Rename gpus_per_task to gpu_limit

GPU on SLURM can be supported by a variety of flags, usually --gres, so
`gpus_per_task` was a misleading name.

pman/cromwell/slurm/wdl.py

@@ -28,7 +28,7 @@
         sharedir: '{{ sharedir }}'
         cpu: '{{ (cpu_limit / 1000)|round(method='ceil')|int }}'
         memory: '{{ (memory_limit * 1.048576)|round(method='ceil')|int }}M'
-        gpus_per_task: '{{ gpu_limit }}'
+        gpu_limit: '{{ gpu_limit }}'
         number_of_workers: '{{ number_of_workers }}'
         timelimit: '{{ timelimit }}'
         {%- if partition %}
@@ -81,15 +81,15 @@ def from_wdl(cls, wdl: StrWdl) -> 'SlurmJob':
         sharedir, end = cls._get_resource(wdl, 'sharedir', end)
         cpu, end = cls._get_resource(wdl, 'cpu', end)
         memory, end = cls._get_resource(wdl, 'memory', end)
-        gpus_per_task, end = cls._get_resource(wdl, 'gpus_per_task', end)
+        gpu_limit, end = cls._get_resource(wdl, 'gpu_limit', end)
         number_of_workers, end = cls._get_resource(wdl, 'number_of_workers', end)
         timelimit, end = cls._get_resource(wdl, 'timelimit', end)
         partition, _ = cls._find_between(wdl, "slurm_partition: '", "'\n", end)
         r = Resources(
             number_of_workers=int(number_of_workers),
             cpu_limit=cls.__serialize_cpu(cpu),
             memory_limit=cls.__serialize_mem(memory),
-            gpu_limit=int(gpus_per_task)
+            gpu_limit=int(gpu_limit)
         )
         return cls(Image(image), command.strip(), sharedir, r, int(timelimit), partition)
 

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name             =   'pman',
-    version          =   '3.4.0',
+    version          =   '3.4.1',
     description      =   'Process Manager',
     long_description =   readme,
     author           =   'FNNDSC Developers',

tests/cromwell/examples/metadata.py

@@ -40,7 +40,7 @@
   ],
   "actualWorkflowLanguageVersion": "1.0",
   "submittedFiles": {
-    "workflow": "\nversion 1.0\n\ntask plugin_instance {\n    command {\n        office_convert /share/incoming /share/outgoing\n    } #ENDCOMMAND\n    runtime {\n        docker: 'docker.io/fnndsc/pl-office-convert:0.0.1'\n        sharedir: '/mounted/storebase/example-jid-1234'\n        cpu: '2'\n        memory: '4195M'\n        gpus_per_task: '0'\n        number_of_workers: '1'\n        timelimit: '5'\n        slurm_partition: 'my-slurm-partition'\n    }\n}\n\nworkflow ChRISJob {\n    call plugin_instance\n}",
+    "workflow": "\nversion 1.0\n\ntask plugin_instance {\n    command {\n        office_convert /share/incoming /share/outgoing\n    } #ENDCOMMAND\n    runtime {\n        docker: 'docker.io/fnndsc/pl-office-convert:0.0.1'\n        sharedir: '/mounted/storebase/example-jid-1234'\n        cpu: '2'\n        memory: '4195M'\n        gpu_limit: '0'\n        number_of_workers: '1'\n        timelimit: '5'\n        slurm_partition: 'my-slurm-partition'\n    }\n}\n\nworkflow ChRISJob {\n    call plugin_instance\n}",
     "workflowType": "WDL",
     "root": "",
     "workflowTypeVersion": "1.0",
@@ -366,7 +366,7 @@
 response_notstarted = r"""
 {
   "submittedFiles": {
-    "workflow": "\nversion 1.0\n\ntask plugin_instance {\n    command {\n        /usr/local/bin/python /usr/local/bin/whatsgood --day sunny  /share/incoming /share/outgoing\n    } #ENDCOMMAND\n    runtime {\n        docker: 'ghcr.io/fnndsc/pl-salute-the-sun:latest'\n        sharedir: '/storebase/key-vitamin-d'\n        cpu: '2'\n        memory: '5954M'\n        gpus_per_task: '2'\n        number_of_workers: '1'\n        timelimit: '50'\n    }\n}\n\nworkflow ChRISJob {\n    call plugin_instance\n}",
+    "workflow": "\nversion 1.0\n\ntask plugin_instance {\n    command {\n        /usr/local/bin/python /usr/local/bin/whatsgood --day sunny  /share/incoming /share/outgoing\n    } #ENDCOMMAND\n    runtime {\n        docker: 'ghcr.io/fnndsc/pl-salute-the-sun:latest'\n        sharedir: '/storebase/key-vitamin-d'\n        cpu: '2'\n        memory: '5954M'\n        gpu_limit: '2'\n        number_of_workers: '1'\n        timelimit: '50'\n    }\n}\n\nworkflow ChRISJob {\n    call plugin_instance\n}",
     "root": "",
     "options": "{\n\n}",
     "inputs": "{}",
@@ -412,7 +412,7 @@
   ],
   "actualWorkflowLanguageVersion": "1.0",
   "submittedFiles": {
-    "workflow": "\nversion 1.0\n\ntask plugin_instance {\n    command {\n        /usr/local/bin/python /usr/local/bin/fruit_machine --salad orange  /share/incoming /share/outgoing\n    } #ENDCOMMAND\n    runtime {\n        docker: 'internal.gitlab:5678/fnndsc/pl-fruit:1.2.3'\n        sharedir: '/storebase/key-fruity-fruit'\n        cpu: '1'\n        memory: '828M'\n        gpus_per_task: '0'\n        number_of_workers: '3'\n        timelimit: '70'\n    }\n}\n\nworkflow ChRISJob {\n    call plugin_instance\n}",
+    "workflow": "\nversion 1.0\n\ntask plugin_instance {\n    command {\n        /usr/local/bin/python /usr/local/bin/fruit_machine --salad orange  /share/incoming /share/outgoing\n    } #ENDCOMMAND\n    runtime {\n        docker: 'internal.gitlab:5678/fnndsc/pl-fruit:1.2.3'\n        sharedir: '/storebase/key-fruity-fruit'\n        cpu: '1'\n        memory: '828M'\n        gpu_limit: '0'\n        number_of_workers: '3'\n        timelimit: '70'\n    }\n}\n\nworkflow ChRISJob {\n    call plugin_instance\n}",
     "root": "",
     "options": "{\n\n}",
     "inputs": "{}",

tests/cromwell/examples/wdl.py

@@ -19,7 +19,7 @@
         sharedir: '/location/of/bribe'
         cpu: '2'
         memory: '5954M'
-        gpus_per_task: '0'
+        gpu_limit: '0'
         number_of_workers: '9'
         timelimit: '12'
     }
@@ -70,7 +70,7 @@
         sharedir: '/neuroimaging/data'
         cpu: '7'
         memory: '10356M'
-        gpus_per_task: '6'
+        gpu_limit: '6'
         number_of_workers: '5'
         timelimit: '300'
         slurm_partition: 'has-gpu'