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a simple bash based scheduler, part two.

june 24, 2011 at 01:35 by felix. no comments.

i recently presented a bash script which schedules computational tasks on multi-core machines. in the meanwhile, i fixed a bug in the display, made the program more flexible, and started to use local variables instead of global variables only. the new version is also more intelligent: it tries to adjust the running times of its controlled processes so that the running times are not far apart.
here is the newest version:

  1#/bin/bash
  2
  3initProfile() {
  4    PROFILEFN=bigprimerunner-$PROFILE.profile
  5    CORES=`grep "^CORES " $PROFILEFN`
  6    CORES=${CORES/CORES }
  7    STARTUP=`grep "^STARTUP " $PROFILEFN`
  8    STARTUP=${STARTUP/STARTUP }
  9    eval STARTUP=$STARTUP
 10}
 11
 12# Startup
 13LOADMODIFIER=0
 14if [ "$1" != "" ]
 15then
 16    PROFILE=$1
 17else
 18    PROFILE=`hostname`
 19fi
 20if [ "$2" != "" ]
 21then
 22    LOADMODIFIER=$2
 23fi
 24initProfile
 25if [ "$CORES" == "" ]
 26then
 27    echo "Cannot load profile $PROFILEFN!"
 28    exit
 29fi
 30echo Cores: $CORES
 31echo Load modifier: $LOADMODIFIER
 32
 33# The command to execute
 34COMMAND=primefinder
 35
 36computeFreecores() {
 37    FREECORES=0
 38    local DAY=`date +%w`
 39    local LINE=`grep "^$DAY " $PROFILEFN`
 40    local LINE=${LINE/$DAY }
 41    local HOUR=`date +%k`
 42    for ((i=0;i<$HOUR;++i));
 43    do
 44        local LINE=${LINE#* }
 45    done
 46    local LINE=${LINE/ *}
 47    eval FREECORES=$LINE
 48    # Also determine how many jobs should be started
 49    STARTUP=`grep "^STARTUP " $PROFILEFN`
 50    STARTUP=${STARTUP/STARTUP }
 51    eval STARTUP=$STARTUP
 52}
 53
 54killProcess() { # One argument: PID of process to kill
 55    local PID=$1
 56    local FILE=`lsof -p $PID -F n 2>/dev/null | grep primedatabase | grep -v "\.nfs"`
 57    kill $PID 2> /dev/null
 58    local A=${FILE#n*}
 59    local A=${A/ (nfs*}
 60    if [ "$A" != "" ]
 61    then
 62        rm $A
 63        echo Killed $PID with open file $A
 64    else
 65        echo Killed $PID with no open file
 66    fi
 67}
 68
 69stopsignal() {
 70    local PIDS=`jobs -p`
 71    echo
 72    echo
 73    echo Terminating...
 74    echo Killing: $PIDS
 75    for PID in $PIDS;
 76    do
 77        killProcess $PID
 78    done
 79    echo done.
 80    exit
 81}
 82
 83trap 'stopsignal' 2
 84
 85computeFreecores
 86
 87echo "Starting $STARTUP instances (in $BINDIR)"
 88
 89filterRunning() { # Removes all PIDs from the arguments which are currently stopped
 90    ps -o pid= -o s= $* | grep R | sed -e "s/R//"
 91}
 92
 93filterStopped() { # Removes all PIDs from the arguments
 94    ps -o pid= -o s= $* | grep T | sed -e "s/T//"
 95}
 96
 97determineToAdd() {
 98    computeFreecores
 99    local LOAD=`uptime`
100    local LOAD=${LOAD#*average: }
101    local LOAD=${LOAD/,*}
102    local LOAD=${LOAD/.*}
103    ADD=$[CORES-FREECORES-(LOAD+LOADMODIFIER)]
104    local JOBS=`jobs -p`
105    local JOBS=`filterRunning $JOBS`
106    echo "Load: $[LOAD+LOADMODIFIER], Intended number of free cores: $FREECORES, Running: `echo $JOBS | wc -w`, Started: `jobs -p | wc -l` (should be $STARTUP)"
107}
108
109continueOne() {
110    local JOBS=`jobs -p`
111    local JOBS=`filterStopped $JOBS`
112    if [ "$JOBS" != "" ]
113    then
114        local PID=`ps -o pid= --sort +time $JOBS | head -1`
115        echo Continuing $PID...
116        kill -SIGCONT $PID
117    fi
118}
119
120stopOne() {
121    local JOBS=`jobs -p`
122    local JOBS=`filterRunning $JOBS`
123    if [ "$JOBS" != "" ]
124    then
125        local PID=`ps -o pid= --sort -time $JOBS | head -1`
126        echo Stopping $PID...
127        kill -SIGSTOP $PID
128    fi
129}
130
131killOne() {
132    local JOBS=`jobs -p`
133    if [ "$JOBS" != "" ]
134    then
135        local PID=`ps -o pid= --sort -time $JOBS | head -1`
136        killProcess $PID
137    fi
138}
139
140launchOne() {
141    echo "Launching \"$COMMAND\"..."
142    $COMMAND &
143    sleep 1.5
144}
145
146computeTotaltimeInSecs() {
147    # Input: $1
148    # Output: $TOTALSECS
149    local I=$1
150    local SECS=${I##*:}
151    local REST=${I%:*}
152    local MINS=${REST##*:}
153    local REST=${REST%:*}
154    local HOURS=${REST##*-}
155    local DAYS=`expr "$REST" : '\([0-9]*-\)'`
156    local DAYS=${DAYS%-}
157    if [ "$DAYS" == "" ]
158    then
159        local DAYS=0
160    fi
161    if [ "$HOURS" == "" ]
162    then
163        local HOURS=0
164    fi
165    if [ "$MINS" == "" ]
166    then
167        local MINS=0
168    fi
169    echo "((($DAYS * 24) + $HOURS) * 60 + $MINS) * 60 + $SECS" | bc
170}
171
172adjustProcesses() {
173    local JOBS=`jobs -p`
174    local JOBS=`filterRunning $JOBS`
175    if [ "$JOBS" != "" ]
176    then
177        local STOPPID=`ps -o pid= --sort -time $JOBS | head -1`
178        local JOBS=`jobs -p`
179        local JOBS=`filterStopped $JOBS`
180        if [ "$JOBS" != "" ]
181        then
182            local CONTPID=`ps -o pid= --sort +time $JOBS | head -1`
183            # Compute times
184            local I=`ps -o time= $STOPPID`
185            local STOPSEC=`computeTotaltimeInSecs $I`
186            local I=`ps -o time= $CONTPID`
187            local CONTSEC=`computeTotaltimeInSecs $I`
188            # Compare times
189            local CT=`echo $CONTSEC+60*5 | bc`
190            if [ $STOPSEC -gt $CT ]
191            then
192                echo Stopping $STOPPID and continuing $CONTPID
193                kill -SIGSTOP $STOPPID
194                kill -SIGCONT $CONTPID
195            fi
196        fi
197    fi
198}
199
200# Start programs in the background
201determineToAdd
202for ((i=1;i<=STARTUP;++i));
203do
204    launchOne
205    if [ $i -gt $ADD ]
206    then
207        sleep 1
208        kill -SIGSTOP %$i
209    fi
210done
211
212# Start mainloop
213while [ 1 ]
214do
215    sleep 60
216    
217    # Determine how many processes should be added/removed
218    determineToAdd
219
220    # Stop/continue processes
221    if [ $ADD -gt 0 ]
222    then
223        # Add processes
224        echo ADD:$ADD
225        for ((i=0;i<ADD;++i))
226        do
227            continueOne
228        done
229    fi
230    if [ $ADD -lt 0 ]
231    then
232        REM=$[-ADD]
233        # Remove processes
234        echo REMOVE:$REM
235        for ((i=0;i<REM;++i))
236        do
237            stopOne
238        done;
239    fi
240
241    # Launch new processes or kill running ones
242    CURRLAUNCHED=`jobs -p | wc -l`
243    if [ $STARTUP != $CURRLAUNCHED ]
244    then
245        if [ $STARTUP -lt $CURRLAUNCHED ]
246        then
247            echo kill: $STARTUP $CURRLAUNCHED
248            for ((i=STARTUP;i<CURRLAUNCHED;++i));
249            do
250                killOne
251            done;
252        else
253            echo add: $CURRLAUNCHED $STARTUP
254            for ((i=CURRLAUNCHED;i<STARTUP;++i));
255            do
256                launchOne
257            done;
258        fi
259    fi
260    sleep 2
261    
262    # Adjust
263    adjustProcesses
264done
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a simple bash based scheduler.

june 15, 2011 at 13:50 by felix. one comment.

ever had the problem that you have access to a big machine (with many cores), and you want to run many (tens of thousands) small computations, but you want to make sure that not too many cores are used?
i’ve had this problem, and since i now have a pretty nice (i think so) solution, i thought that maybe more people are interested in it. so here’s my setup. i have a program, let’s call it primefinder, which, for a certain input n (where n is a natural number ≤ 21000), computes a prime of n bits with special properties. the program loops over all possible n, and checks for each n if a file n.prime exists. if it does not, it creates it (with zero content), computes the prime (which can take between minutes and days), writes the prime into the file and continues with the next file. this simple task distribution technique allows me to run the program in parallel on different machines (since the files are in a nfs folder) with many instances on each machine. now at our institute, we have a big computation machine (64 cores) and four user machines (on which the users work, each 32 cores). since the user machines are often not intensively used (and that only during certain times of the day), i want to use these as well. but there should be enough cores free, so the users won’t notice that there are computations going on in the background. on the computation server, also other people want to run something, so there should also be some free cores. optimally, my program would somehow decide how many cores are used by others, and use the rest. or most of them, to leave some free, especially on the user machines.
after a suggestion by our it guys, i started writing a bash script which controls the instances of my program on the same machine. the first version used the time of the day to determine the number of processes. everything was computed in terms of the number of cores of the machine, the load (with a load modifier applied, since some machines have uninterruptable processes running which do not effectively do something, and which won’t go away until the next reboot) and the hour of the day. but it is not easy to find a good scheme which yields good results on all machines. something which works well on the user machines is wasting processor time on the computation server.
so today i rewrote the program to use profiles. a profile contains information on the number of cores (this is necessary since the computation server has hyperthreading enabled, and thus returns twice the number of cores), the number of processes to be started, and the number of cores to be left free during each hour and day of a week. so on weekends or nights, i choose lower numbers for the free cores for the user machines, while for the computational server the number is always 1.
a profile can look like this (this is from a user machine, the file is called primefinderrunner-user.profile for later reference):

1CORES 32
2STARTUP $[CORES-CORES/8]
30 $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8]
41 $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/4] $[CORES/4] $[CORES/4] $[CORES/8]
52 $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/4] $[CORES/4] $[CORES/4] $[CORES/8]
63 $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/4] $[CORES/4] $[CORES/4] $[CORES/8]
74 $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/4] $[CORES/4] $[CORES/4] $[CORES/8]
85 $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/2] $[CORES/4] $[CORES/4] $[CORES/4] $[CORES/8]
96 $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/8] $[CORES/16] $[CORES/16] $[CORES/16] $[CORES/16]

the line with prefix CORES gives the number of cores. the line prefixed by STARTUP gives the number of processes to run (at most); here, we use 7/8 of the number of cores. the lines prefixed by a number between 0 (sunday) and 6 (saturday) have 24 entries following: every entry (seperated by exactly one space, as the prefix itself is separated by exactly one space from the entries!) says how many cores should be free at each time of the day. usually during night (up to 7 am) at least 1/16 of the total number of cores should be free, while during workday (8 am to 7 pm) half of the cores should be free. of course, the numbers are different for weekends (saturday and sunday) than for the other working days.
now the script itself looks like this (for reference, the filename is primefinderrunner.sh):

  1#/bin/bash
  2 
  3initProfile() {
  4    PROFILEFN=primefinderrunner-$PROFILE.profile
  5    CORES=`grep "^CORES " $PROFILEFN`
  6    CORES=${CORES/CORES }
  7    STARTUP=`grep "^STARTUP " $PROFILEFN`
  8    STARTUP=${STARTUP/STARTUP }
  9    eval STARTUP=$STARTUP
 10}
 11 
 12LOADMODIFIER=0
 13if [ "$1" != "" ]
 14then
 15    PROFILE=$1
 16else
 17    PROFILE=`hostname`
 18fi
 19if [ "$2" != "" ]
 20then
 21    LOADMODIFIER=$2
 22fi
 23initProfile
 24if [ "$CORES" == "" ]
 25then
 26    echo "Cannot load profile $PROFILEFN!"
 27    exit
 28fi
 29echo Cores: $CORES
 30echo Load modifier: $LOADMODIFIER
 31 
 32computeFreecores() { 
 33    # two arguments: day (0..6) and hour (0..23)
 34    FREECORES=0
 35    DAY=`date +%w`
 36    LINE=`grep "^$DAY " $PROFILEFN`
 37    LINE=${LINE/$DAY }
 38    HOUR=`date +%k`
 39    for ((i=0;i<$HOUR;++i));
 40    do
 41        LINE=${LINE#* }
 42    done
 43    LINE=${LINE/ *}
 44    eval FREECORES=$LINE
 45}
 46 
 47computeFreecores
 48 
 49stopsignal() {
 50    for PID in `jobs -p`;
 51    do
 52        FILE=`lsof -p $PID -F n 2>/dev/null | grep primedatabase | grep -v "\\.nfs"`
 53        A=${FILE#n*}
 54        A=${A/ (nfs*}
 55        echo killing $PID with open file $A
 56        rm $A
 57        kill $PID
 58    done
 59    exit
 60}
 61 
 62trap 'stopsignal' 2
 63 
 64echo "Starting $STARTUP instances"
 65 
 66determineToAdd() {
 67    computeFreecores
 68    LOAD=`uptime`
 69    LOAD=${LOAD#*average: }
 70    LOAD=${LOAD/,*}
 71    LOAD=${LOAD/.*}
 72    ADD=$[CORES-FREECORES-LOAD-LOADMODIFIER]
 73    echo Load: $[LOAD-LOADMODIFIER], Intended number of free cores: $FREECORES
 74}
 75 
 76# Start programs in the background
 77determineToAdd
 78for ((i=1;i<=STARTUP;++i));
 79do
 80    primefinder &amp;
 81    sleep 2
 82done
 83sleep 20
 84if [ $ADD -lt 0 ]
 85then
 86    ADD=0
 87fi
 88for ((i=ADD+1;i<=STARTUP;++i));
 89do
 90    kill -SIGSTOP %$i
 91done
 92 
 93CURRRUNNING=$ADD
 94RUNNINGSTART=1 # The first one running
 95RUNNINGSTOP=$CURRRUNNING # The last one running
 96 
 97startOne() {
 98    # Assume that $CURRRUNNING < $STARTUP
 99    RUNNINGSTOP=$[(RUNNINGSTOP % STARTUP) + 1]
100    kill -SIGCONT %$RUNNINGSTOP
101    CURRRUNNING=$[CURRRUNNING+1]
102}
103 
104stopOne() {
105    # Assume that $CURRRUNNING > 0
106    kill -SIGSTOP %$RUNNINGSTART
107    RUNNINGSTART=$[(RUNNINGSTART % STARTUP) + 1]
108    CURRRUNNING=$[CURRRUNNING-1]
109}
110 
111# Start mainloop
112while [ 1 ]
113do
114    sleep 60
115 
116    # Determine how many threads should be added/removed
117    determineToAdd
118    if [ $ADD -gt 0 ]
119    then
120        if [ $[ADD+CURRRUNNING] -gt $STARTUP ]
121        then
122            ADD=$[STARTUP-CURRRUNNING]
123        fi
124        # Add processes
125        echo ADD:$ADD
126        for ((i=0;i<ADD;++i))
127        do
128            startOne
129        done
130    fi
131    if [ $ADD -lt 0 ]
132    then
133        REM=$[-ADD]
134        # Clip
135        if [ $REM -gt $CURRRUNNING ]
136        then
137            REM=$CURRRUNNING
138        fi
139        # Remove processes
140        echo REMOVE:$REM
141        for ((i=0;i<REM;++i))
142        do
143            stopOne
144        done
145    fi
146    sleep 60
147done

the script first starts all instances, then stops the ones which are too many, and then starts the main loop. in the main loop, it waits 60 seconds (for the average load to adjust to the new process count), and then decides how many cores should be left free, and what that means for the number of processes (add/remove some). note that the profile file is read every minute, so it can be changed any time without any need to re-run the whole thing.
in case the script is stopped (with control+c), all primefinder processes are killed and their open file is deleted. to determine the open file, i use lsof with some greps. you have to adjust and test that line before using this script!
note that this script is quite a hack, and far from perfect. and it is somehow system dependent, or at least “setup dependent” since it has certain assumptions on the executables, on how the output of lsof looks like, … so better make sure it works before you use it, especially on bigger systems. also note that in the beginning, all instances are ran (they are started with a two second delay between two instances), and then everything is run for 20 seconds before the first adjustment (i.e. stopping processes which are too many) are made. if you share the system with other people, this might already annoy others when they try to measure timings of their programs (especially if hyperthreading is enabled).

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