Using R to Analyze G1GC Log Files
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Published on Tue, 27 May 2014 20:59:13 +0000
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Using R to Analyze G1GC Log Files
Introduction
Working in Oracle Platform Integration gives an engineer opportunities to work on a wide array of technologies. My team’s goal is to make Oracle applications run best on the Solaris/SPARC platform. When looking for bottlenecks in a modern applications, one needs to be aware of not only how the CPUs and operating system are executing, but also network, storage, and in some cases, the Java Virtual Machine.
I was recently presented with about 1.5 GB of Java Garbage First Garbage Collector log file data. If you’re not familiar with the subject, you might want to review Garbage First Garbage Collector Tuning by Monica Beckwith. The customer had been running Java HotSpot 1.6.0_31 to host a web application server.
I was told that the Solaris/SPARC server was running a Java process launched using a commmand line that included the following flags: -d64 -Xms9g -Xmx9g -XX:+UseG1GC -XX:MaxGCPauseMillis=200 -XX:InitiatingHeapOccupancyPercent=80 -XX:PermSize=256m -XX:MaxPermSize=256m -XX:+PrintGC -XX:+PrintGCTimeStamps -XX:+PrintHeapAtGC -XX:+PrintGCDateStamps -XX:+PrintFlagsFinal -XX:+DisableExplicitGC -XX:+UnlockExperimentalVMOptions -XX:ParallelGCThreads=8
Several sources on the internet indicate that if I were to print out the 1.5 GB of log files, it would require enough paper to fill the bed of a pick up truck. Of course, it would be fruitless to try to scan the log files by hand. Tools will be required to summarize the contents of the log files.
Others have encountered large Java garbage collection log files. There are existing tools to analyze the log files:
- IBM’s GC toolkit
- The chewiebug GCViewer
- gchisto
- HPjmeter
Instead of using one of the other tools listed, I decide to parse the log files with standard Unix tools, and analyze the data with R.
Data Cleansing
The log files arrived in two different formats. I guess that the difference is that one set of log files was generated using a more verbose option, maybe -XX:+PrintHeapAtGC, and the other set of log files was generated without that option.
Format 1
In some of the log files, the log files with the less verbose format, a single trace, i.e. the report of a singe garbage collection event, looks like this:
{Heap before GC invocations=12280 (full 61):
garbage-first heap total 9437184K, used 7499918K [0xfffffffd00000000, 0xffffffff40000000, 0xffffffff40000000)
region size 4096K, 1 young (4096K), 0 survivors (0K)
compacting perm gen total 262144K, used 144077K [0xffffffff40000000, 0xffffffff50000000, 0xffffffff50000000)
the space 262144K, 54% used [0xffffffff40000000, 0xffffffff48cb3758, 0xffffffff48cb3800, 0xffffffff50000000)
No shared spaces configured.
2014-05-14T07:24:00.988-0700: 60586.353: [GC pause (young) 7324M->7320M(9216M), 0.1567265 secs]
Heap after GC invocations=12281 (full 61):
garbage-first heap total 9437184K, used 7496533K [0xfffffffd00000000, 0xffffffff40000000, 0xffffffff40000000)
region size 4096K, 0 young (0K), 0 survivors (0K)
compacting perm gen total 262144K, used 144077K [0xffffffff40000000, 0xffffffff50000000, 0xffffffff50000000)
the space 262144K, 54% used [0xffffffff40000000, 0xffffffff48cb3758, 0xffffffff48cb3800, 0xffffffff50000000)
No shared spaces configured.
}
A simple grep can be used to extract a summary:
$ grep "\[ GC pause (young" g1gc.log
2014-05-13T13:24:35.091-0700: 3.109: [GC pause (young) 20M->5029K(9216M), 0.0146328 secs] 2014-05-13T13:24:35.440-0700: 3.459: [GC pause (young) 9125K->6077K(9216M), 0.0086723 secs] 2014-05-13T13:24:37.581-0700: 5.599: [GC pause (young) 25M->8470K(9216M), 0.0203820 secs] 2014-05-13T13:24:42.686-0700: 10.704: [GC pause (young) 44M->15M(9216M), 0.0288848 secs] 2014-05-13T13:24:48.941-0700: 16.958: [GC pause (young) 51M->20M(9216M), 0.0491244 secs] 2014-05-13T13:24:56.049-0700: 24.066: [GC pause (young) 92M->26M(9216M), 0.0525368 secs] 2014-05-13T13:25:34.368-0700: 62.383: [GC pause (young) 602M->68M(9216M), 0.1721173 secs]
But that format wasn't easily read into R, so I needed to be a bit more tricky. I used the following Unix command to create a summary file that was easy for R to read.
$ echo "SecondsSinceLaunch BeforeSize AfterSize TotalSize RealTime" $ grep "\[GC pause (young" g1gc.log | grep -v mark | sed -e 's/[A-SU-z\(\),]/ /g' -e 's/->/ /' -e 's/: / /g' | more
SecondsSinceLaunch BeforeSize AfterSize TotalSize RealTime 2014-05-13T13:24:35.091-0700 3.109 20 5029 9216 0.0146328 2014-05-13T13:24:35.440-0700 3.459 9125 6077 9216 0.0086723 2014-05-13T13:24:37.581-0700 5.599 25 8470 9216 0.0203820 2014-05-13T13:24:42.686-0700 10.704 44 15 9216 0.0288848 2014-05-13T13:24:48.941-0700 16.958 51 20 9216 0.0491244 2014-05-13T13:24:56.049-0700 24.066 92 26 9216 0.0525368 2014-05-13T13:25:34.368-0700 62.383 602 68 9216 0.1721173
Format 2
In some of the log files, the log files with the more verbose format, a single trace, i.e. the report of a singe garbage collection event, was more complicated than Format 1. Here is a text file with an example of a single G1GC trace in the second format. As you can see, it is quite complicated. It is nice that there is so much information available, but the level of detail can be overwhelming.
I wrote this awk script (download) to summarize each trace on a single line.
#!/usr/bin/env awk -f
BEGIN {
printf("SecondsSinceLaunch IncrementalCount FullCount UserTime SysTime RealTime BeforeSize AfterSize TotalSize\n")
}
######################
# Save count data from lines that are at the start of each G1GC trace.
# Each trace starts out like this:
# {Heap before GC invocations=14 (full 0):
# garbage-first heap total 9437184K, used 325496K [0xfffffffd00000000, 0xffffffff40000000, 0xffffffff40000000)
######################
/{Heap.*full/{
gsub ( "\\)" , "" );
nf=split($0,a,"=");
split(a[2],b," ");
getline;
if ( match($0, "first") ) {
G1GC=1;
IncrementalCount=b[1];
FullCount=substr( b[3], 1, length(b[3])-1 );
} else {
G1GC=0;
}
}
######################
# Pull out time stamps that are in lines with this format:
# 2014-05-12T14:02:06.025-0700: 94.312: [GC pause (young), 0.08870154 secs]
######################
/GC pause/ {
DateTime=$1;
SecondsSinceLaunch=substr($2, 1, length($2)-1);
}
######################
# Heap sizes are in lines that look like this:
# [ 4842M->4838M(9216M)]
######################
/\[ .*]$/ {
gsub ( "\\[" , "" );
gsub ( "\ \]" , "" );
gsub ( "->" , " " );
gsub ( "\\( " , " " );
gsub ( "\ \)" , " " );
split($0,a," ");
if ( split(a[1],b,"M") > 1 ) {BeforeSize=b[1]*1024;}
if ( split(a[1],b,"K") > 1 ) {BeforeSize=b[1];}
if ( split(a[2],b,"M") > 1 ) {AfterSize=b[1]*1024;}
if ( split(a[2],b,"K") > 1 ) {AfterSize=b[1];}
if ( split(a[3],b,"M") > 1 ) {TotalSize=b[1]*1024;}
if ( split(a[3],b,"K") > 1 ) {TotalSize=b[1];}
}
######################
# Emit an output line when you find input that looks like this:
# [Times: user=1.41 sys=0.08, real=0.24 secs]
######################
/\[Times/ {
if (G1GC==1) {
gsub ( "," , "" );
split($2,a,"=");
UserTime=a[2];
split($3,a,"=");
SysTime=a[2];
split($4,a,"=");
RealTime=a[2];
print DateTime,SecondsSinceLaunch,IncrementalCount,FullCount,UserTime,SysTime,RealTime,BeforeSize,AfterSize,TotalSize;
G1GC=0;
}
}
The resulting summary is about 25X smaller that the original file, but still difficult for a human to digest.
SecondsSinceLaunch IncrementalCount FullCount UserTime SysTime RealTime BeforeSize AfterSize TotalSize ... 2014-05-12T18:36:34.669-0700: 3985.744 561 0 0.57 0.06 0.16 1724416 1720320 9437184 2014-05-12T18:36:34.839-0700: 3985.914 562 0 0.51 0.06 0.19 1724416 1720320 9437184 2014-05-12T18:36:35.069-0700: 3986.144 563 0 0.60 0.04 0.27 1724416 1721344 9437184 2014-05-12T18:36:35.354-0700: 3986.429 564 0 0.33 0.04 0.09 1725440 1722368 9437184 2014-05-12T18:36:35.545-0700: 3986.620 565 0 0.58 0.04 0.17 1726464 1722368 9437184 2014-05-12T18:36:35.726-0700: 3986.801 566 0 0.43 0.05 0.12 1726464 1722368 9437184 2014-05-12T18:36:35.856-0700: 3986.930 567 0 0.30 0.04 0.07 1726464 1723392 9437184 2014-05-12T18:36:35.947-0700: 3987.023 568 0 0.61 0.04 0.26 1727488 1723392 9437184 2014-05-12T18:36:36.228-0700: 3987.302 569 0 0.46 0.04 0.16 1731584 1724416 9437184
Reading the Data into R
Once the GC log data had been cleansed, either by processing the first format with the shell script, or by processing the second format with the awk script, it was easy to read the data into R.
g1gc.df = read.csv("summary.txt", row.names = NULL, stringsAsFactors=FALSE,sep="")
str(g1gc.df)
## 'data.frame': 8307 obs. of 10 variables:
## $ row.names : chr "2014-05-12T14:00:32.868-0700:" "2014-05-12T14:00:33.179-0700:" "2014-05-12T14:00:33.677-0700:" "2014-05-12T14:00:35.538-0700:" ...
## $ SecondsSinceLaunch: num 1.16 1.47 1.97 3.83 6.1 ...
## $ IncrementalCount : int 0 1 2 3 4 5 6 7 8 9 ...
## $ FullCount : int 0 0 0 0 0 0 0 0 0 0 ...
## $ UserTime : num 0.11 0.05 0.04 0.21 0.08 0.26 0.31 0.33 0.34 0.56 ...
## $ SysTime : num 0.04 0.01 0.01 0.05 0.01 0.06 0.07 0.06 0.07 0.09 ...
## $ RealTime : num 0.02 0.02 0.01 0.04 0.02 0.04 0.05 0.04 0.04 0.06 ...
## $ BeforeSize : int 8192 5496 5768 22528 24576 43008 34816 53248 55296 93184 ...
## $ AfterSize : int 1400 1672 2557 4907 7072 14336 16384 18432 19456 21504 ...
## $ TotalSize : int 9437184 9437184 9437184 9437184 9437184 9437184 9437184 9437184 9437184 9437184 ...
head(g1gc.df)
## row.names SecondsSinceLaunch IncrementalCount
## 1 2014-05-12T14:00:32.868-0700: 1.161 0
## 2 2014-05-12T14:00:33.179-0700: 1.472 1
## 3 2014-05-12T14:00:33.677-0700: 1.969 2
## 4 2014-05-12T14:00:35.538-0700: 3.830 3
## 5 2014-05-12T14:00:37.811-0700: 6.103 4
## 6 2014-05-12T14:00:41.428-0700: 9.720 5
## FullCount UserTime SysTime RealTime BeforeSize AfterSize TotalSize
## 1 0 0.11 0.04 0.02 8192 1400 9437184
## 2 0 0.05 0.01 0.02 5496 1672 9437184
## 3 0 0.04 0.01 0.01 5768 2557 9437184
## 4 0 0.21 0.05 0.04 22528 4907 9437184
## 5 0 0.08 0.01 0.02 24576 7072 9437184
## 6 0 0.26 0.06 0.04 43008 14336 9437184
Basic Statistics
Once the data has been read into R, simple statistics are very easy to generate. All of the numbers from high school statistics are available via simple commands. For example, generate a summary of every column:
summary(g1gc.df)
## row.names SecondsSinceLaunch IncrementalCount FullCount
## Length:8307 Min. : 1 Min. : 0 Min. : 0.0
## Class :character 1st Qu.: 9977 1st Qu.:2048 1st Qu.: 0.0
## Mode :character Median :12855 Median :4136 Median : 12.0
## Mean :12527 Mean :4156 Mean : 31.6
## 3rd Qu.:15758 3rd Qu.:6262 3rd Qu.: 61.0
## Max. :55484 Max. :8391 Max. :113.0
## UserTime SysTime RealTime BeforeSize
## Min. :0.040 Min. :0.0000 Min. : 0.0 Min. : 5476
## 1st Qu.:0.470 1st Qu.:0.0300 1st Qu.: 0.1 1st Qu.:5137920
## Median :0.620 Median :0.0300 Median : 0.1 Median :6574080
## Mean :0.751 Mean :0.0355 Mean : 0.3 Mean :5841855
## 3rd Qu.:0.920 3rd Qu.:0.0400 3rd Qu.: 0.2 3rd Qu.:7084032
## Max. :3.370 Max. :1.5600 Max. :488.1 Max. :8696832
## AfterSize TotalSize
## Min. : 1380 Min. :9437184
## 1st Qu.:5002752 1st Qu.:9437184
## Median :6559744 Median :9437184
## Mean :5785454 Mean :9437184
## 3rd Qu.:7054336 3rd Qu.:9437184
## Max. :8482816 Max. :9437184
Q: What is the total amount of User CPU time spent in garbage collection?
sum(g1gc.df$UserTime)
## [1] 6236
As you can see, less than two hours of CPU time was spent in garbage collection. Is that too much? To find the percentage of time spent in garbage collection, divide the number above by total_elapsed_time*CPU_count. In this case, there are a lot of CPU’s and it turns out the the overall amount of CPU time spent in garbage collection isn’t a problem when viewed in isolation.
When calculating rates, i.e. events per unit time, you need to ask yourself if the rate is homogenous across the time period in the log file. Does the log file include spikes of high activity that should be separately analyzed? Averaging in data from nights and weekends with data from business hours may alias problems. If you have a reason to suspect that the garbage collection rates include peaks and valleys that need independent analysis, see the “Time Series” section, below.
Q: How much garbage is collected on each pass?
The amount of heap space that is recovered per GC pass is surprisingly low:
- At least one collection didn’t recover any data. (“Min.=0”)
- 25% of the passes recovered 3MB or less. (“1st Qu.=3072”)
- Half of the GC passes recovered 4MB or less. (“Median=4096”)
- The average amount recovered was 56MB. (“Mean=56390”)
- 75% of the passes recovered 36MB or less. (“3rd Qu.=36860”)
- At least one pass recovered 2GB. (“Max.=2121000”)
g1gc.df$Delta = g1gc.df$BeforeSize - g1gc.df$AfterSize
summary(g1gc.df$Delta)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0 3070 4100 56400 36900 2120000
Q: What is the maximum User CPU time for a single collection?
The worst garbage collection (“Max.”) is many standard deviations away from the mean. The data appears to be right skewed.
summary(g1gc.df$UserTime)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.040 0.470 0.620 0.751 0.920 3.370
sd(g1gc.df$UserTime)
## [1] 0.3966
Basic Graphics
Once the data is in R, it is trivial to plot the data with formats including dot plots, line charts, bar charts (simple, stacked, grouped), pie charts, boxplots, scatter plots histograms, and kernel density plots.
Histogram of User CPU Time per Collection
I don't think that this graph requires any explanation.
hist(g1gc.df$UserTime,
main="User CPU Time per Collection",
xlab="Seconds", ylab="Frequency")
Box plot to identify outliers
When the initial data is viewed with a box plot, you can see the one crazy outlier in the real time per GC. Save this data point for future analysis and drop the outlier so that it’s not throwing off our statistics. Now the box plot shows many outliers, which will be examined later, using times series analysis. Notice that the scale of the x-axis changes drastically once the crazy outlier is removed.
par(mfrow=c(2,1))
boxplot(g1gc.df$UserTime,g1gc.df$SysTime,g1gc.df$RealTime,
main="Box Plot of Time per GC\n(dominated by a crazy outlier)",
names=c("usr","sys","elapsed"),
xlab="Seconds per GC", ylab="Time (Seconds)",
horizontal = TRUE,
outcol="red")
crazy.outlier.df=g1gc.df[g1gc.df$RealTime > 400,]
g1gc.df=g1gc.df[g1gc.df$RealTime < 400,]
boxplot(g1gc.df$UserTime,g1gc.df$SysTime,g1gc.df$RealTime,
main="Box Plot of Time per GC\n(crazy outlier excluded)",
names=c("usr","sys","elapsed"),
xlab="Seconds per GC", ylab="Time (Seconds)",
horizontal = TRUE,
outcol="red")
box(which = "outer", lty = "solid")
Here is the crazy outlier for future analysis:
crazy.outlier.df
## row.names SecondsSinceLaunch IncrementalCount
## 8233 2014-05-12T23:15:43.903-0700: 20741 8316
## FullCount UserTime SysTime RealTime BeforeSize AfterSize TotalSize
## 8233 112 0.55 0.42 488.1 8381440 8235008 9437184
## Delta
## 8233 146432
R Time Series Data
To analyze the garbage collection as a time series, I’ll use Z’s Ordered Observations (zoo). “zoo is the creator for an S3 class of indexed totally ordered observations which includes irregular time series.”
require(zoo)
## Loading required package: zoo
##
## Attaching package: 'zoo'
##
## The following objects are masked from 'package:base':
##
## as.Date, as.Date.numeric
head(g1gc.df[,1])
## [1] "2014-05-12T14:00:32.868-0700:" "2014-05-12T14:00:33.179-0700:"
## [3] "2014-05-12T14:00:33.677-0700:" "2014-05-12T14:00:35.538-0700:"
## [5] "2014-05-12T14:00:37.811-0700:" "2014-05-12T14:00:41.428-0700:"
options("digits.secs"=3)
times=as.POSIXct( g1gc.df[,1], format="%Y-%m-%dT%H:%M:%OS%z:")
g1gc.z = zoo(g1gc.df[,-c(1)], order.by=times)
head(g1gc.z)
## SecondsSinceLaunch IncrementalCount FullCount
## 2014-05-12 17:00:32.868 1.161 0 0
## 2014-05-12 17:00:33.178 1.472 1 0
## 2014-05-12 17:00:33.677 1.969 2 0
## 2014-05-12 17:00:35.538 3.830 3 0
## 2014-05-12 17:00:37.811 6.103 4 0
## 2014-05-12 17:00:41.427 9.720 5 0
## UserTime SysTime RealTime BeforeSize AfterSize
## 2014-05-12 17:00:32.868 0.11 0.04 0.02 8192 1400
## 2014-05-12 17:00:33.178 0.05 0.01 0.02 5496 1672
## 2014-05-12 17:00:33.677 0.04 0.01 0.01 5768 2557
## 2014-05-12 17:00:35.538 0.21 0.05 0.04 22528 4907
## 2014-05-12 17:00:37.811 0.08 0.01 0.02 24576 7072
## 2014-05-12 17:00:41.427 0.26 0.06 0.04 43008 14336
## TotalSize Delta
## 2014-05-12 17:00:32.868 9437184 6792
## 2014-05-12 17:00:33.178 9437184 3824
## 2014-05-12 17:00:33.677 9437184 3211
## 2014-05-12 17:00:35.538 9437184 17621
## 2014-05-12 17:00:37.811 9437184 17504
## 2014-05-12 17:00:41.427 9437184 28672
Example of Two Benchmark Runs in One Log File
The data in the following graph is from a different log file, not the one of primary interest to this article. I’m including this image because it is an example of idle periods followed by busy periods. It would be uninteresting to average the rate of garbage collection over the entire log file period. More interesting would be the rate of garbage collect in the two busy periods. Are they the same or different?
Your production data may be similar, for example, bursts when employees return from lunch and idle times on weekend evenings, etc. Once the data is in an R Time Series, you can analyze isolated time windows.
Clipping the Time Series data
Flashing back to our test case… Viewing the data as a time series is interesting. You can see that the work intensive time period is between 9:00 PM and 3:00 AM. Lets clip the data to the interesting period:
par(mfrow=c(2,1))
plot(g1gc.z$UserTime, type="h",
main="User Time per GC\nTime: Complete Log File",
xlab="Time of Day", ylab="CPU Seconds per GC",
col="#1b9e77")
clipped.g1gc.z=window(g1gc.z,
start=as.POSIXct("2014-05-12 21:00:00"),
end=as.POSIXct("2014-05-13 03:00:00"))
plot(clipped.g1gc.z$UserTime, type="h",
main="User Time per GC\nTime: Limited to Benchmark Execution",
xlab="Time of Day", ylab="CPU Seconds per GC",
col="#1b9e77")
box(which = "outer", lty = "solid")
Cumulative Incremental and Full GC count
Here is the cumulative incremental and full GC count. When the line is very steep, it indicates that the GCs are repeating very quickly. Notice that the scale on the Y axis is different for full vs. incremental.
plot(clipped.g1gc.z[,c(2:3)],
main="Cumulative Incremental and Full GC count",
xlab="Time of Day",
col="#1b9e77")
GC Analysis of Benchmark Execution using Time Series data
In the following series of 3 graphs:
plot(clipped.g1gc.z[,c("AfterSize","RealTime","FullCount")],
xlab="Time of Day",
col=c("#1b9e77","red","#1b9e77"))
GC Analysis of heap recovered
Each GC trace includes the amount of heap space in use before and after the individual GC event. During garbage coolection, unreferenced objects are identified, the space holding the unreferenced objects is freed, and thus, the difference in before and after usage indicates how much space has been freed.
The following box plot and bar chart both demonstrate the same point - the amount of heap space freed per garbage colloection is surprisingly low.
par(mfrow=c(2,1))
boxplot(as.vector(clipped.g1gc.z$Delta),
main="Amount of Heap Recovered per GC Pass",
xlab="Size in KB",
horizontal = TRUE,
col="red")
hist(as.vector(clipped.g1gc.z$Delta),
main="Amount of Heap Recovered per GC Pass",
xlab="Size in KB",
breaks=100,
col="red")
box(which = "outer", lty = "solid")
This graph is the most interesting. The dark blue area shows how much heap is occupied by referenced Java objects. This represents memory that holds live data. The red fringe at the top shows how much data was recovered after each garbage collection.
barplot(clipped.g1gc.z[,c("AfterSize","Delta")],
col=c("#7570b3","#e7298a"),
xlab="Time of Day",
border=NA)
legend("topleft",
c("Live Objects","Heap Recovered on GC"),
fill=c("#7570b3","#e7298a"))
box(which = "outer", lty = "solid")
When I discuss the data in the log files with the customer, I will ask for an explaination for the large amount of referenced data resident in the Java heap. There are two are posibilities:
- There is a memory leak and the amount of space required to hold referenced objects will continue to grow, limited only by the maximum heap size. After the maximum heap size is reached, the JVM will throw an “Out of Memory” exception every time that the application tries to allocate a new object. If this is the case, the aplication needs to be debugged to identify why old objects are referenced when they are no longer needed.
- The application has a legitimate requirement to keep a large amount of data in memory. The customer may want to further increase the maximum heap size. Another possible solution would be to partition the application across multiple cluster nodes, where each node has responsibility for managing a unique subset of the data.
Conclusion
In conclusion, R is a very powerful tool for the analysis of Java garbage collection log files. The primary difficulty is data cleansing so that information can be read into an R data frame. Once the data has been read into R, a rich set of tools may be used for thorough evaluation.
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