Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/tests/test_mpi.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """Tests of the experimental MPI extension.""" |
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2 import json |
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3 import os.path |
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4 import sys |
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5 from io import StringIO |
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6 from pathlib import Path |
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7 from typing import Any, Generator, List, MutableMapping, Optional, Tuple |
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8 |
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9 import pkg_resources |
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10 import pytest |
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11 from ruamel import yaml |
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12 from ruamel.yaml.comments import CommentedMap, CommentedSeq |
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13 from schema_salad.avro.schema import Names |
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14 |
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15 import cwltool.load_tool |
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16 import cwltool.singularity |
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17 import cwltool.udocker |
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18 from cwltool.command_line_tool import CommandLineTool |
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19 from cwltool.context import LoadingContext, RuntimeContext |
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20 from cwltool.main import main |
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21 from cwltool.mpi import MpiConfig, MPIRequirementName |
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22 |
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23 from .util import get_data, windows_needs_docker, working_directory |
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24 |
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25 |
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26 def test_mpi_conf_defaults() -> None: |
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27 mpi = MpiConfig() |
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28 assert mpi.runner == "mpirun" |
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29 assert mpi.nproc_flag == "-n" |
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30 assert mpi.default_nproc == 1 |
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31 assert mpi.extra_flags == [] |
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32 assert mpi.env_pass == [] |
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33 assert mpi.env_pass_regex == [] |
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34 assert mpi.env_set == {} |
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35 |
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36 |
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37 def test_mpi_conf_unknownkeys() -> None: |
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38 with pytest.raises(TypeError): |
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39 MpiConfig(runner="mpiexec", foo="bar") # type: ignore |
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40 |
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41 |
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42 @pytest.fixture(scope="class") |
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43 def fake_mpi_conf(tmp_path_factory: Any) -> Generator[str, None, None]: |
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44 """ |
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45 Make a super simple mpirun-alike for applications that don't actually use MPI. |
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46 |
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47 It just runs the command multiple times (in serial). |
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48 |
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49 Then create a plaform MPI config YAML file that should make it work |
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50 for the testing examples. |
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51 """ |
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52 mpirun_text = """#!{interpreter} |
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53 import argparse |
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54 import sys |
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55 import subprocess |
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56 from io import StringIO |
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57 from typing import List |
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58 |
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59 def make_parser(): |
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60 p = argparse.ArgumentParser() |
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61 p.add_argument("--num", type=int, help="number of times to run the application") |
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62 p.add_argument( |
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63 "--no-fail", help="add this flag to actually work", action="store_true" |
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64 ) |
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65 p.add_argument( |
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66 "progargs", nargs=argparse.REMAINDER, help="The program and its arguments" |
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67 ) |
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68 return p |
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69 |
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70 class Runner: |
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71 def __init__(self): |
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72 if sys.stdin.isatty(): |
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73 self.indata = None |
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74 else: |
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75 self.indata = sys.stdin.read().encode(sys.stdin.encoding) |
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76 |
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77 def run_once(self, args: List[str]): |
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78 subprocess.run( |
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79 args, input=self.indata, stdout=sys.stdout, stderr=sys.stderr |
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80 ).check_returncode() |
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81 |
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82 def run_many(self, n: int, args: List[str]): |
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83 for i in range(n): |
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84 self.run_once(args) |
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85 |
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86 if __name__ == "__main__": |
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87 args = make_parser().parse_args() |
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88 assert args.no_fail == True, "Didn't set the --no-fail flag" |
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89 r = Runner() |
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90 r.run_many(args.num, args.progargs) |
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91 """.format( |
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92 interpreter=sys.executable |
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93 ) |
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94 mpitmp = tmp_path_factory.mktemp("fake_mpi") |
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95 mpirun_file = mpitmp / "fake_mpirun" |
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96 mpirun_file.write_text(mpirun_text) |
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97 mpirun_file.chmod(0o755) |
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98 |
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99 plat_conf = { |
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100 "runner": str(mpirun_file), |
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101 "nproc_flag": "--num", |
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102 "extra_flags": ["--no-fail"], |
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103 "env_set": {"TEST_MPI_FOO": "bar"}, |
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104 "env_pass": ["USER"], |
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105 } |
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106 plat_conf_file = mpitmp / "plat_mpi.yml" |
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107 plat_conf_file.write_text(yaml.main.round_trip_dump(plat_conf)) |
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108 |
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109 yield str(plat_conf_file) |
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110 |
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111 plat_conf_file.unlink() |
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112 mpirun_file.unlink() |
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113 mpitmp.rmdir() |
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114 |
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115 |
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116 def make_processes_input(np: int, tmp_path: Path) -> Path: |
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117 input_file = tmp_path / "input.yml" |
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118 with input_file.open("w") as f: |
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119 f.write("processes: %d\n" % np) |
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120 return input_file |
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121 |
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122 |
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123 def cwltool_args(fake_mpi_conf: str) -> List[str]: |
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124 return ["--enable-ext", "--enable-dev", "--mpi-config-file", fake_mpi_conf] |
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125 |
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126 |
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127 class TestMpiRun: |
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128 def test_fake_mpi_config(self, fake_mpi_conf: str) -> None: |
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129 conf_obj = MpiConfig.load(fake_mpi_conf) |
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130 runner = conf_obj.runner |
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131 assert os.path.dirname(runner) == os.path.dirname(fake_mpi_conf) |
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132 assert os.path.basename(runner) == "fake_mpirun" |
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133 assert conf_obj.nproc_flag == "--num" |
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134 assert conf_obj.default_nproc == 1 |
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135 assert conf_obj.extra_flags == ["--no-fail"] |
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136 |
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137 @windows_needs_docker |
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138 def test_simple_mpi_tool(self, fake_mpi_conf: str, tmp_path: Path) -> None: |
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139 stdout = StringIO() |
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140 stderr = StringIO() |
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141 with working_directory(tmp_path): |
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142 rc = main( |
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143 argsl=cwltool_args(fake_mpi_conf) |
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144 + [get_data("tests/wf/mpi_simple.cwl")], |
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145 stdout=stdout, |
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146 stderr=stderr, |
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147 ) |
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148 assert rc == 0 |
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149 |
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150 output = json.loads(stdout.getvalue()) |
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151 pid_path = output["pids"]["path"] |
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152 with open(pid_path) as pidfile: |
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153 pids = [int(line) for line in pidfile] |
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154 assert len(pids) == 2 |
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155 |
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156 @windows_needs_docker |
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157 def test_simple_mpi_nproc_expr(self, fake_mpi_conf: str, tmp_path: Path) -> None: |
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158 np = 4 |
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159 input_file = make_processes_input(np, tmp_path) |
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160 stdout = StringIO() |
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161 stderr = StringIO() |
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162 with working_directory(tmp_path): |
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163 rc = main( |
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164 argsl=cwltool_args(fake_mpi_conf) |
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165 + [get_data("tests/wf/mpi_expr.cwl"), str(input_file)], |
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166 stdout=stdout, |
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167 stderr=stderr, |
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168 ) |
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169 assert rc == 0 |
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170 |
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171 output = json.loads(stdout.getvalue()) |
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172 pid_path = output["pids"]["path"] |
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173 with open(pid_path) as pidfile: |
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174 pids = [int(line) for line in pidfile] |
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175 assert len(pids) == np |
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176 |
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177 @windows_needs_docker |
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178 def test_mpi_workflow(self, fake_mpi_conf: str, tmp_path: Path) -> None: |
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179 np = 3 |
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180 input_file = make_processes_input(np, tmp_path) |
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181 stdout = StringIO() |
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182 stderr = StringIO() |
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183 with working_directory(tmp_path): |
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184 rc = main( |
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185 argsl=cwltool_args(fake_mpi_conf) |
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186 + [get_data("tests/wf/mpi_simple_wf.cwl"), str(input_file)], |
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187 stdout=stdout, |
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188 stderr=stderr, |
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189 ) |
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190 assert rc == 0 |
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191 |
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192 output = json.loads(stdout.getvalue()) |
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193 lc_path = output["line_count"]["path"] |
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194 with open(lc_path) as lc_file: |
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195 lc = int(lc_file.read()) |
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196 assert lc == np |
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197 |
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198 @windows_needs_docker |
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199 def test_environment( |
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200 self, fake_mpi_conf: str, tmp_path: Path, monkeypatch: Any |
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201 ) -> None: |
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202 stdout = StringIO() |
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203 stderr = StringIO() |
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204 monkeypatch.setenv("USER", "tester") |
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205 with working_directory(tmp_path): |
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206 rc = main( |
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207 argsl=cwltool_args(fake_mpi_conf) + [get_data("tests/wf/mpi_env.cwl")], |
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208 stdout=stdout, |
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209 stderr=stderr, |
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210 ) |
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211 assert rc == 0 |
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212 |
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213 output = json.loads(stdout.getvalue()) |
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214 env_path = output["environment"]["path"] |
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215 with open(env_path) as envfile: |
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216 e = {} |
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217 for line in envfile: |
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218 k, v = line.strip().split("=", 1) |
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219 e[k] = v |
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220 assert e["USER"] == "tester" |
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221 assert e["TEST_MPI_FOO"] == "bar" |
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222 |
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223 |
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224 def test_env_passing(monkeypatch: Any) -> None: |
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225 config = MpiConfig( |
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226 env_pass=["A", "B", "LONG_NAME"], |
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227 env_pass_regex=["TOOLNAME", "MPI_.*_CONF"], |
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228 ) |
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229 |
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230 env = {} # type: MutableMapping[str, str] |
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231 |
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232 with monkeypatch.context() as m: |
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233 m.setattr(os, "environ", {}) |
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234 env = {} |
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235 config.pass_through_env_vars(env) |
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236 assert env == {} |
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237 |
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238 with monkeypatch.context() as m: |
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239 m.setattr(os, "environ", {"A": "a"}) |
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240 env = {} |
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241 config.pass_through_env_vars(env) |
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242 assert env == {"A": "a"} |
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243 |
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244 with monkeypatch.context() as m: |
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245 m.setattr(os, "environ", {"A": "a", "C": "c"}) |
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246 env = {} |
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247 config.pass_through_env_vars(env) |
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248 assert env == {"A": "a"} |
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249 |
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250 with monkeypatch.context() as m: |
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251 m.setattr(os, "environ", {"A": "a", "B": "b", "C": "c"}) |
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252 env = {"PATH": "one:two:three", "HOME": "/tmp/dir", "TMPDIR": "/tmp/dir"} |
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253 config.pass_through_env_vars(env) |
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254 assert env == { |
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255 "PATH": "one:two:three", |
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256 "HOME": "/tmp/dir", |
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257 "TMPDIR": "/tmp/dir", |
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258 "A": "a", |
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259 "B": "b", |
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260 } |
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261 |
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262 with monkeypatch.context() as m: |
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263 m.setattr(os, "environ", {"TOOLNAME": "foobar"}) |
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264 env = {} |
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265 config.pass_through_env_vars(env) |
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266 assert env == {"TOOLNAME": "foobar"} |
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267 |
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268 with monkeypatch.context() as m: |
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269 m.setattr(os, "environ", {"_TOOLNAME_": "foobar"}) |
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270 env = {} |
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271 config.pass_through_env_vars(env) |
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272 # Cos we are matching not searching |
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273 assert env == {} |
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274 |
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275 with monkeypatch.context() as m: |
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276 m.setattr(os, "environ", {"MPI_A_CONF": "A", "MPI_B_CONF": "B"}) |
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277 |
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278 env = {} |
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279 config.pass_through_env_vars(env) |
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280 # Cos we are matching not searching |
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281 assert env == {"MPI_A_CONF": "A", "MPI_B_CONF": "B"} |
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282 |
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283 |
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284 # Reading the schema is super slow - cache for the session |
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285 @pytest.fixture(scope="session") |
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286 def schema_ext11() -> Generator[Names, None, None]: |
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287 with pkg_resources.resource_stream("cwltool", "extensions-v1.1.yml") as res: |
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288 ext11 = res.read().decode("utf-8") |
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289 cwltool.process.use_custom_schema("v1.1", "http://commonwl.org/cwltool", ext11) |
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290 schema = cwltool.process.get_schema("v1.1")[1] |
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291 assert isinstance(schema, Names) |
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292 yield schema |
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293 |
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294 |
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295 mpiReq = CommentedMap({"class": MPIRequirementName, "processes": 1}) |
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296 containerReq = CommentedMap({"class": "DockerRequirement"}) |
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297 basetool = CommentedMap( |
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298 {"cwlVersion": "v1.1", "inputs": CommentedSeq(), "outputs": CommentedSeq()} |
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299 ) |
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300 |
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301 |
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302 def mk_tool( |
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303 schema: Names, |
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304 opts: List[str], |
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305 reqs: Optional[List[CommentedMap]] = None, |
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306 hints: Optional[List[CommentedMap]] = None, |
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307 ) -> Tuple[LoadingContext, RuntimeContext, CommentedMap]: |
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308 tool = basetool.copy() |
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309 |
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310 if reqs is not None: |
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311 tool["requirements"] = CommentedSeq(reqs) |
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312 if hints is not None: |
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313 tool["hints"] = CommentedSeq(hints) |
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314 |
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315 args = cwltool.argparser.arg_parser().parse_args(opts) |
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316 args.enable_ext = True |
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317 rc = RuntimeContext(vars(args)) |
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318 lc = cwltool.main.setup_loadingContext(None, rc, args) |
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319 lc.avsc_names = schema |
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320 return lc, rc, tool |
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321 |
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322 |
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323 def test_singularity(schema_ext11: Names) -> None: |
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324 lc, rc, tool = mk_tool(schema_ext11, ["--singularity"], reqs=[mpiReq, containerReq]) |
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325 clt = CommandLineTool(tool, lc) |
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326 jr = clt.make_job_runner(rc) |
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327 assert jr is cwltool.singularity.SingularityCommandLineJob |
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328 |
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329 |
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330 def test_udocker(schema_ext11: Names) -> None: |
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331 lc, rc, tool = mk_tool(schema_ext11, ["--udocker"], reqs=[mpiReq, containerReq]) |
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332 clt = CommandLineTool(tool, lc) |
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333 jr = clt.make_job_runner(rc) |
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334 assert jr is cwltool.udocker.UDockerCommandLineJob |
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335 |
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336 |
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337 def test_docker_hint(schema_ext11: Names) -> None: |
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338 # Docker hint, MPI required |
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339 lc, rc, tool = mk_tool(schema_ext11, [], hints=[containerReq], reqs=[mpiReq]) |
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340 clt = CommandLineTool(tool, lc) |
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341 jr = clt.make_job_runner(rc) |
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342 assert jr is cwltool.job.CommandLineJob |
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343 |
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344 |
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345 def test_docker_required(schema_ext11: Names) -> None: |
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346 # Docker required, MPI hinted |
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347 lc, rc, tool = mk_tool(schema_ext11, [], reqs=[containerReq], hints=[mpiReq]) |
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348 clt = CommandLineTool(tool, lc) |
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349 jr = clt.make_job_runner(rc) |
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350 assert jr is cwltool.docker.DockerCommandLineJob |
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351 |
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352 |
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353 def test_docker_mpi_both_required(schema_ext11: Names) -> None: |
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354 # Both required - error |
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355 with pytest.raises(cwltool.errors.UnsupportedRequirement): |
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356 lc, rc, tool = mk_tool(schema_ext11, [], reqs=[mpiReq, containerReq]) |
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357 clt = CommandLineTool(tool, lc) |
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358 jr = clt.make_job_runner(rc) |
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359 |
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360 |
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361 def test_docker_mpi_both_hinted(schema_ext11: Names) -> None: |
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362 # Both hinted - error |
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363 with pytest.raises(cwltool.errors.UnsupportedRequirement): |
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364 lc, rc, tool = mk_tool(schema_ext11, [], hints=[mpiReq, containerReq]) |
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365 clt = CommandLineTool(tool, lc) |
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366 jr = clt.make_job_runner(rc) |