Working abroad

Sometimes for some reason some VPN might not work as one expects. Then one can login to a node with a key.

First, check if you have a public key already. On your own computer in a terminal run:

cat ~/.ssh/

If this command worked, then skip the next step. If an error appeared, run this:


It will ask for a password. This is the password you give to the key. You can make one without password, in which case it will not ask for a password each time you try to use it.

You must have an access to the cluster somehow to run the following command:

ssh-copy-id <your-username>@cluster

This trick does not work for all machines. So, you might use the established connection to connect to other machines. In my case I wanted to work with some notebooks, so I did:

ssh -N -L localhost:PORT1:localhost:PORT2 <your-username>@cluster

and so it worked.

Installing Gromacs and Lammps


./configure –enable-float –enable-shared –enable-sse2
make -j N
make install



$ tar xvfz gromacs-x.y.z.tar.gz
$ ls
$ mkdir build
$ cd build
$ cmake ../gromacs-x.y.z -DCMAKE_INSTALL_PREFIX=/home/yourUser/opt/gromacs.x.y.z -DGMX_CPU_ACCELERATION=SSE2 -DGMX_SIMD=SSE2
$ make -j N
$ make install



$ git clone git:// LAMMPS
$ make yes-molecule
$ make mpi


To the .bashrc add:


source /home/yourUser/opt/gromacs.x.y.z/bin/GMXRC
#or source /your/installation/prefix/here/bin/GMXRC

export PATH=~/LAMMPS/src:$PATH

gsissh at ubuntu

To access one of the PRACE supercomputers, I was required to use gsissh. The corresponding gsi-openssh-clients package is not in the standard Ubuntu repositories. I have downloaded it from that also globus-proxy-utils is needed. This one was easy to install via apt-get install globus-proxy-utils. Finally, everything got working when the bundle of X509 trusted certificates was downloaded from Note, for some reason .globus folder did not appear in my home directory. To use gsissh, I had to create it and then move my user certificate to it with proper correct permissions -rw-------.

P.S. Do not forget to create a proxy certificate (grid-proxy-init) before login to your supercomputer.