feat: Set tmpspace with help of gres="tmpspace:10G" syntax

docs/further.md

@@ -380,7 +380,6 @@ To adapt the workflow for an application using `mpiexec`, you can override the `
 ``` console
 $ snakemake --set-resources calc_pi:mpi="mpiexec" ...
 ```
-
 ##### Resource Specifications for MPI Jobs
 
 When configuring MPI jobs, it's essential to accurately define the resources to match the requirements of your application.
@@ -518,6 +517,28 @@ In this configuration:
 
 By defining these resource specifications in a profile, you maintain a clean and organized workflow, ensuring that resource allocations are consistent and easily adjustable.
 
+### Setting tmpspace with GRES
+On certain clusters the amount of scratch/tmpspace on the worker node can be set with: 
+`--gres=tmpspace:10G`
+
+*this depends on the cluser config and is not a default*
+
+You can specify the amount of tmpspace using the `gres` resource:
+
+```Python
+rule tmpspace_task:
+    input:
+        "input_file"
+    output:
+        "output_file"
+    resources:
+         gres="tmpspace:15G"
+    shell:
+        "tmpspace_task --input {input} --output {output}"
+```
+
+
+
 ### Running Jobs locally
 
 In Snakemake workflows executed within cluster environments, certain tasks -- such as brief data downloads or plotting -- are better suited for local execution on the head node rather than being submitted as cluster jobs.

snakemake_executor_plugin_slurm/utils.py

@@ -253,6 +253,10 @@ def set_gres_string(job: JobExecutorInterface) -> str:
     # generic resources (GRES) arguments can be of type
     # "string:int" or "string:string:int"
     gres_re = re.compile(r"^[a-zA-Z0-9_]+(:[a-zA-Z0-9_\.]+)?:\d+$")
+
+    # generic resources (GRES) arguments can be of type
+    # "string:int[TGM]" when a tmpspace is specified.
+    gres_tmpspace_re = re.compile(r"^tmpspace:\d+[TGM]?$")
     # gpu model arguments can be of type "string"
     # The model string may contain a dot for variants, see
     # https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/387
@@ -283,20 +287,23 @@ def set_gres_string(job: JobExecutorInterface) -> str:
         # Validate GRES format (e.g., "gpu:1", "gpu:tesla:2")
         gres = job.resources.gres
         if not gres_re.match(gres):
-            if not string_check.match(gres):
-                raise WorkflowError(
-                    "GRES format should not be a nested string (start "
-                    "and end with ticks or quotation marks). "
-                    "Expected format: "
-                    "'<name>:<number>' or '<name>:<type>:<number>' "
-                    "(e.g., 'gpu:1' or 'gpu:tesla:2')"
-                )
-            else:
-                raise WorkflowError(
-                    f"Invalid GRES format: {gres}. Expected format: "
-                    "'<name>:<number>' or '<name>:<type>:<number>' "
-                    "(e.g., 'gpu:1' or 'gpu:tesla:2')"
-                )
+            if not gres_tmpspace_re.match(gres):
+                if not string_check.match(gres):
+                    raise WorkflowError(
+                        "GRES format should not be a nested string (start "
+                        "and end with ticks or quotation marks). "
+                        "Expected format: "
+                        "'<name>:<number>' or '<name>:<type>:<number>' or "
+                        "'tmpspace:<number>[TGM]' "
+                        "(e.g., 'gpu:1' or 'gpu:tesla:2') or tmpspace:10G "
+                    )
+                else:
+                    raise WorkflowError(
+                        f"Invalid GRES format: {gres}. Expected format: "
+                        "'<name>:<number>' or '<name>:<type>:<number>' "
+                        "or 'tmpspace:<number>[TGM]' "
+                        "(e.g., 'gpu:1' or 'gpu:tesla:2') or tmpspace:10G "
+                    )
         return f" --gres={job.resources.gres}"
 
     if gpu_model and gpu_string:

tests/tests.py

@@ -368,6 +368,20 @@ def test_gpu_model_without_gpu(self, mock_job):
             ):
                 set_gres_string(job)
 
+    def test_tmpspace_gres_10G(self, mock_job):
+        """Test with valid GRES format (simple)."""
+        job = mock_job(gres="tmpspace:10G")
+
+        # Patch subprocess.Popen to capture the sbatch command
+        with patch("subprocess.Popen") as mock_popen:
+            # Configure the mock to return successful submission
+            process_mock = MagicMock()
+            process_mock.communicate.return_value = ("123", "")
+            process_mock.returncode = 0
+            mock_popen.return_value = process_mock
+
+        assert set_gres_string(job) == " --gres=tmpspace:10G"
+
     def test_both_gres_and_gpu_set(self, mock_job):
         """Test error case when both GRES and GPU are specified."""
         job = mock_job(gres="gpu:1", gpu="2")