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exercises:2018_uzh_cmest:login [2018/09/17 12:52] – external edit 127.0.0.1exercises:2018_uzh_cmest:login [2020/08/21 10:15] (current) – external edit 127.0.0.1
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     * on Microsoft Windows: you need to install [[http://sourceforge.net/projects/xming/files/latest/download|XMing]]     * on Microsoft Windows: you need to install [[http://sourceforge.net/projects/xming/files/latest/download|XMing]]
   * 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://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 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 Mac OS X/OSX/macOS Sierra: use [[https://cyberduck.io/|Cyberduck]]     * on Mac OS X/OSX/macOS Sierra: use [[https://cyberduck.io/|Cyberduck]]
     * one Windows: use [[https://winscp.net/|WinSCP]] or [[https://cyberduck.io/|Cyberduck]]     * one Windows: use [[https://winscp.net/|WinSCP]] or [[https://cyberduck.io/|Cyberduck]]
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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)
   * Open a terminal (Konsole, xterm or similar)   * Open a terminal (Konsole, xterm or similar)
-  * Connect to the server by entering the command: ''ssh -X studentXX@tcopt3.chem.uzh.ch''+  * Connect to the server by entering the command: ''ssh -X studentXX@tcopt2.chem.uzh.ch''
  
  
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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)
   * Open a X-Windows terminal in the X11 application if you want to run graphical applications on the server, otherwise use the pre-installed //Terminal// application or an alternative like //iTerm2//   * Open a X-Windows terminal in the X11 application if you want to run graphical applications on the server, otherwise use the pre-installed //Terminal// application or an alternative like //iTerm2//
-  * Connect to the server by entering the command: ''ssh -X studentXX@tcopt3.chem.uzh.ch''+  * Connect to the server by entering the command: ''ssh -X studentXX@tcopt2.chem.uzh.ch''
  
 ==== Login using Windows ==== ==== Login using Windows ====
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   - Start the application PuTTY from the Windows menu (in the folder PuTTY)   - Start the application PuTTY from the Windows menu (in the folder PuTTY)
-  - Fill in the //Host Name//: ''tcopt3.chem.uzh.ch''+  - Fill in the //Host Name//: ''tcopt2.chem.uzh.ch''
   - Set //Connection type// to ''SSH''   - Set //Connection type// to ''SSH''
-  - Type ''tcopt3'' as the name of the session below Saved Sessions and save the settings a first time+  - Type ''tcopt2'' as the name of the session below Saved Sessions and save the settings a first time
   - In the Category tree on the left side, select //Connection > Data// and enter the username you have been given in the lecture in the field //Auto-login username//   - In the Category tree on the left side, select //Connection > Data// and enter the username you have been given in the lecture in the field //Auto-login username//
   - Select the tab ''Connection > SSH > X11'' from the ''Category'' list and enable the option ''Enable X11 Forwarding''   - Select the tab ''Connection > SSH > X11'' from the ''Category'' list and enable the option ''Enable X11 Forwarding''
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   * Start Xming (optional, only required if you want to run graphical applications on the server)   * Start Xming (optional, only required if you want to run graphical applications on the server)
   * Start Putty   * Start Putty
-  * Double click the session ''tcopt3'' to start the connection+  * Double click the session ''tcopt2'' to start the connection
   * Enter (username and) password as requested   * Enter (username and) password as requested
  
-==== First steps ==== 
- 
-<note important>Change the password of your account after your first login, using: 
- 
-<code> 
-$ passwd 
-</code> 
-</note> 
  
 ===== Part II: Loading and running a program ===== ===== Part II: Loading and running a program =====
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 <code> <code>
-$ module load cp2k/r18057_2017_09_18+$ module load cp2k
 </code> </code>
  
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 <code> <code>
-$ cp2k.sopt --help+$ cp2k.popt --help
 </code> </code>
  
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 <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>
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  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:
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 </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>
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 <code> <code>
-$ module initadd cp2k/r18057_2017_09_18+$ module initadd cp2k
 </code> </code>
  
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 </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 ====
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 and accept the defaults proposed and do no set a password. and accept the defaults proposed and do no set a password.
  
-Upload the public key **from your local machine** to tcopt3:+Upload the public key **from your local machine** to tcopt2:
  
 <code> <code>
-$ scp ~/.ssh/id_rsa.pub studentXX@tcopt3.chem.uzh.ch:~/+$ scp ~/.ssh/id_rsa.pub studentXX@tcopt2.chem.uzh.ch:~/
 </code> </code>
  
-Now login to ''tcopt3.chem.uzh.ch'' and move the uploaded public key to the right place and set the access permissions correct:+Now login to ''tcopt2.chem.uzh.ch'' and move the uploaded public key to the right place and set the access permissions correct:
  
 <code> <code>
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 <code> <code>
-$ ssh -i ~/.ssh/id_rsa studentXX@tcopt3.chem.uzh.ch+$ ssh -i ~/.ssh/id_rsa studentXX@tcopt2.chem.uzh.ch
 </code> </code>
  
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   - Restart //PuTTY//   - Restart //PuTTY//
-  - Select the //Session// ''tcopt3'' and press //Load//+  - Select the //Session// ''tcopt2'' and press //Load//
   - Select //Connection > SSH > Auth//   - Select //Connection > SSH > Auth//
   - Use the //Browse...// button in //Authentication parameters// to selected the ''condensed_matter.ppk'' you generated earlier   - Use the //Browse...// button in //Authentication parameters// to selected the ''condensed_matter.ppk'' you generated earlier
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 <code> <code>
-Host tcopt3 +Host tcopt2 
-  HostName tcopt3.chem.uzh.ch+  HostName tcopt2.chem.uzh.ch
   User studentXX   User studentXX
 </code> </code>
  
-after which you will be able to connect to ''tcopt3'' simply by using+after which you will be able to connect to ''tcopt2'' simply by using
  
 <code> <code>
-$ ssh tcopt3+$ ssh tcopt2
 </code> </code>
  
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 <code> <code>
-Host tcopt3 +Host tcopt2 
-  HostName tcopt3.chem.uzh.ch+  HostName tcopt2.chem.uzh.ch
   User studentXX   User studentXX
   IdentityFile ~/.ssh/id_rsa   IdentityFile ~/.ssh/id_rsa
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