[arvados] updated: 2.5.0-260-g765604b09
git repository hosting
git at public.arvados.org
Tue Mar 7 18:43:25 UTC 2023
Summary of changes:
doc/user/cwl/cwl-extensions.html.textile.liquid | 18 +++++
sdk/cwl/arvados_cwl/__init__.py | 1 +
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.0.yml | 27 +++++++
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.1.yml | 27 +++++++
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml | 28 +++++++
sdk/cwl/arvados_cwl/arvcontainer.py | 100 ++++++++++++++++++++----
sdk/cwl/tests/arvados-tests.yml | 15 ++++
sdk/cwl/tests/oom/19975-oom.cwl | 18 +++++
sdk/cwl/tests/oom/19975-oom3.cwl | 19 +++++
sdk/cwl/tests/oom/fakeoom.py | 13 +++
sdk/cwl/tests/{octo.yml => oom/fakeoom.yml} | 4 +-
sdk/cwl/tests/oom/fakeoom2.py | 13 +++
sdk/cwl/tests/{octo.yml => oom/fakeoom2.yml} | 4 +-
sdk/cwl/tests/oom/fakeoom3.py | 14 ++++
sdk/cwl/tests/{octo.yml => oom/fakeoom3.yml} | 4 +-
15 files changed, 283 insertions(+), 22 deletions(-)
create mode 100644 sdk/cwl/tests/oom/19975-oom.cwl
create mode 100644 sdk/cwl/tests/oom/19975-oom3.cwl
create mode 100644 sdk/cwl/tests/oom/fakeoom.py
copy sdk/cwl/tests/{octo.yml => oom/fakeoom.yml} (72%)
create mode 100644 sdk/cwl/tests/oom/fakeoom2.py
copy sdk/cwl/tests/{octo.yml => oom/fakeoom2.yml} (72%)
create mode 100644 sdk/cwl/tests/oom/fakeoom3.py
copy sdk/cwl/tests/{octo.yml => oom/fakeoom3.yml} (72%)
via 765604b096c464b242e60860ace75bd6645fd4e7 (commit)
via adb11a544a649b24196b38b6b614a95585728240 (commit)
via a7bb7c84d2e84eeb92810c319f54a8456011288a (commit)
via 1e55288da627c93d8fa01abaf4611f114a20525d (commit)
via 82de91b57218abf4f74a38f1bf53d0cc28cd8da9 (commit)
via 9e76a12ff0b25322f86caf6d5ea70c09cbfd8829 (commit)
via 5d73c8c825577b65d48b9dec05428f3db104efb2 (commit)
via fe18471f4f1a04af7444d2162cab16eef2685677 (commit)
via 39fc2f223fae40dc4fb160758e76ca39304b44af (commit)
from efd62fdeffaef4d47710511f7e1ac37d5b4cc5a7 (commit)
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 765604b096c464b242e60860ace75bd6645fd4e7
Merge: efd62fdef adb11a544
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Tue Mar 7 13:42:58 2023 -0500
Merge branch '19975-oom-resubmit' refs #19975
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
commit adb11a544a649b24196b38b6b614a95585728240
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Tue Mar 7 13:42:05 2023 -0500
19975: s/request/specify
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/doc/user/cwl/cwl-extensions.html.textile.liquid b/doc/user/cwl/cwl-extensions.html.textile.liquid
index ade588f14..e05072ddf 100644
--- a/doc/user/cwl/cwl-extensions.html.textile.liquid
+++ b/doc/user/cwl/cwl-extensions.html.textile.liquid
@@ -195,7 +195,7 @@ table(table table-bordered table-condensed).
h2(#OutOfMemoryRetry). arv:OutOfMemoryRetry
-Request that when a workflow step appears to have failed because it did not request enough RAM, it should be re-submitted with more RAM. Out of memory conditions are detected either by the container being unexpectedly killed (exit code 137) or by matching a pattern in the container's output (see @memoryErrorRegex@). Retrying will increase the base RAM request by the value of @memoryRetryMultipler at . For example, if the original RAM request was 10 GiB and the multiplier is 1.5, then it will re-submit with 15 GiB.
+Specify that when a workflow step appears to have failed because it did not request enough RAM, it should be re-submitted with more RAM. Out of memory conditions are detected either by the container being unexpectedly killed (exit code 137) or by matching a pattern in the container's output (see @memoryErrorRegex@). Retrying will increase the base RAM request by the value of @memoryRetryMultipler at . For example, if the original RAM request was 10 GiB and the multiplier is 1.5, then it will re-submit with 15 GiB.
Containers are only re-submitted once. If it fails a second time after increasing RAM, then the worklow step will still fail.
commit a7bb7c84d2e84eeb92810c319f54a8456011288a
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Tue Mar 7 13:40:48 2023 -0500
19975: Add note about runtime.ram
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/doc/user/cwl/cwl-extensions.html.textile.liquid b/doc/user/cwl/cwl-extensions.html.textile.liquid
index 41a7d393d..ade588f14 100644
--- a/doc/user/cwl/cwl-extensions.html.textile.liquid
+++ b/doc/user/cwl/cwl-extensions.html.textile.liquid
@@ -195,7 +195,11 @@ table(table table-bordered table-condensed).
h2(#OutOfMemoryRetry). arv:OutOfMemoryRetry
-Request that when a workflow step appears to have failed because it did not request enough RAM, it should be re-submitted with more RAM. Out of memory conditions are detected either by the container being unexpectedly killed (exit code 137) or by matching a pattern in the container's output (see @memoryErrorRegex@). Retrying will increase the base RAM request by the value of @memoryRetryMultipler at . For example, if the original RAM request was 10 GiB and the multiplier is 1.5, then it will re-submit with 15 GiB. Containers are only re-submitted once. If it fails a second time after increasing RAM, then the worklow step will still fail.
+Request that when a workflow step appears to have failed because it did not request enough RAM, it should be re-submitted with more RAM. Out of memory conditions are detected either by the container being unexpectedly killed (exit code 137) or by matching a pattern in the container's output (see @memoryErrorRegex@). Retrying will increase the base RAM request by the value of @memoryRetryMultipler at . For example, if the original RAM request was 10 GiB and the multiplier is 1.5, then it will re-submit with 15 GiB.
+
+Containers are only re-submitted once. If it fails a second time after increasing RAM, then the worklow step will still fail.
+
+Also note that expressions that use @$(runtime.ram)@ (such as dynamic command line parameters) are not reevaluated when the container is resubmitted.
table(table table-bordered table-condensed).
|_. Field |_. Type |_. Description |
commit 1e55288da627c93d8fa01abaf4611f114a20525d
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Tue Mar 7 13:36:00 2023 -0500
19975: Typo fix.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/doc/user/cwl/cwl-extensions.html.textile.liquid b/doc/user/cwl/cwl-extensions.html.textile.liquid
index 0b8562de1..41a7d393d 100644
--- a/doc/user/cwl/cwl-extensions.html.textile.liquid
+++ b/doc/user/cwl/cwl-extensions.html.textile.liquid
@@ -200,7 +200,7 @@ Request that when a workflow step appears to have failed because it did not requ
table(table table-bordered table-condensed).
|_. Field |_. Type |_. Description |
|memoryRetryMultipler|float|Required, the retry will multiply the base memory request by this factor to get the retry memory request.|
-|memoryErrorRegex|string|Optional, a custom regex that, if found in the stdout, stderr or crunch-run logging of a program, will trigger a retry with greater RAM. If not provided, the default pattern matches "out of memory" (with or without spaces), "memory error" (with or without spaces), "bad_alloc" and "container using over 90% of memory"|
+|memoryErrorRegex|string|Optional, a custom regex that, if found in the stdout, stderr or crunch-run logging of a program, will trigger a retry with greater RAM. If not provided, the default pattern matches "out of memory" (with or without spaces), "memory error" (with or without spaces), "bad_alloc" and "container using over 90% of memory".|
h2. arv:dockerCollectionPDH
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list