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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>
  • Loading branch information...
bors and hirschsn committed Apr 15, 2019
2 parents 01d1b12 + dbeae30 commit 75894c87f715dc24cef27804974f5d3b6904274c
Showing with 143 additions and 1 deletion.
  1. +1 −1 src/core/io/mpiio/mpiio.cpp
  2. +1 −0 testsuite/python/CMakeLists.txt
  3. +141 −0 testsuite/python/mpiio.py
@@ -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
@@ -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)
@@ -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()

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