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--- exercises:2017_uzh_cp2k-tutorial:login [2017/06/26 08:06] – created jglan
+++ exercises:2017_uzh_cp2k-tutorial:login [2017/07/05 16:23] – [Module loading] Change CP2K version to load. agloess
@@ Line 21: / Line 21: @@
   * 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://tcopt6.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]]
     * one Windows: use [[https://winscp.net/|WinSCP]] or [[https://cyberduck.io/|Cyberduck]]
   * a plain text editor to edit input files if you are uncomfortable with using ''vim'', ''nano'' or ''emacs'' via SSH. Please note: It is important that your editor supports Unix line endings. If in doubt, use one of the mentioned editors on the server, or an advanced plain text editor like [[https://atom.io/|Atom]] (plus the [[https://atom.io/packages/line-ending-selector-unix|line-ending-selector-unix]] plugin) or [[https://notepad-plus-plus.org/|Notepad++]] on your local machine.
-Use the instructions giving in the lecture/available via OLAT to login on the server ''tcopt3.chem.uzh.ch'' using your assigned student account.
+Use the instructions giving in the lecture/available via OLAT to login on the server ''tcopt6.chem.uzh.ch'' using your assigned account.
-<note important>Change the password of your account after your first login, using:
-<code>
-$ passwd
-</code>
-</note>
 <note important>Login the remote machine using (if you use Linux or MacOS):
 <code>
-$ ssh -X username@tcopt3.chem.uzh.ch
+$ ssh -X username@tcopt6.chem.uzh.ch
 </code>
 </note>
-===== The bash terminal=====
-Many tasks in the following weeks will need to be performed on the terminal (or 'command line').
-<note tip>
-If you use Mac OS X:
-In order to keep the terminal in the dock also after you close it, right click on the symbol and select 'Options' -> 'keep in dock'.
-</note>
-Let's start with a list of useful commands -- just type them into the command line and confirm with ''RETURN''.
-<code bash>
-ls             # get list of files in the current directory
-mkdir molsim   # make directory 'molsim'
-cd             # change into your home directory
-cd molsim      # change into directory 'molsim'
-cd ..          # go up one directory
-pwd            # print path to the current working directory
-</code>
-Now it is time to copy some files from the teacher account.
-<code bash>
-cp ~student10/whatever.txt .               # copy 'whatever.txt' to you current folder
-scp your_username@remotehost.edu:foobar.txt /some/local/directory  #Copy the file "foobar.txt" from a remote host to the local host
-scp foobar.txt your_username@remotehost.edu:/some/remote/directory #Copy the file "foobar.txt" from the local host to a remote host
-</code>
-After this, please close and reopen your terminal in order to activate the course-specific
-settings you copied.
-We are now ready to get started. Below you find some additional commands that will come in handy later.
-<code bash>
-vim myfile      # opens 'myfile' in vim (less intuitive but more powerful command line text editor)
-vi myfile       # opens 'myfile' in vim (less intuitive but more powerful command line text editor)
-</code>
@@ Line 106: / Line 62: @@
 <code>
-$ module load cp2k/r17408_2016_09_19
+$ module load cp2k/r17968_2017_06_27
 </code>
@@ Line 157: / Line 113: @@
 <code>
 $ cp2k.sopt -i cp2k.inp -o cp2k.out &
+$ mpirun -n $NUM_PROC cp2k.popt -i cp2k.inp -o cp2k.out &
 </code>
@@ Line 205: / Line 162: @@
-===== Part III: Advanced account configuration =====
-==== Make module loading persistent ====
-Upon login, the shell (''bash'' in our case) executes a number of files if they exist. One of them is the ''.bashrc''. To prepare it for management using the the ''module'' command, simply execute the following **once**:
-<code>
-$ 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>