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exercises:2016_uzh_cmest:first_simulation_run [2016/09/21 09:19] – [Module loading] tmuellerexercises:2016_uzh_cmest:login [2016/09/22 09:48] tmueller
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-====== 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 ===== ===== Part I: Login =====
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 optionally you may want: optionally you may want:
  
-  * a file transfer tool to copy files from/to the server +  * a file transfer tool to copy files from/to the server
-  * a plain text editor to edit input files if you are uncomfortable with using ''nano'', ''vim'' or ''emacs'' via SSH+    * 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.
  
-<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 loginusing:
 <code> <code>
 $ passwd $ passwd
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 </code> </code>
  
-When you now list the loaded modules again, you will see that the list changed.+When you list the loaded modules again at this point (see command above), you will notice that the list has changed.
  
-Run the following command to verify that the CP2K executable is now available:+ 
 +Now run the following command to verify that the CP2K executable is available:
  
 <code> <code>
-$ cp2k.popt --help+$ cp2k.sopt --help
 </code> </code>
  
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 <code> <code>
- cp2k.popt [-c|--check] [-e|--echo] [-h|--help] [--html-manual]+ cp2k.sopt [-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.popt <input_file>+ The easiest way is cp2k.sopt <input_file>
  
  The following options can be used:  The following options can be used:
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   --xml             : dumps the whole CP2K input structure as a XML file   --xml             : dumps the whole CP2K input structure as a XML file
                       xml2htm generates a HTML manual from this 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> </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>
  
-==== Running a simulation using CP2K ==== 
  
 +===== 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 ''vmd'' and ''cp2k'', run for example:
 +
 +<code>
 +$ module initadd vmd
 +$ module initadd cp2k/r17408_2016_09_19
 +</code>
 +
 +to remove ''vmd'' again from the list of modules to load:
 +
 +<code>
 +$ module initrm vmd
 +</code>
 +
 +Alternatively you can of course simply edit ''.bashrc'' using your favorite editor and add a line like ''module load vmd cp2k/r17408_2016_09_19'' by yourself.
 +
 +==== Setup key-based authentication ====
 +
 +To avoid having to type the password every time you log in (and to increase the security), keys can be used for authentication instead. The following instructions are **for OSX and Linux**.
 +
 +First generate a key-pair **on your local machine** using
 +
 +<code>
 +$ ssh-keygen
 +</code>
 +
 +and accept the defaults proposed and do not set a password.
 +
 +Upload the public key **from your local machine** to tcopt3:
 +
 +<code>
 +$ scp ~/.ssh/id_rsa.pub studentXX@tcopt3.chem.uzh.ch:~/
 +</code>
 +
 +Now login to ''tcopt3.chem.uzh.ch'' and move the uploaded public key to the right place:
 +
 +<code>
 +$ mkdir -p .ssh
 +$ chmod 0700 .ssh
 +$ mv id_rsa.pub .ssh/authorized_keys
 +</code>
 +
 +When connecting to the server **from your local machine** now, use:
 +
 +<code>
 +$ ssh -i ~/.ssh/id_rsa studentXX@tcopt3.chem.uzh.ch
 +</code>
 +
 +==== Simplify the login ====
 +
 +The following instructions apply **apply to OSX and Linux**.
 +
 +**On your local machine** add the following part to the file ''.ssh/config'' in your home directory:
 +
 +<code>
 +Host tcopt3
 +  HostName tcopt3.chem.uzh.ch
 +  User studentXX
 +</code>
 +
 +after which you will be able to connect to ''tcopt3'' simply by using
 +
 +<code>
 +$ ssh tcopt3
 +</code>
 +
 +If you have setup key-based authentication as shown above, augment the entry to the following instead, to always use key-based authentication without having to specify ''-i ~/.ssh/id_rsa'' manually:
 +
 +<code>
 +Host tcopt3
 +  HostName tcopt3.chem.uzh.ch
 +  User studentXX
 +  IdentityFile ~/.ssh/id_rsa
 +  IdentitiesOnly yes
 +  PreferredAuthentications publickey
 +</code>
exercises/2016_uzh_cmest/login.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1