Merge pull request #376 from djarecka/nicolocin-pytest-slurm-tmpdir

fixing issues with workflow on cluster with slurm (closes #369, #368)

Author: djarecka

pydra/engine/submitter.py

@@ -1,5 +1,6 @@
 """Handle execution backends."""
 import asyncio
+import time
 from .workers import SerialWorker, ConcurrentFuturesWorker, SlurmWorker, DaskWorker
 from .core import is_workflow
 from .helpers import get_open_loop, load_and_run_async
@@ -150,15 +151,31 @@ async def _run_workflow(self, wf, rerun=False):
             The computed workflow
 
         """
+        for nd in wf.graph.nodes:
+            if nd.allow_cache_override:
+                nd.cache_dir = wf.cache_dir
+
         # creating a copy of the graph that will be modified
         # the copy contains new lists with original runnable objects
         graph_copy = wf.graph.copy()
         # keep track of pending futures
         task_futures = set()
         tasks, tasks_follow_errored = get_runnable_tasks(graph_copy)
-        while tasks or len(task_futures):
+        while tasks or task_futures or graph_copy.nodes:
             if not tasks and not task_futures:
-                raise Exception("Nothing queued or todo - something went wrong")
+                # it's possible that task_futures is empty, but not able to get any
+                # tasks from graph_copy (using get_runnable_tasks)
+                # this might be related to some delays saving the files
+                # so try to get_runnable_tasks for another minut
+                ii = 0
+                while not tasks and graph_copy.nodes:
+                    tasks, follow_err = get_runnable_tasks(graph_copy)
+                    ii += 1
+                    time.sleep(1)
+                    if ii > 60:
+                        raise Exception(
+                            "graph is not empty, but not able to get more tasks - something is wrong (e.g. with the filesystem)"
+                        )
             for task in tasks:
                 # grab inputs if needed
                 logger.debug(f"Retrieving inputs for {task}")

pydra/engine/tests/test_boutiques.py

@@ -26,11 +26,12 @@
     "maskfile", ["test_brain.nii.gz", "test_brain", "test_brain.nii"]
 )
 @pytest.mark.parametrize("results_function", [result_no_submitter, result_submitter])
-def test_boutiques_1(maskfile, plugin, results_function):
+def test_boutiques_1(maskfile, plugin, results_function, tmpdir):
     """ simple task to run fsl.bet using BoshTask"""
     btask = BoshTask(name="NA", zenodo_id="1482743")
     btask.inputs.infile = Infile
     btask.inputs.maskfile = maskfile
+    btask.cache_dir = tmpdir
     res = results_function(btask, plugin)
 
     assert res.output.return_code == 0
@@ -97,11 +98,12 @@ def test_boutiques_spec_2():
 @pytest.mark.parametrize(
     "maskfile", ["test_brain.nii.gz", "test_brain", "test_brain.nii"]
 )
-def test_boutiques_wf_1(maskfile, plugin):
+def test_boutiques_wf_1(maskfile, plugin, tmpdir):
     """ wf with one task that runs fsl.bet using BoshTask"""
     wf = Workflow(name="wf", input_spec=["maskfile", "infile"])
     wf.inputs.maskfile = maskfile
     wf.inputs.infile = Infile
+    wf.cache_dir = tmpdir
 
     wf.add(
         BoshTask(
@@ -128,11 +130,12 @@ def test_boutiques_wf_1(maskfile, plugin):
 @pytest.mark.parametrize(
     "maskfile", ["test_brain.nii.gz", "test_brain", "test_brain.nii"]
 )
-def test_boutiques_wf_2(maskfile, plugin):
+def test_boutiques_wf_2(maskfile, plugin, tmpdir):
     """ wf with two BoshTasks (fsl.bet and fsl.stats) and one ShellTask"""
     wf = Workflow(name="wf", input_spec=["maskfile", "infile"])
     wf.inputs.maskfile = maskfile
     wf.inputs.infile = Infile
+    wf.cache_dir = tmpdir
 
     wf.add(
         BoshTask(

pydra/engine/tests/test_node_task.py

@@ -365,9 +365,10 @@ def test_odir_init():
 
 
 @pytest.mark.flaky(reruns=2)  # when dask
-def test_task_nostate_1(plugin_dask_opt):
+def test_task_nostate_1(plugin_dask_opt, tmpdir):
     """ task without splitter"""
     nn = fun_addtwo(name="NA", a=3)
+    nn.cache_dir = tmpdir
     assert np.allclose(nn.inputs.a, [3])
     assert nn.state is None
 
@@ -405,9 +406,10 @@ def test_task_nostate_1_call():
 
 
 @pytest.mark.flaky(reruns=2)  # when dask
-def test_task_nostate_1_call_subm(plugin_dask_opt):
+def test_task_nostate_1_call_subm(plugin_dask_opt, tmpdir):
     """ task without splitter"""
     nn = fun_addtwo(name="NA", a=3)
+    nn.cache_dir = tmpdir
     assert np.allclose(nn.inputs.a, [3])
     assert nn.state is None
 
@@ -422,9 +424,10 @@ def test_task_nostate_1_call_subm(plugin_dask_opt):
 
 
 @pytest.mark.flaky(reruns=2)  # when dask
-def test_task_nostate_1_call_plug(plugin_dask_opt):
+def test_task_nostate_1_call_plug(plugin_dask_opt, tmpdir):
     """ task without splitter"""
     nn = fun_addtwo(name="NA", a=3)
+    nn.cache_dir = tmpdir
     assert np.allclose(nn.inputs.a, [3])
     assert nn.state is None
 
@@ -450,9 +453,10 @@ def test_task_nostate_1_call_updateinp():
     assert nn.output_dir.exists()
 
 
-def test_task_nostate_2(plugin):
+def test_task_nostate_2(plugin, tmpdir):
     """ task with a list as an input, but no splitter"""
     nn = moment(name="NA", n=3, lst=[2, 3, 4])
+    nn.cache_dir = tmpdir
     assert np.allclose(nn.inputs.n, [3])
     assert np.allclose(nn.inputs.lst, [2, 3, 4])
     assert nn.state is None
@@ -467,9 +471,10 @@ def test_task_nostate_2(plugin):
     assert nn.output_dir.exists()
 
 
-def test_task_nostate_3(plugin):
+def test_task_nostate_3(plugin, tmpdir):
     """ task with a dictionary as an input"""
     nn = fun_dict(name="NA", d={"a": "ala", "b": "bala"})
+    nn.cache_dir = tmpdir
     assert nn.inputs.d == {"a": "ala", "b": "bala"}
 
     with Submitter(plugin=plugin) as sub:
@@ -489,6 +494,7 @@ def test_task_nostate_4(plugin, tmpdir):
         f.write("hello from pydra\n")
 
     nn = fun_file(name="NA", filename=file1)
+    nn.cache_dir = tmpdir
 
     with Submitter(plugin) as sub:
         sub(nn)
@@ -719,13 +725,14 @@ def test_task_nostate_cachelocations_updated(plugin, tmpdir):
 
 @pytest.mark.flaky(reruns=2)  # when dask
 @pytest.mark.parametrize("input_type", ["list", "array"])
-def test_task_state_1(plugin_dask_opt, input_type):
+def test_task_state_1(plugin_dask_opt, input_type, tmpdir):
     """ task with the simplest splitter"""
     a_in = [3, 5]
     if input_type == "array":
         a_in = np.array(a_in)
 
     nn = fun_addtwo(name="NA").split(splitter="a", a=a_in)
+    nn.cache_dir = tmpdir
 
     assert nn.state.splitter == "NA.a"
     assert nn.state.splitter_rpn == ["NA.a"]
@@ -761,11 +768,12 @@ def test_task_state_1(plugin_dask_opt, input_type):
         assert odir.exists()
 
 
-def test_task_state_1a(plugin):
+def test_task_state_1a(plugin, tmpdir):
     """ task with the simplest splitter (inputs set separately)"""
     nn = fun_addtwo(name="NA")
     nn.split(splitter="a")
     nn.inputs.a = [3, 5]
+    nn.cache_dir = tmpdir
 
     assert nn.state.splitter == "NA.a"
     assert nn.state.splitter_rpn == ["NA.a"]
@@ -781,11 +789,12 @@ def test_task_state_1a(plugin):
         assert results[i].output.out == res[1]
 
 
-def test_task_state_singl_1(plugin):
+def test_task_state_singl_1(plugin, tmpdir):
     """ Tasks with two inputs and a splitter (no combiner)
         one input is a single value, the other is in the splitter and combiner
     """
     nn = fun_addvar(name="NA").split(splitter="a", a=[3, 5], b=10)
+    nn.cache_dir = tmpdir
 
     assert nn.inputs.a == [3, 5]
     assert nn.inputs.b == 10
@@ -839,7 +848,14 @@ def test_task_state_singl_1(plugin):
 )
 @pytest.mark.parametrize("input_type", ["list", "array", "mixed"])
 def test_task_state_2(
-    plugin, splitter, state_splitter, state_rpn, expected, expected_ind, input_type
+    plugin,
+    splitter,
+    state_splitter,
+    state_rpn,
+    expected,
+    expected_ind,
+    input_type,
+    tmpdir,
 ):
     """ Tasks with two inputs and a splitter (no combiner)"""
     a_in, b_in = [3, 5], [10, 20]
@@ -848,6 +864,8 @@ def test_task_state_2(
     elif input_type == "mixed":
         a_in = np.array(a_in)
     nn = fun_addvar(name="NA").split(splitter=splitter, a=a_in, b=b_in)
+    nn.cache_dir = tmpdir
+
     assert (nn.inputs.a == np.array([3, 5])).all()
     assert (nn.inputs.b == np.array([10, 20])).all()
     assert nn.state.splitter == state_splitter
@@ -883,9 +901,10 @@ def test_task_state_2(
         assert odir.exists()
 
 
-def test_task_state_3(plugin):
+def test_task_state_3(plugin, tmpdir):
     """ task with the simplest splitter, the input is an empty list"""
     nn = fun_addtwo(name="NA").split(splitter="a", a=[])
+    nn.cache_dir = tmpdir
 
     assert nn.state.splitter == "NA.a"
     assert nn.state.splitter_rpn == ["NA.a"]
@@ -904,12 +923,14 @@ def test_task_state_3(plugin):
 
 
 @pytest.mark.parametrize("input_type", ["list", "array"])
-def test_task_state_4(plugin, input_type):
+def test_task_state_4(plugin, input_type, tmpdir):
     """ task with a list as an input, and a simple splitter """
     lst_in = [[2, 3, 4], [1, 2, 3]]
     if input_type == "array":
         lst_in = np.array(lst_in)
     nn = moment(name="NA", n=3, lst=lst_in).split(splitter="lst")
+    nn.cache_dir = tmpdir
+
     assert np.allclose(nn.inputs.n, 3)
     assert np.allclose(nn.inputs.lst, [[2, 3, 4], [1, 2, 3]])
     assert nn.state.splitter == "NA.lst"
@@ -935,9 +956,11 @@ def test_task_state_4(plugin, input_type):
         assert odir.exists()
 
 
-def test_task_state_4a(plugin):
+def test_task_state_4a(plugin, tmpdir):
     """ task with a tuple as an input, and a simple splitter """
     nn = moment(name="NA", n=3, lst=[(2, 3, 4), (1, 2, 3)]).split(splitter="lst")
+    nn.cache_dir = tmpdir
+
     assert np.allclose(nn.inputs.n, 3)
     assert np.allclose(nn.inputs.lst, [[2, 3, 4], [1, 2, 3]])
     assert nn.state.splitter == "NA.lst"
@@ -955,11 +978,13 @@ def test_task_state_4a(plugin):
         assert odir.exists()
 
 
-def test_task_state_5(plugin):
+def test_task_state_5(plugin, tmpdir):
     """ task with a list as an input, and the variable is part of the scalar splitter"""
     nn = moment(name="NA", n=[1, 3], lst=[[2, 3, 4], [1, 2, 3]]).split(
         splitter=("n", "lst")
     )
+    nn.cache_dir = tmpdir
+
     assert np.allclose(nn.inputs.n, [1, 3])
     assert np.allclose(nn.inputs.lst, [[2, 3, 4], [1, 2, 3]])
     assert nn.state.splitter == ("NA.n", "NA.lst")
@@ -977,13 +1002,15 @@ def test_task_state_5(plugin):
         assert odir.exists()
 
 
-def test_task_state_5_exception(plugin):
+def test_task_state_5_exception(plugin, tmpdir):
     """ task with a list as an input, and the variable is part of the scalar splitter
         the shapes are not matching, so exception should be raised
     """
     nn = moment(name="NA", n=[1, 3, 3], lst=[[2, 3, 4], [1, 2, 3]]).split(
         splitter=("n", "lst")
     )
+    nn.cache_dir = tmpdir
+
     assert np.allclose(nn.inputs.n, [1, 3, 3])
     assert np.allclose(nn.inputs.lst, [[2, 3, 4], [1, 2, 3]])
     assert nn.state.splitter == ("NA.n", "NA.lst")
@@ -994,11 +1021,13 @@ def test_task_state_5_exception(plugin):
     assert "shape" in str(excinfo.value)
 
 
-def test_task_state_6(plugin):
+def test_task_state_6(plugin, tmpdir):
     """ ask with a list as an input, and the variable is part of the outer splitter """
     nn = moment(name="NA", n=[1, 3], lst=[[2, 3, 4], [1, 2, 3]]).split(
         splitter=["n", "lst"]
     )
+    nn.cache_dir = tmpdir
+
     assert np.allclose(nn.inputs.n, [1, 3])
     assert np.allclose(nn.inputs.lst, [[2, 3, 4], [1, 2, 3]])
     assert nn.state.splitter == ["NA.n", "NA.lst"]
@@ -1016,11 +1045,13 @@ def test_task_state_6(plugin):
         assert odir.exists()
 
 
-def test_task_state_6a(plugin):
+def test_task_state_6a(plugin, tmpdir):
     """ ask with a tuple as an input, and the variable is part of the outer splitter """
     nn = moment(name="NA", n=[1, 3], lst=[(2, 3, 4), (1, 2, 3)]).split(
         splitter=["n", "lst"]
     )
+    nn.cache_dir = tmpdir
+
     assert np.allclose(nn.inputs.n, [1, 3])
     assert np.allclose(nn.inputs.lst, [[2, 3, 4], [1, 2, 3]])
     assert nn.state.splitter == ["NA.n", "NA.lst"]
@@ -1039,9 +1070,10 @@ def test_task_state_6a(plugin):
 
 
 @pytest.mark.flaky(reruns=2)  # when dask
-def test_task_state_comb_1(plugin_dask_opt):
+def test_task_state_comb_1(plugin_dask_opt, tmpdir):
     """ task with the simplest splitter and combiner"""
     nn = fun_addtwo(name="NA").split(a=[3, 5], splitter="a").combine(combiner="a")
+    nn.cache_dir = tmpdir
 
     assert (nn.inputs.a == np.array([3, 5])).all()
 
@@ -1173,13 +1205,15 @@ def test_task_state_comb_2(
     state_rpn_final,
     expected,
     expected_val,
+    tmpdir,
 ):
     """ Tasks with scalar and outer splitters and  partial or full combiners"""
     nn = (
         fun_addvar(name="NA")
         .split(a=[3, 5], b=[10, 20], splitter=splitter)
         .combine(combiner=combiner)
     )
+    nn.cache_dir = tmpdir
 
     assert (nn.inputs.a == np.array([3, 5])).all()
 
@@ -1219,11 +1253,12 @@ def test_task_state_comb_2(
         assert odir.exists()
 
 
-def test_task_state_comb_singl_1(plugin):
+def test_task_state_comb_singl_1(plugin, tmpdir):
     """ Tasks with two inputs;
      one input is a single value, the other is in the splitter and combiner
      """
     nn = fun_addvar(name="NA").split(splitter="a", a=[3, 5], b=10).combine(combiner="a")
+    nn.cache_dir = tmpdir
 
     assert nn.inputs.a == [3, 5]
     assert nn.inputs.b == 10
@@ -1248,9 +1283,10 @@ def test_task_state_comb_singl_1(plugin):
         assert odir.exists()
 
 
-def test_task_state_comb_3(plugin):
+def test_task_state_comb_3(plugin, tmpdir):
     """ task with the simplest splitter, the input is an empty list"""
     nn = fun_addtwo(name="NA").split(splitter="a", a=[]).combine(combiner=["a"])
+    nn.cache_dir = tmpdir
 
     assert nn.state.splitter == "NA.a"
     assert nn.state.splitter_rpn == ["NA.a"]