.

Please note that in the wharf you only have access to upload your files to the directory that is named

<username>-<projid>
ex.
myuser-sens2016999

so you will want to cd to that directory the first thing you do.

sftp> cd myuser-sens2016999

Alternatively, you can specify this at the end of the sftp command, so that you will always end up in the correct folder directly.

$ sftp <username>-<projid>@bianca-sftp.uppmax.uu.se:<username>-<projid>
Ex.
$ sftp myuser-sens2016999@bianca-sftp.uppmax.uu.se:myuser-sens2016999