SSH Keypair

Setting Up your local hosts for password-less login via SSH

This is a technology based on public-key cryptography.   The idea is to set up your desktop/laptop so that you are recognized by our login servers without you having to enter your password every time . In the documentation below your desktop/laptop is referred to as the “local host” and our login server(s) are referred to as the “remote host”. There is a one-time setup for each of the local hosts that you want to set up with keypair authentication.

Instructions for unix-based machines (e.g. linux and mac osx)

First, on your local laptop/desktop, cd into your home directory  and invoke the ssh key generator:

ssh-keygen -t rsa

You will be prompted for a passphrase.  For security reasons, we recommend that you use a passphrase to protect your key.  For the other questions, you can select the default values.

The key generator will put two files in the .ssh subdirectory of your home directory, i.e.  ~/.ssh/id_rsa and  ~/.ssh/ . The former contains your private key while the latter contains your public key. You should only ever have to run the ssh key generator once on your local host.  If you have already configured passwordless login and you run the key generator a second time, it will overwrite your previous public and private key files. This will break all password-less logins that you set up with your previous keys.

Next you want to copy your public key file to the remote host and append it to the authorized_keys file in the .ssh subdirectory of your home directory on the remote host (one of the jhpce login servers, e.g. jhpce01 – jhpce04). If there is no ~/.ssh directory in the remote host, you will need to login to the remote host and create a .ssh subdirectory in your home directory. You can perform the copy and append operations in one line as follows;

cat ~/.ssh/ | ssh <your_userid> \
'cat >> ~/.ssh/authorized_keys'

Where you replace <your_userid> with your JHPCE userid and where you enter your JHPCE password when you are prompted for it by ssh.

To test that everything is working you should be able to log into the remote host from your local host with the following command:

ssh <your_userid>

When you start ssh, you will be prompted for the passphrase that you used to protect your key.  To avoid having to enter your passphrase every time you use ssh, you can use the “ssh-agent” program.  To use ssh-agent, run

ssh-add  (you will be prompted for the passphrase you used)

You should now be able to use ssh without entering a password.  The ssh-agent will remain active for as long as your desktop or laptop is up and running.  If you reboot your desktop/laptop, you will need to rerun the ssh-add and ssh-agent commands.

Lastly, on the JHPCE cluster, you will need generate ssh keys within the cluster to allow you to qrsh between nodes without using a password.  The steps are similar to the steps for your laptop.  First, on the cluster, cd into the .ssh directory.  Once in the .ssh dirctory. run “ls -al” to see if you already have an id_rsa and file.  If you don’t have these files, generate them with the “ssh-keygen -t rsa”.  Finally append the file to the authorized_keys file.  The steps should look similar to the following example:

[jhpce01 /users/mmill116]$ cd .ssh

[jhpce01 /users/mmill116/.ssh]$ ls -al
total 854
drwx------ 2 mmill116 mmi 26 Feb 4 21:32 .
drwxr-x--- 153 mmill116 mmi 250 Feb 4 21:27 ..
-rw------- 1 mmill116 mmi 10939 Aug 26 11:03 authorized_keys
-rw-r--r-- 1 mmill116 mmi 11994 Dec 1 15:03 known_hosts

[jhpce01 /users/mmill116/.ssh]$ ssh-keygen -t rsa
Generating public/private rsa key pair.
Enter file in which to save the key (/users/mmill116/.ssh/id_rsa): 
Enter passphrase (empty for no passphrase): 
Enter same passphrase again: 
Your identification has been saved in /users/mmill116/.ssh/id_rsa.
Your public key has been saved in /users/mmill116/.ssh/
The key fingerprint is:
The key's randomart image is:
+---[RSA 2048]----+
| .++ooOO.    +++ |
| .+oo.++ o .+ .o.|
| .o.o. .+. o +  +|
[jhpce01 /users/mmill116/.ssh]$ ls -al
total 854
drwx------   2 mmill116 mmi      26 Feb  4 21:32 .
drwxr-x--- 153 mmill116 mmi     250 Feb  4 21:27 ..
-rw-------   1 mmill116 mmi   10939 Aug 26 11:03 authorized_keys
-rw-------   1 mmill116 mmi    1675 Feb  4 21:32 id_rsa
-rw-r--r--   1 mmill116 mmi     409 Feb  4 21:32
-rw-r--r--   1 mmill116 mmi   11994 Dec  1 15:03 known_hosts

[jhpce01 /users/mmill116/.ssh]$ cat >> authorized_keys

Fine points and troubleshooting

1. Many users set up an alias for the ssh command so they don’t have to type as much to log into the remote host. For example, suppose I want to setup my local host so all I have to do is type ‘hpc’ to log into the cluster, i.e.:


You can do this by adding the following line to your ~/.bashrc

alias hpc='ssh -X <your_userid>'

2. If you followed the directions and ssh is still asking for a password, then it is likely that the permissions of the  ~/.ssh directory (or the files in it) on the remote host, are not set correctly. To fix the permissions, execute the following command on the remote host:

chmod -R o-rwx ~/.ssh

Finally, if your changed the permissions of your .ssh directory and you are still being asked for a password, then perhaps the permissions on your home directory are such that others are allowed to write to it. If this is the case, then this needs to be changed so that only you can write to it. Contact bit support to have this changed.

Instructions for Windows machines 

If your desktop/laptop runs MIcrosoft Windows then you first need to install either puTTY or MobaXterm on your windows machine. If you are using MobaXterm, please use the steps at the bottom of the MobaXterm Configuration Page.   If you are using puTTY, you can follow the these directions:

1. Launch puttygen.exe.

2. Click “generate” and move your mouse around randomly in the blank area. Add a passphrase if you’d like, though this is not necessary. Click ‘Save private key’ and type in a file name.

3. Select and copy the text from  the area labeled “Public key for pasting into Open Ssh …”. Next SSH to jhpce01.

4. log into our login server using your password and cd to your .ssh directory.  Edit your “authorized_keys” file. Paste the text  you just copied into the end of your authorized_keys file and save it. Close puTTY.

5. Next create and save a session in puTTY.  Open up puTTY again. For the hostname type in In the left had panel click on “ssh” and then “auth”. Browse to you private key that saved earlier. In the left hand panel, click on “session” then under “saved session” type a name. Any name will do buy “” is memorable. Click on save.

You should only have to perform the setup steps (1-5) just once. From now on to get to get to jhpce01, open putty, load your saved session, and click on “open”.

You can create a shortcut for this by right clicking in a directory then “new” then “shortcut”. Have the target of the shortcut be:


For example, we use:

     "C:\Users\my_dirname\putty\PUTTY.EXE" -load ""

Now you can double click on that icon and it will automatically bring up a putty session on jhpce01 without requiring a password.

Configuring SSH Keys in Filezilla

– Open a Terminal window on your Mac
– Do you already have SSH keys? You can check by running “ls -la ~/.ssh/id_*”
– If you do not already have SSH keys for your account on your Mac, Run “ssh-keygen -t rsa” , and just hit “Enter” when prompted for questions.
– You will need to copy your public key to the JHPCE cluster, so on your mac. The easiest way is to run:
$ cat .ssh/ | ssh “cat >> ~/.ssh/authorized_keys”
– If you hadn’t set up ssh keys, this will allow you to ssh into the JHPCE cluster without a password. You can test this by running “ssh”

To then add your key to Filezilla:

– Start Filezilla, and go to “Filezilla” -> “Settings”
– In the Settings screen, go to “Connections -> SFTP”
– Click the “Add keyfile…” button
– You will need to go to the hidden .ssh directory on your Mac. To do so, press <CMD>-<SHIFT>-G . This will open the “Go to the folder” prompt.
– Enter “~/.ssh” , and click on “Go”
– Select “id_rsa”
– You will then get a Filezilla prompt about converting the file to a supported format. Click “Yes”
– Give the file a name (like JHPCE-rsa) , and click “Save”

– Now, in Filezilla, go to “File” -> “Site Manager” Click “New Site”
– In the Host field, enter (The transfer01 system should be used instead of jhpce01 for transferring files)
– For “Protocol”, select “SFTP
– For “Login Type”, select “Normal”
– For “User”, enter your JHPCE User ID.
– Clear out the “Password” field.
– On the left side, rename “New Site” to “JHPCE” (or something similar)
– Click “OK”

You can now connect to the JHPCE cluster using Filezilla by clicking “Connect” for that site.  There is a shortcut to the “Sites” list at the upper left corner of the main Filezilla screen.