IFCA Datacenter usage guidelines

1. Introduction

The GridUI (Grid User Interface) cluster is the interactive gateway to the Advanced Computing and e-Science resources at IFCA. This cluster is comprised of a pool of Scientific Linux machines reachable through a single entry point. The connections to the internal machines are managed by a director node that tries to ensure that proper balancing is made across the available nodes at a given moment.

Please note that this cluster is not intended for the execution of CPU intensive tasks, for this purpose use any of the available computing resources. Every process spawned are limited to a maximum CPU time of 2 hours.

Login on these machines is provided via Secure Shell. The RSA key fingerprint of them is 46:85:91:c1:eb:61:55:34:25:2c:d6:0a:08:22:1f:77.

Outgoing SSH connections are not allowed by default from this cluster. Inactive SSH sessions will be closed after 12h.

2. Authentication

Authentication is centralized via secured LDAP. All the changes made to a user account in one node take immediate effect in the whole cluster. There is also a secured web interface, that allows a user to change his/her details, available at https://cerbero.ifca.es/. If you need to reset your account password, please contact the system administrators.

With this username you should be able to access also the ticketing system at http://support.ifca.es/

3. Grid resources

As the several virtual organizations supported use its own set of resources, it is commonly required to set up the correct environment variables in order to use the grid tools. Environment scripts are located under /nfs4/usr/etc/env/:

$ source /nfs4/usr/etc/env/ibergrid-env.sh

4. PBS Cluster

PBS cluster was decommissioned in December 2009. Please use the new SGE Cluster instead.

5. SGE Cluster

The SGE Cluster is based on Scientific Linux CERN SLC release 5.5 machines, running on x86_64. The exact number or resources available is shown on the monitorization page.

Local submission is allowed for certain projects. As stated below, there are some shared areas that can be accessed from the computing nodes. The underlying batch system is Son of Grid Engine 8.0.0d. Refer to the following sources for information:

• Using /GridEngine.

• Some useful HOWTOS.

• SGE basic usage.

6. Shared areas

The $HOME directories (/home/$USER) are shared between the UIs and the computing nodes. There is a projects shared area (located at /gpfs/csic_projects/), also accessible from the UI and the computing nodes. If your group does not have this area, please open an Incidence ticket.

6.1. Usage

The shared directories are not intended for scratch, use the temporal areas of the local filesystems instead. In other words, instruct every job you send to copy the input from the shared directory to the local scratch ($TMPDIR), execute all operations there, then copy the output back to some shared area where you will be able to retrieve it comfortably from the UI.

As mentioned above, the contents of $TMPDIR are removed after job execution.

6.2. Disk quotas

Disk quotas are enabled on both user and projects filesystems. A message with this information should be shown upon login. If you need more quota on your user space (not in the project shared area), please contact the system administrators explaining your reasons.

If you wish to check your quota at a later time, you can use the commands mmlsquota gpfs_csic (for user quotas) and mmlsquota -g id -g gpfs_projects (for group quotas). A script reporting both quotas is located on /nfs4/usr/bin/rep-user-quotas.py. A sample output of the latter could be:

**********************************************************************
                    INFORMATION ABOUT YOUR CURRENT DISK USAGE

USER                Used      Soft      Hard     Doubt     Grace
Space (GB):         3.41     20.00      0.00      0.06      none
Files (x1000):        64         0         0         0      none

GROUP               Used      Soft      Hard     Doubt     Grace
Space (GB):         0.00   1000.00   1500.00      0.00      none
Files (x1000):         0         0         0         0      none
**********************************************************************

For a basic interpretation of this output, note that the "Used" column will tell you about how much disk space you are using, whereas "Soft" denotes the limit this "Used" amount should not exceed. The "Hard" column is the value of the limit "Used" plus "Doubt" should not cross. A healthy disk space management would require that you periodically delete unused files in your $HOME directory, keeping its usage below the limits at all times. In the event that the user exceeds a limit, a grace period will be shown in the "Grace" column. If the user does not correct the situation within the grace period, she will be banned from writing to the disk.

For further information you can read the mmlsquota command manual page.

7. Extra utils/Software

Some extra packages as latest Python versions and Intel Non-Commercial Compilers can be found at /nfs4/opt/. Here also is the preferred location for some other piece of software commonly used like:

• Matlab's like octave language for numerical anaylisis.

• Data plotting gnuplot program.

• Profiling and debugging valgrind tools.

Please note that these packages are provided as-is, without further support from IFCA staff.

8. Support

Before opening a new incidence, please check the Frequently Asked Questions page

Questions, support and/or feedback should be directed through the use the Helpdesk.

CategoryUserSupport CategoryLocalCluster