added gcbd benchmark;

added power-off option

benchmark-gcbd.R

@@ -0,0 +1,81 @@
+# source: CRAN gcbd package
+
+size = c(100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 3500, 4000, 4500, 5000)
+runs = c( 50,  50,  50,  50,  50,  50,  50,  50,  50,   30,   30,   30,   30,   20,   20,    5,    5,    5,    5,    5)
+meanTrim = 0.1
+
+results = data.frame(t1=numeric(), t2=numeric(), t3=numeric(), t4=numeric())
+
+library(Matrix)
+
+# functions
+
+getMatrix <- function(N) {
+    a <- rnorm(N*N)
+    dim(a) <- c(N,N)
+    invisible(gc())
+    invisible(a)
+}
+
+matmultBenchmark <- function(N, n, trim=0.1) {
+    a <- getMatrix(N)
+    traw <- replicate(n, system.time(crossprod(a))[3])
+    tmean <- mean(traw,trim=trim)
+}
+
+
+qrBenchmark <- function(N, n, trim=0.1) {
+    a <- getMatrix(N)
+    traw <- replicate(n, system.time(qr(a, LAPACK=TRUE))[3])
+    tmean <- mean(traw,trim=trim)
+}
+
+svdBenchmark <- function(N, n, trim=0.1) {
+    a <- getMatrix(N)
+    traw <- replicate(n, system.time(svd(a))[3])
+    tmean <- mean(traw,trim=trim)
+}
+
+luBenchmark <- function(N, n, trim=0.1) {
+    a <- getMatrix(N)
+    traw <- replicate(n, system.time(lu(a))[3])
+    tmean <- mean(traw,trim=trim)
+}
+
+
+# Initialization
+
+set.seed (1)
+
+cat(paste0("Mean trim : ", meanTrim, "\n"))
+
+for (i in 1:length(size))
+{
+    n = size[i]
+    r = runs[i]
+    
+    cat(paste0("Size : ", n, "\n"))
+    cat(paste0("Runs : ", r, "\n"))
+    
+    t1 = matmultBenchmark(n, r, meanTrim)
+    cat(paste0("Matrix Multiply             : ", t1, "\n"))
+    
+    t2 = qrBenchmark(n, r, meanTrim)
+    cat(paste0("QR Decomposition            : ", t2, "\n"))
+    
+    t3 = svdBenchmark(n, r, meanTrim)
+    cat(paste0("Singular Value Deomposition : ", t3, "\n"))
+    
+    t4 = luBenchmark(n, r, meanTrim)
+    cat(paste0("Triangular Decomposition    : ", t4, "\n"))
+    
+    results = rbind(results, data.frame(t1=t1, t2=t2, t3=t3, t4=t4))
+}
+
+colnames(results) = c("Matrix Multiply", "QR Decomposition", 
+                      "Singular Value Deomposition", "Triangular Decomposition")
+
+attr(results, "size") = size
+attr(results, "runs") = runs
+attr(results, "meanTrim") = meanTrim
+saveRDS(results, paste0("test-gcbd-", ifelse(exists("blasLibName"), blasLibName, ""), ".rds"))

master-ctrl-slaves.sh

@@ -13,7 +13,7 @@ function configure_hosts {
         echo -n "${host} ... "
         
         echo -n "config-push "
-        scp ${SSH_OPTIONS} -i ssh/${SSH_KEY_PRIV} slave-cmds.sh cpuinfo benchmark-sample.R benchmark-urbanek.R benchmark-revolution.R root@${host}:/root
+        scp ${SSH_OPTIONS} -i ssh/${SSH_KEY_PRIV} slave-cmds.sh cpuinfo benchmark-sample.R benchmark-urbanek.R benchmark-revolution.R benchmark-gcbd.R root@${host}:/root
         ret=$?
         if [ $ret -ne 0 ] ; then
             echo "error $ret"; continue
@@ -49,6 +49,23 @@ function configure_hosts {
 
 }
 
+function power_off {
+
+    echo "* Power-off hosts:"
+
+    for host in `cat hosts-list.txt`
+    do
+        echo -n "${host} ... "
+        
+        echo "power off "
+        ssh ${SSH_OPTIONS} -i ssh/${SSH_KEY_PRIV} root@${host} 'poweroff'
+        
+    done
+
+    echo "* Done"
+
+}
+
 function benchmark {
 
     echo "* Benchmark: ${BENCHMARK_TEST}"
@@ -99,6 +116,9 @@ else
             configure_hosts)
                 configure_hosts
                 ;;
+            power_off)
+                power_off
+                ;;
             test_sample)
                 BENCHMARK_TEST="sample"
                 benchmark
@@ -111,6 +131,10 @@ else
                 BENCHMARK_TEST="revolution"
                 benchmark
                 ;;
+            test_gcbd)
+                BENCHMARK_TEST="gcbd"
+                benchmark
+                ;;
             *)
                 echo "unknown command"
         esac

slave-cmds.sh

@@ -55,6 +55,7 @@ function mro_install {
     sed -i "1i\library(checkpoint); checkpoint('${CHECKPOINT_DATE}', scanForPackages=FALSE, verbose=FALSE)" benchmark-sample.R
     sed -i "1i\library(checkpoint); checkpoint('${CHECKPOINT_DATE}', scanForPackages=FALSE, verbose=FALSE)" benchmark-urbanek.R
     sed -i "1i\library(checkpoint); checkpoint('${CHECKPOINT_DATE}', scanForPackages=FALSE, verbose=FALSE)" benchmark-revolution.R
+    sed -i "1i\library(checkpoint); checkpoint('${CHECKPOINT_DATE}', scanForPackages=FALSE, verbose=FALSE)" benchmark-gcbd.R
 
     # make directory for BLAS and LAPACK libraries
     mkdir -p ${DIR_BLAS}
@@ -631,6 +632,9 @@ else
             test_revolution)
                 R_BENCHMARK_SCRIPT="benchmark-revolution.R"
                 ;;
+            test_gcbd)
+                R_BENCHMARK_SCRIPT="benchmark-gcbd.R"
+                ;;
             *)
                 $i
         esac