exercises:2020_uzh_acpc2:installation
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exercises:2020_uzh_acpc2:installation [2020/04/06 10:22] – [0.4 Visualization with VMD] jglan | exercises:2020_uzh_acpc2:installation [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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===== First CP2K simulation ===== | ===== First CP2K simulation ===== | ||
- | It is possible to run cp2k from any directory on your own machine by adding a line to your '' | ||
- | To do this change to the directory where the '' | + | ==== Module loading ==== |
- | To edit the '' | + | |
+ | Since there are numerous applications with different and possibly conflicting requirements, | ||
+ | |||
+ | To list all available modules: | ||
< | < | ||
- | vim ~/.bashrc | + | $ module avail |
</ | </ | ||
- | Add the following line, replacing ''/ | + | |
+ | while using | ||
< | < | ||
- | export PATH=${PATH}:/ | + | $ module list |
</ | </ | ||
- | Save the '' | + | |
- | In the terminal after typing | + | gives the list of loaded moules. |
+ | |||
+ | To load the CP2K module used in this course, | ||
< | < | ||
- | source ~/.bashrc | + | $ module load cp2k/6.1-gcc-7.3.1-d43qc6l |
</ | </ | ||
+ | |||
+ | When you list the loaded modules again at this point (see command above), you will notice that the list has changed. | ||
+ | |||
+ | |||
you can run cp2k from any directory. To do this enter | you can run cp2k from any directory. To do this enter | ||
< | < | ||
- | cp2k.sopt --help | + | cp2k.popt --help |
</ | </ | ||
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</ | </ | ||
- | Now, make a new directory, for instance called '' | + | Now, make a new directory, for instance called '' |
+ | |||
+ | To download the file and extract the zip: | ||
< | < | ||
- | cp2k.sopt -i argon.inp -o out_ex0.out | + | wget https:// |
+ | |||
+ | mv exercises: | ||
+ | |||
+ | unzip argon.zip | ||
</ | </ | ||
+ | |||
+ | < | ||
+ | cp2k.popt -i argon.inp -o out_ex0.out | ||
+ | </ | ||
+ | |||
+ | To run cp2k with MPI, for instance with 2 CPU, one can use | ||
+ | < | ||
+ | mpirun -n 2 cp2k.popt -i argon.inp -o out_ex0.out | ||
+ | </ | ||
+ | |||
You just ran a short Molecular Dynamics trajectory of liquid argon. | You just ran a short Molecular Dynamics trajectory of liquid argon. | ||
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===== Visualization with VMD ===== | ===== 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:// | ||
- | The current official release doesn' | + | ===== Part II: Loading and running a 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.</ | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | 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:// | ||
+ | |||
Open VMD. From '' | Open VMD. From '' | ||
< | < | ||
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{{: | {{: | ||
+ | |||
===== Plotting tools ===== | ===== Plotting tools ===== | ||
- | Throughout the course you will also need to plot some graphs. You can use any tool you like for that. '' | + | Throughout the course, you will also need to plot some graphs. You can use any tool you like for that. '' |
exercises/2020_uzh_acpc2/installation.1586168525.txt.gz · Last modified: 2020/08/21 10:15 (external edit)