property1: value1
property2: $(inputs.value2)
+ arv:OutputCollectionProperties:
+ outputProperties:
+ property1: value1
+ property2: $(inputs.value2)
+
cwltool:CUDARequirement:
cudaVersionMin: "11.0"
- cudaComputeCapabilityMin: "9.0"
- deviceCountMin: 1
- deviceCountMax: 1
+ cudaComputeCapability: "9.0"
+ cudaDeviceCountMin: 1
+ cudaDeviceCountMax: 1
arv:UsePreemptible:
usePreemptible: true
+
+ arv:OutOfMemoryRetry:
+ memoryRetryMultiplier: 2
+ memoryErrorRegex: "custom memory error"
{% endcodeblock %}
h2(#RunInSingleContainer). arv:RunInSingleContainer
table(table table-bordered table-condensed).
|_. Field |_. Type |_. Description |
-|processProperties|key-value map, or list of objects with the fields {propertyName, propertyValue}|The properties that will be set on the container request. May include expressions that reference `$(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
table(table table-bordered table-condensed).
|_. Field |_. Type |_. Description |
|cudaVersionMin|string|Required. The CUDA SDK version corresponding to the minimum driver version supported by the container (generally, the SDK version 'X.Y' the application was compiled against).|
-|cudaComputeCapabilityMin|string|Required. The minimum CUDA hardware capability (in 'X.Y' format) required by the application's PTX or C++ GPU code (will be JIT compiled for the available hardware).|
-|deviceCountMin|integer|Minimum number of GPU devices to allocate on a single node. Required.|
-|deviceCountMax|integer|Maximum number of GPU devices to allocate on a single node. Optional. If not specified, same as @minDeviceCount@.|
+|cudaComputeCapability|string|Required. The minimum CUDA hardware capability (in 'X.Y' format) required by the application's PTX or C++ GPU code (will be JIT compiled for the available hardware).|
+|cudaDeviceCountMin|integer|Minimum number of GPU devices to allocate on a single node. Required.|
+|cudaDeviceCountMax|integer|Maximum number of GPU devices to allocate on a single node. Optional. If not specified, same as @cudaDeviceCountMin@.|
h2(#UsePreemptible). arv:UsePreemptible
|_. 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 @memoryRetryMultiplier@. 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 |
+|memoryRetryMultiplier|float|Optional, default value is 2. 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@.
projects / arvados.git / blobdiff