0001-add-timing-tests.patch

From 9cfae509b03a69de267fe58f15e1e902468f3bbf Mon Sep 17 00:00:00 2001
From: Daniel King <[email protected]>
Date: Mon, 8 May 2017 11:12:30 -0400
Subject: [PATCH] add timing tests

---
 .../is/hail/variant/GenericDatasetSuite.scala      | 44 ++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/src/test/scala/is/hail/variant/GenericDatasetSuite.scala b/src/test/scala/is/hail/variant/GenericDatasetSuite.scala
index 00b9250..9e23057 100644
--- a/src/test/scala/is/hail/variant/GenericDatasetSuite.scala
+++ b/src/test/scala/is/hail/variant/GenericDatasetSuite.scala
@@ -1,13 +1,57 @@
 package is.hail.variant
 
 import is.hail.SparkSuite
+import is.hail.check.{Gen, Parameters, Prop}
 import is.hail.check.Prop._
 import is.hail.utils._
 import is.hail.expr.{TDouble, TGenotype, TInt, TString, TStruct}
+import org.apache.commons.math3.random.RandomDataGenerator
 import org.testng.annotations.Test
 
 class GenericDatasetSuite extends SparkSuite {
 
+  private val runs = 10
+  private def timeIt[T](g: Gen[VariantSampleMatrix[T]])(
+    write: (VariantSampleMatrix[T], String) => Unit,
+    read: String => VariantSampleMatrix[T]): (Double, Double) = {
+    var readTimes = Array[Long]()
+
+    val rng = new RandomDataGenerator()
+    rng.reSeed(Prop.seed)
+
+    val p = forAll(g) { gds =>
+      val f = tmpDir.createTempFile(extension = "vds")
+      write(gds, f)
+      val (readBack, t) = time(read(f).rdd.map(_._2._2.size).fold(0)(_ + _))
+      readTimes = readTimes :+ t
+      // readBack.same(gds)
+      true
+    }(Parameters(rng, 10000, runs))
+
+    val mean = readTimes.sum.toDouble / runs
+    val stddev = math.sqrt(readTimes.map(x => (x - mean) * (x - mean)).sum / runs)
+
+    println(s"mean: $mean, stddev: $stddev")
+    (mean, stddev)
+  }
+
+  @Test def timingTest() {
+    timeIt(VariantSampleMatrix.genGeneric(hc))(_.write(_), hc.readGDS(_))
+    timeIt(VariantSampleMatrix.genGeneric(hc))(_.write(_), hc.readGDS(_, sitesOnly = true))
+    timeIt(VariantSampleMatrix.genGeneric(hc))(_.write(_), hc.readGDS(_, sitesOnly = true, samplesOnly = true))
+    timeIt(VariantSampleMatrix.genGeneric(hc))(_.write(_), hc.readGDS(_, samplesOnly = true))
+
+    timeIt(VariantSampleMatrix.gen(hc, VSMSubgen.realistic))(_.write(_), hc.readVDS(_))
+    timeIt(VariantSampleMatrix.gen(hc, VSMSubgen.realistic))(_.write(_), hc.readVDS(_, sitesOnly = true))
+    timeIt(VariantSampleMatrix.gen(hc, VSMSubgen.realistic))(_.write(_), hc.readVDS(_, sitesOnly = true, samplesOnly = true))
+    timeIt(VariantSampleMatrix.gen(hc, VSMSubgen.realistic))(_.write(_), hc.readVDS(_, samplesOnly = true))
+
+    timeIt(VariantSampleMatrix.gen(hc, VSMSubgen.realistic))(_.write(_, parquetGenotypes = true), hc.readVDS(_))
+    timeIt(VariantSampleMatrix.gen(hc, VSMSubgen.realistic))(_.write(_, parquetGenotypes = true), hc.readVDS(_, sitesOnly = true))
+    timeIt(VariantSampleMatrix.gen(hc, VSMSubgen.realistic))(_.write(_, parquetGenotypes = true), hc.readVDS(_, sitesOnly = true, samplesOnly = true))
+    timeIt(VariantSampleMatrix.gen(hc, VSMSubgen.realistic))(_.write(_, parquetGenotypes = true), hc.readVDS(_, samplesOnly = true))
+  }
+
   @Test def testReadWrite() {
     val path = tmpDir.createTempFile(extension = ".vds")
 
-- 
2.10.1 (Apple Git-78)