Each grant has a Unix group associated with it. Every file is "owned" by a Unix group, and that file ownership determines which grant is charged for the file space. See Managing multiple grants for a further explanation of Unix groups, and how to manage file ownership if you have more than one grant. If you have multiple grants on Bridges, you should ensure that the work you do under each grant is assigned correctly to that grant. The files created under or associated with that grant should belong to it, to make them easily available to others on the same grant. Unix groups determine which pylon5 allocation the storage space for files is deducted from, and who owns and can access a file or directory.
One of your grants has been designated as your default grant, and the account id and Unix group associated with the grant are your default account id and default Unix group. When a Bridges job runs, any SUs it uses are deducted from the default grant. Any files created by that job are owned by the default Unix group. It will display all the grants you belong to. It will also list your default account id called charge id in the projects output at the top. Your default Unix group is the same. In this example, the user has two grants with account ids account-1 and account The default account id is account To use a grant other than your default grant on Bridges, you must specify the appropriate account id with the -A option to the SLURM sbatch command.
Note that using the -A option does not change your default Unix group. Any files created during a job are owned by your default Unix group, no matter which account id is used for the job, and the space they use will be deducted from the pylon allocation for the default Unix group. To temporarily change your Unix group, use the newgrp command. Any files created subsequently during this login session will be owned by the new group you have specified. Their storage will be deducted from the pylon allocation of the new group. After logging out of the session, your default Unix group will be in effect again.
Note that the newgrp command has no effect on the account id in effect. Any Bridges usage will be deducted from the default account id or the one specified with the -A option to sbatch.
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Your default account id changes immediately. Bridges use by any batch jobs or interactive sessions following this command are deducted from the new account by default. Your default Unix group does not change immediately. It takes about an hour for the change to take effect. You must log out and log back in after that window for the new Unix group to be the default. There are several ways to track your Bridges usage: the xdusage command, the projects command, and the Grant Management System.
Type man xdusage on Bridges for information. The projects command shows information on all Bridges grants, including usage and the pylon directories associated with the grant. You can search the Knowledge Base to get help. Some common questions:. This command is only available on the login nodes. You must log out and back in again for the new shell to take effect.
Three months after your grant expires all of your Bridges files associated with that grant will be deleted, no matter which file space they are in. You will be able to login during this 3-month period to transfer files, but you will not be able to run jobs or create new files.
Access to files in any Bridges space is governed by Unix file permissions. If your data has additional security or compliance requirements, please contact compliance psc. For detailed information on Unix file protections, see the man page for the chmod command. To share files with your group, give the group read and execute access for each directory from your top-level directory down to the directory that contains the files you want to share:.
If you want more fine-grained control than Unix file permissions allow, e. Suppose, for example, that you want to give janeuser access to a file in a directory, but no one else in the group. Then give janeuser access to the specific file with:. User janeuser will now be able to read this file, but no one else in the group will have access to it.
This is your Bridges home directory. It is the usual location for your batch scripts, source code and parameter files. Your home directory is visible to all of the Bridges nodes.
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Your home directory is backed up daily, although it is still a good idea to store copies of your important files in another location, such as the pylon5 file system or on a local file system at your site. If you need to recover a home directory file from backup send email to remarks psc.
One last thing…
The process of recovery will take 3 to 4 days. Your home directory has a 10GB quota. You can check your home directory usage using the quota command or the command du -sh. To improve the access speed to your home directory files you should stay as far below your home directory quota as you can.
Three months after a grant expires, the files in your home directory associated with that grant will be deleted. Pylon5 is a Lustre file system shared across all of Bridges' nodes. The pylon5 file system is persistent storage, and can be used as working space for your running jobs. It provides fast access for data read or written by running jobs. Files on pylon5 are not backed up, so you should store copies of important pylon5 files in another location. Use the id command to find your group name. If you have more than one grant, you will have a pylon5 directory for each grant. Be sure to use the appropriate directory when working with multiple grants.
Your usage quota for each of your grants is the Pylon storage allocation you received when your proposal was approved. If your total use in pylon5 exceeds this quota your access to the partitions on Bridges will be shut off until you are under quota. Use the du -sh or projects command to check your pylon5 usage. If you have multiple grants, it is very important that you store your files in the correct pylon5 directory.
Three months after a grant expires, the files in any pylon5 directories associated with that grant will be deleted. Each Bridges node has a local file system attached to it. This local file system is only visible to the node to which it is attached. The local file system provides fast access to local storage. Once your job finishes, your local files are inaccessible and deleted.
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The maximum amount of local space varies by node type. The following script is an example of how to do this:. This code will try at most 20 times to copy your files. If it succeeds, the loop will exit.
If an invocation of rsync was unsuccessful, the loop will try again and pick up where it left off. The following script will do this:. This code fragment copies your files to a directory in your pylon5 file space named results, which you must have created previously with the mkdir command.
Again it will loop at most 20 times and stop if it is successful. The amount of memory space available to you depends on the size of the memory on the nodes and the number of nodes you are using. If you do not use all of the cores on a node, you are allocated memory in proportion to the number of cores you are using.
Once your job ends this space is inaccessible. If your job terminates abnormally, your memory files are lost. Use the command du -sh to see how much space you are using. For all file transfer methods other than cp, you must always use the full path for your Bridges files. The start of the full paths for your Bridges directories are:. The command id -Gn will show all of your valid Unix-groups.
You have a pylon5 directory for each grant you have. Your home directory quota is 10GB, so large files cannot be stored there; they should be copied into one of your pylon file spaces instead. Exceeding your home directory quota will prevent you from writing more data into your home directory and will adversely impact other operations you might want to perform.https://meister-walter.de/images/2019-10-01/cepa-handy-verloren-orten.php
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You can use the rsync command to copy files to and from Bridges. A sample rsync command to copy to a Bridges directory is. Substitute your userid for 'joeuser'. Make sure you use the correct group name in your target directory. By default, rsync will not copy older files with the same name in place of newer files in the target directory.
It will overwrite older files.
We recommend the rsync options -rltDvp. See the rsync man page for information on these options and other options you might want to use. We also recommend the option.
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