fix remdsort postprocess

configs/threadpool.yaml

@@ -9,6 +9,7 @@ ModelTraining:
   gpu: true
   use_threadpool: true
   max_training_time: 1
+  max_workers: 1  # suppress assertion for multigpu training
 CP2K:
   cores_per_worker: 2
   max_evaluation_time: 0.3

psiflow/execution.py

@@ -42,13 +42,15 @@ def __init__(
         cores_per_worker: int,
         use_threadpool: bool,
         worker_prepend: str,
+        max_workers: Optional[int] = None,
     ) -> None:
         self.parsl_provider = parsl_provider
         self.gpu = gpu
         self.cores_per_worker = cores_per_worker
         self.use_threadpool = use_threadpool
         self.worker_prepend = worker_prepend
         self.name = self.__class__.__name__
+        self._max_workers = max_workers
 
     @property
     def cores_available(self):
@@ -62,7 +64,10 @@ def cores_available(self):
 
     @property
     def max_workers(self):
-        return max(1, math.floor(self.cores_available / self.cores_per_worker))
+        if self._max_workers is not None:
+            return self._max_workers
+        else:
+            return max(1, math.floor(self.cores_available / self.cores_per_worker))
 
     @property
     def max_runtime(self):
@@ -239,7 +244,7 @@ def __init__(
             assert max_training_time * 60 < self.max_runtime
         self.max_training_time = max_training_time
         if self.max_workers > 1:
-            message = ('the max_simulation_time keyword does not work '
+            message = ('the max_training_time keyword does not work '
                        'in combination with multi-gpu training. Adjust '
                        'the maximum number of epochs to control the '
                        'duration of training')

psiflow/sampling/server.py

@@ -1,7 +1,7 @@
 import argparse
+import os
 import ast
 import glob
-import shutil
 import signal
 import xml.etree.ElementTree as ET
 from copy import deepcopy
@@ -132,8 +132,14 @@ def remdsort(inputfile, prefix="SRT_"):
                                     }
                                 )
                             else:
-                                filename = filename + "_" + padb + "." + o.format
-                                ofilename = ofilename + "_" + padb + "." + o.format
+                                # FIX
+                                if o.format == 'ase':
+                                    extension = 'extxyz'
+                                else:
+                                    extension = o.format
+                                filename = filename + "_" + padb + "." + extension
+                                ofilename = ofilename + "_" + padb + "." + extension
+                                print(filename, ofilename)
                                 ntraj.append(
                                     {
                                         "filename": filename,
@@ -380,10 +386,13 @@ def cleanup(args):
         if "remd" in content:
             remdsort("input.xml")
             for filepath in glob.glob("SRT_*"):
+                # does not use shutil because it is not instantaneous
                 source = filepath
                 target = filepath.replace("SRT_", "")
-                assert Path(target).exists()  # should exist
-                shutil.copyfile(source, target)
+                os.remove(target)
+                assert not Path(target).exists()
+                os.rename(source, target)
+                assert Path(target).exists()
         i = 0
         while i < len(states):
             # try all formattings of bead index (i-PI inconsistency)
@@ -449,19 +458,19 @@ def main():
     if not args.cleanup:
         start(args)
     else:
-        try:
-            cleanup(args)
-        except BaseException as e:  # noqa: B036
-            print(e)
-            print("i-PI cleanup failed!")
-            print("files in directory:")
-            for filepath in Path.cwd().glob("*"):
-                print(filepath)
-            print("")
-
-            names = [p.name for p in Path.cwd().glob("*")]
-            if "output.checkpoint" in names:
-                with open("output.checkpoint", "r") as f:
-                    print(f.read())
-            else:
-                print("no output.checkpoint found")
+        #try:
+        cleanup(args)
+        #except BaseException as e:  # noqa: B036
+        #    print(e)
+        #    print("i-PI cleanup failed!")
+        #    print("files in directory:")
+        #    for filepath in Path.cwd().glob("*"):
+        #        print(filepath)
+        #    print("")
+
+        #    names = [p.name for p in Path.cwd().glob("*")]
+        #    if "output.checkpoint" in names:
+        #        with open("output.checkpoint", "r") as f:
+        #            print(f.read())
+        #    else:
+        #        print("no output.checkpoint found")

tests/test_sampling.py

@@ -425,7 +425,8 @@ def test_rex(dataset):
     assert len(partition(walkers)) == 1
     assert len(partition(walkers)[0]) == 2
 
-    _ = sample(walkers, steps=50, step=10)
+    outputs = sample(walkers, steps=50, step=10)
+    assert outputs[0].trajectory.length().result() == 6
 
     swaps = np.loadtxt(walkers[0].coupling.swapfile.result().filepath)
     assert len(swaps) > 0  # at least some successful swaps