Merge remote-tracking branch 'upstream/master' into python3.13

Author: brownbaerchen

.github/workflows/ci_pipeline.yml

@@ -203,8 +203,6 @@ jobs:
         run: |
           . venv-pySDC/bin/activate
           pip install -e /repositories/pySDC
-          pip install qmat
-          pip install pytest-isolate-mpi
           # test installation
           python -c "import pySDC; print(f'pySDC module: {pySDC}')"
       - name: Install gusto

README.md

@@ -118,7 +118,7 @@ and innovation programme and Belgium, France, Germany, and Switzerland.
 This project also received funding from the [German Federal Ministry of
 Education and Research](https://www.bmbf.de/bmbf/en/home/home_node.html)
 (BMBF) grants  16HPC047 and 16ME0679K. Supported by the European Union - NextGenerationEU. 
-The project also received help from the [Helmholtz Platform for Research Software Engineering - Preparatory Study (HiRSE_PS)](https://www.helmholtz-hirse.de/).
+The project also received help from the [Joint Lab "Helmholtz Information -  Research Software Engineering" (HiRSE)](https://www.helmholtz-hirse.de/).
 
 <p align="center">
   <img src="./docs/img/EuroHPC.jpg" height="105"/> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

pySDC/helpers/fieldsIO.py

@@ -44,14 +44,13 @@
 
 Warning
 -------
-To use MPI collective writing, you need to call first the class methods :class:`Rectilinear.initMPI` (cf their docstring).
+To use MPI collective writing, you need to call first the class methods :class:`Rectilinear.setupMPI` (cf their docstring).
 Also, `Rectilinear.setHeader` **must be given the global grids coordinates**, whether the code is run in parallel or not.
 """
 import os
 import numpy as np
 from typing import Type, TypeVar
 import logging
-import itertools
 
 T = TypeVar("T")
 
@@ -61,11 +60,17 @@
     except ImportError:
         pass
     from mpi4py import MPI
+    from mpi4py.util.dtlib import from_numpy_dtype as MPI_DTYPE
 except ImportError:
 
     class MPI:
         COMM_WORLD = None
         Intracomm = T
+        File = T
+        Datatype = T
+
+    def MPI_DTYPE():
+        pass
 
 
 # Supported data types
@@ -493,7 +498,6 @@ def toVTR(self, baseName, varNames, idxFormat="{:06d}"):
     # MPI-parallel implementation
     # -------------------------------------------------------------------------
     comm: MPI.Intracomm = None
-    _nCollectiveIO = None
 
     @classmethod
     def setupMPI(cls, comm: MPI.Intracomm, iLoc, nLoc):
@@ -513,21 +517,9 @@ def setupMPI(cls, comm: MPI.Intracomm, iLoc, nLoc):
         cls.comm = comm
         cls.iLoc = iLoc
         cls.nLoc = nLoc
-        cls.mpiFile = None
-        cls._nCollectiveIO = None
-
-    @property
-    def nCollectiveIO(self):
-        """
-        Number of collective IO operations over all processes, when reading or writing a field.
-
-        Returns:
-        --------
-        int: Number of collective IO accesses
-        """
-        if self._nCollectiveIO is None:
-            self._nCollectiveIO = self.comm.allreduce(self.nVar * np.prod(self.nLoc[:-1]), op=MPI.MAX)
-        return self._nCollectiveIO
+        cls.mpiFile: MPI.File = None
+        cls.mpiType: MPI.Datatype = None
+        cls.mpiFileType: MPI.Datatype = None
 
     @property
     def MPI_ON(self):
@@ -543,13 +535,25 @@ def MPI_ROOT(self):
             return True
         return self.comm.Get_rank() == 0
 
+    def MPI_SETUP_FILETYPE(self):
+        """Setup subarray masks for each processes"""
+        self.mpiType = MPI_DTYPE(self.dtype)
+        self.mpiFileType = self.mpiType.Create_subarray(
+            [self.nVar, *self.gridSizes],  # Global array sizes
+            [self.nVar, *self.nLoc],  # Local array sizes
+            [0, *self.iLoc],  # Global starting indices of local blocks
+        )
+        self.mpiFileType.Commit()
+
     def MPI_FILE_OPEN(self, mode):
         """Open the binary file in MPI mode"""
         amode = {
             "r": MPI.MODE_RDONLY,
             "a": MPI.MODE_WRONLY | MPI.MODE_APPEND,
         }[mode]
         self.mpiFile = MPI.File.Open(self.comm, self.fileName, amode)
+        if self.mpiType is None:
+            self.MPI_SETUP_FILETYPE()
 
     def MPI_WRITE(self, data):
         """Write data (np.ndarray) in the binary file in MPI mode, at the current file cursor position."""
@@ -567,7 +571,8 @@ def MPI_WRITE_AT_ALL(self, offset, data: np.ndarray):
         data : np.ndarray
             Data to be written in the binary file.
         """
-        self.mpiFile.Write_at_all(offset, data)
+        self.mpiFile.Set_view(disp=offset, etype=self.mpiType, filetype=self.mpiFileType)
+        self.mpiFile.Write_all(data)
 
     def MPI_READ_AT_ALL(self, offset, data: np.ndarray):
         """
@@ -581,7 +586,8 @@ def MPI_READ_AT_ALL(self, offset, data: np.ndarray):
         data : np.ndarray
             Array on which to read the data from the binary file.
         """
-        self.mpiFile.Read_at_all(offset, data)
+        self.mpiFile.Set_view(disp=offset, etype=self.mpiType, filetype=self.mpiFileType)
+        self.mpiFile.Read_all(data)
 
     def MPI_FILE_CLOSE(self):
         """Close the binary file in MPI mode"""
@@ -632,33 +638,15 @@ def addField(self, time, field):
             *self.nLoc,
         ), f"expected {(self.nVar, *self.nLoc)} shape, got {field.shape}"
 
-        offset0 = self.fileSize
+        offset = self.fileSize
         self.MPI_FILE_OPEN(mode="a")
-        nWrites = 0
-        nCollectiveIO = self.nCollectiveIO
 
         if self.MPI_ROOT:
             self.MPI_WRITE(np.array(time, dtype=T_DTYPE))
-        offset0 += self.tSize
-
-        for (iVar, *iBeg) in itertools.product(range(self.nVar), *[range(n) for n in self.nLoc[:-1]]):
-            offset = offset0 + self.iPos(iVar, iBeg) * self.itemSize
-            self.MPI_WRITE_AT_ALL(offset, field[(iVar, *iBeg)])
-            nWrites += 1
-
-        for _ in range(nCollectiveIO - nWrites):
-            # Additional collective write to catch up with other processes
-            self.MPI_WRITE_AT_ALL(offset0, field[:0])
-
+        offset += self.tSize
+        self.MPI_WRITE_AT_ALL(offset, field)
         self.MPI_FILE_CLOSE()
 
-    def iPos(self, iVar, iX):
-        iPos = iVar * self.nDoF
-        for axis in range(self.dim - 1):
-            iPos += (self.iLoc[axis] + iX[axis]) * np.prod(self.gridSizes[axis + 1 :])
-        iPos += self.iLoc[-1]
-        return iPos
-
     def readField(self, idx):
         """
         Read one field stored in the binary file, corresponding to the given
@@ -684,26 +672,15 @@ def readField(self, idx):
             return super().readField(idx)
 
         idx = self.formatIndex(idx)
-        offset0 = self.hSize + idx * (self.tSize + self.fSize)
+        offset = self.hSize + idx * (self.tSize + self.fSize)
         with open(self.fileName, "rb") as f:
-            t = float(np.fromfile(f, dtype=T_DTYPE, count=1, offset=offset0)[0])
-        offset0 += self.tSize
+            t = float(np.fromfile(f, dtype=T_DTYPE, count=1, offset=offset)[0])
+        offset += self.tSize
 
         field = np.empty((self.nVar, *self.nLoc), dtype=self.dtype)
 
         self.MPI_FILE_OPEN(mode="r")
-        nReads = 0
-        nCollectiveIO = self.nCollectiveIO
-
-        for (iVar, *iBeg) in itertools.product(range(self.nVar), *[range(n) for n in self.nLoc[:-1]]):
-            offset = offset0 + self.iPos(iVar, iBeg) * self.itemSize
-            self.MPI_READ_AT_ALL(offset, field[(iVar, *iBeg)])
-            nReads += 1
-
-        for _ in range(nCollectiveIO - nReads):
-            # Additional collective read to catch up with other processes
-            self.MPI_READ_AT_ALL(offset0, field[:0])
-
+        self.MPI_READ_AT_ALL(offset, field)
         self.MPI_FILE_CLOSE()
 
         return t, field

pySDC/tests/test_benchmarks/test_collocation.py

@@ -3,8 +3,8 @@
 
 from pySDC.core.collocation import CollBase
 
-t_start = float(np.random.rand(1) * 0.2)
-t_end = float(0.8 + np.random.rand(1) * 0.2)
+t_start = float(np.random.rand(1)[0] * 0.2)
+t_end = float(0.8 + np.random.rand(1)[0] * 0.2)
 
 tolQuad = 1e-13
 

pySDC/tests/test_helpers/test_gusto_coupling.py

@@ -621,7 +621,7 @@ def test_pySDC_integrator_with_adaptivity(dt_initial, setup):
 
 
 @pytest.mark.firedrake
-@pytest.mark.parametrize('n_steps', [1, 2, 4])
+@pytest.mark.parametrize('n_steps', [1, 4])
 @pytest.mark.parametrize('useMPIController', [True, False])
 def test_pySDC_integrator_MSSDC(n_steps, useMPIController, setup, submit=True, n_tasks=4):
     if submit and useMPIController: