source: tests/Calculations/testsuite-calculations-jobmarket-1_2-dimethylbenzene.at@ 854a1e

Action_Thermostats Add_AtomRandomPerturbation Add_RotateAroundBondAction Add_SelectAtomByNameAction Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph_documentation Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_ChronosMutex Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion GeometryObjects Gui_displays_atomic_force_velocity IndependentFragmentGrids_IntegrationTest JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PartialCharges_OrthogonalSummation PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks RotateToPrincipalAxisSystem_UndoRedo StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps Ubuntu_1604_changes stable
Last change on this file since 854a1e was fbf005, checked in by Frederik Heber <heber@…>, 8 years ago

HUGE: Extracted libmolecuilder_mpqc that is now linked to poolworker.

  • This stops the problems with MemDebug and mpqc when linking against libLinearAlgebra in debug mode: static global variables in libLinAlg are allocated using MemDebug (prefixed with a checksum) but are deallocated using normal libc's free() on exit. This causes an invalid free() as the ptr given to free points inside the block and not at its start. The problem comes from mpqc's use of own new and delete implementation. I'm guessing its reference counting is the culprit. Hence, we need to separate these two compilations from another in different units/libraries. Therefore, we have split off libmolecuilder_mpqc, .._mpqc_extract and additionally place the MPQCJob::Work() implementation inside libMolecuilderJobs_Work.
  • libmolecuilder_mpqc contains all MPQC's code in mpqc.cc (and linked libraries) that is not the main() function.
  • libmolecuilder_mpqc_extract contains functions that extract results such as energies, forces, charge grids from the obtained mpqc solution. These were added by myself to the mpqc code before.
  • molecuilder_mpqc is then linked against a NoOp .._extract library version. Thereby, it does not use any of the Molecuilder or related libraries and does not come in contact with MemDebug.
  • molecuilder_poolworker however is linked with the full .._extract library and hence performs these extractions.
  • poolworker now executes MPQCJob, MPQCCommandJob, and VMGJob and therefore needs to enforce binding to all of them.
  • TESTS: renamed molecuilder_mpqc.in to molecuilder_poolworker.in.
  • Property mode set to 100644
File size: 3.4 KB
Line 
1#
2# MoleCuilder - creates and alters molecular systems
3# Copyright (C) 2014 Frederik Heber
4#
5# This program is free software: you can redistribute it and/or modify
6# it under the terms of the GNU General Public License as published by
7# the Free Software Foundation, either version 3 of the License, or
8# (at your option) any later version.
9#
10# This program is distributed in the hope that it will be useful,
11# but WITHOUT ANY WARRANTY; without even the implied warranty of
12# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13# GNU General Public License for more details.
14#
15# You should have received a copy of the GNU General Public License
16# along with this program. If not, see <http://www.gnu.org/licenses/>.
17#
18### 1_2-dimethylbenzene
19
20AT_SETUP([Calculations - 1_2-dimethylbenzene])
21AT_KEYWORDS([Calculations 1_2-dimethylbenzene xyz])
22
23# check that ports are unique over all tests such that they may run in parallel
24WORKERPORT=3010
25CONTROLLERPORT=3011
26WORKERLISTENPORT=3012
27
28# start service in background
29${AUTOTEST_PATH}/molecuilder_server --workerport $WORKERPORT --controllerport $CONTROLLERPORT &
30server_pid=$!
31AT_CHECK([sleep 2], 0, [ignore], [ignore], [kill $server_pid])
32AT_CHECK([kill -s 0 $server_pid], 0, [ignore], [ignore], [kill $server_pid])
33
34# enlist a worker to work on jobs
35../../molecuilder_poolworker -v 5 --server 127.0.0.1:${WORKERPORT} --hostname 127.0.0.1 --listen $WORKERLISTENPORT &
36worker_pid=$!
37AT_CHECK([sleep 2], 0, [ignore], [ignore], [kill $worker_pid $server_pid])
38AT_CHECK([kill -s 0 $worker_pid], 0, [ignore], [ignore], [kill $worker_pid $server_pid])
39
40MOL=1_2-dimethylbenzene
41DISTANCE="2."
42FILENAME="BondFragment"
43ENERGY="-307.7013126"
44
45file=${MOL}.xyz
46AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/Fragmentations/Fragmenting/${MOL}/pre/$file $file], 0)
47AT_CHECK([chmod u+w $file], 0)
48
49AT_CHECK([../../molecuilder \
50 -i $file \
51 --subgraph-dissection \
52 --select-molecule-by-id 0 \
53 --select-molecules-atoms \
54 --fragment-molecule $FILENAME \
55 --order 3 \
56 --distance $DISTANCE \
57 --fragment-automation --server-address 127.0.0.1 --server-port $CONTROLLERPORT --DoLongrange 0 \
58 --analyse-fragment-results \
59 --fragment-prefix $FILENAME],
60 0, [stdout], [stderr], [kill $worker_pid $server_pid])
61AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat | awk '{print $2}' >energy_stdout], 0, [stdout], [stderr], [kill $worker_pid $server_pid])
62
63# send removeall to server such that all workers shutdown
64AT_CHECK([${AUTOTEST_PATH}/molecuilder_controller --server 127.0.0.1:$CONTROLLERPORT --command removeall], 0, [ignore], [ignore], [kill $worker_pid $server_pid])
65
66# shutdown controller socket
67AT_CHECK([sleep 1], 0, [ignore], [ignore], [kill $worker_pid $server_pid])
68AT_CHECK([${AUTOTEST_PATH}/molecuilder_controller --server 127.0.0.1:$CONTROLLERPORT --command shutdown], 0, [stdout], [ignore], [kill $worker_pid $server_pid])
69
70# check that worker is truly down
71AT_CHECK([sleep 1], 0, [ignore], [ignore], [kill $worker_pid $server_pid])
72AT_CHECK([kill $worker_pid], 1, [ignore], [ignore], [kill $server_pid])
73
74# check that server is truly down
75AT_CHECK([sleep 1], 0, [ignore], [ignore], [kill $server_pid])
76AT_CHECK([kill $server_pid], 1, [ignore], [ignore])
77
78# check calculated energy
79AT_CHECK([cat energy_stdout | awk -v energy=$ENERGY 'function abs(x){return ((x < 0.0) ? -x : x)} {if (abs(($1 - energy)/energy) > 1e-5) exit(1)}'], 0, [stdout], [stderr])
80
81AT_CLEANUP
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