Added code to support Singularity on HiperGator

.gitignore

@@ -11,3 +11,6 @@ __pycache__/
 .tox/
 .cache/
 htmlcov/
+build/
+.eggs
+

examples/plugin_example/gwexample/analyses/tasks.py

@@ -10,3 +10,32 @@ def fibonacci(n):
     if n == 1 or n == 2:
         return 1
     return fibonacci(n-1) + fibonacci(n-2)
+
+@app.task
+# @argument('image_name', 'slide_name', 'path')
+def nuclei(image_name, slide_name, path):
+    "running nuclei"
+    print(app, '++++++++++')
+    if path:
+        print('using arg path !!')
+        os.chdir(path)
+    else:
+        print('using default path !!')
+        os.chdir('/home/rc-svc-pinaki.sarder-web/digital_slide_archive/devops/singularity-minimal')
+    print('Current Path => ', os.getcwd())
+    path = os.getcwd()
+    flags = os.O_RDWR | os.O_CREAT
+    sif_image = os.open('sarderlab_histomicstk_latest.sif', flags)
+    sif_image_path = path + image_name if image_name else '/sarderlab_histomicstk_latest.sif'
+    slide_image = os.open(slide_name, flags)
+    slide_image_path = path + slide_name if slide_name else '18-142_PAS_1of6.svs'
+    output = os.open('Nuclei-outputNucleiAnnotationFile.anot', flags)
+    output_path = path + '/Nuclei-outputNucleiAnnotationFile.anot'
+    run_container = f'apptainer run --pwd /HistomicsTK/histomicstk/cli {sif_image} NucleiDetection {slide_image} {output}'
+    try:
+        res = subprocess.call(f'apptainer run --pwd /HistomicsTK/histomicstk/cli {sif_image_path} NucleiDetection {slide_image_path} {output_path}', shell=True, bufsize=0,stdin=subprocess.PIPE,stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding="UTF8")
+        print(res, '----1')
+
+    except Exception as e:
+        print(f"Exception occured {e}")
+

girder_worker/app.py

@@ -132,7 +132,8 @@ def gw_task_prerun(task=None, sender=None, task_id=None,
             raise
 
     try:
-        task.girder_client = GirderClient(apiUrl=task.request.girder_api_url)
+        #task.girder_client = GirderClient(apiUrl=task.request.girder_api_url)
+        task.girder_client = GirderClient(apiUrl='http://0.0.0.0:8101/api/v1')
         task.girder_client.token = task.request.girder_client_token
     except AttributeError:
         task.girder_client = None

girder_worker/docker/nvidia.py

@@ -1,3 +1,24 @@
 def is_nvidia_image(api, image):
     labels = api.inspect_image(image).get('Config', {}).get('Labels')
     return bool(labels and labels.get('com.nvidia.volumes.needed') == 'nvidia_driver')
+
+def set_nvidia_params(kwargs:dict,singularity_command:list,gpus:int=1):
+    '''
+    This function is used to set the gpu parameters based on the user input and plugin job. 
+
+    Parameters:
+    kwargs (dict, required): The keyword arguments dictionary sent to the celery task as an input, part of the request
+
+    singularity_command (list, required): A list that container all the arguments to construct a singularity command that will be sent to the HPC job
+
+    gps (int, optional): If the plugin doesn't have a --gpu parameter in contianer_args, then a default of 1 gpu is allocated, else the user specified number of gpus is allocated.
+
+    Returns:
+    None
+    '''
+    kwargs['--gres'] = f"gres:gpu:a100:{gpus}" if gpus > 1 else f"gres:gpu:a100:1"
+    kwargs['--partition'] = 'gpu'
+    kwargs['--mem'] = '32000'
+    #Reducing CPU count for gpu-based job for resource conservation 
+    kwargs['--cpus-per-task'] = '8'
+    singularity_command.append('--nv')