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The CheckPointing software DMTCP https://dmtcp.sourceforge.io is available in O2.
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DMTCP software is NOT guaranteed to work or to support all applications and languages. A given process might fail to run or restart from a saved checkpoint. We strongly encourage you to test DMTCP on your workflow before depending on it. |
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The process of CheckPointing consists in creating periodic snapshots of the running process and the active memory (RAM). Those snapshots can then be used to restart the execution of that process from the recorded point. The process is similar to creating manual restart points inside your code by saving important data with a given period. However, it is handled outside your code by the DMTCP software. It attempts to save all relevant data, allowing you to restart (e.g. after a crash) and get the same results you would have gotten by simply running the original program to completion.
How does it work
The two most common approaches for using DMTCP are to either checkpoint your execution at a given constant interval or to manually initiate checkpointing from within the code (when possible).
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where CKP_FREQ is the checkpointing frequency in seconds and your_program is the command you need to run within the job. In this case DMTCP will create a memory checkpoint every CKP_FREQ seconds. (See the CAUTION below about choosing CKP_FREQs that are too small.)
Custom CheckPointing:
It is also possible to manually create checkpoints by starting the command without specifying an interval
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def main():
# something here
for it in range(0,some_number_here):
print(it)
# do something here that takes
# a very long time
os.system('dmtcp_command --checkpoint')
if __name__ == '__main__':
main() |
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CAUTION: The creation of a checkpoint is a potentially time consuming process that can also generate very large files, depending on the RAM (memory) used by the running processes. When a checkpoint is created DMTCP will write to file all data currently loaded in RAM. Therefore, a job using ~100GB of RAM will create a similar size of data, which could fill up your storage quota. |
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from the folder where the job’s checkpoint was created. The file dmtcp_restart_script.sh is created by the DMTCP software.
You can also build a script that will automatically restart a program from its last checkpoint if one is available using a sbatch script like:
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with the assumption that each job is executed in a separate folder and therefore no dmtcp_restart_script.sh file is present when a job is dispatched the first time.
If you start a job with the above template and you don’t want it to restart from the saved checkpoints make sure to delete any local file created by DMTCP.
Important additional information
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