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# System prepended metadata

title: Untitled

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Just a short tutorial for reproducability

## Start Container with some Options
docker volume create cocalc-volume-2
docker run --name=200916-cocalc-10 -d -v cocalc-volume-2:/projects -p 1337:443 -v /usr/local/MATLAB/R2020a:/matlab:ro -e TZ=Europe/Berlin sagemathinc/cocalc:48049298903c


## Make User a CoCalc Admin (to change template of website for example)
docker exec -it [cocalc|containerHash] bash
make-user-admin usermail@userprovider.com


## General Link to already existing Linux software on turbine (such as MATLAB)
* Start docker container with special “link”-instruction, e.g. for MATLAB:
* docker run --name=cocalc_test2 -d -v ~/cocalc_test:/projects -v /usr/local/MATLAB/R2020a:/matlab:ro -p 443:443 sagemathinc/cocalc
* This will expose the MATLAB directory into the container and students can run MATLAB with  /matlab/bin/matlab


## VMD (https://www.ks.uiuc.edu/Research/vmd/)
* Login to running docker with: docker exec -it [cocalc|containerHash] bash
* Download VMD inside container: wget https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/vmd-1.9.4a43.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz
* Unpack it: tar xvf vmd-1.9.4a43.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz
* Follow installation instructions. i.a.:
* umask 022 # NEEDED for permission!, see https://github.com/sagemathinc/cocalc-docker#adding-custom-software-to-your-cocalc-instance
* ./configure
* cd src
* make install
* Students can now execute vmd either in terminal with vmd or even use graphical X11 interface :sonnenbrille:


## LAMMPS (NOT NEEDED FOR THE CWP, OBSOLETE)
* Guide: https://lammps.sandia.gov/doc/Install_linux.html
* Simply follow their guide inside the docker container
* Download cmake in advance: apt-get install cmake


## GROMACS
* TODO :doppeltes_ausrufezeichen:
* Guide: http://manual.gromacs.org/documentation/2019.4/install-guide/index.html
