19524: configurable vcpus/ram

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/slicenumpy.go b/slicenumpy.go
index 41f9f5eb43fb2af737fcc4a64a64679f64b54094..feab8b0cd79596a0983698ed0df9686408e61068 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -64,6 +64,8 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
        flags.SetOutput(stderr)
        pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
        runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
+       arvadosRAM := flags.Int("arvados-ram", 750000000000, "amount of memory to request for arvados container (`bytes`)")
+       arvadosVCPUs := flags.Int("arvados-vcpus", 96, "number of VCPUs to request for arvados container")
        projectUUID := flags.String("project", "", "project `UUID` for output data")
        priority := flags.Int("priority", 500, "container request priority")
        inputDir := flags.String("input-dir", "./in", "input `directory`")
@@ -79,7 +81,7 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
        onlyPCA := flags.Bool("pca", false, "generate pca matrix")
        pcaComponents := flags.Int("pca-components", 4, "number of PCA components")
        debugTag := flags.Int("debug-tag", -1, "log debugging details about specified tag")
-       flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
+       flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads, and number of VCPUs to request for arvados container")
        flags.StringVar(&cmd.chi2CaseControlFile, "chi2-case-control-file", "", "tsv file or directory indicating cases and controls for Χ² test (if directory, all .tsv files will be read)")
        flags.StringVar(&cmd.chi2CaseControlColumn, "chi2-case-control-column", "", "name of case/control column in case-control files for Χ² test (value must be 0 for control, 1 for case)")
        flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test and omit columns with p-value above this threshold")
@@ -109,8 +111,8 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
                        Name:        "lightning slice-numpy",
                        Client:      arvados.NewClientFromEnv(),
                        ProjectUUID: *projectUUID,
-                       RAM:         750000000000,
-                       VCPUs:       96,
+                       RAM:         int64(*arvadosRAM),
+                       VCPUs:       *arvadosVCPUs,
                        Priority:    *priority,
                        KeepCache:   2,
                        APIAccess:   true,