Differences

This shows you the differences between two versions of the page.

--- exercises:2016_uzh_cmest:first_simulation_run [2016/09/21 10:29] – [Part I: Login] tmueller
+++ exercises:2016_uzh_cmest:login [2016/09/22 09:06] – [Make module loading persistent] tmueller
@@ Line 1: / Line 1: @@
-====== 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 =====
@@ Line 19: / Line 19: @@
   * 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 login and browser your home directory
+    * 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.
+  * 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.
-<note important>Change the password of your account after your first login using:
+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
@@ Line 62: / Line 64: @@
 <code>
-$ cp2k.popt --help
+$ cp2k.sopt --help
 </code>
@@ Line 68: / Line 70: @@
 <code>
- cp2k.popt [-c|--check] [-e|--echo] [-h|--help] [--html-manual]
+ cp2k.sopt [-c|--check] [-e|--echo] [-h|--help] [--html-manual]
            [-i] <input_file>
            [-mpi-mapping|--mpi-mapping] <method>
@@ Line 76: / Line 78: @@
  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:
@@ Line 99: / Line 101: @@
   --xml             : dumps the whole CP2K input structure as a XML file
                       xml2htm generates a HTML manual from this XML file
+</code>
+Another program we need for visualization is [[http://www.ks.uiuc.edu/Research/vmd/|VMD]].
+Load the respective module (since there is only one version available, the shorthand ''vmd'' can be used when specifying the module to load) and start it using:
+<code>
+$ vmd
+</code>
+Two new windows named ''VMD Main'' and ''VMD 1.9.2 ... Display'' should open on your local machine while the server shows:
+<code>
+Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
+Info) http://www.ks.uiuc.edu/Research/vmd/
+Info) Email questions and bug reports to vmd@ks.uiuc.edu
+Info) Please include this reference in published work using VMD:
+Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
+Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
+Info) -------------------------------------------------------------
+Info) Multithreading available, 32 CPUs detected.
+Info) Free system memory: 256213MB (99%)
+Warning) Detected a mismatch between CUDA runtime and GPU driver
+Warning) Check to make sure that GPU drivers are up to date.
+Info) No CUDA accelerator devices available.
+Warning) Detected X11 'Composite' extension: if incorrect display occurs
+Warning) try disabling this X server option.  Most OpenGL drivers
+Warning) disable stereoscopic display when 'Composite' is enabled.
+libGL error: failed to load driver: swrast
+libGL error: Try again with LIBGL_DEBUG=verbose for more details.
+Info) OpenGL renderer: GeForce GTX 760 (192-bit)/PCIe/SSE2
+Info)   Features: STENCIL MSAA(4) MDE MTX NPOT PP PS
+Info)   GLSL rendering mode is NOT available.
+Info)   Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (4)
+Info) Dynamically loaded 2 plugins in directory:
+Info) /sw/build/generic/app/vmd/vmd-1.9.2/lib/vmd/plugins/LINUXAMD64/molfile
+vmd >
+</code>
+If you only get the output on the server but not the 2 windows there is something wrong with your setup and you should check the lecture notes again. You can exit VMD by either closing the ''VMD Main'' or by giving the ''quit'' command at the ''vmd >'' prompt:
+<code>
+vmd > quit
 </code>
@@ Line 104: / Line 149: @@
+===== 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''. For example:
+<code>
+$ module initadd vmd
+$ module initadd cp2k/r17408_2016_09_19
+</code>
+to remove ''vmd'' from the list of modules to load at login:
+<code>
+$ module initrm vmd
+</code>