exercises:2021_uzh_acpc2:installation
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exercises:2021_uzh_acpc2:installation [2021/04/13 11:02] – external edit 127.0.0.1 | exercises:2021_uzh_acpc2:installation [2021/04/14 12:30] (current) – [Part II: Loading and running a program] Update VMD instructions mrossmannek | ||
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< | < | ||
- | $ module avail | + | module avail |
</ | </ | ||
- | while using | + | To list all modules which are currently loaded use: |
< | < | ||
- | $ module list | + | module list |
</ | </ | ||
- | |||
- | gives the list of loaded moules. | ||
To load the CP2K module used in this course, use: | To load the CP2K module used in this course, use: | ||
< | < | ||
- | $ module load cp2k/6.1-gcc-7.3.1-d43qc6l | + | module load cp2k/8.1-intel-20.0.2-gimphmw |
</ | </ | ||
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- | you can run cp2k from any directory. To do this enter | + | You can run cp2k from any directory. To do this enter |
< | < | ||
cp2k.popt --help | cp2k.popt --help | ||
Line 36: | Line 34: | ||
< | < | ||
- | cp2k.sopt [-c|--check] [-e|--echo] [-h|--help] [--html-manual] | + | cp2k.popt [-c|--check] [-e|--echo] [-h|--help] |
[-i] < | [-i] < | ||
| | ||
[-o] < | [-o] < | ||
- | | + | |
| | ||
- | The easiest way is cp2k.sopt < | + | The easiest way is cp2k.popt < |
The following options can be used: | The following options can be used: | ||
- | -i < | + | -i < |
- | argument, the -i flag is not needed | + | |
- | -o < | + | -o < |
These switches skip the simulation, unless [-r|-run] is specified: | These switches skip the simulation, unless [-r|-run] is specified: | ||
- | --check, -c | + | --check, -c : performs a syntax check of the < |
- | --echo, -e : echos the < | + | --echo, -e |
- | The input is also checked, but only a failure is reported | + | |
- | --help, -h : writes this message | + | --help, -h |
- | --html-manual | + | --license |
- | in the current directory. The file index.html is a good | + | --mpi-mapping |
- | starting point for browsing | + | --run, -r : forces a CP2K run regardless of other specified flags |
- | --license | + | --shell, -s : start interactive shell mode |
- | --mpi-mapping | + | --version, -v : prints the CP2K version and the revision number |
- | --run, -r | + | --xml : dumps the whole CP2K input structure as a XML file |
- | --version, -v | + | |
- | --xml | + | --set, -E name=value : set the initial value of a preprocessor value |
- | xml2htm generates a HTML manual from this XML file | + | |
</ | </ | ||
- | Now, make a new directory, for instance called '' | + | Now, make a new directory, for instance called '' |
+ | < | ||
+ | mkdir exercise0 | ||
- | To download the file and extract the zip: | + | cd exercise0 |
+ | </ | ||
+ | |||
+ | Download | ||
< | < | ||
wget https:// | wget https:// | ||
Line 78: | Line 80: | ||
unzip argon.zip | unzip argon.zip | ||
- | |||
</ | </ | ||
+ | Finally, you can run cp2K by typing: | ||
< | < | ||
cp2k.popt -i argon.inp -o out_ex0.out | cp2k.popt -i argon.inp -o out_ex0.out | ||
</ | </ | ||
- | To run cp2k with MPI, for instance with 2 CPU, one can use | + | To run cp2k with MPI, for instance with 2 CPUs, you can use: |
< | < | ||
mpirun -n 2 cp2k.popt -i argon.inp -o out_ex0.out | 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! |
+ | Now, let's look at the results. | ||
Line 99: | Line 102: | ||
- | We need for visualization is [[http:// | + | The software we need for visualization is [[http:// |
- | Load the respective module (since there is only one version available, the shorthand | + | You can either use our provided installation on '' |
+ | === Starting VMD on '' | ||
+ | |||
+ | Load the respective module: | ||
+ | < | ||
+ | module load vmd/ | ||
+ | </ | ||
+ | |||
+ | Pay **attention** to load the correct version of VMD (i.e. '' | ||
+ | |||
+ | You can start '' | ||
< | < | ||
- | $ vmd | + | vmd |
</ | </ | ||
- | Two new windows named '' | + | Two new windows named '' |
< | < | ||
- | Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014) | + | Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016) |
- | Info) http:// | + | Info) http:// |
- | Info) Email questions and bug reports to vmd@ks.uiuc.edu | + | Info) Email questions and bug reports to vmd@ks.uiuc.edu |
- | Info) Please include this reference in published work using VMD: | + | Info) Please include this reference in published work using VMD: |
- | Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual | + | Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual |
Info) Molecular Dynamics', | Info) Molecular Dynamics', | ||
Info) ------------------------------------------------------------- | Info) ------------------------------------------------------------- | ||
- | Info) Multithreading available, | + | Info) Multithreading available, |
- | Info) Free system memory: | + | Info) CPU features: SSE2 AVX AVX2 FMA |
- | Warning) Detected a mismatch between CUDA runtime and GPU driver | + | Info) Free system memory: |
- | Warning) Check to make sure that GPU drivers are up to date. | + | |
Info) No CUDA accelerator devices available. | Info) No CUDA accelerator devices available. | ||
Warning) Detected X11 ' | Warning) Detected X11 ' | ||
Warning) try disabling this X server option. | Warning) try disabling this X server option. | ||
Warning) disable stereoscopic display when ' | Warning) disable stereoscopic display when ' | ||
- | libGL error: failed to load driver: swrast | + | Info) OpenGL renderer: |
- | libGL error: Try again with LIBGL_DEBUG=verbose for more details. | + | Info) |
- | Info) OpenGL renderer: | + | Info) Full GLSL rendering mode is available. |
- | Info) | + | Info) |
- | Info) GLSL rendering mode is NOT available. | + | |
- | Info) | + | |
Info) Dynamically loaded 2 plugins in directory: | Info) Dynamically loaded 2 plugins in directory: | ||
- | Info) /sw/build/generic/app/vmd/vmd-1.9.2/lib/vmd/ | + | Info) /sw-ng/spack/opt/spack/linux-opensuse_leap15-sandybridge/ |
vmd > | 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 '' | + | 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 setup instructions |
+ | You can exit VMD by either closing the '' | ||
< | < | ||
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<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.</ | ||
+ | === Installing VMD on your **local** machine === | ||
+ | Simply download and install VMD for your operating system as indicated [[http:// | ||
+ | If you are using MacOS Catalina and are experiencing issue, please download VMD from [[https:// | ||
- | 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:// | ||
+ | === Getting the input data === | ||
+ | |||
+ | Before you can try out VMD, we must get some data to visualize. | ||
+ | For now, we simply want to view all the Argon atoms from our previous simulation. | ||
+ | To do so, we need to extract their coordinates from the input file. | ||
+ | The easiest solution to this, is to copy them into an [[https:// | ||
+ | < | ||
+ | cp argon.inp argon.xyz | ||
+ | </ | ||
+ | Now, you must remove everything but the atoms coordinates. | ||
+ | You should end up with 108 lines in your file, each containing the coordinate of a single Ar atom. | ||
+ | |||
+ | To make this a fully functional '' | ||
+ | - The number of atoms on the first line | ||
+ | - A blank line (or a comment) | ||
+ | - The rest of the file | ||
+ | < | ||
+ | 108 | ||
+ | |||
+ | Ar -8.53869012951987116 -15.5816257770688615 2.85663672298278293 | ||
+ | ... | ||
+ | </ | ||
+ | |||
+ | === Using VMD === | ||
+ | |||
+ | Now, we are ready for our first visualization with VMD. | ||
Open VMD. From '' | Open VMD. From '' | ||
Line 156: | Line 195: | ||
pbc wrap -all | pbc wrap -all | ||
</ | </ | ||
+ | |||
+ | <note tip>'' | ||
+ | |||
+ | <note tip> | ||
+ | If you prefer to load the file and set the drawing methods via commands, you can do the following: | ||
+ | < | ||
+ | mol new argon.xyz | ||
+ | mol modstyle 0 0 vdw | ||
+ | </ | ||
+ | The first commands loads the file '' | ||
+ | The second command assumes this is the first file you load (the first index '' | ||
+ | </ | ||
A snapshot of the molecular dynamics trajectory should approximately look like this: | A snapshot of the molecular dynamics trajectory should approximately look like this: | ||
{{: | {{: | ||
- | |||
- | |||
===== 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/2021_uzh_acpc2/installation.1618311776.txt.gz · Last modified: 2021/04/13 11:02 by 127.0.0.1