Merge branch '19099-singularity-container-shell'

[arvados.git] / lib / crunchrun / singularity.go

diff --git a/lib/crunchrun/singularity.go b/lib/crunchrun/singularity.go
index 2d8962e96a39472e4fa8bb375c7decdec69e3576..1da401f859f94b36655f771e5fea5af750b0cbe7 100644 (file)
--- a/lib/crunchrun/singularity.go
+++ b/lib/crunchrun/singularity.go
@@ -16,6 +16,7 @@ import (
        "regexp"
        "sort"
        "strconv"
+       "strings"
        "syscall"
        "time"
 
@@ -43,7 +44,13 @@ func newSingularityExecutor(logf func(string, ...interface{})) (*singularityExec
        }, nil
 }
 
-func (e *singularityExecutor) Runtime() string { return "singularity" }
+func (e *singularityExecutor) Runtime() string {
+       buf, err := exec.Command("singularity", "--version").CombinedOutput()
+       if err != nil {
+               return "singularity (unknown version)"
+       }
+       return strings.TrimSuffix(string(buf), "\n")
+}
 
 func (e *singularityExecutor) getOrCreateProject(ownerUuid string, name string, containerClient *arvados.Client) (*arvados.Group, error) {
        var gp arvados.GroupList
@@ -310,6 +317,14 @@ func (e *singularityExecutor) execCmd(path string) *exec.Cmd {
                // us to select specific devices we need to propagate that.
                env = append(env, "SINGULARITYENV_CUDA_VISIBLE_DEVICES="+cudaVisibleDevices)
        }
+       // Singularity's default behavior is to evaluate each
+       // SINGULARITYENV_* env var with a shell as a double-quoted
+       // string and pass the result to the contained
+       // process. Singularity 3.10+ has an option to pass env vars
+       // through literally without evaluating, which is what we
+       // want. See https://github.com/sylabs/singularity/pull/704
+       // and https://dev.arvados.org/issues/19081
+       env = append(env, "SINGULARITY_NO_EVAL=1")
 
        args = append(args, e.imageFilename)
        args = append(args, e.spec.Command...)