[ARVADOS] updated: 2.1.0-1062-geec5086af

[Git user]

Summary of changes:
 doc/admin/upgrading.html.textile.liquid              |  6 +++++-
 lib/crunchrun/crunchrun.go                           |  1 +
 lib/crunchrun/singularity.go                         |  2 ++
 .../crunch-dispatch-local/crunch-dispatch-local.go   | 20 ++++++++++++++++++++
 4 files changed, 28 insertions(+), 1 deletion(-)

  discards  ac42f50a4f44c4cade2346aaad176847989f2985 (commit)
       via  eec5086af5c2d1c1f17bbc525cc68d394c9680f4 (commit)
       via  ec5fd6d8072cc038648b254a5500868dfdf6a17b (commit)
       via  f2ee5bac37391ce9fe084306da332becd7620ca7 (commit)

This update added new revisions after undoing existing revisions.  That is
to say, the old revision is not a strict subset of the new revision.  This
situation occurs when you --force push a change and generate a repository
containing something like this:

 * -- * -- B -- O -- O -- O (ac42f50a4f44c4cade2346aaad176847989f2985)
            \
             N -- N -- N (eec5086af5c2d1c1f17bbc525cc68d394c9680f4)

When this happens we assume that you've already had alert emails for all
of the O revisions, and so we here report only the revisions in the N
branch from the common base, B.

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit eec5086af5c2d1c1f17bbc525cc68d394c9680f4
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Thu Jul 15 15:05:41 2021 -0400

    17816: Also fix logging by flushing before getting the manifest.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/lib/crunchrun/crunchrun.go b/lib/crunchrun/crunchrun.go
index 3c9c38161..e83203b31 100644
--- a/lib/crunchrun/crunchrun.go
+++ b/lib/crunchrun/crunchrun.go
@@ -1244,6 +1244,7 @@ func (runner *ContainerRunner) saveLogCollection(final bool) (response arvados.C
 	updates := arvadosclient.Dict{
 		"name": "logs for " + runner.Container.UUID,
 	}
+	runner.LogCollection.Flush(".", true)
 	mt, err1 := runner.LogCollection.MarshalManifest(".")
 	if err1 == nil {
 		// Only send updated manifest text if there was no
diff --git a/lib/crunchrun/singularity.go b/lib/crunchrun/singularity.go
index 2a294cf03..c108a6abe 100644
--- a/lib/crunchrun/singularity.go
+++ b/lib/crunchrun/singularity.go
@@ -131,6 +131,8 @@ func (e *singularityExecutor) Stop() error {
 
 func (e *singularityExecutor) Wait(context.Context) (int, error) {
 	err := e.child.Wait()
+	e.spec.Stdout.Close()
+	e.spec.Stderr.Close()
 	if err, ok := err.(*exec.ExitError); ok {
 		return err.ProcessState.ExitCode(), nil
 	}

commit ec5fd6d8072cc038648b254a5500868dfdf6a17b
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Thu Jul 15 13:50:22 2021 -0400

    17816: Set the current working directory in the singularity container
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/lib/crunchrun/singularity.go b/lib/crunchrun/singularity.go
index 4bec8c3eb..2a294cf03 100644
--- a/lib/crunchrun/singularity.go
+++ b/lib/crunchrun/singularity.go
@@ -74,7 +74,7 @@ func (e *singularityExecutor) Create(spec containerSpec) error {
 }
 
 func (e *singularityExecutor) Start() error {
-	args := []string{"singularity", "exec", "--containall", "--no-home", "--cleanenv"}
+	args := []string{"singularity", "exec", "--containall", "--no-home", "--cleanenv", "--pwd", e.spec.WorkingDir}
 	if !e.spec.EnableNetwork {
 		args = append(args, "--net", "--network=none")
 	}

-----------------------------------------------------------------------


hooks/post-receive
--