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  • Using R to Analyze G1GC Log Files

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    Using R to Analyze G1GC Log Files body, td { font-family: sans-serif; background-color: white; font-size: 12px; margin: 8px; } tt, code, pre { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, monospace; } h1 { font-size:2.2em; } h2 { font-size:1.8em; } h3 { font-size:1.4em; } h4 { font-size:1.0em; } h5 { font-size:0.9em; } h6 { font-size:0.8em; } a:visited { color: rgb(50%, 0%, 50%); } pre { margin-top: 0; max-width: 95%; border: 1px solid #ccc; white-space: pre-wrap; } pre code { display: block; padding: 0.5em; } code.r, code.cpp { background-color: #F8F8F8; } table, td, th { border: none; } blockquote { color:#666666; margin:0; padding-left: 1em; border-left: 0.5em #EEE solid; } hr { height: 0px; border-bottom: none; border-top-width: thin; border-top-style: dotted; border-top-color: #999999; } @media print { * { background: transparent !important; color: black !important; filter:none !important; -ms-filter: none !important; } body { 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  Using R to Analyze G1GC Log Files   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: The “After Size” show the amount of heap space in use after each garbage collection. Many Java objects are still referenced, i.e. alive, during each garbage collection. This may indicate that the application has a memory leak, or may indicate that the application has a very large memory footprint. Typically, an application's memory footprint plateau's in the early stage of execution. One would expect this graph to have a flat top. The steep decline in the heap space may indicate that the application crashed after 2:00. The second graph shows that the outliers in real execution time, discussed above, occur near 2:00. when the Java heap seems to be quite full. The third graph shows that Full GCs are infrequent during the first few hours of execution. The rate of Full GC's, (the slope of the cummulative Full GC line), changes near midnight.   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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  • rJava - how to call an abstract class method?

    - by Sarah
    I am trying to create an R function that taps into my JAVA code. I have an abstract class, let's say StudentGroup, that has abstract methods, and one method "getAppropriateStudentGroup" which returns (based on config) a class which extends StudentGroup. This allows calling classes to behave the same regardless of which StudentGroups is actually appropriate. 1) How can I use rJava to call getAppropriateStudentGroup? and 2) How can I call the methods on the returned class? Thank you!

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  • how many sites IIS 6 can handle

    - by Sarah Nasir
    Is there a limit for creating Sites in IIS. i have searched and some forums have it in discussion which says there is no limit. Someone mentioned that he has created upto 100,000 sites in IIS 6 but i dont know his server specs though. Personally i feel that whatever the limit of IIS, the resources will be run out well before the limit reaches. how do big sites like blogger and wordpress handle a huge number of sites on their server. Questions: 1) Is there an upper limit for IIS 6.0? if yes then what is it 2) What should be a good number of requests IIS should serve for a decent server? (I am not talking about dynamic requests on server or logs.) 3) Is there a way I can do the test run on my cloud to test the capability of my server. what factors should i keep in view. db request, page size, disk read/writes etc ? Response shall be highly appreciated.

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  • how many sites IIS 6 can handle

    - by Sarah Nasir
    Is there a limit for creating Sites in IIS. i have searched and some forums have it in discussion which says there is no limit. Someone mentioned that he has created upto 100,000 sites in IIS 6 but i dont know his server specs though. Personally i feel that whatever the limit of IIS, the resources will be run out well before the limit reaches. how do big sites like blogger and wordpress handle a huge number of sites on their server. Questions: 1) Is there an upper limit for IIS 6.0? if yes then what is it 2) What should be a good number of requests IIS should serve for a decent server? (I am not talking about dynamic requests on server or logs.) 3) Is there a way I can do the test run on my cloud to test the capability of my server. what factors should i keep in view. db request, page size, disk read/writes etc ? Response shall be highly appreciated.

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  • Standby Internet connection by means of 3G Modem if Internet Fails

    - by Sarah Boss
    In my office I have 4 computers connected to the Internet with a DIR-615 Wireless N 300 router which gives Internet to all pc's via Ethernet cable. But sometimes this Internet goes off and I have to call the ISP and it takes them 2 days to repair it. I wanted to know if in such cases, can I connect my two zte 3g usb modems to this DIR-615 Wirless N300 router and get emergency Internet in my office? What other steps are required to set up this fail-safe connection?

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  • VIM autocompletion: Making ^X^U expand to longest match

    - by Sarah
    I'm using eclim to bring some eclipse functionality to VIM, however the code completion functions seem to work less than ideal. When I press ctrl+x ctrl+u after, for instance, System.out. with the curser right after the last dot, I get the completion popup-menu. This menu is really rather cumbersome to use, and the functionality that I would ideally want is something like: ctrl+x ctrl+u (expands to longest match) fill in more characters (expand to longest match). Is this possible somehow? I've tried fiddling with the completeopts settings, but they don't seem to do what I want.

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  • Lost Powerpoint document somewhere between Explorer and C drive

    - by Sarah Frank
    Opened (and not saving) a Powerpoint presentation attached to an online email message. Modified the document and clicked on the Save (not Save As) and now the presentation is nowhere to be found. How do I find this document? I have run a serious search on the C drive to no avail. It's not even in the Temporary Internet Files. Computer system Windows XP Professional version 5.1.2600 Explorer version 6.0.2900

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  • CentOS Latency High Troubleshooting

    - by Sarah Weinberger
    I have two CentOS servers connected via a 10 Gb fiber optic cable with a network emulator connected between them. All three units sit on a desk in the lab. There is also a regular 1 Gbit Ethernet cable connected to each of the machines, which provide internet connectivity. When I set the latency to something roughly below 30 ms, all is fine. When the latency gets to 70ms and above, and definitely 130ms, the network layer suspends. For instance, if I set the latency (delay) to 70ms, then launching TeamViewer (or any other application that uses network connectivity) never happens or does not work. There is no timeout message, simply no response. I have to lower to latency back down to zero to see any response and have the box start working. What is the problem and how would I go about fixing it? It seems to me some sort of setting in Linux causes one of the CentOS networking drivers to sit in an infinite loop or something. eth0 is the connection to the internet, all settings are default eth2 is the 10 Gbit fiber optic connection to the other computer with the MTU set to 9600 with all other parameters at default values.

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  • Calling the LWRP from the Exception Handler

    - by Sarah Haskins
    Is it possible to call out to a Provider (LWRP) from a Chef Exception Handler? I think my Provider is out of scope, but I don't know if what I am trying to do is possible? or advisable? Here is my provider code (cookbooks/config/provider/signal.rb): action :failure do Chef::Log.info("Yeah success") end Here is my exception handler code (exception_handler/handlers/exceptionHandler.rb): require 'chef/handler' config_signal "signal" do action :nothing end class Chef class Handler class LogCollector < Chef::Handler notifies :failure, resources(:config_signal => signal) end end end Also, if anyone has a good recommendation for general reading about scope in the context of Chef I'd appreciate it.

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  • How to create hash or yml from top level attributes values of node?

    - by Sarah Haskins
    I have a chef recipe where I want to take all of the attributes under node['cfn']['environment'] and write them to a yml file. I could do something like this (it works fine): content = { "environment_class" => node['cfn']['environment']['environment_class'], "node_id" => node['cfn']['environment']['node_id'], "reporting_prefix" => node['cfn']['environment']['reporting_prefix'], "cfn_signal_url" => node['cfn']['environment']['signal_url'] } yml_string = YAML::dump(content) file "/etc/configuration/environment/platform.yml" do mode 0644 action :create content "#{yml_string}" end But I don't like that I have to explicitly list out the names of the attributes. If later I add a new attributes it would be nice if it automatically was included in the written out yml file. So I tried something like this: yml_string = node['cfn']['environment'].to_yaml But because the node is actually a Mash, I get a platform.yml file like this (it contains a lot of unexpected nesting that I don't want): --- !ruby/object:Chef::Node::Attribute normal: tags: [] cfn: environment: &25793640 reporting_prefix: Platform2 signal_url: https://cloudformation-waitcondition-us-east-1.s3.amazonaws.com/... environment_class: Dev node_id: i-908adf9 ... But what I want is this: ---- reporting_prefix: Platform2 signal_url: https://cloudformation-waitcondition-us-east-1.s3.amazonaws.com/... environment_class: Dev node_id: i-908adf9 How can I achieve the desired yml output w/o explicitly listing the attributes by name?

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  • Nginx flv audio pseudo stream works but video is not loading

    - by sarah
    I am working on a development server for a company & they want nginx webserver to work with. So the requirements for their company is, it should be capable of doing following things i.e hotlink protection, mp4 & flv pseudo stream & secure streaming. However nginx fulfills their requirements and i am configuring their server from past 2 days as i am new to this field so i've only acheived hotlinking prevention in past 2 days. But the problem on which i am stuck is flv pseudo streaming, to make work to mp4 pseudo stream it was just a piece of paper but i am really fuc*ed up with flv pseudo stream. I have converted my flv videos with flvmdi tools to insert many keyframes but the problem is , when i try to seek video from following keyframes that are generated by flvmdi i.e test.flv?start=2681223, video does not load but audio pseudo works fine. So it means no problem with my flv configuration in nginx.conf file. And the forum that i used to compile my nginx-1.2.1 is http://h264.code-shop.com/trac/wiki/Mod-H264-Streaming-Nginx-Version2 & by adding additional module --with-http_flv_module. This forum is really active, hopes i will resolve my problem as soon as you guys will provide me some guide.

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  • Loading the preview function of AUCTeX 11.86 on macports Emacs-app 23.2.1 port.

    - by Sarah
    I've installed Emacs-app 23.2.1 via MacPorts and I'm trying to install AUCTeX 11.86 so that it will work on this installation. I've run the following configure line for AUCTeX and that seems to work. ./configure --with-emacs=/Applications/MacPorts/Emacs.app/Contents/MacOS/Emacs --with-lispdir=/Applications/MacPorts/Emacs.app/Contents/Resources/site-lisp/ --with-texmf-dir=/usr/local/texlive/2010basic/texmf-local/ make and make install seem to work, and I've added the following line to my init.el (require 'tex-site) as per the installation instructions. However, when I open a TeX file, the Preview menu does not show up (although the LaTeX menu does.) The following are some of my tests: M-x load-library RET preview-latex RET doesn't seem to do anything. M-x load-library RET preview RET brings up the Preview menu. Is it safe to somehow add the load-library preview to my init.el? Or do I risk mucking up something? I'm new to Emacs and primarily trying to learn it because of the AUCTeX preview features, but I don't feel very safe in this environment yet.

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  • Repair corrupt hard disk on Mac without install CD

    - by Sarah
    The hard disk of my late 2009 MacBook Pro appears to have become corrupted. I am traveling and do not have my install CD (and won't for several weeks, nor will I be anywhere near an Apple store). The hard disk is not the original, which failed in June 2011. It's some Hitachi replacement installed by IT. History: I was typing an email this afternoon, my computer suddenly started making soft clicking sounds and then froze. I was not moving around. I rebooted, which took a while. I heard more clicking sounds and the computer froze at least once again. It's now kind of working, with mdworker sucking up one CPU. There are no awkward hard drive sounds when I run Chrome or play music. However, when I launched Stickies, I found no trace of my saved Stickies. I ran a live disk verification from within Disk Utility, and it reported Problem: As reported, I don't have access to an installation disc and am nowhere near an area where I can get one for at least two weeks. I have the option of asking someone to go to some trouble and expense to get one for me, but I'm not sure it's worth it: I've read that I can use fsck from single-user mode to repair the disk. Should I just try this? Is it risky? I'm concerned that the clicky sound portends imminent (mechanical) hard drive failure, so it's not worth doing a silly repair. This hard disk is backed up, but I definitely won't be able to access the backup while traveling. I'd like to maximize the probability that I can keep using my computer (and all its current files) while traveling. Update I bit the bullet and ran fsck -fy from single-user mode. It only needed one pass (modification) to reach the "okay" stage. However, rebooting took nearly 5 min and involved several rounds of scratchy sounds and a few bad clicks. I'm now back to kind of using my computer (the same files are missing as before). When I ran live disk verification from Disk Utility this time, however, it reported that the volume appears to be OK. Am I right to infer from the scratchy sounds, however, that my hard drive is still rapidly on its way out? Is there anything else I can do to increase its functionality over the next few weeks?

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  • Easy to use database with views for a medical student doing research?

    - by Sarah
    I'm having trouble finding a tool that does this for my friend (without designing it myself). What is needed is a simple program with a database where input forms and views can be designed and saved. A patient table might consist of, say, 50 columns, so it is imperative that it is possible to make columns be able to default, say, through a form for submission of data. By views I mean something like "saved selections" based on various criteria (WHERE runny_nose=True...) but as friendly as possible to save, and export options would be nice. Does this exist at all? It seems at one hand trivial and on the other, my Google fu is failing.

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  • How to change the URL on my Amazon EC2 webserver

    - by Sarah
    I am at the point in playing around with EC2 that I have launched a webserver. Right now, the website URL looks like http://ec2-<some numbers>.compute-1.amazonaws.com/ I am evaluating the usefulness of these services for my small business purposes; is there a way I can get my URL to look something more like http://<mybusiness>.com. Ideally, I would like to get it to look cleaner, and furthermore I would rather not have "amazonaws" as part of it. Is this possible? I'm a newb to AWS, so apologies if this is an easy question

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  • System Issues and Major Malfuctions after Failed hibernation Exit

    - by Sarah Seguin
    I have a HP G71-340US that went into hibernation mode for a while and when I tried coming out of it, I got an error message: You're computer cannot come out if hibernation . Status: 0xc000009a Info: A fatal error occurred processing the restoration data. File: \hiberfil.sys Any information that was not saved before the computer went into hybernation will be lost enter=continue So I hit continue and it ran soooo super slow it. It was seriously crawling. Finally I gave up and turned it off manually (IE press and hold the button). It's been a week or two since then and EVERY SINGLE TIME I have tried to to do ANYTHING it takes forever. When I say forever, I literally mean takes 5-7 minutes to load the internet, then the page itself, then to click a link, so on so forth. Eventually everything just goes not responding and I have to give up (4-6 HOURS later). I also cannot access my thumb/jump drives once I've managed to load windows. I was going to try runing malware bytes incase of a virus, but it's windows explorer developes errors and goes not responding on me. Currently I'm running scan disk or check disk and like every file is coming back unreadable. I let it run the last 2 hours straight in chkdesk and I'm only at 6 percent with around 500+ errors and still going. Yes, I've taken logs of the errors via cell phone camera and patience. A week or two prior to this happening I had to change our the hard drive due to blunt force trama next to the mouse. OH! Running on Windows 7: ) And I've tried loading the computer in safe mode and it makes absolutely no difference. Any and all help would be appreciated. I really don't know what to do from here and I'm kind of freaking out. I've googled different part of the error and things that I've done/seen and there are so many different answers/topics that I thought it best to just post the questions.

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  • Word 2010 doc skips pages

    - by Sarah
    A Word document with 9 pages, 3 section brakes next page (no odd and even breaks used) and inserted page numbers shows the correct sequence of pages when moving thru the document. When I change the page numbers in section 2 to start from 1 (Section 1 is only one page numbered with a roman numeral.) Then two strange things happen: The sequence in the status bar goes from 1 to 3. Page 2 disappeared (no text is missing) and my total number of pages reads 10 when i actually only have 9. The first page has a table of contents. Page 2 is listed, but when I press ctrl + click the shortcut it goes to page 4?

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  • Mysql: Working With 192 Trillion Records... (Yes, 192 Trillion)

    - by Sarah
    Here's the question... Considering 192 trillion records, what should my considerations be? My main concern is speed. Here's the table... CREATE TABLE `ref` ( `id` INTEGER(13) AUTO_INCREMENT DEFAULT NOT NULL, `rel_id` INTEGER(13) NOT NULL, `p1` INTEGER(13) NOT NULL, `p2` INTEGER(13) DEFAULT NULL, `p3` INTEGER(13) DEFAULT NULL, `s` INTEGER(13) NOT NULL, `p4` INTEGER(13) DEFAULT NULL, `p5` INTEGER(13) DEFAULT NULL, `p6` INTEGER(13) DEFAULT NULL, PRIMARY KEY (`id`), KEY (`s`), KEY (`rel_id`), KEY (`p3`), KEY (`p4`) ); Here's the queries... SELECT id, s FROM ref WHERE red_id="$rel_id" AND p3="$p3" AND p4="$p4" SELECT rel_id, p1, p2, p3, p4, p5, p6 FROM ref WHERE id="$id" INSERT INTO rel (rel_id, p1, p2, p3, s, p4, p5, p6) VALUES ("$rel_id", "$p1", "$p2", "$p3", "$s", "$p4", "$p5", "$p6") Here's some notes... The SELECT's will be done much more frequently than the INSERT. However, occasionally I want to add a few hundred records at a time. Load-wise, there will be nothing for hours then maybe a few thousand queries all at once. Don't think I can normalize any more (need the p values in a combination) The database as a whole is very relational. This will be the largest table by far (next largest is about 900k) UPDATE (08/11/2010) Interestingly, I've been given a second option... Instead of 192 trillion I could store 2.6*10^16 (15 zeros, meaning 26 Quadrillion)... But in this second option I would only need to store one bigint(18) as the index in a table. That's it - just the one column. So I would just be checking for the existence of a value. Occasionally adding records, never deleting them. So that makes me think there must be a better solution then mysql for simply storing numbers... Given this second option, should I take it or stick with the first... [edit] Just got news of some testing that's been done - 100 million rows with this setup returns the query in 0.0004 seconds [/edit]

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  • Odd SQL Results

    - by Ryan Burnham
    So i have the following query Select id, [First], [Last] , [Business] as contactbusiness, (Case When ([Business] != '' or [Business] is not null) Then [Business] Else 'No Phone Number' END) from contacts The results look like id First Last contactbusiness (No column name) 2 John Smith 3 Sarah Jane 0411 111 222 0411 111 222 6 John Smith 0411 111 111 0411 111 111 8 NULL No Phone Number 11 Ryan B 08 9999 9999 08 9999 9999 14 David F NULL No Phone Number I'd expect record 2 to also show No Phone Number If i change the "[Business] is not null" to [Business] != null then i get the correct results id First Last contactbusiness (No column name) 2 John Smith No Phone Number 3 Sarah Jane 0411 111 222 0411 111 222 6 John Smith 0411 111 111 0411 111 111 8 NULL No Phone Number 11 Ryan B 08 9999 9999 08 9999 9999 14 David F NULL No Phone Number Normally you need to use is not null rather than != null. whats going on here?

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  • Updating Xml attributes with new values in a SQL Server 2008 table

    - by SMD
    I have a table in SQL Server 2008 that it has some columns. One of these columns is in Xml format and I want to update some attributes. For example my Xml column's name is XmlText and it's value in 5 first rows is such as: <Identification Name="John" Family="Brown" Age="30" /> <Identification Name="Smith" Family="Johnson" Age="35" /> <Identification Name="Jessy" Family="Albert" Age="60" /> <Identification Name="Mike" Family="Brown" Age="23" /> <Identification Name="Sarah" Family="Johnson" Age="30" /> and I want to change all Age attributes that are 30 to 40 such as below: <Identification Name="John" Family="Brown" Age="40" /> <Identification Name="Smith" Family="Johnson" Age="35" /> <Identification Name="Jessy" Family="Albert" Age="60" /> <Identification Name="Mike" Family="Brown" Age="23" /> <Identification Name="Sarah" Family="Johnson" Age="40" />

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  • SQL Query to retrieve highest item up to a point in a group

    - by James
    The best way of describing this is I have a table of people with their names and ages. Assume that people with the same surname are from the same family. I need a query in oracle which will retrieve a list of the oldest person in each family, but not older than a certain age. Table: person name surname age =============================== James Smith 23 Sarah Powell 17 Barry Smith 31 Mark Smith 35 Mary Smith 18 Bob Powell 30 How do I retrieve the oldest person in each family under 30? Results I'm after name surname age =============================== James Smith 23 Sarah Powell 17

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  • Operator== in derived class never gets called.

    - by Robin Welch
    Can someone please put me out of my misery with this? I'm trying to figure out why a derived operator== never gets called in a loop. To simplify the example, here's my Base and Derived class: class Base { // ... snipped bool operator==( const Base& other ) const { return name_ == other.name_; } }; class Derived : public Base { // ... snipped bool operator==( const Derived& other ) const { return ( static_cast<const Base&>( *this ) == static_cast<const Base&>( other ) ? age_ == other.age_ : false ); }; Now when I instantiate and compare like this ... Derived p1("Sarah", 42); Derived p2("Sarah", 42); bool z = ( p1 == p2 ); ... all is fine. Here the operator== from Derived gets called, but when I loop over a list, comparing items in a list of pointers to Base objects ... list<Base*> coll; coll.push_back( new Base("fred") ); coll.push_back( new Derived("sarah", 42) ); // ... snipped // Get two items from the list. Base& obj1 = **itr; Base& obj2 = **itr2; cout << obj1.asString() << " " << ( ( obj1 == obj2 ) ? "==" : "!=" ) << " " << obj2.asString() << endl; Here asString() (which is virtual and not shown here for brevity) works fine, but obj1 == obj2 always calls the Base operator== even if the two objects are Derived. I know I'm going to kick myself when I find out what's wrong, but if someone could let me down gently it would be much appreciated.

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  • Blank Processes (?) in Natty Narwhal

    - by A Hylian Human
    I've noticed that there a seemingly blank processes (no process name, no cmdline info, only an ID), which also appear to cause my CPU to be running like crazy. My fans are going pretty much full speed and I have no idea what to do. Restarting does not help. Whenever I try to kill the process IDs, nothing happens. It's like new blank processes are continuously being created. I am really surprised that I am able to write up this question without Firefox lagging like crazy (and trust me, it's not Firefox causing the issue, as far as I can tell).

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