Table of Contents
In this exercise you will learn how to login and run commands on our infrastructure.
Part I: Login
As mentioned in the lecture, you absolutely need
- a X11-Server:
- a terminal emulator:
- on Linux: this can be one of Konsole, Gnome Terminal, Terminal, XTerm, …
- on Mac OS X/OSX/macOS Sierra: use the X-Windows terminal from XQuartz
- on Windows: use Putty
optionally you may want:
- a file transfer tool to copy files from/to the server:
- on Linux: put
sftp://tcopt3.chem.uzh.chas the address in your file browser and you should be able to browse your home directory after logging in
- on Mac OS X/OSX/macOS Sierra: use Cyberduck
- a plain text editor to edit input files if you are uncomfortable with using
emacsvia SSH. Please note: It is important that your editor supports Unix line endings. If in doubt, use one of the mentioned editors on the server, or an advanced plain text editor like Atom (plus the line-ending-selector-unix plugin) or Notepad++ on your local machine.
Use the instructions giving in the lecture/available via OLAT to login on the server
tcopt3.chem.uzh.ch using your assigned student account.
$ ssh -X firstname.lastname@example.org
The bash terminal
Many tasks in the following weeks will need to be performed on the terminal (or 'command line').
Let's start with a list of useful commands – just type them into the command line and confirm with
ls # get list of files in the current directory mkdir molsim # make directory 'molsim' cd # change into your home directory cd molsim # change into directory 'molsim' cd .. # go up one directory pwd # print path to the current working directory
Now it is time to copy some files from the teacher account.
cp ~student10/whatever.txt . # copy 'whatever.txt' to you current folder scp email@example.com:foobar.txt /some/local/directory #Copy the file "foobar.txt" from a remote host to the local host scp foobar.txt firstname.lastname@example.org:/some/remote/directory #Copy the file "foobar.txt" from the local host to a remote host
After this, please close and reopen your terminal in order to activate the course-specific settings you copied.
We are now ready to get started. Below you find some additional commands that will come in handy later.
vim myfile # opens 'myfile' in vim (less intuitive but more powerful command line text editor) vi myfile # opens 'myfile' in vim (less intuitive but more powerful command line text editor)
Part II: Loading and running a program
Since there are numerous applications with different and possibly conflicting requirements, the module system is used. This means that only basic commands are available until explicitly loaded.
To list all available modules:
$ module avail
$ module list
gives the list of loaded moules.
To load the CP2K module used in this course, use:
$ module load cp2k/r17408_2016_09_19
When you list the loaded modules again at this point (see command above), you will notice that the list has changed.
Now run the following command to verify that the CP2K executable is available:
$ cp2k.sopt --help
Which should give you the output
cp2k.sopt [-c|--check] [-e|--echo] [-h|--help] [--html-manual] [-i] <input_file> [-mpi-mapping|--mpi-mapping] <method> [-o] <output_file> [-r|-run] [--xml] starts the CP2K program, see <https://www.cp2k.org/> The easiest way is cp2k.sopt <input_file> The following options can be used: -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: --check, -c : performs a syntax check of the <input_file> --echo, -e : echos the <input_file>, and make all defaults explicit The input is also checked, but only a failure is reported --help, -h : writes this message --html-manual : writes a HTML reference manual of the CP2K input in the current directory. The file index.html is a good starting point for browsing --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
Now you can run cp2k using:
$ cp2k.sopt -i cp2k.inp -o cp2k.out &
Another program we need for visualization is VMD.
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:
Two new windows named
VMD Main and
VMD 1.9.2 … Display should open on your local machine while the server shows:
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 email@example.com 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 >
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:
vmd > quit
Part III: Advanced account configuration
Make module loading persistent
Upon login, the shell (
bash in our case) executes a number of files if they exist. One of them is the
.bashrc. To prepare it for management using the the
module command, simply execute the following once:
$ echo 'module load ' >> ~/.bashrc
after that you can add and remove modules to be loaded at startup using
module initadd or
cp2k, run for example:
$ module initadd vmd $ module initadd cp2k/r17408_2016_09_19
vmd again from the list of modules to load:
$ module initrm vmd
Alternatively you can of course simply edit
.bashrc using your favorite editor and add a line like
module load vmd cp2k/r17408_2016_09_19 by yourself.
Setup key-based authentication
To avoid having to type the password every time you log in (and to increase the security), keys can be used for authentication instead. The following instructions are for OSX and Linux.
First generate a key-pair on your local machine using
and accept the defaults proposed and do not set a password.
Upload the public key from your local machine to tcopt3:
$ scp ~/.ssh/id_rsa.pub studentXX@tcopt3.chem.uzh.ch:~/
Now login to
tcopt3.chem.uzh.ch and move the uploaded public key to the right place:
$ mkdir -p .ssh $ chmod 0700 .ssh $ mv id_rsa.pub .ssh/authorized_keys
When connecting to the server from your local machine now, use:
$ ssh -i ~/.ssh/id_rsa studentXX@tcopt3.chem.uzh.ch
Simplify the login
The following instructions apply apply to OSX and Linux.
On your local machine add the following part to the file
.ssh/config in your home directory:
Host tcopt3 HostName tcopt3.chem.uzh.ch User studentXX
after which you will be able to connect to
tcopt3 simply by using
$ ssh tcopt3
If you have setup key-based authentication as shown above, augment the entry to the following instead, to always use key-based authentication without having to specify
-i ~/.ssh/id_rsa manually:
Host tcopt3 HostName tcopt3.chem.uzh.ch User studentXX IdentityFile ~/.ssh/id_rsa IdentitiesOnly yes PreferredAuthentications publickey