File system

Users of SCAYLE HPC computing systems have two predefined file systems to perform their work (frontend11-frontend12). Each system user has access to the $HOME, $SOFT and $SCRATCH directories.

These directories are stored on SCAYLE storage systems and are designed to allow high-performance access to data and programs from compute nodes in parallel program execution.


When the user logs into the system he is redirected to his home working directory $HOME. The absolute path is /home/user_group/user.
It is private access for the user, i.e., no other user will be able to access the information contained within the directory. Each user will have 50GB available in $HOME and will be able to store maximum 10,000 inodes. All compute nodes and login computers (frontend) have access to this directory.

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 directory structure of the group and the users of the group is:

 /home 
    /group
         /COMUNES ($HOME_GROUP) 
         /user1 ($HOME) 
         /user2 ($HOME) 
         ... 
         /userN ($HOME)


This environment variable corresponds to the absolute path /soft. Within this directory are installed the programs available to the users 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 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 apr 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 in the software directory OpenMPI .


This work path must be the storage location for saving large files as input and output data for calculations. No backup of the data stored in $SCRATCH will be performed.

It has the same directory structure as $HOME, but with the following features:

  • All input and output files from job runs must go here.
  • It is the user's responsibility to delete files after execution is complete.
  • There are no disk quotas in $SCRATCH but, to prevent abuse, an automatic process may delete any file that has not been accessed for more than 45 days .

IMPORTANT: Do not install any software (executables, scripts, job submission scripts, etc.) in this path as it may be deleted.


Last update: 06/02/2025 13:09