Cray R

tests/utils/R/rscript.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python3
+"""
+R benchmarks
+
+These tests checks that the R programming language is functional.
+
+"""
+
+import os
+import reframe as rfm
+import reframe.utility.sanity as sn
+
+
+class RscriptBase(rfm.RunOnlyRegressionTest):
+    """A base class for R functionality tests."""
+
+    descr = "A base class for R functionality tests.  "
+    valid_prog_environs = ["PrgEnv-gnu"]
+    modules = ["cray-R"]
+    executable = "Rscript"
+
+    @sanity_function
+    def validate_job_run(self):
+        """Basic check that any output was produced and the job run until completion"""
+        return sn.assert_found("Success", self.stdout)
+
+
+class RscriptInstall(RscriptBase):
+    """Tests installing packages with R on the login nodes"""
+
+    descr = "Tests that R packages can be installed locally. Requires internet access."
+    valid_systems = ["archer2:login"]
+    local = True
+    executable_opts = ["install_benchmark_packages.R"]
+    libs_path = None
+    env_vars = {}
+    prerun_cmds = []
+
+    @run_before("run")
+    def setup_r_library(self):
+        """Setup R library path
+
+        The default R library directory is on the home folder,
+        which is not writable on the compute nodes and pollute user's environment.
+        This sets environment variables so that packages are written/read in a local directory.
+        """
+
+        self.libs_path = os.path.join(self.stagedir, ".libs")
+
+        self.env_vars = {"R_LIBS_USER": self.libs_path}
+
+        self.prerun_cmds = [f"mkdir -p {self.libs_path}"]
+
+
+@rfm.simple_test
+class RscriptRun(RscriptBase):
+    """Runs a basic R functionality test."""
+
+    descr = """
+            Runs a basic R functionality test.
+            Uses packages installed locally
+            in a previous test.
+            """
+    valid_systems = ["archer2:login", "archer2:compute"]
+    executable_opts = ["run_benchmark.R"]
+    library = fixture(RscriptInstall, scope="session")
+    libs_path = None
+    env_vars = {}
+
+    @run_before("run")
+    def setup_r_library(self):
+        """Setup R library path
+
+        Set the library path to where packages were installed in the R package install test.
+        """
+
+        self.libs_path = self.library.libs_path
+
+        self.env_vars = {"R_LIBS_USER": self.libs_path}

tests/utils/R/src/install_benchmark_packages.R

@@ -0,0 +1,5 @@
+
+install.packages("plyr",NCores=8,repos="https://www.stats.bris.ac.uk/R")
+library(plyr)
+
+print("Success")

tests/utils/R/src/run_benchmark.R

@@ -0,0 +1,23 @@
+
+library("plyr")
+
+# declaring first data frame
+data_frame1 <- data.frame(col1 = c(2,4,6), 
+                          col2 = c(4,6,8), 
+                          col3 = c(8,10,12), 
+                          col4 = LETTERS[1:3])
+print ("First Dataframe")
+print (data_frame1)
+
+# declaring second data frame
+data_frame2 <- data.frame(col4 = letters[1:4], 
+                          col5 = TRUE)
+print ("Second Dataframe")
+print (data_frame2)
+
+print ("Combining Dataframe")
+
+# binding data frames
+rbind.fill(data_frame1,data_frame2)
+
+print("Success")