CP2K Open Source Molecular Dynamics

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exercises:2020_uzh_acpc2:login [2020/04/06 10:15] – created jglanexercises:2020_uzh_acpc2:login [2020/08/21 10:15] (current) – external edit 127.0.0.1
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     * on Linux: it is enough to be logged-in in a graphical environment (Unity, Gnome, KDE, ...)     * 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 to install [[https://www.xquartz.org/|XQuartz]]     * on Mac OS X/OSX/macOS Sierra: you need to install [[https://www.xquartz.org/|XQuartz]]
-    * on Microsoft Windows: you need to install [[http://sourceforge.net/projects/xming/files/latest/download|XMing]]+    * on Microsoft Windows: you need to install [[https://sourceforge.net/projects/vcxsrv/files/latest/download|VcXsrv]]
   * 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://tcopt2.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://tcopt2.chem.uzh.ch%%'' as the address in your file browser and you should be able to browse your home directory after logging in
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   * Connect to the server by entering the command: ''ssh -X studentXX@tcopt2.chem.uzh.ch''   * Connect to the server by entering the command: ''ssh -X studentXX@tcopt2.chem.uzh.ch''
  
-==== Login using Windows ====+==== Login using Windows with SSH (Windows 10 and later) ==== 
 + 
 +  * Connect to Internet (use VPN when not in the UZH network) 
 +  * Start VcXsrv (optional, only required if you want to run graphical applications on the server) 
 +  * Start the Powershell console 
 +  * Type the command ''ssh studentXY@tcopt2.chem.uzh.ch'' 
 +  * Enter (username and) password as requested 
 + 
 +==== Login using Windows with Putty ====
  
 First configure Putty (only required on the first run) as follows: First configure Putty (only required on the first run) as follows:
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   * Connect to Internet (use VPN when not on the UZH network)   * Connect to Internet (use VPN when not on the UZH network)
-  * Start Xming (optional, only required if you want to run graphical applications on the server)+  * Start VcXsrv (optional, only required if you want to run graphical applications on the server)
   * Start Putty   * Start Putty
   * Double click the session ''tcopt2'' to start the connection   * Double click the session ''tcopt2'' to start the connection
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 </note> </note>
  
-===== Part II: Loading and running a program ===== 
  
-==== Module loading ==== +===== Part II: Advanced account configuration =====
- +
-Since there are numerous applications with different and possibly conflicting requirements, the //module// system is used. This means that only basic commands are available until **explicitly** loaded. +
- +
-To list all available modules: +
- +
-<code> +
-$ module avail +
-</code> +
- +
-while using +
- +
-<code> +
-$ module list +
-</code> +
- +
-gives the list of loaded moules. +
- +
-To load the CP2K module used in this course, use: +
- +
-<code> +
-$ module load cp2k/r18057_2017_09_18 +
-</code> +
- +
-When you list the loaded modules again at this point (see command above), you will notice that the list has changed. +
- +
- +
-Now run the following command to verify that the CP2K executable is available: +
- +
-<code> +
-$ cp2k.sopt --help +
-</code> +
- +
-Which should give you the output +
- +
-<code> +
- cp2k.sopt [-c|--check] [-e|--echo] [-h|--help] [--html-manual] +
-           [-i] <input_file> +
-           [-mpi-mapping|--mpi-mapping] <method> +
-           [-o] <output_file> +
-           [-r|-run] [--xml] +
- +
- starts the CP2K program, see <https://www.cp2k.org/> +
- +
- The easiest way is cp2k.sopt <input_file> +
- +
- The following options can be used: +
- +
-  -i <input_file>   : provides an input file name, if it is the last +
-                      argument, the -i flag is not needed +
-  -o <output_file>  : provides an output file name [default: screen] +
- +
- These switches skip the simulation, unless [-r|-run] is specified: +
- +
-  --check, -c       : performs a syntax check of the <input_file> +
-  --echo, -e        : echos the <input_file>, and make all defaults explicit +
-                      The input is also checked, but only a failure is reported +
-  --help, -h        : writes this message +
-  --html-manual     : writes a HTML reference manual of the CP2K input +
-                      in the current directory. The file index.html is a good +
-                      starting point for browsing +
-  --license         : prints the CP2K license +
-  --mpi-mapping     : applies a given MPI reordering to CP2K +
-  --run, -r         : forces a CP2K run regardless of other specified flags +
-  --version, -v     : prints the CP2K version and the SVN revision number +
-  --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> +
- +
-<note tip>The module loading is **not** persistent. You have to reload the modules every time you log back in.</note> +
- +
- +
-===== 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 ''cp2k'', run for example: +
- +
-<code> +
-$ module initadd cp2k/r18057_2017_09_18 +
-</code> +
- +
-to remove ''cp2k'' again from the list of modules to load: +
- +
-<code> +
-$ module initrm cp2k +
-</code>+
  
-Alternatively you can of course simply edit ''.bashrc'' using your favorite editor and add a line like ''module load vmd cp2k/r18057_2017_09_18'' by yourself. 
  
 ==== Setup key-based authentication ==== ==== Setup key-based authentication ====
exercises/2020_uzh_acpc2/login.1586168108.txt.gz · Last modified: (external edit)