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exercises:2016_uzh_cmest:login [2016/09/21 10:53]
tmueller [Part I: Login]
exercises:2016_uzh_cmest:login [2016/09/22 09:48] (current)
tmueller
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-====== ​Your first simulation ​======+====== ​First Login ======
  
-In this exercise you will learn how to run your first calculation.+In this exercise you will learn how to login and run commands on our infrastructure.
  
 ===== Part I: Login ===== ===== Part I: Login =====
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   * a file transfer tool to copy files from/to the server:   * a file transfer tool to copy files from/to the server:
-    * on Linux: put ''​sftp:​////​tcopt3.chem.uzh.ch''​ as the address in your file browser and you should be able to browse your home directory after logging in+    * on Linux: put ''​%%sftp://​tcopt3.chem.uzh.ch%%''​ as the address in your file browser and you should be able to browse your home directory after logging in
     * on Mac OS X/OSX/macOS Sierra: use [[https://​cyberduck.io/​|Cyberduck]]     * on Mac OS X/OSX/macOS Sierra: use [[https://​cyberduck.io/​|Cyberduck]]
     * one Windows: use [[https://​winscp.net/​|WinSCP]] or [[https://​cyberduck.io/​|Cyberduck]]     * one Windows: use [[https://​winscp.net/​|WinSCP]] or [[https://​cyberduck.io/​|Cyberduck]]
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 <​code>​ <​code>​
-$ cp2k.popt --help+$ cp2k.sopt --help
 </​code>​ </​code>​
  
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 <​code>​ <​code>​
- cp2k.popt [-c|--check] [-e|--echo] [-h|--help] [--html-manual]+ cp2k.sopt [-c|--check] [-e|--echo] [-h|--help] [--html-manual]
            [-i] <​input_file>​            [-i] <​input_file>​
            ​[-mpi-mapping|--mpi-mapping] <​method>​            ​[-mpi-mapping|--mpi-mapping] <​method>​
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  ​starts the CP2K program, see <​https://​www.cp2k.org/>​  ​starts the CP2K program, see <​https://​www.cp2k.org/>​
  
- The easiest way is cp2k.popt <​input_file>​+ The easiest way is cp2k.sopt <​input_file>​
  
  The following options can be used:  The following options can be used:
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 +===== Part III: Advanced account configuration =====
 +
 +==== Make module loading persistent ====
 +
 +Upon login, the shell (''​bash''​ in our case) executes a number of files if they exist. One of them is the ''​.bashrc''​. To prepare it for management using the the ''​module''​ command, simply execute the following **once**:
 +
 +<​code>​
 +$ echo '​module load ' >> ~/.bashrc
 +</​code>​
 +
 +after that you can add and remove modules to be loaded at startup using ''​module initadd''​ or ''​module initrm''​.
 +
 +To add ''​vmd''​ and ''​cp2k'',​ run for example:
 +
 +<​code>​
 +$ module initadd vmd
 +$ module initadd cp2k/​r17408_2016_09_19
 +</​code>​
 +
 +to remove ''​vmd''​ again from the list of modules to load:
 +
 +<​code>​
 +$ module initrm vmd
 +</​code>​
 +
 +Alternatively you can of course simply edit ''​.bashrc''​ using your favorite editor and add a line like ''​module load vmd cp2k/​r17408_2016_09_19''​ by yourself.
 +
 +==== Setup key-based authentication ====
 +
 +To avoid having to type the password every time you log in (and to increase the security), keys can be used for authentication instead. The following instructions are **for OSX and Linux**.
 +
 +First generate a key-pair **on your local machine** using
 +
 +<​code>​
 +$ ssh-keygen
 +</​code>​
 +
 +and accept the defaults proposed and do not set a password.
 +
 +Upload the public key **from your local machine** to tcopt3:
 +
 +<​code>​
 +$ scp ~/​.ssh/​id_rsa.pub studentXX@tcopt3.chem.uzh.ch:​~/​
 +</​code>​
 +
 +Now login to ''​tcopt3.chem.uzh.ch''​ and move the uploaded public key to the right place:
 +
 +<​code>​
 +$ mkdir -p .ssh
 +$ chmod 0700 .ssh
 +$ mv id_rsa.pub .ssh/​authorized_keys
 +</​code>​
 +
 +When connecting to the server **from your local machine** now, use:
 +
 +<​code>​
 +$ ssh -i ~/​.ssh/​id_rsa studentXX@tcopt3.chem.uzh.ch
 +</​code>​
 +
 +==== Simplify the login ====
 +
 +The following instructions apply **apply to OSX and Linux**.
 +
 +**On your local machine** add the following part to the file ''​.ssh/​config''​ in your home directory:
 +
 +<​code>​
 +Host tcopt3
 +  HostName tcopt3.chem.uzh.ch
 +  User studentXX
 +</​code>​
 +
 +after which you will be able to connect to ''​tcopt3''​ simply by using
 +
 +<​code>​
 +$ ssh tcopt3
 +</​code>​
 +
 +If you have setup key-based authentication as shown above, augment the entry to the following instead, to always use key-based authentication without having to specify ''​-i ~/​.ssh/​id_rsa''​ manually:
 +
 +<​code>​
 +Host tcopt3
 +  HostName tcopt3.chem.uzh.ch
 +  User studentXX
 +  IdentityFile ~/​.ssh/​id_rsa
 +  IdentitiesOnly yes
 +  PreferredAuthentications publickey
 +</​code>​
exercises/2016_uzh_cmest/login.1474455196.txt.gz ยท Last modified: 2016/09/21 10:53 by tmueller