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--- exercises:2020_uzh_acpc2:installation [2020/04/07 08:04] – jglan
+++ exercises:2020_uzh_acpc2:installation [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 22: / Line 22: @@
 <code>
-$ module load cp2k/r18057_2017_09_18
+$ module load cp2k/6.1-gcc-7.3.1-d43qc6l
 </code>
@@ Line 28: / Line 28: @@
-Now run the following command to verify that the CP2K executable is available:
+you can run cp2k from any directory. To do this enter
 <code>
-$ cp2k.sopt --help
+cp2k.popt --help
 </code>
@@ Line 70: / Line 69: @@
 </code>
-you can run cp2k from any directory. To do this enter
+Now, make a new directory, for instance called ''exercise0''. Download and extract the file {{ :exercises:2019_uzh_acpc2:argon.zip |argon.inp}} into this directory and run cp2k by typing
+To download the file and extract the zip:
 <code>
-cp2k.sopt --help
+wget https://www.cp2k.org/_media/exercises:2019_uzh_acpc2:argon.zip
+mv exercises:2019_uzh_acpc2:argon.zip argon.zip
+unzip argon.zip
 </code>
-Which should give you the output
+<code>
+cp2k.popt -i argon.inp -o out_ex0.out
+</code>
+To run cp2k with MPI, for instance with 2 CPU, one can use
 <code>
- cp2k.sopt [-c|--check] [-e|--echo] [-h|--help] [--html-manual]
+mpirun -n 2 cp2k.popt -i argon.inp -o out_ex0.out
-           [-i] <input_file>
+</code>
-           [-mpi-mapping|--mpi-mapping] <method>
-           [-o] <output_file>
-           [-r|-run] [--xml]
- starts the CP2K program, see <https://www.cp2k.org/>
+You just ran a short Molecular Dynamics trajectory of liquid argon.
- The easiest way is cp2k.sopt <input_file>
- The following options can be used:
+===== Visualization with VMD =====
-  -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:
+===== Part II: Loading and running a program =====
-  --check, -c       : performs a syntax check of the <input_file>
-  --echo, -e        : echos the <input_file>, and make all defaults explicit
+We need for visualization is [[http://www.ks.uiuc.edu/Research/vmd/|VMD]].
-                      The input is also checked, but only a failure is reported
-  --help, -h        : writes this message
+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:
-  --html-manual     : writes a HTML reference manual of the CP2K input
-                      in the current directory. The file index.html is a good
+<code>
-                      starting point for browsing
+$ vmd
-  --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>
-Now, make a new directory, for instance called ''exercise0''. Download and extract the file {{argon.zip|}} into this directory and run cp2k by typing
+Two new windows named ''VMD Main'' and ''VMD 1.9.2 ... Display'' should open on your local machine while the server shows:
 <code>
-cp2k.sopt -i argon.inp -o out_ex0.out
+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>
-You just ran a short Molecular Dynamics trajectory of liquid argon.
+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>
-===== Visualization with VMD =====
 We will visualize this trajectory with VMD, a molecular visualization program. First of all, download and install VMD for your operating system as indicated [[http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD|here]].The current official release doesn't support MacOS Catalina. For those who have Catalina OS, please download VMD [[https://www.dropbox.com/s/700vi9kkpglf6m6/VMD%201.9.4a38.zip?dl=0|here]].