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--- cluster:190 [2020/01/14 14:50]
hmeij07 created
+++ cluster:190 [2020/09/28 07:38] (current)
hmeij07
@@ Line 3: / Line 3: @@
 ==== DMTCP ====
+  * https://sourceforge.net/projects/dmtcp/
+  * DMTCP (Distributed MultiThreaded Checkpointing)
+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
+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 [[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.
+Write your checkpoint files in ''/sanscratch/checkpoints/JOBPID'' so it does not add into your quota.  The scheduler will not create this directory for you, you must do this in your submit job.  Directories will automatically be delete if 120 days old.
+<code>
+# sample steps to put in your scripts
+# make a directory (first one done by scheduler, second one done by your script)
+mkdir -p /sanscratch/111 /sanscratch/checkpoints/111
+cd /sanscratch/111
+# invoke sample rpogram which generates one line of output
+time ./a.out
+[1]+  Done                    time ./a.out
+real    64m0.513s
+user    64m0.813s
+sys     0m0.022s
+total 1108
+-rwxr--r-- 1 hmeij its 1126428 Jan 14 14:36 a.out
+-rw-r--r-- 1 hmeij its      49 Jan 14 15:41 fid.txt
+[hmeij@cottontail2 111]$ cat fid.txt
+.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 above  with interval 300 (every 5 mins)
+[hmeij@cottontail2 111]$ ps
+  PID TTY          TIME CMD
+pts/1    00:00:00 time
+pts/1    00:00:00 dmtcp_coordinat
+pts/1    00:03:02 a.out
+pts/1    00:00:00 ps
+pts/1    00:00:00 bash
+# the coordinator to which application process was attached
+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
+# the random port (in case somebody else is also checkpointing on this host
+[hmeij@cottontail2 111]$ cat port.txt
+# 5 mins checkpoints, little impact
+[hmeij@cottontail2 111]$ sleep 6m; ll /sanscratch/checkpoints/111/
+total 2960
+-rw------- 1 hmeij its 3011726 Jan 16 13:53 ckpt_a.out_24945f6ae3823bbf-40000-fb2d136b9b544.dmtcp\\
+-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\\
+[hmeij@cottontail2 111]$
+real    63m57.287s
+user    63m54.703s
+sys     0m0.444s
+# lets try a termination of processes and restart
+[hmeij@cottontail2 111]$ time dmtcp_launch \\
+--new-coordinator --coord-port 0 --port-file port.txt \\
+-i 300 --ckptdir /sanscratch/checkpoints/111  ./a.out &
+[1] 29201
+[hmeij@cottontail2 111]$ ps
+  PID TTY          TIME CMD
+pts/1    00:00:00 bash
+pts/1    00:00:00 bash
+pts/1    00:00:01 a.out
+pts/1    00:00:00 dmtcp_coordinat
+pts/1    00:00:00 ps
+# terminate half way through
+[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
+# ps
+S hmeij    20891 20890  -bash
+R hmeij    31136 20891 [DMTCP:a.out]
+S hmeij    31201     1  /usr/bin/dmtcp_coordinator --quiet --exit-on-last --daemon
+# You must make sure the old directory and file exists, otherwise
+[40000] ERROR at fileconnection.cpp:737 in refill;
+REASON='JASSERT(jalib::Filesystem::FileExists(_path)) failed'
+     _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>
 ==== Quick-Start Guide ====

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