Workstation tips

Remote connection

Typically, work on the workstation is done from your notebook or remote desktop.

General procedure for the remote connection

Required software

It is mandatory the installation of the software GlobalProtect from the UNITO intranet network (VPN - Accesso da remoto - Servizi - Intranet UNITO).

Ask to your director for the VPN activation.

Download and install the free version of MobaXTerm (MobaXterm Xserver with SSH, telnet, RDP, VNC and X11 - Download (mobatek.net))

Remote connection

Run GlobalProtect and login using the UNITO credentials to activate the VPN
Run MobaXTerm
The first time you have to create a New Session

Menu Session - New Session

Click on SSH icon
Specify the remote host IP (ask to the director)
Specify the username (it is not mandatory, you can specify it later)
Click ok
A terminal window appears

Specify your login name that you uses on the workstation

The credentials on the workstation are not the UNITO credentials
Workstation credential are released from CASSMedChem director

Bash shell is opened with your environment

Background job

Many jobs take a long time, so it is advisable to run the job in background and close the MobaXterm session.

To do this you need to use nohup and & commands following the general syntax:

nohup COMMAND &

e.g.:

nohup oeomega classic -commentEnergy true -ewindow 10 -maxconfs 1000000 -strict -in mol_sz.mol2 -out mol_oel.mol2 -prefix mol_oel -mpi_np 4 &

WARNING: background jobs ONLY works if you exit the MobaXterm session using CRTL d keys sequence. If you exit by clicking on the cross at the top right of the MobaXterm window or using OTHER METHODS, the JOB STOPS.

Some basic Linux commands

Basic syntax

The basic syntax of a Linux command is: command option variables

Often, the option are letters following minus symbol
E.g. ls -l ./ : where ls is the command, -l is the option and ./ is the variable

Working with the file tree

To know where you are

pwd

You can see the directory where your are (i.e. at the beginning your are in your home directory /home/yourusername)

Copy command

cp file1 file2

copy file1 in file2

cp -rL source.file destination.file

-r: recursively option
-L: copy the original file that is linked with as symbolic link

man command

show help for the command

nvidia-smi

monitoring Nvidia GPU
in particular, chem GPU-Util that show the percentage of utilization of the CPU

module

The setup of the environment can be done using the module tool installed by Aethia

Use

To setup an environment present in the modulefiles

module load modulefile

Checking the list of the modulefiles

module avail

Showing the list of loaded modules

module list

Setup of a new modulefile

Modulefiles are located in two directories

/usr/share/Modules/modulefiles
/etc/modulefiles

In such directories, some sub-directories contain the modulefiles that will be loaded with module tool.

New modulfiles added in such directories are immediately recognized by the module tool.

To use the correct syntax, it is better to copy an old file and modified it.

Warning: check the permissions of sub-directories (drwxr-xr-x) and modlefiles (-rw-r--r--)