Merge #2703

2703: Mpiio test r=KaiSzuttor a=hirschsn

Fixes missing MPI-IO test (see #2071).

Description of changes:
 - Add a test that creates random particles, dumps them, reads them in, again and verifies the read particles.


PR Checklist
------------
 - [ ] Tests?
   - [ ] Interface
   - [ ] Core 
 - [ ] Docs?


Co-authored-by: Steffen Hirschmann <steffen.hirschmann@ipvs.uni-stuttgart.de>

src/core/io/mpiio/mpiio.cpp

@@ -312,10 +312,10 @@ static void read_head(const std::string &fn, int rank, unsigned *fields) {
       errexit();
     }
     MPI_Bcast(fields, 1, MPI_UNSIGNED, 0, MPI_COMM_WORLD);
+    fclose(f);
   } else {
     MPI_Bcast(fields, 1, MPI_UNSIGNED, 0, MPI_COMM_WORLD);
   }
-  free(f);
 }
 
 /** Reads the pref file and fills pref and nlocalpart with their

testsuite/python/CMakeLists.txt

@@ -192,6 +192,7 @@ python_test(FILE p3m_electrostatic_pressure.py MAX_NUM_PROC 2)
 python_test(FILE sigint.py DEPENDENCIES sigint_child.py MAX_NUM_PROC 1)
 python_test(FILE lb_density.py MAX_NUM_PROC 1)
 python_test(FILE observable_chain.py MAX_NUM_PROC 4)
+python_test(FILE mpiio.py MAX_NUM_PROC 4)
 python_test(FILE gpu_availability.py MAX_NUM_PROC 1)
 
 if(PY_H5PY)

testsuite/python/mpiio.py

@@ -0,0 +1,141 @@
+#
+# Copyright (C) 2013-2019 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# ESPResSo is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+"""
+Testmodule for MPI-IO.
+"""
+
+from __future__ import print_function
+import espressomd
+import espressomd.io
+from espressomd.interactions import AngleHarmonic
+import numpy
+import unittest as ut
+import random
+import os
+from argparse import Namespace
+#from tests_common import abspath
+
+# Number of particles
+npart = 1023
+# Number of different bond types
+nbonds = 100
+
+filename = "testdata.mpiio"
+exts = ["head", "pref", "id", "type", "pos", "vel", "boff", "bond"]
+filenames = [filename + "." + ext for ext in exts]
+
+
+def clean_files():
+    for f in filenames:
+        if os.path.isfile(f):
+            os.remove(f)
+
+
+def randint_different_from(a, b, n):
+    """Returns a random integer in [a, b) that is not n."""
+    r = n
+    while r == n:
+        r = random.randint(a, b - 1)
+    return r
+
+
+def random_particles():
+    """Returns a list of random particle descriptions."""
+    parts = []
+    for i in range(npart):
+        p = Namespace()
+        p.id = i
+        p.type = random.randint(0, 100)
+        p.pos = numpy.random.rand(3)
+        p.v = numpy.random.rand(3)
+        p.bonds = []
+        # Up to 20 bonds; otherwise this test will take ages
+        for _ in range(random.randint(0, 20)):
+            btype = random.randint(0, nbonds - 1)
+            # Don't create loops, i.e. exclude "i" itself
+            p1 = randint_different_from(0, npart, i)
+            p2 = randint_different_from(0, npart, i)
+            p.bonds.append((btype, p1, p2))
+        parts.append(p)
+    return parts
+
+
+class MPIIOTest(ut.TestCase):
+
+    """
+    Test class for the MPI-IO core functionality.
+    Generates random particles, dumps them, reads them in,
+    again and then checks the input against the initially created random
+    particles.
+    """
+    s = espressomd.system.System(box_l=[1, 1, 1])
+    # Just a bunch of random interaction such that add_bond does not throw
+    for i in range(nbonds):
+        s.bonded_inter[i] = AngleHarmonic(bend=i, phi0=i)
+    test_particles = random_particles()
+
+    def setUp(self):
+        """Sets up a system from test_particles and prepares environment
+        for the tests."""
+        clean_files()  # Prior call might not have completed sucecssfully
+        for p in self.test_particles:
+            self.s.part.add(id=p.id, type=p.type, pos=p.pos, v=p.v)
+            for b in p.bonds:
+                self.s.part[p.id].add_bond(b)
+
+    def tearDown(self):
+        clean_files()
+
+    def check_files_exist(self):
+        """Checks if all necessary files have been written."""
+        for fn in filenames:
+            self.assertTrue(os.path.isfile(fn))
+
+    def check_sample_system(self):
+        """Checks the particles in the ESPResSo system "self.s" against the
+        true values in "self.test_particles"."""
+        for p, q in zip(self.s.part, self.test_particles):
+            self.assertEqual(p.id, q.id)
+            self.assertEqual(p.type, q.type)
+            numpy.testing.assert_array_equal(numpy.copy(p.pos), q.pos)
+            numpy.testing.assert_array_equal(numpy.copy(p.v), q.v)
+            self.assertEqual(len(p.bonds), len(q.bonds))
+            # Check all bonds
+            for bp, bq in zip(p.bonds, q.bonds):
+                # Bond type - "bend" stores the index of the bond
+                self.assertEqual(bp[0].params["bend"], bq[0])
+                # Bond partners
+                numpy.testing.assert_array_equal(bp[1:], bq[1:])
+
+    def test_mpiio(self):
+        espressomd.io.mpiio.mpiio.write(
+            filename, types=True, positions=True, velocities=True, bonds=True)
+
+        self.check_files_exist()
+
+        self.s.part.clear()  # Clear to be on the safe side
+        espressomd.io.mpiio.mpiio.read(
+            filename, types=True, positions=True, velocities=True, bonds=True)
+
+        self.check_sample_system()
+
+
+if __name__ == '__main__':
+    ut.main()