Merge pull request #12775 from gulsumgudukbay/dev

Adding GPU support to Galaxy

lib/galaxy/tool_util/deps/requirements.py

@@ -233,6 +233,11 @@ ResourceType = Literal[
     "ram_max",
     "tmpdir_min",
     "tmpdir_max",
+    "cuda_version_min",
+    "cuda_compute_capability",
+    "gpu_memory_min",
+    "cuda_device_count_min",
+    "cuda_device_count_max",
 ]
 VALID_RESOURCE_TYPES = get_args(ResourceType)
 
@@ -272,6 +277,11 @@ def resource_requirements_from_list(requirements) -> List[ResourceRequirement]:
         "ramMax": "ram_max",
         "tmpdirMin": "tmpdir_min",
         "tmpdirMax": "tmpdir_max",
+        "cudaVersionMin": "cuda_version_min",
+        "cudaComputeCapability": "cuda_compute_capability",
+        "gpuMemoryMin": "gpu_memory_min",
+        "cudaDeviceCountMin": "cuda_device_count_min",
+        "cudaDeviceCountMax": "cuda_device_count_max",
     }
     rr = []
     for r in requirements:

lib/galaxy/tool_util/xsd/galaxy.xsd

@@ -6793,6 +6793,31 @@ and ``bibtex`` are the only supported options.</xs:documentation>
           <xs:documentation xml:lang="en">Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20 bytes), if runtime allows it (not yet implemented in Galaxy).</xs:documentation>
         </xs:annotation>
       </xs:enumeration>
+       <xs:enumeration value="cuda_version_min">
+        <xs:annotation>
+          <xs:documentation xml:lang="en">Minimum CUDA (runtime link library) runtime version, if runtime allows it (not yet implemented in Galaxy).</xs:documentation>
+        </xs:annotation>
+      </xs:enumeration>
+      <xs:enumeration value="cuda_compute_capability">
+        <xs:annotation>
+          <xs:documentation xml:lang="en">Minimum NVIDIA (hardware+driver) Compute capabilities (major, minor (can be a range or a list), if runtime allows it (not yet implemented in Galaxy).</xs:documentation>
+        </xs:annotation>
+      </xs:enumeration>
+      <xs:enumeration value="gpu_memory_min">
+        <xs:annotation>
+          <xs:documentation xml:lang="en">Minimum Memory of the GPU in mebibytes, if runtime allows it (not yet implemented in Galaxy).</xs:documentation>
+        </xs:annotation>
+      </xs:enumeration>
+      <xs:enumeration value="cuda_device_count_min">
+        <xs:annotation>
+          <xs:documentation xml:lang="en">Minimum CUDA device count, if runtime allows it (not yet implemented in Galaxy).</xs:documentation>
+        </xs:annotation>
+      </xs:enumeration>
+      <xs:enumeration value="cuda_device_count_max">
+        <xs:annotation>
+          <xs:documentation xml:lang="en">Maximum CUDA device count, if runtime allows it (not yet implemented in Galaxy).</xs:documentation>
+        </xs:annotation>
+      </xs:enumeration>
     </xs:restriction>
   </xs:simpleType>
   <xs:simpleType name="ContainerType">

test/functional/tools/resource_requirements.xml

@@ -6,6 +6,11 @@
         <resource type="ram_max">2></resource>
         <resource type="tmpdir_min"><![CDATA[$(inputs.input1.size)]]></resource>
         <resource type="tmpdir_max"><![CDATA[$(inputs.input1.size * 2)]]></resource>
+        <resource type="cuda_version_min">10.2</resource>
+        <resource type="cuda_compute_capability">6.1</resource>
+        <resource type="gpu_memory_min">4042</resource>
+        <resource type="cuda_device_count_min">1</resource>
+        <resource type="cuda_device_count_max">2</resource>
     </requirements>
     <command><![CDATA[
 echo "\$GALAXY_SLOTS" > $output

test/unit/tool_util/test_parsing.py

@@ -31,6 +31,11 @@ TOOL_XML_1 = """
         <container type="docker">mycool/bwa</container>
         <requirement type="package" version="1.0">bwa</requirement>
         <resource type="cores_min">1</resource>
+        <resource type="cuda_version_min">10.2</resource>
+        <resource type="cuda_compute_capability">6.1</resource>
+        <resource type="gpu_memory_min">4042</resource>
+        <resource type="cuda_device_count_min">1</resource>
+        <resource type="cuda_device_count_max">2</resource>
     </requirements>
     <outputs>
         <data name="out1" format="bam" from_work_dir="out1.bam" />
@@ -125,6 +130,16 @@ requirements:
     version: 1.0.1
   - type: resource
     cores_min: 1
+  - type: resource
+    cuda_version_min: 10.2
+  - type: resource
+    cuda_compute_capability: 6.1
+  - type: resource
+    gpu_memory_min: 4042
+  - type: resource
+    cuda_device_count_min: 1
+  - type: resource
+    cuda_device_count_max: 2
 containers:
   - type: docker
     identifier: "awesome/bowtie"
@@ -311,6 +326,11 @@ class TestXmlLoader(BaseLoaderTestCase):
         assert requirements[0].type == "package"
         assert list(containers)[0].identifier == "mycool/bwa"
         assert resource_requirements[0].resource_type == "cores_min"
+        assert resource_requirements[1].resource_type == "cuda_version_min"
+        assert resource_requirements[2].resource_type == "cuda_compute_capability"
+        assert resource_requirements[3].resource_type == "gpu_memory_min"
+        assert resource_requirements[4].resource_type == "cuda_device_count_min"
+        assert resource_requirements[5].resource_type == "cuda_device_count_max"
         assert not resource_requirements[0].runtime_required
 
     def test_outputs(self):
@@ -486,8 +506,22 @@ class TestYamlLoader(BaseLoaderTestCase):
             "resolve_dependencies": False,
             "shell": "/bin/sh",
         }
-        assert len(resource_requirements) == 1
+        assert len(resource_requirements) == 6
         assert resource_requirements[0].to_dict() == {"resource_type": "cores_min", "value_or_expression": 1}
+        assert resource_requirements[1].to_dict() == {"resource_type": "cuda_version_min", "value_or_expression": 10.2}
+        assert resource_requirements[2].to_dict() == {
+            "resource_type": "cuda_compute_capability",
+            "value_or_expression": 6.1,
+        }
+        assert resource_requirements[3].to_dict() == {"resource_type": "gpu_memory_min", "value_or_expression": 4042}
+        assert resource_requirements[4].to_dict() == {
+            "resource_type": "cuda_device_count_min",
+            "value_or_expression": 1,
+        }
+        assert resource_requirements[5].to_dict() == {
+            "resource_type": "cuda_device_count_max",
+            "value_or_expression": 2,
+        }
 
     def test_outputs(self):
         outputs, output_collections = self._tool_source.parse_outputs(object())