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DMTCP

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​Distributed Multithreaded checkpointing (DMTCP) checkpoints a running program on Linux with no modifications to the program or OS. It allows to restart running the program from a checkpoint. 
Modules
To access dmtcp, load a dmtcp module. For example:
module load dmtcp/2.6.0
Example Programs
The following example programs can be copied from /gpfs/runtime/oftware_examples/dmtcp/
dmtcp_serial
dmtcp_serial.c
dmtcp_serial_job.sh
Basic Usage
Launch a Program
The dmtcp_lanuch command launches a program, and automatically checkpoints the program. To specify the interval (seconds) for checkpoints, add the "-i num_seconds" option to the dmtcp_lauch command. 
Example: the following command launches the program dmtcp_serial and checkpoints every 8 seconds.
$port=$(shuf -i 40000-60000 -n 1)
$dmtcp_launch -p$port -i 8 ./dmtcp_serial  
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^C
[yliu385@node1317 interact]$ ll
total 2761
-rw------- 1 yliu385 ccvstaff 2786466 May 18 11:18 ckpt_dmtcp_serial_24f183c2194a7dc4-40000-42af86bb59385.dmtcp
lrwxrwxrwx 1 yliu385 ccvstaff      60 May 18 11:18 dmtcp_restart_script.sh -> dmtcp_restart_script_24f183c2194a7dc4-40000-42af82ef922a7.sh
-rwxr--r-- 1 yliu385 ccvstaff   12533 May 18 11:18 dmtcp_restart_script_24f183c2194a7dc4-40000-42af82ef922a7.sh
-rwxr-xr-x 1 yliu385 ccvstaff    8512 May 18 08:36 dmtcp_serial
As shown in the example above, a checkpoint file (ckpt_dmtcp_serial_24f183c2194a7dc4-40000-42af86bb59385.dmtcpp) is created, and can be used to restart the program
Restart from a checkpoint
The dmtcp_resart command restarts a program from a checkpoint, and also automatically checkpoints the program. To specify the interval (seconds) for checkpoints, add the "-i num_seconds" option to the dmtcp_restart command. 
Example: the following command restarts the dmtcp_serial program from a checkpoint, and checkpoints every 12 seconds
$port=$(shuf -i 40000-60000 -n 1)
$dmtcp_restart -p $port -i 12 ckpt_dmtcp_serial_24f183c2194a7dc4-40000-42af86bb59385.dmtcp 
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^C
[yliu385@node1317 interact]$ dmtcp_restart -p $port -i 12 ckpt_dmtcp_serial_24f183c2194a7dc4-40000-42af86bb59385.dmtcp 
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^C
​
Batch Jobs
It is desirable goal that single job script can 
launch a program if there is checkpoints, or
automatically restarts from a checkpoint if there is one or more checkpoints
The job script dmtcp_serial_job.sh below is an example which shows how to achieve the goal:
If there is no checkpoint in the current directory, launch the program dmtcp_serial 
If one or more checkpoints exist in the current directory, restart the program dmtcp_serial from the latest checkpoint
$ cat dmtcp_serial_job.sh 
#!/bin/bash
​
#SBATCH -n 1
#SBATCH -t 5:00
#SBATCH -J dmtcp_serial
​
checkpoint_file=`ls ckpt_*.dmtcp -t|head -n 1`
checkpoint_interval=8
port=$(shuf -i 40000-60000 -n 1)
​
if [ -z $checkpoint_file ]; then
    dmtcp_launch -p $port -i $checkpoint_interval ./dmtcp_serial
else
    dmtcp_restart -p $port -i $checkpoint_interval $checkpoint_file
fi
​
First Submission - Launch a Program
Submit dmtcp_serial_job.sh and then wait for the job to run until time out. Below shows the beginning and end of the job output file
$ head  slurm-5157871.out -n 15
## SLURM PROLOG ###############################################################
##    Job ID : 5157871
##  Job Name : dmtcp_serial
##  Nodelist : node1139
##      CPUs : 1
##   Mem/CPU : 2800 MB
##  Mem/Node : 65536 MB
## Directory : /gpfs/data/ccvstaff/yliu385/Test/dmtcp/serial/batch_job
##   Job Started : Wed May 18 09:38:39 EDT 2022
###############################################################################
ls: cannot access ckpt_*.dmtcp: No such file or directory
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$ tail slurm-5157871.out
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slurmstepd: error: *** JOB 5157871 ON node1139 CANCELLED AT 2022-05-18T09:43:58 DUE TO TIME LIMIT ***
​
Later Submissions - Restart from a Checkpoint
Submit dmtcp_serial_job.sh and then wait for the job to run until time out.  Below shows the beginning of the job output file, which demonstrate that the job restarts from the checkpoint of the previous job.
$ head  slurm-5158218.out -n 15
## SLURM PROLOG ###############################################################
##    Job ID : 5158218
##  Job Name : dmtcp_serial
##  Nodelist : node1327
##      CPUs : 1
##   Mem/CPU : 2800 MB
##  Mem/Node : 65536 MB
## Directory : /gpfs/data/ccvstaff/yliu385/Test/dmtcp/serial/batch_job
##   Job Started : Wed May 18 09:50:39 EDT 2022
###############################################################################
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​
Job Array
The following example script
creates a sub directory for each task of a job array, and then saves a task's checkpoint in the task's own sub directory when the job script is submitted for the first time
restarts checkpoints in task subdirectories when the job script is submitted for the second time or later
#!/bin/bash
​
#SBATCH -n 1
#SBATCH --array=1-4
#SBATCH -t 5:00
#SBATCH -J dmtcp_job_array
​
checkpoint_interval=8
port=$((SLURM_JOB_ID %20000 + 40000))
task_dir=jobtask_$SLURM_ARRAY_TASK_ID
​
if [ ! -d $task_dir ]; then
    mkdir $task_dir
    cd $task_dir
    dmtcp_launch -p $port -i $checkpoint_interval ../dmtcp_serial
else
    cd $task_dir
    checkpoint_file=`ls ckpt_*.dmtcp -t|head -n 1`
    if [ -z $checkpoint_file ]; then
        dmtcp_launch -p $port -i $checkpoint_interval ../dmtcp_serial
    else
        dmtcp_restart -p $port -i $checkpoint_interval $checkpoint_file
    fi
fi
​
​
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