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Steps to Migrate to the New Home System Manually

If you are currently using more than 100GB of space in your home directory, you will need to take some manual steps to migrate to the new home system. Since all quotas on the new system are a maximum of 100GB of space, you will need to choose what to copy over to the new system.

Steps

Migrating to the new system consists of two steps:

  1. Moving files
  2. Initiating the transfer

Moving files

There are two workflows for moving files. Choose the tab below that best matches your situation.

  1. Check your home space usage with the powertool file-sizes:

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    module load powertools/1.3.9
file-sizes --detail

    Take note of how much space you are using over 100GB.

    Important: don't use the quota command or any other tool to check your usage

    There is a difference between the way that the old and new home systems compress files. The output from the quota command and most other tools will therefore be inaccurate on the old home system.

    Please only use the file-sizes command described above to get usage information that will be more accurate for the new home system.

    You can also use this tool to view how the space is being used within a directory, e.g.,

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    file-sizes --detail ~/project

    to break down the space usage within ~/project.

  2. Move excess files manually. There are a few choices:

    • Move files to a shared research space. If your PI does not have one that you have access to, please ask them to create one or update your membership using this form. Each PI can request up to 3TB of space for free. See additional information for using research spaces below.
    • Delete files that you are no longer using.
    • Sync files to a non-HPCC location (like a personal computer, OneDrive, etc) and remove them from the HPCC. The recommended tool for this is Globus.
    • As a last resort, you may consider temporarily using your scratch space. However, this is not recommended, as any files you move here will be deleted within 45 days. This should only be used as a temporary measure while implementing one of the solutions above.

  3. After repeating Step 1 and verifying that you are using less than 100GB in your home directory, you can sync the entire contents of your home directory using these steps:

    1. Go to Globus
    2. Log in with MSU credentials
    3. Select the File Manager tab
    4. Select the Collection "Michigan State University MSU ICER msu#hpcc msuhpcc" on both sides
    5. On the left, navigate to /mnt/ufs18/gpfs-home/<USER> replacing <USER> with your MSU username
    6. On the right, navigate to /mnt/ffs24/home/<USER> replacing <USER> with your MSU username
    7. On the left, check the "select all" box
    8. On the left, click the Start button
    9. You will receive an email when your sync is complete

    The File Manager setup is depicted in this screenshot:

    The Globus file manager with the Collection and Paths set as described above. The "select all" checkbox and left-side "Start" button are circled.

    Use the command:

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    rsync -avP /mnt/ufs18/gpfs-home/$USER/ /mnt/ffs24/home/$USER/

    Note that the trailing slashes are necessary. If your sync is interrupted for any reason, you can restart it using the same command.

  1. Select directories you wish to copy to the new home system.

  2. Copy these directories manually using these steps:

    1. Go to Globus
    2. Log in with MSU credentials
    3. Select the File Manager tab
    4. Select the Collection "Michigan State University MSU ICER msu#hpcc msuhpcc" on both sides
    5. On the left, navigate to /mnt/ufs18/gpfs-home/<USER> replacing <USER> with your MSU username
    6. On the right, navigate to /mnt/ffs24/home/<USER> replacing <USER> with your MSU username
    7. On the left, check the boxes next to all files/directories you would like to copy
    8. On the left, click the Start button
    9. You will receive an email when your sync is complete

    The File Manager setup is depicted in this screenshot:

    The Globus file manager with the Collection and Paths set as described above. The left-side "Start" button is circled.

    Suppose you wish to only copy the directory ~/project to your new home directory. Use the command:

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    rsync -avP /mnt/ufs18/gpfs-home/$USER/project /mnt/ffs24/home/$USER/

    Repeat for any other directories or files you would like to keep. Note that if you remove any files in your old home and want to resync this directory, you should use the --delete option, like

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    rsync -avP --delete /mnt/ufs18/gpfs-home/$USER/project /mnt/ffs24/home/$USER/

    This will ensure that these deletions are replicated in your new home directory.

    Transferring files that are too large

    If you transfer files that total more than 100GB to your new home directory, you will exceed your quota. In this case, you will have to remove those files from your new home directory before trying again with fewer files.

  3. Note that all files that you do not copy will be removed from the system.

Initiating the transfer

To start the transition, you just need to tell ICER that you are ready for your home directory to be moved. Note that you will not be able to use the HPCC for up to 30 minutes while this is taking effect, and any running jobs will not function as expected.

Do not access HPCC while home directory is being moved

After completing the step below, you should:

  1. Ensure you have no running or queued SLURM jobs with

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    scancel --me

  2. Log out of the HPCC (including all OnDemand and tmux/screen sessions)

  3. Wait up to 30 minutes for an email confirming that your home directory migration is complete
  1. Go to your home directory in the OnDemand File Browser
  2. Click the button that says "New File"
  3. Name the file .move.my.home (note that the initial . is important)!

The process is depicted in this screenshot:

The OnDemand file browser with the New File dialog open, and the filename .move.my.home entered.

Run the command:

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touch ~/.move.my.home

Tips

Managing files graphically via OnDemand

You can also use OnDemand's file browser to perform many operations like moving, copying, and deleting files. You can also download files to your personal computer, though this is limited to files that are 1GB or smaller.

However, note that the file sizes reported on OnDemand may be inaccurate on the new home system. Please use the file-sizes powertool, e.g., by starting a new command line via the Development Nodes tab, and running the commands

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module purge
module load powertools/1.3.9
file-sizes --detail

Managing files on the command line

  • To move files on the command line use the mv command:

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    mv ~/project ~/other_project_location

    Don't use mv with research spaces

    Using mv with a research space may preserve undesired group ownership. It is better to copy to a research space first (e.g., using cp), then delete the original version (e.g., using rm).

  • To copy files on the command line, use the cp command. When you are copying a directory, you need to use the -r option to copy everything inside:

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    cp -r ~/project /mnt/research/my_group

    You can also use the rsync command as shown above for a more robust option.

  • To remove files on the command line, use the rm command. When you are removing a directory, you need to use the -r option to remove everything inside. Be careful with using rm because deletions cannot be undone:

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    rm -r ~/project

Moving files to research spaces

We recommend checking with your PI to see if there are any conventions for moving files to your shared research space (e.g., putting your files underneath a directory with your username).

The most important considerations when using research spaces are to:

  1. Use the newgrp command to change to the corresponding research group before copying any files
  2. Copy files and remove the originals rather than move them directly

For example, to move the directory ~/my_project from the home space to the research space /mnt/research/my_group, use the commands:

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newgrp - my_group  # Change group to match the research space
cp -r ~/my_project /mnt/research/my_group  # Copy files
ls /mnt/research/my_group  # Check files transferred correctly
rm -r ~/my_project  # Remove the originals

Before moving files to research spaces please see our additional tips for Using Research Spaces.