CP2K Open Source Molecular Dynamics

User Tools

Site Tools

Trace:
exercises:2018_uzh_cmest:login

Differences

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

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
exercises:2018_uzh_cmest:login [2018/09/19 11:00] – [First steps] tmuellerexercises:2018_uzh_cmest:login [2020/08/21 10:15] (current) – external edit 127.0.0.1
Line 83: Line 83:
  
 <code> <code>
-$ module load cp2k/r18057_2017_09_18+$ module load cp2k
 </code> </code>
  
Line 92: Line 92:
  
 <code> <code>
-$ cp2k.sopt --help+$ cp2k.popt --help
 </code> </code>
  
Line 98: Line 98:
  
 <code> <code>
- cp2k.sopt [-c|--check] [-e|--echo] [-h|--help] [--html-manual]+ cp2k.popt [-c|--check] [-e|--echo] [-h|--help] [--html-manual]
            [-i] <input_file>            [-i] <input_file>
            [-mpi-mapping|--mpi-mapping] <method>            [-mpi-mapping|--mpi-mapping] <method>
Line 106: Line 106:
  starts the CP2K program, see <https://www.cp2k.org/>  starts the CP2K program, see <https://www.cp2k.org/>
  
- The easiest way is cp2k.sopt <input_file>+ The easiest way is cp2k.popt <input_file>
  
  The following options can be used:  The following options can be used:
Line 131: Line 131:
 </code> </code>
  
-Another program we need for visualization is [[http://www.ks.uiuc.edu/Research/vmd/|VMD]]. +Another program we need for visualization is [[http://www.ks.uiuc.edu/Research/vmd/|VMD]]. Running this remotely is unfortunately error prone which is why you should download it from the link above and install it locally on your machine.
- +
-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> <note tip>The module loading is **not** persistent. You have to reload the modules every time you log back in.</note>
Line 192: Line 151:
  
 <code> <code>
-$ module initadd cp2k/r18057_2017_09_18+$ module initadd cp2k
 </code> </code>
  
Line 201: Line 160:
 </code> </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.+Alternatively you can of course simply edit ''.bashrc'' using your favorite editor and add a line like ''module load vmd cp2k'' by yourself.
  
 ==== Setup key-based authentication ==== ==== Setup key-based authentication ====
exercises/2018_uzh_cmest/login.1537354845.txt.gz · Last modified: (external edit)