exercises:2020_uzh_acpc2:login
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exercises:2020_uzh_acpc2:login [2020/04/06 10:15] – created jglan | exercises: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:// | * on Mac OS X/OSX/macOS Sierra: you need to install [[https:// | ||
- | * on Microsoft Windows: you need to install [[http:// | + | * on Microsoft Windows: you need to install [[https:// |
* 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 '' | * on Linux: put '' | ||
Line 38: | Line 38: | ||
* Connect to the server by entering the command: '' | * Connect to the server by entering the command: '' | ||
- | ==== Login using Windows ==== | + | ==== Login using Windows |
+ | |||
+ | * 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 '' | ||
+ | * 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: | ||
Line 54: | Line 62: | ||
* 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 |
* Start Putty | * Start Putty | ||
* Double click the session '' | * Double click the session '' | ||
Line 68: | Line 76: | ||
</ | </ | ||
- | ===== 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, | + | |
- | + | ||
- | To list all available modules: | + | |
- | + | ||
- | < | + | |
- | $ module avail | + | |
- | </ | + | |
- | + | ||
- | while using | + | |
- | + | ||
- | < | + | |
- | $ module list | + | |
- | </ | + | |
- | + | ||
- | gives the list of loaded moules. | + | |
- | + | ||
- | To load the CP2K module used in this course, use: | + | |
- | + | ||
- | < | + | |
- | $ module load cp2k/ | + | |
- | </ | + | |
- | + | ||
- | 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: | + | |
- | + | ||
- | < | + | |
- | $ cp2k.sopt --help | + | |
- | </ | + | |
- | + | ||
- | Which should give you the output | + | |
- | + | ||
- | < | + | |
- | | + | |
- | [-i] < | + | |
- | | + | |
- | [-o] < | + | |
- | | + | |
- | + | ||
- | | + | |
- | + | ||
- | The easiest way is cp2k.sopt < | + | |
- | + | ||
- | The following options can be used: | + | |
- | + | ||
- | -i < | + | |
- | argument, the -i flag is not needed | + | |
- | -o < | + | |
- | + | ||
- | These switches skip the simulation, unless [-r|-run] is specified: | + | |
- | + | ||
- | --check, -c : performs a syntax check of the < | + | |
- | --echo, -e : echos the < | + | |
- | The input is also checked, but only a failure is reported | + | |
- | --help, -h : writes this message | + | |
- | --html-manual | + | |
- | in the current directory. The file index.html is a good | + | |
- | starting point for browsing | + | |
- | --license | + | |
- | --mpi-mapping | + | |
- | --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 | + | |
- | </ | + | |
- | + | ||
- | Another program we need for visualization is [[http:// | + | |
- | + | ||
- | Load the respective module (since there is only one version available, the shorthand '' | + | |
- | + | ||
- | < | + | |
- | $ vmd | + | |
- | </ | + | |
- | + | ||
- | Two new windows named '' | + | |
- | + | ||
- | < | + | |
- | Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014) | + | |
- | Info) http:// | + | |
- | 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', | + | |
- | 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 ' | + | |
- | Warning) try disabling this X server option. | + | |
- | Warning) disable stereoscopic display when ' | + | |
- | 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)/ | + | |
- | Info) | + | |
- | Info) GLSL rendering mode is NOT available. | + | |
- | Info) | + | |
- | Info) Dynamically loaded 2 plugins in directory: | + | |
- | Info) / | + | |
- | vmd > | + | |
- | </ | + | |
- | + | ||
- | 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 > quit | + | |
- | </ | + | |
- | + | ||
- | <note tip>The module loading is **not** persistent. You have to reload the modules every time you log back in.</ | + | |
- | + | ||
- | + | ||
- | ===== Part III: Advanced account configuration ===== | + | |
- | + | ||
- | ==== Make module loading persistent ==== | + | |
- | + | ||
- | Upon login, the shell ('' | + | |
- | + | ||
- | < | + | |
- | $ echo ' | + | |
- | </ | + | |
- | + | ||
- | after that you can add and remove modules to be loaded at startup using '' | + | |
- | + | ||
- | To add '' | + | |
- | + | ||
- | < | + | |
- | $ module initadd cp2k/ | + | |
- | </ | + | |
- | + | ||
- | to remove '' | + | |
- | + | ||
- | < | + | |
- | $ module initrm cp2k | + | |
- | </ | + | |
- | Alternatively you can of course simply edit '' | ||
==== Setup key-based authentication ==== | ==== Setup key-based authentication ==== |
exercises/2020_uzh_acpc2/login.1586168108.txt.gz · Last modified: 2020/08/21 10:15 (external edit)