1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
|
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright 2019- The GROMACS Authors
# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
# as published by the Free Software Foundation; either version 2.1
# of the License, or (at your option) any later version.
#
# GROMACS 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
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with GROMACS; if not, see
# https://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# If you want to redistribute modifications to GROMACS, please
# consider that scientific software is very special. Version
# control is crucial - bugs must be traceable. We will be happy to
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at https://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out https://www.gromacs.org.
import os
import pytest
import gmxapi as gmx
try:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank_number = comm.Get_rank()
comm_size = comm.Get_size()
except ImportError:
comm = None
rank_number = 0
comm_size = 1
rank_tag = ""
MPI = None
else:
rank_tag = "rank{}:".format(rank_number)
mpi_support = pytest.mark.skipif(
comm_size > 1
and gmx.utility.config()["gmx_mpi_type"] == "library"
and not gmx.version.has_feature("mpi_comm_integration"),
reason="Multi-rank MPI contexts require gmxapi 0.4.",
)
@gmx.function_wrapper(output={"data": float})
def add_float(a: float, b: float) -> float:
return a + b
@gmx.function_wrapper(output={"data": bool})
def less_than(lhs: float, rhs: float, output=None):
output.data = lhs < rhs
def test_subgraph_function():
subgraph = gmx.subgraph(variables={"float_with_default": 1.0, "bool_data": True})
with subgraph:
# Define the update for float_with_default to come from an add_float operation.
subgraph.float_with_default = add_float(
subgraph.float_with_default, 1.0
).output.data
subgraph.bool_data = less_than(
lhs=subgraph.float_with_default, rhs=6.0
).output.data
operation_instance = subgraph()
operation_instance.run()
assert operation_instance.values["float_with_default"] == 2.0
loop = gmx.while_loop(operation=subgraph, condition=subgraph.bool_data)
handle = loop()
assert handle.output.float_with_default.result() == 6
_previous_cpt = [""] * comm_size
@gmx.function_wrapper(output={"data": bool})
def _is_new(current_cpt: str, output):
# Is the simulation new or is it continuing from a checkpoint?
global _previous_cpt
# TODO: Don't use private details of the publishing data proxy.
# Either use another subgraph variable for previous_cpt, distribute function_wrapper tasks by MPI rank,
# or develop the interface for session resources provided to tasks.
executing_member = output._client_identifier
previous_cpt = _previous_cpt[executing_member]
_previous_cpt[executing_member] = current_cpt
if current_cpt != previous_cpt and os.path.exists(previous_cpt):
output.data = False
else:
output.data = True
@mpi_support
def test_subgraph_simulation_extension(spc_water_box, mdrun_kwargs):
tpr_list = gmx.read_tpr([spc_water_box] * comm_size)
input_list = gmx.modify_input(tpr_list, parameters={"nsteps": 10**6})
subgraph = gmx.subgraph(
variables={
"new": True,
"checkpoint": "",
# 'previous': '',
}
)
with subgraph:
md = gmx.mdrun(
input_list,
runtime_args={
"-cpi": subgraph.checkpoint,
"-maxh": "0.001",
"-noappend": None,
},
)
subgraph.new = _is_new(md.output.checkpoint).output.data
subgraph.checkpoint = md.output.checkpoint
trajectory_continuation_loop = gmx.while_loop(
operation=subgraph, condition=subgraph.new
)()
trajectory_continuation_loop.run()
_cpt_output = trajectory_continuation_loop.output.checkpoint
final_checkpoint = _cpt_output.result()
loop_condition = trajectory_continuation_loop.output.new.result()
if comm_size > 1:
final_checkpoint = final_checkpoint[rank_number]
loop_condition = loop_condition[rank_number]
assert isinstance(final_checkpoint, str)
assert isinstance(loop_condition, bool)
assert os.path.exists(final_checkpoint)
def test_local_tools_and_assumptions():
const = gmx.make_constant(1.0)
assert add_float(const, const).output.data.result() == 2
assert gmx.logical_not(less_than(const, const).output.data).result()
# Note: It may not be safe to assume that keyword argument order (lhs, rhs) is preserved.
assert less_than(const, add_float(const, const).output.data).output.data.result()
|
