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--- exercises:2017_uzh_acpc2:login [2017/04/11 10:51] – [The bash terminal] jglan
+++ exercises:2017_uzh_acpc2:login [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 3: / Line 3: @@
 In this exercise you will learn how to login and run commands on our infrastructure.
-====== The bash terminal======
+===== Part I: Login =====
+As mentioned in the lecture, you absolutely need
+  * a X11-Server:
+    * on Linux: it is enough to be logged-in in a graphical environment (Unity, Gnome, KDE, ...)
+    * on Mac OS X/OSX/macOS Sierra: you need [[https://www.xquartz.org/|XQuartz]]
+    * on Microsoft Windows: you need [[http://sourceforge.net/projects/xming/files/latest/download|XMing]]
+  * a terminal emulator:
+    * on Linux: this can be one of Konsole, Gnome Terminal, Terminal, XTerm, ...
+    * on Mac OS X/OSX/macOS Sierra: use the X-Windows terminal from XQuartz
+    * on Windows: use [[http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html|Putty]]
+optionally you may want:
+  * 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 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.
+<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
+</code>
+</note>
+===== The bash terminal=====
 Many tasks in the following weeks will need to be performed on the terminal (or 'command line').
@@ Line 17: / Line 56: @@
 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
-open .         # opens current directory in Finder (Mac OS X)
 </code>
@@ Line 26: / Line 66: @@
 <code bash>
-cd                                    # change into your home directory
-cp ~student10/.bashrc .               # copy course-specific system settings
+cp ~student10/whatever.txt .               # copy 'whatever.txt' to you current folder
-cd intro                              # change into directory 'intro'
 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
@@ Line 40: / Line 79: @@
 <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>
-(on Mac OS X): In order to take a screen shot, hit ''CMD''+ ''SHIFT'' + ''4''.
-===== Part I: Login =====
-As mentioned in the lecture, you absolutely need
-  * a X11-Server:
-    * on Linux: it is enough to be logged-in in a graphical environment (Unity, Gnome, KDE, ...)
-    * on Mac OS X/OSX/macOS Sierra: you need [[https://www.xquartz.org/|XQuartz]]
-    * on Microsoft Windows: you need [[http://sourceforge.net/projects/xming/files/latest/download|XMing]]
-  * a terminal emulator:
-    * on Linux: this can be one of Konsole, Gnome Terminal, Terminal, XTerm, ...
-    * on Mac OS X/OSX/macOS Sierra: use the X-Windows terminal from XQuartz
-    * on Windows: use [[http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html|Putty]]
-optionally you may want:
-  * 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 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.
-<note important>Change the password of your account after your first login, using:
-<code>
-$ passwd
-</code>
-</note>
 ===== Part II: Loading and running a program =====
@@ Line 142: / Line 152: @@
   --xml             : dumps the whole CP2K input structure as a XML file
                       xml2htm generates a HTML manual from this XML file
+</code>
+Now you can run cp2k using:
+<code>
+$ cp2k.sopt -i cp2k.inp -o cp2k.out &
 </code>