How to schedule tasks (e.g the execution of a shell
script or a gromacs command) using the crontab command, for example the transfer of files from a remote host using
sftp/scp.

First you define the text editor you want to use for editing the crontab
file, where the scheduling is defined

export EDITOR=nedit (or your favourite text editor)

Then, you edit the crontab file by issuing

crontab -e

A crontab file entry has the following format

minute (0-59) hour (0-23, 0 = midnight) day (1-31) month (1-12) weekday
(0-6, 0 =
Sunday) command
Example:

55 22 21 12 6 cd /home/george/Arp23/; bash do_sftp

On Saturday (day 6), 21st of December at 22:55 the cron daemon will do the
following:

 - Change to dir /home/george/Arp23/
 - Execute the do_sftp script located in this dir

You can have as many commands separated by the character ;
as you want.

Please don't forget the cd command as shown above because cron executes
commands by
default in the home dir

If you want to run a GROMACS command, make sure to source the version you
want to
use, like for example

55 22 21 12 6 cd /home/george/Arp23/; source
gromacs-installation-dir/bin/GMXRC;
g_cluster -s ...

To download from the CURIE cluster in France, the do_sftp script mentioned
above
will look like this

#! /bin/bash
sshpass -p 'password' sftp [email protected] << !
cd /ccc/work/cont005/ra1260/patargig/act_MG_DUMMY
get prod1_out*
bye
!

This script downloads all files that contain "prod1_out" in their name.The
program sshpass is used for establishing an ssh/sftp connection non
interactively. If it is not installed in your machine, you issue

sudo apt-get install sshpass

In this way, we can transfer files after working hours but the fact that
the password is contained in plain text in the script, poses a security
risk.

George