converted more getting started pages

account/huquota.md

+# How to get a local account on Star
+
+## To get a local account on Star, you need to provide us with:
+
+-   Your full name, date of birth, and nationality.
+-   Your position (master student, PhD, PostDoc, staff member,
+    visitor/guest).
+-   Your mobile phone number. This is necessary for recovery of
+    passwords.
+-   Your institutional mail address (i.e. your work email at the
+    research institution to which you belong)
+-   The name and address of the instruction you belong to; also
+    including name of the center, institute etc.
+-   A preferred username. Note: If you already have a Notur user account
+    name, please enter that one. A username is defined as a sequence of
+    two to thirty lowercase alphanumeric characters where the first
+    letter may only be a lowercase letter.
+-   Necessary additional group and account memberships.
+-   Optional: If you know in advance, please let us know: how many CPU
+    hours you expect to use, how much long-term storage space (GB) you
+    will need, and what software you will use. Partial answers are also
+    welcome. The more we know about the needs of our users, the better
+    services we can provide and the better we can plan for the future.
+
+**If you are a staff member and need to get a local project,** we need information about the project:  
+-   Name of the project
+-   Brief description of the project
+-   Field of science for the project
+-   Name of additonal members of the project
+
+**If you are a student, PhD or post-doc,** you need to also provide us
+with the name of your advisor and name of the project you are to be a
+member of.
+
+Compile this list in a proper manner and send to <starhpc-support@hofstra.edu>
+with a comment that the application is for a local account on Star.

account/login.md

+# Logging in for the first time
+
+## Log in with SSH
+
+An *SSH* client (Secure SHell) is the required tool to connect to
+Star. An *SSH* client provides secure encrypted communications between
+two hosts over an insecure network.
+
+If you already have *ssh* installed on your UNIX-like system, have a
+user account and password on a Notur system, login may be as easy as
+typing
+
+    ssh <machine name>         (for instance: ssh star.hofstra.edu)
+
+into a terminal window.
+
+If your user name on the machine differs from your user name on the
+local machine, use the -l option to specify the user name on the machine
+to which you connect. For example:
+
+    ssh <machine name> -l [username]
+
+And if you need X-forwarding (for instance, if you like to run Emacs in
+it's own window) you must log in like this:
+
+    ssh -X -Y <machine name>
+
+No matter how you login, you will need to confirm that the connection
+shall be trusted. The SHA256 key fingerprint of `star.hofstra.edu` is:
+
+    SHA256:YJpwZ91X5FNXTc/5SE1j9UR1UAAI4FFWVwNSoWoq6Hc
+
+So you should get precisely this message the first time you login via
+ssh:
+
+    The authenticity of host 'star.hofstra.edu (129.242.2.68)' can't be established.
+    RSA key fingerprint is SHA256:YJpwZ91X5FNXTc/5SE1j9UR1UAAI4FFWVwNSoWoq6Hc.
+    Are you sure you want to continue connecting (yes/no)?
+
+If you see this message with precisely this code, you can continue by
+typing `yes` and pressing *Enter*. If you connect to Star for the
+first time and ssh does *not* show you this key, please contact
+<starhpc-support@hofstra.edu> immediately.
+
+### Log in with an ssh key
+
+To avoid entering your password every time you login and to increase
+security, you can log in with an ssh keypair. This keypair consists of a
+private key that you have to store on your computer and a public key
+that you can store on Star. On Linux or OSX simply type:
+
+    ssh-keygen
+
+and follow the instructions on the screen. Please use a good passphrase.
+You will have to enter this passphrase the first time you log in after a
+reboot of the computer, but not anymore afterwards. To copy the public
+key to Star, type:
+
+    ssh-copy-id <username>@star.hofstra.edu
+
+To learn more about ssh keys, have a look at
+[this](https://wiki.archlinux.org/index.php/SSH_keys) page.
+
+On Windows, you can use PuTTYgen that comes with PuTTY. More information
+on [ssh.com](https://www.ssh.com/ssh/putty/windows/puttygen).
+
+### SSH clients for Windows and Mac
+
+At the [OpenSSH page](https://www.openssh.com) you will find several
+*SSH* alternatives for both Windows and Mac.
+
+Please note that Mac OS X comes with its own implementation of
+*OpenSSH*, so you don't need to install any third-party software to take
+advantage of the extra security *SSH* offers. Just open a terminal
+window and jump in.
+
+### Learning more about SSH
+
+To learn more about using SSH, please also consult the [OpenSSH
+page](https://www.openssh.com) page and take a look at the manual page
+on your system (*man ssh*).
+
+## Obtain a new password
+
+When you have been granted an account on star.hofstra.edu, your username
+and password is sent to you separately. The username by email and the
+password by SMS. The password you receive by SMS is temporally and only
+valid for 7 days.
+
+### The passwd command does not seem to work. My password is reset back to the old one after a while. Why is this happening?
+
+The Star system is using a centralised database for user management.
+This will override the password changes done locally on Star.
+
+The password can be changed
+[here](https://www.metacenter.no/user/password/), log in using your
+username on star and the NOTUR domain.
+
+## Logging on the compute nodes
+
+Information on how to log in on a compute node.
+
+Some times you may want to log on a compute node (for instance to check
+out output files on the local work area on the node), and this is also
+done by using SSH. From star.hofstra.edu you can log in to compute-x-y the
+following way:
+
+    ssh -Y compute-x-y     (for instance: ssh compute-5-8)
+
+or short
+
+    ssh -Y cx-y        (for instance: ssh c5-8)
+
+If you don't need display forwarding you can omit the "-Y" option above.
+
+If you for instance want to run a program interactively on a compute
+node, and with display forwarding to your desktop you should in stead do
+something like this:
+
+1.  first login to Star with display forwarding,
+2.  then you should reserve a node through the queuing system
+
+Below is an example on how you can do this:
+
+    1) Log in on Star with display forwarding.
+
+       $ ssh -Y star.hofstra.edu
+
+    2) Reserve and log in on a compute node with display forwarding.
+       (start an interactive job.)
+
+       $ srun -N 1 -t 1:0:0 --pty bash -i
+
+    3) Open a new terminal window, type squeue -j <jobid> (it shows you which node(s) was allocated
+       to that specific job). Then ssh -Y <nodename> to that node and start your preferred gui.
+
+## Graphical logon to Star
+
+If you want to run applications with graphical user interfaces we
+recommend you to use the [remote desktop
+service](http://star-gui.hofstra.edu/vnc/) on Star.
+
+If you have a new account and you have never logged in on Star before,
+first log in with a classical ssh connection (see above). Afterwards you
+can use the graphical logon. Otherwise it can happen that your /home
+will not be created and you will get an error message of the type:
+"Could not chdir to home directory /home/your_user_name: No such file or
+directory"
+
+**Important:**
+
+If you are connecting from outside the networks of UNINETT and partners
+you need to log into star-gui.hofstra.edu with ssh to verify that you have
+a valid username and password on the Star system. After a successful
+login the service will automatically allow you to connect from the
+ip-address your client currently has. The connection will be open for at
+least 5 minutes after you log in. There is no need to keep the
+ssh-connection open after you have connected to the remote desktop, in
+fact you will be automatically logged off after 5 seconds.

star/getting_started.md

+# Getting started
+
+Here you will get the basics to work with Stallo. Please study carefully
+the links at the end of each paragraph to get more detailed information.
+
+## Get an account
+
+If you are associated with UiT The Arctic University of Norway, you may
+apply locally. `/account/uitquota`
+
+You can also apply for an account for Stallo or any of the other
+Norwegian computer clusters at the [Metacenter account
+application](https:/www.metacenter.no/user/application/form/notur/).
+This is also possible if you already have a local account.
+`/account/account`
+
+## Change temporary password
+
+The password you got by SMS has to be changed on
+[MAS](https://www.metacenter.no/user/login/?next=/user/password/) within
+one week, or else the loginaccount will be closed again - and you need
+to contact us for reopening. You can't use the temporary password for
+logging in to Stallo.
+
+## Connect to Stallo
+
+You may connect to Stallo via *SSH* to `stallo.uit.no`. This means that
+on Linux and OSX you may directly connect by opening a terminal and
+writing `ssh username@stallo.uit.no`. From Windows, you may connect via
+PuTTY which is available in the Software Center. X-forwarding for
+graphical applications is possible. There exists also a webinterface to
+allow easy graphical login. Please see the following link for details to
+all mentioned methods. `/account/login`
+
+## On nodes and files
+
+When you login, you will be on a login node. Do *not* run any
+long-lasting programs here. The login node shall only be used for job
+preparation (see below) and simple file operations.
+
+You will also be in your home directory `/home/username`. Here, you have
+300 GB at your disposal that will be backed up regularly. For actual
+work, please use the global work area at `/global/work/username`. This
+space is not backed up, but it has a good performance and is 1000 TB in
+size. Please remove old files regularly. `/storage/storage`
+
+To move files from your computer to Stallo or vice versa, you may use
+any tool that works with *ssh*. On Linux and OSX, these are scp, rsync,
+or similar programs. On Windows, you may use WinSCP.
+`/storage/file_transfer`
+
+## Run a program
+
+There are many programs pre-installed. You may get a list of all
+programs by typing `module avail`. You can also search within that list.
+`module avail blast` will search for Blast (case-insensitive). When you
+found your program of choice, you may load it using
+`module load BLAST+/2.7.1-intel-2017b-Python-2.7.14`. All program files
+will now be available, i.e. you can now simply call `blastp -version` to
+run Blast and check the loaded version. You can also compile your own
+software, if necessary. `/software/modules`
+
+To eventually run the program, you have to write a job script. In this
+script, you can define how long the job (i.e. the program) will run and
+how much memory and compute cores it needs. For the actual computation,
+you need to learn at least the basics of Linux shell scripting. You can
+learn some basics here: `/account/linux`.
+
+When you wrote the job script, you can start it with
+`sbatch jobscript.sh`. This will put the script in the queue, where it
+will wait until an appropriate compute node is available. You can see
+the status of your job with `squeue -u username`. `/jobs/batch` and
+`/jobs/examples`
+
+Every job that gets started will be charged to your quota. Your quota is
+calculated in hours of CPU time and is connected to your specific
+project. To see the status of your quota account(s), type `cost`
+`/account/accounting`
+
+## Get help
+
+Do you need help with Stallo? Write us an email to
+<support@metacenter.no>. You can also request new software (either an
+update or entirely new software), suggest changes to this documentation,
+or send us any other suggestions or issues concerning Stallo to that
+email address. Please also read the rest of this documentation.
+
+Happy researching!