large refactor

Author: nfultz

DESCRIPTION

@@ -1,30 +1,26 @@
 Package: gcbc
 Type: Package
 Title: 'GPU'/CPU Benchmarking in Centos Systems
-Version: 0.2.6
-Date: 2016-09-27
+Version: 0.1.0
+Date: 2020-04-15
 Author: Dirk Eddelbuettel (Debian Version), Neal Fultz (Centos Port)
 Maintainer: Neal Fultz <[email protected]>
 Description: 'GPU'/CPU Benchmarking on Centos-package based systems
  This package benchmarks performance of a few standard linear algebra
  operations (such as a matrix product and QR, SVD and LU decompositions)
  across a number of different 'BLAS' libraries as well as a 'GPU' implementation.
- To do so, it takes advantage of the ability to 'plug and play' different
- 'BLAS' implementations easily on a Debian and/or Ubuntu system.  The current
- version supports
+ The current version supports
   - 'Reference BLAS' ('refblas') which are un-accelerated as a baseline
   - Atlas which are tuned but typically configure single-threaded
   - Atlas39 which are tuned and configured for multi-threaded mode
   - 'Goto Blas' which are accelerated and multi-threaded
   - 'Intel MKL' which is a commercial accelerated and multithreaded version.
  As for 'GPU' computing, we use the CRAN package
-  - 'gputools'
- For 'Goto Blas', the 'gotoblas2-helper' script from the ISM in Tokyo can be
- used. For 'Intel MKL' we use the Revolution R packages from Ubuntu 9.10.
+  - 'gpuR'
 License: GPL (>= 2)
 LazyLoad: yes
 Depends: R (>= 2.11.1)
-Imports: Matrix, DBI, RSQLite, plyr, reshape, lattice
+Imports: Matrix, DBI, RSQLite, plyr, reshape2, lattice
 Suggests: gpuR
 SystemRequirements: Centos or RHEL system with access to Goto Blas, Intel
  MKL, Atlas development build as well as a Nvidia GPU with CUDA support

NAMESPACE

@@ -5,7 +5,7 @@ importFrom("DBI", "dbDriver", "dbConnect", "dbDisconnect", "dbGetQuery", "dbWrit
 importFrom("RSQLite", "dbBuildTableDefinition")
 importFrom("lattice", "trellis.par.get", "trellis.par.set", "xyplot", "simpleKey", "dotplot")
 importFrom("plyr", "ddply")
-importFrom("reshape", "melt", "melt.data.frame")
+importFrom("reshape2", "melt", "melt.data.frame")
 importFrom("Matrix", "lu")
 
 export(

R/benchmark.R

@@ -4,16 +4,16 @@
 #    1 / outer(i - 1, i, "+")
 #}
 
-getMatrix <- function(N, type="matrix") {
+getMatrix <- function(N) {
     on.exit(invisible(gc()))
     a <- rnorm(N*N)
     #a <- hilbert(N)
     dim(a) <- c(N,N)
-    invisible(as(a, "type"))
+    invisible(as(a, Sys.getenv("GCBC_MATRIX_TYPE", "matrix")))
 }
 
-matmultBenchmark <- function(N, n, trim=0.1, type="matrix") {
-    a <- getMatrix(N, type)
+matmultBenchmark <- function(N, n, trim=0.1) {
+    a <- getMatrix(N)
     traw <- replicate(n, system.time(crossprod(a))[3])
     tmean <- mean(traw,trim=trim)
 }

R/utilities.R

@@ -1,27 +1,8 @@
 
-.dbfile <- "/var/tmp/gcbd.sqlite"
+.dbfile <- "~/gcbc.sqlite"
 
 requirements <- function() {
 
-    # are we on Unix ?
-    stopifnot(.Platform$OS.type == "unix")
-
-    # are we on a Debian or Ubuntu system ?
-    stopifnot(file.exists("/etc/debian_version"))
-
-    # reference blas as minimum standard installed ?
-    stopifnot(file.exists("/usr/share/doc/libblas3gf/copyright"))
-    stopifnot(file.exists("/usr/share/doc/liblapack3gf/copyright"))
-
-    # wajig frontend to dpkg, apt, ... ?
-    stopifnot(file.exists("/usr/bin/wajig"))
-
-    # "littler" scripting frontend to R
-    stopifnot(file.exists("/usr/bin/r"))
-
-    # is Goto available -- gotoblas2-help installs this
-    stopifnot(file.exists("/etc/default/gotoblas2-helper"))
-
     # is database available ?
     if ( ! file.exists(.dbfile)) {
         createDatabase(.dbfile)
@@ -30,63 +11,14 @@ requirements <- function() {
     invisible(TRUE)
 }
 
-installAtlas <- function() {
-    res <- system("sudo apt-get -y --force-yes install libatlas3gf-base", intern=TRUE, ignore.stderr=TRUE)
-    invisible(res)
-}
-
-purgeAtlas <- function() {
-    ##-- old local build wajig purge libatlas-base-dev libatlas-dev  libatlas3gf-amd64sse3  libatlas3gf-base
-    res <- system("sudo apt-get -y --force-yes purge libatlas3gf-base", intern=TRUE, ignore.stderr=TRUE)
-    invisible(res)
-}
-
-installMKL <- function() {
-    res <- system("sudo apt-get -y --force-yes install revolution-mkl r-revolution-revobase revolution-r", intern=TRUE, ignore.stderr=TRUE)
-    invisible(res)
-}
-
-purgeMKL <- function() {
-    res <- system("sudo apt-get -y --force-yes purge revolution-mkl r-revolution-revobase revolution-r", intern=TRUE, ignore.stderr=TRUE)
-    invisible(res)
-}
-
-installGoto <- function() {
-    res <- system("sudo wajig -y install /var/spool/gotoblas2-helper/archive/gotoblas2_1.13-1_amd64.deb", intern=TRUE, ignore.stderr=TRUE)
-    invisible(res)
-}
-
-purgeGoto <- function() {
-    res <- system("sudo apt-get -y --force-yes purge gotoblas2", intern=TRUE, ignore.stderr=TRUE)
-    invisible(res)
-}
-
-installAtlas39 <- function() {
-    res <- system("sudo wajig -y install /var/spool/atlas39/libatlas39_3.9.25-1_amd64.deb", intern=TRUE, ignore.stderr=TRUE)
-    invisible(res)
-}
-
-purgeAtlas39 <- function() {
-    res <- system("sudo apt-get -y --force-yes purge libatlas39", intern=TRUE, ignore.stderr=TRUE)
-    invisible(res)
-}
 
 createDatabase <- function(dbfile=.dbfile) {
-
-    dbi <- dbDriver("SQLite")
-    dframe <- data.frame(host="", datum="",
-                         type="", nobs=NA, nrun=NA,
-                         ref=NA, atlas=NA, atl39=NA,
-                         mkl=NA, gotob=NA, gpu=NA)
-    dftypes <- list(host="text", datum="text", type="text",
-                    nobs="integer", nrun="integer",
-                    ref="real", atlas="real", atl39="real",
-                    mkl="real", gotob="real", gpu="real")
-    sql <- dbBuildTableDefinition(dbi, name="benchmark", value=dframe,
-                                  field.types=dftypes, row.names=FALSE)
     dbcon <- dbConnect(dbDriver("SQLite"), dbname=dbfile)
-    res <- dbGetQuery(dbcon, sql)
-    dbDisconnect(dbcon)
+    on.exit(dbDisconnect(dbcon))
+    dftypes <- list(host="text", datum="text", env="text", type="text",
+                    nobs="integer", nrun="integer")
+    sql <- sqlCreateTable(dbcon, "benchmark", fields=dftypes, row.names = FALSE)
+    dbExecute(dbcon, sql)
 }
 
 databaseResult <- function(data,dbfile=.dbfile) {
@@ -101,20 +33,16 @@ databaseResult <- function(data,dbfile=.dbfile) {
 }
 
 isPackageInstalled <- function(package) { 	# Henrik Bengtsson, r-devel, 24 Aug 2010
-    path <- system.file(package=package)
-    (path != "")
+    system.file(package=package)  != ""
 }
 
-#hasMagma <- function() {
-#    isPackageInstalled("magma")
-#}
 
-hasGputools <- function() {
-    isPackageInstalled("gputools")
+hasGpuR <- function() {
+    isPackageInstalled("gpuR")
 }
 
-getBenchmarkData <- function(host) {
-    dbcon <- dbConnect(dbDriver("SQLite"), dbname=system.file("sql", "gcbd.sqlite", package="gcbd"))
+getBenchmarkData <- function(host, dbfile=.dbfile) {
+    dbcon <- dbConnect(dbDriver("SQLite"), dbname=.dbfile)
     data <- dbGetQuery(dbcon, paste('select * from benchmark where host="',
                                     host, '" order by nobs', sep=""))
     invisible(dbDisconnect(dbcon))

inst/scripts/benchmark.r

@@ -1,6 +1,6 @@
 #!/usr/bin/r -t
 
-suppressMessages(library(gcbd))
+suppressMessages(library(gcbc))
 suppressMessages(library(getopt))
 
 ## default values
@@ -39,35 +39,42 @@ if (verbose) {
 
 requirements()
 
-purgeAtlas()
-purgeAtlas39()
-purgeMKL()
-purgeGoto()
-
-cmd      <- paste('r -lgcbd,Matrix   -e"cat(', benchmark, 'Benchmark(', N, ",", n, '))"', sep="")
-cmdgpu   <- paste('r -lgcbd,gpuR -e"cat(', benchmark, 'Benchmarkgputools(', N, ",", n, '))"', sep="")
-cmdtest  <- paste('r -lgcbd,Matrix   -e"cat(', benchmark, 'BenchmarkTEST(', N, ",", n, '))"', sep="")
+cmd      <- paste('r -lgcbc,Matrix   -e"cat(', benchmark, 'Benchmark(', N, ",", n, '))"', sep="")
+cmdgpu   <- paste('r -lgcbc,gpuR -e"cat(', benchmark, 'Benchmarkgputools(', N, ",", n, '))"', sep="")
+cmdtest  <- paste('r -lgcbc,Matrix   -e"cat(', benchmark, 'BenchmarkTEST(', N, ",", n, '))"', sep="")
 
 ref <- as.numeric(system(cmd, intern=TRUE))
 
-installAtlas()
+##SETENV
+
+# for b in lu qr svd matmult;
+# do 
+# ##for n in 250 500 750 1000 1250 1500 1750 2000 2250 2500 2750 3000 3250 3500 3750 4000; 
+# for n in 100 200 300 400 500 600 700 800 900 1000 1250 1500 1750 2000 2500 3000 3500 4000 4500 5000;
+# do
+# if [ $n -lt 1000 ]; then
+# r=50
+# elif [ $n -lt 2000 ]; then
+# r=30
+# elif [ $n -lt 3000 ]; then
+# r=20
+# elif [ $n -ge 3000 ]; then
+# r=5
+# fi
+# echo "Now starting $n $r $b"
+# ./benchmark.r -n $n -r $r -b $b -v
+# done
+# done
+
 atlas      <- as.numeric(system(cmd,      intern=TRUE))
-purgeAtlas()
 
-installAtlas39()
 atl39      <- as.numeric(system(cmd,      intern=TRUE))
-purgeAtlas39()
 
-installMKL()
 mkl      <- as.numeric(system(cmd,      intern=TRUE))
-purgeMKL()
 
-installGoto()
 goto      <- as.numeric(system(cmd,      intern=TRUE))
-#magmaGoto <- ifelse( hasMagma(), as.numeric(system(cmdmagma, intern=TRUE)), NA)
-purgeGoto()
 
-gpu <- ifelse( hasGputools(), as.numeric(system(cmdgpu, intern=TRUE)), NA)
+gpu <- ifelse( hasGpuR(), as.numeric(system(cmdgpu, intern=TRUE)), NA)
 
 res <- data.frame(type=benchmark, nobs=N, nrun=n,
                   ref=ref, atlas=atlas, atl39=atl39,