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--- exercises:2016_uzh_cmest:first_simulation_run [2016/09/21 09:11] – [Part I: Login] tmueller
+++ exercises:2016_uzh_cmest:login [2016/09/22 09:48] – tmueller
@@ Line 1: / Line 1: @@
-====== 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 =====
@@ Line 18: / Line 18: @@
 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 login, using:
 <code>
 $ passwd
@@ Line 33: / Line 38: @@
 Since there are numerous applications with different and possibly conflicting requirements, the //module// system is used. This means that only basic commands are available until **explicitly** loaded.
-To load the CP2K module, use:
+To list all available modules:
 <code>
-$ module load cp2k/r17408_2016_09_19
+$ module avail
 </code>
-while
+while using
 <code>
-$ module avail
 $ module list
 </code>
-gives you the complete list of available modules, respectively the list of loaded modules.
+gives the list of loaded moules.
-After loading the CP2K module, the command
+To load the CP2K module used in this course, use:
 <code>
-$ cp2k.popt --version
+$ module load cp2k/r17408_2016_09_19
 </code>
-should give you the output
+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:
 <code>
- CP2K version 4.0 (Development Version)
+$ cp2k.sopt --help
- SVN source code revision svn:17408
- cp2kflags: libint fftw3 libxc parallel mpi3 scalapack libderiv_max_am1=5 libint_max_am=6
 </code>
-<note tip>The module loading is **not** persistent. You have to reload the modules every time you log back in.
+Which should give you the output
+<code>
+ cp2k.sopt [-c|--check] [-e|--echo] [-h|--help] [--html-manual]
+           [-i] <input_file>
+           [-mpi-mapping|--mpi-mapping] <method>
+           [-o] <output_file>
+           [-r|-run] [--xml]
-</note>
+ starts the CP2K program, see <https://www.cp2k.org/>
-==== Running a simulation using CP2K ====
+ The easiest way is cp2k.sopt <input_file>
+ The following options can be used:
+  -i <input_file>   : provides an input file name, if it is the last
+                      argument, the -i flag is not needed
+  -o <output_file>  : provides an output file name [default: screen]
+ These switches skip the simulation, unless [-r|-run] is specified:
+  --check, -c       : performs a syntax check of the <input_file>
+  --echo, -e        : echos the <input_file>, and make all defaults explicit
+                      The input is also checked, but only a failure is reported
+  --help, -h        : writes this message
+  --html-manual     : writes a HTML reference manual of the CP2K input
+                      in the current directory. The file index.html is a good
+                      starting point for browsing
+  --license         : prints the CP2K license
+  --mpi-mapping     : applies a given MPI reordering to CP2K
+  --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
+</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>
+<note tip>The module loading is **not** persistent. You have to reload the modules every time you log back in.</note>
+===== 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>