exercises:2020_uzh_acpc2:installation
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exercises:2020_uzh_acpc2:installation [2020/04/07 08:04] – jglan | exercises:2020_uzh_acpc2:installation [2020/04/07 09:22] – jglan | ||
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< | < | ||
- | $ module load cp2k/r18057_2017_09_18 | + | $ module load cp2k/6.1-gcc-7.3.1-d43qc6l |
</ | </ | ||
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 |
< | < | ||
- | $ cp2k.sopt --help | + | cp2k.popt --help |
</ | </ | ||
Line 70: | Line 69: | ||
</ | </ | ||
- | you can run cp2k from any directory. | + | Now, make a new directory, for instance called '' |
+ | |||
+ | To download the file and extract the zip: | ||
< | < | ||
- | cp2k.sopt --help | + | wget https:// |
+ | |||
+ | mv exercises: | ||
+ | |||
+ | unzip argon.zip | ||
</ | </ | ||
- | Which should give you the output | + | < |
+ | cp2k.popt -i argon.inp -o out_ex0.out | ||
+ | </ | ||
+ | To run cp2k with MPI, for instance with 2 CPU, one can use | ||
< | < | ||
- | cp2k.sopt [-c|--check] [-e|--echo] [-h|--help] [--html-manual] | + | mpirun -n 2 cp2k.popt -i argon.inp |
- | [-i] < | + | </code> |
- | [-mpi-mapping|--mpi-mapping] < | + | |
- | [-o] <output_file> | + | |
- | | + | |
- | | + | You just ran a short Molecular Dynamics trajectory of liquid argon. |
- | The easiest way is cp2k.sopt < | ||
- | The following options can be used: | + | ===== Visualization with VMD ===== |
- | -i < | ||
- | argument, the -i flag is not needed | ||
- | -o < | ||
- | 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 < | + | |
- | | + | We need for visualization |
- | The input is also checked, but only a failure is reported | + | |
- | --help, -h | + | Load the respective module (since there is only one version |
- | --html-manual | + | |
- | in the current directory. The file index.html is a good | + | < |
- | | + | $ vmd |
- | | + | |
- | --mpi-mapping | + | |
- | --run, -r : forces a CP2K run regardless of other specified flags | + | |
- | --version, | + | |
- | | + | |
- | | + | |
</ | </ | ||
- | Now, make a new directory, for instance called | + | Two new windows named '' |
< | < | ||
- | cp2k.sopt -i argon.inp -o out_ex0.out | + | 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 > | ||
</ | </ | ||
- | 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 > quit | ||
+ | </ | ||
+ | |||
+ | <note tip>The module loading is **not** persistent. | ||
- | ===== 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:// | 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:// |
exercises/2020_uzh_acpc2/installation.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1