X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/9d706659aa362728270f02b7d18d12b1f68f3e36..544f1dceeb4e5fcc63b683d3edac48e62bca5958:/doc/user/cwl/cwl-extensions.html.textile.liquid

diff --git a/doc/user/cwl/cwl-extensions.html.textile.liquid b/doc/user/cwl/cwl-extensions.html.textile.liquid
index 0e97e07da3..e05072ddf6 100644
--- a/doc/user/cwl/cwl-extensions.html.textile.liquid
+++ b/doc/user/cwl/cwl-extensions.html.textile.liquid
@@ -58,6 +58,11 @@ hints:
       property1: value1
       property2: $(inputs.value2)
 
+  arv:OutputCollectionProperties:
+    outputProperties:
+      property1: value1
+      property2: $(inputs.value2)
+
   cwltool:CUDARequirement:
     cudaVersionMin: "11.0"
     cudaComputeCapability: "9.0"
@@ -66,6 +71,10 @@ hints:
 
   arv:UsePreemptible:
     usePreemptible: true
+
+  arv:OutOfMemoryRetry:
+    memoryRetryMultipler: 2
+    memoryErrorRegex: "custom memory error"
 {% endcodeblock %}
 
 h2(#RunInSingleContainer). arv:RunInSingleContainer
@@ -154,7 +163,15 @@ Specify extra "properties":{{site.baseurl}}/api/methods.html#subpropertyfilters
 
 table(table table-bordered table-condensed).
 |_. Field |_. Type |_. Description |
-|processProperties|key-value map, or list of objects with the fields {propertyName, propertyValue}|The properties that will be set on the container request.  May include expressions that reference `$(inputs)` of the current workflow or tool.|
+|processProperties|key-value map, or list of objects with the fields {propertyName, propertyValue}|The properties that will be set on the container request.  May include expressions that reference @$(inputs)@ of the current workflow or tool.|
+
+h2(#OutputCollectionProperties). arv:OutputCollectionProperties
+
+Specify custom "properties":{{site.baseurl}}/api/methods.html#subpropertyfilters that will be set on the output collection of the workflow step.
+
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
+|outputProperties|key-value map, or list of objects with the fields {propertyName, propertyValue}|The properties that will be set on the output collection.  May include expressions that reference @$(inputs)@ of the current workflow or tool.|
 
 h2(#CUDARequirement). cwltool:CUDARequirement
 
@@ -175,6 +192,20 @@ table(table table-bordered table-condensed).
 |_. Field |_. Type |_. Description |
 |usePreemptible|boolean|Required, true to opt-in to using preemptible instances, false to opt-out.|
 
+
+h2(#OutOfMemoryRetry). arv:OutOfMemoryRetry
+
+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@.  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 |
+|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".|
+
 h2. arv:dockerCollectionPDH
 
 This is an optional extension field appearing on the standard @DockerRequirement@.  It specifies the portable data hash of the Arvados collection containing the Docker image.  If present, it takes precedence over @dockerPull@ or @dockerImageId@.