From: Tom Clegg <tom@curii.com>
Date: Tue, 17 May 2022 18:13:34 +0000 (-0400)
Subject: Merge branch '19081-singularity-no-eval'
X-Git-Tag: 2.5.0~170
X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/844ff7cc1dc1c93a29b7ad8eca2987b987cf89e6?hp=-c

Merge branch '19081-singularity-no-eval'

refs #19081

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

844ff7cc1dc1c93a29b7ad8eca2987b987cf89e6
diff --combined lib/crunchrun/singularity.go
index 879c46c898,61992b312d..1af0d420e4
--- a/lib/crunchrun/singularity.go
+++ b/lib/crunchrun/singularity.go
@@@ -10,7 -10,6 +10,7 @@@ import 
  	"os"
  	"os/exec"
  	"sort"
 +	"strings"
  	"syscall"
  	"time"
  
@@@ -37,13 -36,7 +37,13 @@@ func newSingularityExecutor(logf func(s
  	}, 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
@@@ -299,6 -292,14 +299,14 @@@ func (e *singularityExecutor) execCmd(p
  		// 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...)