exercises:2016_uzh_cmest:login
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exercises:2016_uzh_cmest:first_simulation_run [2016/09/21 09:23] – [Module loading] tmueller | exercises:2016_uzh_cmest:login [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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- | ====== | + | ====== |
- | 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 ===== | ||
Line 18: | Line 18: | ||
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 '' | + | * on Linux: put '' |
+ | * on Mac OS X/OSX/macOS Sierra: use [[https:// | ||
+ | * one Windows: use [[https:// | ||
+ | * a plain text editor to edit input files if you are uncomfortable with using '' | ||
- | <note important> | + | Use the instructions giving in the lecture/ |
+ | |||
+ | <note important> | ||
< | < | ||
$ passwd | $ passwd | ||
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< | < | ||
- | $ cp2k.popt --help | + | $ cp2k.sopt --help |
</ | </ | ||
Line 65: | Line 70: | ||
< | < | ||
- | cp2k.popt [-c|--check] [-e|--echo] [-h|--help] [--html-manual] | + | cp2k.sopt [-c|--check] [-e|--echo] [-h|--help] [--html-manual] |
[-i] < | [-i] < | ||
| | ||
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| | ||
- | The easiest way is cp2k.popt < | + | The easiest way is cp2k.sopt < |
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 | ||
+ | </ | ||
+ | |||
+ | 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.</ | <note tip>The module loading is **not** persistent. You have to reload the modules every time you log back in.</ | ||
- | ==== Running a simulation using CP2K ==== | ||
+ | ===== 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 vmd | ||
+ | $ module initadd cp2k/ | ||
+ | </ | ||
+ | |||
+ | to remove '' | ||
+ | |||
+ | < | ||
+ | $ module initrm vmd | ||
+ | </ | ||
+ | |||
+ | Alternatively you can of course simply edit '' | ||
+ | |||
+ | ==== 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 | ||
+ | |||
+ | < | ||
+ | $ ssh-keygen | ||
+ | </ | ||
+ | |||
+ | and accept the defaults proposed and do not set a password. | ||
+ | |||
+ | Upload the public key **from your local machine** to tcopt3: | ||
+ | |||
+ | < | ||
+ | $ scp ~/ | ||
+ | </ | ||
+ | |||
+ | Now login to '' | ||
+ | |||
+ | < | ||
+ | $ mkdir -p .ssh | ||
+ | $ chmod 0700 .ssh | ||
+ | $ mv id_rsa.pub .ssh/ | ||
+ | </ | ||
+ | |||
+ | When connecting to the server **from your local machine** now, use: | ||
+ | |||
+ | < | ||
+ | $ ssh -i ~/ | ||
+ | </ | ||
+ | |||
+ | ==== Simplify the login ==== | ||
+ | |||
+ | The following instructions apply **apply to OSX and Linux**. | ||
+ | |||
+ | **On your local machine** add the following part to the file '' | ||
+ | |||
+ | < | ||
+ | Host tcopt3 | ||
+ | HostName tcopt3.chem.uzh.ch | ||
+ | User studentXX | ||
+ | </ | ||
+ | |||
+ | after which you will be able to connect to '' | ||
+ | |||
+ | < | ||
+ | $ ssh tcopt3 | ||
+ | </ | ||
+ | |||
+ | 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 '' | ||
+ | |||
+ | < | ||
+ | Host tcopt3 | ||
+ | HostName tcopt3.chem.uzh.ch | ||
+ | User studentXX | ||
+ | IdentityFile ~/ | ||
+ | IdentitiesOnly yes | ||
+ | PreferredAuthentications publickey | ||
+ | </ |
exercises/2016_uzh_cmest/login.1474449796.txt.gz · Last modified: 2020/08/21 10:15 (external edit)