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This user's guide is intended to provide the minimum amount of information needed by a new user of this system. As such, it assumes that the user is familiar with basic notions on scientific computing, in particular the basic commands of the Unix operating system, and also with basic techniques for the execution of applications in a supercomputer.
The information in this guide includes basic technical documentation about the the software environment, and also on available applications.
Please read it carefully and if any doubt arises don't hesitate to contact our support mail (see below in Support).
Batch System
The Batch System is based on CentOs 7 machines, running on x86_64.
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Usage
The $HOME directories are shared between the UIs and the computing nodes.
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Connecting to Login1 and Login2
This cluster is comprised of a pool of machines reachable through a single entry point. The connections to the internal machines are managed by a director node that tries to ensure that proper balancing is made across the available nodes at a given moment.
Please note that this cluster is not intended for the execution of CPU intensive tasks, for this purpose use any of the available computing resources. Every process spawned is limited to a maximum CPU time of 2 hours.
Login on these machines is provided via Secure Shell. Outgoing SSH connections are not allowed by default from this cluster. Inactive SSH sessions may be closed after 12h. It is highly recommended that you set up SSH Keys for authentication, instead of using your username and password.
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Hostname
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Operating System
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SSH server key fingerprint
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CentOs 7
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SHA256:iuRWTlWP7db1cM0d58m5TyGzPnZoDCNoBM3RuTtxddU
There is a projects shared area (located at /gpfs/projects/), also accessible from the UI and the computing nodes. If your group does not have this area, please open an Incidence ticket.
The shared directories are not intended for scratch, use the temporal areas of the local filesystems instead. In other words, instruct every job you send to copy the input from the shared directory to the local scratch ($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.
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).
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INFORMATION ABOUT YOUR CURRENT DISK USAGE
USER Used Soft Hard Doubt Grace
Space (GB): 3.41 50.00 0.00 0.06 none
Files (x1000): 64 0 0 0 none
GROUPUsage
The $HOME directories are shared between the UIs and the computing nodes. There is a projects shared area (located at /gpfs/projects/), also accessible from the UI and the computing nodes. If your group does not have this area, please open an Incidence ticket.
The shared directories are not intended for scratch, use the temporal areas of the local filesystems instead. In other words, instruct every job you send to copy the input from the shared directory to the local scratch ($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.
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).
********************************************************************** Used INFORMATION ABOUTSoft YOUR CURRENT DISK USAGE USER Hard Doubt Used Soft Hard Doubt Grace Space (Grace Space (GB): 30.4100 501000.00 000.00 0.0600 none Files (x1000): 640 0 0 0 none GROUP Used Soft Hard Doubt Grace Space (GB): 0.00 1000.00 00.00 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 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.
Connecting to Grid cluster
This cluster is comprised of a pool of 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 is limited to a maximum CPU time of 2 hours.
Login on these machines is provided via Secure Shell. Outgoing SSH connections are not allowed by default from this cluster. Inactive SSH sessions may be closed after 12h. It is highly recommended that you set up SSH Keys for authentication, instead of using your username and password.
Hostname
Operating System
SSH server key fingerprint
CentOs 7
SHA256:iuRWTlWP7db1cM0d58m5TyGzPnZoDCNoBM3RuTtxddU
Batch System
The Batch System is based on CentOs 7 machines, running on x86_64.
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 SlurmFor further information you can read the mmlsquota command manual page.
SLURM Concept
SLURM manages user jobs with the followingkey characteristics:
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