File system

Users of SCAYLE's HPC calculation systems have two predefined file systems at their disposal to carry out their work.
Each user of the system has access to the $HOME, $SOFT and $SCRATCH directories. These directories are stored in SCAYLE's storage systems and are designed to allow high-performance access to data and programs from the calculation nodes in the execution of parallel programs.

This directory is the initial working directory when the user logs on to the system. The absolute path is /home/user/user_group. It is of private access for the user, that is to say, no other user will be able to access the information contained in it. All calculation nodes and frontends have access to it.
To return to this directory from anywhere in the file system, the user can execute any of the following commands:

 frontend$ cd
 frontend$ cd ~ 
 frontend$ cd $HOME

For projects that have requested multiple user accounts, there is an additional resource accessible via the $HOME_GROUP environment variable that allows all those users to access information shared by the project.
The structure of the group directories and group users is:

 /home 
    /group
         /COMUNES ($HOME_GROUP) 
         /user ($HOME) 
         /user2 ($HOME) 
         ... 
         /userN ($HOME)

This environment variable corresponds to the absolute path /soft. Inside this directory are installed the programs that the users have for their work. An example of its content is:

 $ ls -la /soft 
 total 132 
 drwxr-xr-x 4 user group 4096 nov 20 11:08 bedtools
 drwxr-xr-x 4 user group 4096 oct 29 14:08 blast 
 drwxr-xr-x 4 user group 4096 oct 21 12:27 boost_c++ 
 drwxr-xr-x 4 user group 4096 oct 21 11:49 bowtie2 
 drwxr-xr-x 4 user group 4096 oct 22 17:37 cmake 
 drwxr-xr-x 3 user group 4096 abr 18 2013 COMPSs 
 drwxr-xr-x 4 user group 4096 nov 5 14:38 cufflinks 
 drwxr-xr-x 4 user group 4096 nov 21 17:25 emboss
 drwxr-xr-x 5 user group 4096 oct 17 18:53 gcc 
 drwxr-xr-x 16 user group 4096 may 20 2013 gipsy 
 drwxr-xr-x 9 user group 4096 sep 10 13:25 intel 
 drwxr-xr-x 4 user group 4096 sep 9 12:37 joe 
 drwxr-xr-x 4 user group 4096 nov 6 10:09 microbiomeutil 
 drwxr-xr-x 4 user group 4096 oct 30 10:19 mira 
 drwxrwxr-x 6 user group 4096 sep 16 13:34 Modules 
 drwxr-xr-x 4 user group 4096 oct 29 14:48 mpiBlast 
 drwxrwxr-x 11 user group 4096 oct 24 13:34 OpenFOAM 
 drwxrwxr-x 6 user group 4096 oct 22 13:00 openmpi

Within the directory of a program there are one or more directories with the different versions of the program, for example:

  [user@frontend1 ~]$ cd /soft/openmpi/; ll 
  total 16 
  drwxr-xr-x 7 user group 4096 oct 22 12:53 1.4.2 
  drwxr-xr-x 7 user group 4096 oct 17 19:12 1.6 
  drwxr-xr-x 7 user group 4096 oct 17 16:24 1.6.5 
  drwxrwx--- 2 user group 4096 oct 22 12:57 sources

three different versions 1.4.2, 1.6 and 1.6.5 are installed inside the OpenMPI software directory.

$SCRATCH is the working directory for users. It has the same directory structure as $HOME. All input and output files of job runs should go here. It is the user's responsibility to delete the files once their execution is complete. There are no disk quotas in $SCRATCH but, to avoid abuse, an automatic process can delete any file that has not been accessed for more than 45 days .

In short:

This working path must be the storage place to store large files as input and output data for calculations.
There will be no backup of the data stored in $SCRATCH.
IMPORTANT: Do not install any software (executables, scripts, job submission scripts, etc.) in this path as it can be deleted.