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cluster:190 [2020/01/17 08:07]
hmeij07 		cluster:190 [2020/01/24 13:33]
hmeij07
Line 7: Line 7:
   * DMTCP (Distributed MultiThreaded Checkpointing)   * DMTCP (Distributed MultiThreaded Checkpointing)
  
-DMTCP Checkpoint/Restart allows one to transparently checkpoint to disk +DMTCP Checkpoint/Restart allows one to transparently checkpoint to disk a distributed computation.  It works under Linux, with no modifications to the Linux kernel nor to the application binaries.  It can be used by 
-a distributed computation.  It works under Linux, with no modifications +unprivileged users (no root privilege needed).  One can later restart from a checkpoint, or even migrate the processes by moving the checkpoint files to another host prior to restarting.
-to the Linux kernel nor to the application binaries.  It can be used by +
-unprivileged users (no root privilege needed).  One can later restart +
-from a checkpoint, or even migrate the processes by moving the checkpoint +
-files to another host prior to restarting.+
  
-This is a replacement for THE BLCR methods we used to use.+This is a replacement for THE BLCR methods we used [[cluster:147|BLCR Checkpoint in OL3 -serial]] or [[cluster:148|BLCR Checkpoint in OL3 - parallel]] ... BLCR is not being developed anymore. Today's brief power outage removed the BLCR kernel module HPCC wide. So learn DMTCP. I have not provided wrappers but you can follow the same logic as we used with BLCR.
  
 <code> <code>
Line 20: Line 16:
 # sample steps to put in your scripts # sample steps to put in your scripts
  
-# make a directory (done by scheduler) +# make a directory (first one done by scheduler, second one done by your script) 
-mkdir -p /sanscratch/111 /snascratch/checkpoints/111+mkdir -p /sanscratch/111 /sanscratch/checkpoints/111
 cd /sanscratch/111 cd /sanscratch/111
 +
 +# invoke sample rpogram which generates one line of output
 time ./a.out time ./a.out
  
Line 36: Line 34:
 [hmeij@cottontail2 111]$ cat fid.txt [hmeij@cottontail2 111]$ cat fid.txt
   0.999578495067887       7.978578277139264E-005   0.999578495067887       7.978578277139264E-005
 +
 +# for example, with 24 hours checkpoint interval
 +# launch new coordinator on random port, log port, 24 hour checkpoints 
 +# make sure you create destination dir for checkpoints
 +dmtcp_launch --new-coordinator \
 +  --coord-port 0 --port-file port.txt --interval 86400 \
 +  --ckptdir /sanscratch/checkpoints/111 \
 +  time ./a.out
 +
      
-# run command below with interval 300 (every 5 mins)+# run command above  with interval 300 (every 5 mins) 
 [hmeij@cottontail2 111]$ ps [hmeij@cottontail2 111]$ ps
   PID TTY          TIME CMD   PID TTY          TIME CMD
Line 49: Line 57:
 1 S hmeij    20008     1  0  80   0 -  4665 ep_pol 07:46 pts/1    00:00:00 \\ 1 S hmeij    20008     1  0  80   0 -  4665 ep_pol 07:46 pts/1    00:00:00 \\
 /usr/bin/dmtcp_coordinator --quiet --exit-on-last --daemon /usr/bin/dmtcp_coordinator --quiet --exit-on-last --daemon
 +
 # the random port (in case somebody else is also checkpointing on this host # the random port (in case somebody else is also checkpointing on this host
 [hmeij@cottontail2 111]$ cat port.txt [hmeij@cottontail2 111]$ cat port.txt
Line 59: Line 68:
 -rwxr--r-- 1 hmeij its   12440 Jan 16 13:53 dmtcp_restart_script_24945f6ae3823bbf-40000-fb2d11ea62fa0.sh\\ -rwxr--r-- 1 hmeij its   12440 Jan 16 13:53 dmtcp_restart_script_24945f6ae3823bbf-40000-fb2d11ea62fa0.sh\\
 lrwxrwxrwx 1 hmeij its      60 Jan 16 13:53 dmtcp_restart_script.sh -> dmtcp_restart_script_24945f6ae3823bbf-40000-fb2d11ea62fa0.sh\\ lrwxrwxrwx 1 hmeij its      60 Jan 16 13:53 dmtcp_restart_script.sh -> dmtcp_restart_script_24945f6ae3823bbf-40000-fb2d11ea62fa0.sh\\
 +
 [hmeij@cottontail2 111]$ [hmeij@cottontail2 111]$
 real    63m57.287s real    63m57.287s
Line 69: Line 79:
 -i 300 --ckptdir /sanscratch/checkpoints/111  ./a.out & -i 300 --ckptdir /sanscratch/checkpoints/111  ./a.out &
 [1] 29201 [1] 29201
 +
 [hmeij@cottontail2 111]$ ps [hmeij@cottontail2 111]$ ps
   PID TTY          TIME CMD   PID TTY          TIME CMD
Line 76: Line 87:
 29210 pts/1    00:00:00 dmtcp_coordinat 29210 pts/1    00:00:00 dmtcp_coordinat
 29212 pts/1    00:00:00 ps 29212 pts/1    00:00:00 ps
 +
 +# terminate half way through
 [hmeij@cottontail2 111]$ sleep 32m; kill -9 29202 29210 [hmeij@cottontail2 111]$ sleep 32m; kill -9 29202 29210
  
 +# restart from checkpoints directory (or copy files into desired location)
 +cd /sanscratch/checkpoints/111
 +./dmtcp_restart_script.sh
  
-# launch new coordinator on random port, log port, 24 hour checkpoints  +# ps  
-# make sure you create destination dir for checkpoints+0 S hmeij    20891 20890  -bash 
 +0 R hmeij    31136 20891 [DMTCP:a.out] 
 +1 S hmeij    31201     1  /usr/bin/dmtcp_coordinator --quiet --exit-on-last --daemon
  
-dmtcp_launch --new-coordinator \ +# You must make sure the old directory and file exists, otherwise 
-  --coord-port 0 --port-file port.txt --interval 86400 \ +[40000] ERROR at fileconnection.cpp:737 in refill;  
-  --ckptdir /sanscratch/checkpoints/111 \ +REASON='JASSERT(jalib::Filesystem::FileExists(_path)) failed' 
-  time ./a.out+     _path = /sanscratch/111/fid.txt 
 +Message: File not found. 
 +a.out (40000): Terminating... 
 +# that is because at checkpoint time that file was opened by a.out
  
 +
 +# The process will pick up from last checkpoint
 +# and write output to original work directory
  
 </code> </code>
 +
 ==== Quick-Start Guide ==== ==== Quick-Start Guide ====
  
cluster/190.txt · Last modified: 2020/09/28 07:38 by hmeij07

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