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added slurm unit test for Langevin solver
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@jcschaff
jcschaff committed Aug 22, 2024
1 parent ddd6f41 commit 4c12990
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17 changes: 17 additions & 0 deletions vcell-server/src/test/java/cbit/vcell/message/server/htc/slurm/SlurmProxyTest.java
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Expand Up @@ -207,6 +207,23 @@ public void testSimJobScriptCVODE() throws IOException, XmlParseException, Expre
Assertions.assertEquals(expectedSlurmScript.trim(), slurmScript.trim());
}

@Test
public void testSimJobScriptLangevin() throws IOException, XmlParseException, ExpressionException {
String simTaskResourcePath = "slurm_fixtures/langevin/SimID_274672135_0__0.simtask.xml";
String JOB_NAME = "V_REL_274672135_0_0";

String executable = "/usr/local/app/localsolvers/linux64/langevin_x64";
String outputLog = "/share/apps/vcell3/users/schaff/SimID_274672135_0_.log";
String messagingConfig = "/share/apps/vcell3/users/schaff/SimID_274672135_0_.langevinMessagingConfig";
String inputFilePath = "/share/apps/vcell3/users/schaff/SimID_274672135_0_.langevinInput";
String[] command = new String[] { executable, "simulate", "--output-log="+outputLog,
"--vc-send-status-config="+messagingConfig, inputFilePath, "0", "-tid", "0" };

String slurmScript = createScriptForNativeSolvers(simTaskResourcePath, command, JOB_NAME);
String expectedSlurmScript = readTextFileFromResource("slurm_fixtures/langevin/V_REL_274672135_0_0.slurm.sub");
Assertions.assertEquals(expectedSlurmScript.trim(), slurmScript.trim());
}

@Test
public void testSimJobScriptNFsim() throws IOException, XmlParseException, ExpressionException {
String simTaskResourcePath = "slurm_fixtures/nfsim/SimID_274642453_0__0.simtask.xml";
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206 changes: 206 additions & 0 deletions vcell-server/src/test/resources/slurm_fixtures/langevin/SimID_274672135_0__0.simtask.xml
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@@ -0,0 +1,206 @@
<SimulationTask xmlns="http://sourceforge.net/projects/vcell/vcml" TaskId="0" JobIndex="0" isPowerUser="false">
<MathDescription Name="Application1_generated">
<LangevinParticleMolecularType Name="MT0">
<Component Name="Site0" Radius="1.0" DiffusionRate="1.0" Location="Intracellular" SiteCoordX="0.0" SiteCoordY="0.0" SiteCoordZ="0.0" NamedColor="RED">
<AllowableState Name="state0" />
</Component>
</LangevinParticleMolecularType>
<LangevinParticleMolecularType Name="MT1">
<Component Name="Site0" Radius="1.0" DiffusionRate="1.0" Location="Intracellular" SiteCoordX="0.0" SiteCoordY="0.0" SiteCoordZ="0.0" NamedColor="RED">
<AllowableState Name="state0" />
</Component>
</LangevinParticleMolecularType>
<Constant Name="_F_">96485.3321</Constant>
<Constant Name="_F_nmol_">9.64853321E-5</Constant>
<Constant Name="_N_pmol_">6.02214179E11</Constant>
<Constant Name="_PI_">3.141592653589793</Constant>
<Constant Name="_R_">8314.46261815</Constant>
<Constant Name="_T_">300.0</Constant>
<Constant Name="Kf">1.0</Constant>
<Constant Name="KMOLE">0.001660538783162726</Constant>
<Constant Name="Kr">0.0</Constant>
<Constant Name="s0_Count_init_uM">0.0</Constant>
<Constant Name="s1_Count_init_uM">0.0</Constant>
<Constant Name="Size_Extracellular">1.0499999999999999E-4</Constant>
<Constant Name="Size_Intracellular">8.949999999999999E-4</Constant>
<Constant Name="Size_Membrane">0.009999999999999827</Constant>
<Constant Name="UnitFactor_molecules_uM_neg_1_um_neg_3">(1.0 * pow(KMOLE, - 1.0))</Constant>
<Constant Name="UnitFactor_uM_um3_molecules_neg_1">(1.0 * pow(KMOLE,1.0))</Constant>
<Constant Name="Voltage_Membrane">0.0</Constant>
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern0" Domain="Intracellular">
<MolecularType Name="MT0" MatchLabel="*">
<Component Name="Site0" State="*" Bond="?" />
</MolecularType>
</VolumeParticleSpeciesPattern>
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern1" Domain="Intracellular">
<MolecularType Name="MT1" MatchLabel="*">
<Component Name="Site0" State="*" Bond="?" />
</MolecularType>
</VolumeParticleSpeciesPattern>
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern2" Domain="Intracellular">
<MolecularType Name="MT0" MatchLabel="*">
<Component Name="Site0" State="*" Bond="-" />
</MolecularType>
</VolumeParticleSpeciesPattern>
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern3" Domain="Intracellular">
<MolecularType Name="MT1" MatchLabel="*">
<Component Name="Site0" State="*" Bond="-" />
</MolecularType>
</VolumeParticleSpeciesPattern>
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern4" Domain="Intracellular">
<MolecularType Name="MT0" MatchLabel="*">
<Component Name="Site0" State="*" Bond="1" />
</MolecularType>
<MolecularType Name="MT1" MatchLabel="*">
<Component Name="Site0" State="*" Bond="1" />
</MolecularType>
</VolumeParticleSpeciesPattern>
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern5" Domain="Intracellular">
<MolecularType Name="MT0" MatchLabel="*">
<Component Name="Site0" State="state0" Bond="-" />
</MolecularType>
</VolumeParticleSpeciesPattern>
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern6" Domain="Intracellular">
<MolecularType Name="MT1" MatchLabel="*">
<Component Name="Site0" State="state0" Bond="-" />
</MolecularType>
</VolumeParticleSpeciesPattern>
<VolumeParticleObservable Name="O0_MT0_tot_Count" Domain="Intracellular" MolecularType="Molecules" SequenceType="Multimolecular">
<VolumeParticleSpeciesPatterns>
<VolumeParticleSpeciesPattern Name="speciesPattern0" />
</VolumeParticleSpeciesPatterns>
</VolumeParticleObservable>
<VolumeParticleObservable Name="O0_MT1_tot_Count" Domain="Intracellular" MolecularType="Molecules" SequenceType="Multimolecular">
<VolumeParticleSpeciesPatterns>
<VolumeParticleSpeciesPattern Name="speciesPattern1" />
</VolumeParticleSpeciesPatterns>
</VolumeParticleObservable>
<VolumeParticleObservable Name="s0_Count" Domain="Intracellular" MolecularType="Species" SequenceType="Multimolecular">
<VolumeParticleSpeciesPatterns>
<VolumeParticleSpeciesPattern Name="speciesPattern5" />
</VolumeParticleSpeciesPatterns>
</VolumeParticleObservable>
<VolumeParticleObservable Name="s1_Count" Domain="Intracellular" MolecularType="Species" SequenceType="Multimolecular">
<VolumeParticleSpeciesPatterns>
<VolumeParticleSpeciesPattern Name="speciesPattern6" />
</VolumeParticleSpeciesPatterns>
</VolumeParticleObservable>
<Function Name="O0_MT0_tot" Domain="Intracellular">((O0_MT0_tot_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
<Function Name="O0_MT1_tot" Domain="Intracellular">((O0_MT1_tot_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
<Function Name="P_r0_probabilityRate" Domain="Intracellular">Kf</Function>
<Function Name="P_r0_reverse_probabilityRate" Domain="Intracellular">Kr</Function>
<Function Name="s0" Domain="Intracellular">((UnitFactor_uM_um3_molecules_neg_1 * s0_Count) / Size_Intracellular)</Function>
<Function Name="s0_Count_initCount" Domain="Intracellular">(Size_Intracellular * UnitFactor_molecules_uM_neg_1_um_neg_3 * s0_Count_init_uM)</Function>
<Function Name="s1" Domain="Intracellular">((UnitFactor_uM_um3_molecules_neg_1 * s1_Count) / Size_Intracellular)</Function>
<Function Name="s1_Count_initCount" Domain="Intracellular">(Size_Intracellular * UnitFactor_molecules_uM_neg_1_um_neg_3 * s1_Count_init_uM)</Function>
<CompartmentSubDomain Name="Intracellular">
<BoundaryType Boundary="Xm" Type="Flux" />
<BoundaryType Boundary="Xp" Type="Flux" />
<BoundaryType Boundary="Ym" Type="Flux" />
<BoundaryType Boundary="Yp" Type="Flux" />
<BoundaryType Boundary="Zm" Type="Flux" />
<BoundaryType Boundary="Zp" Type="Flux" />
<LangevinParticleJumpProcess Name="r0" Subtype="Binding" BondLength="1.0" ProcessSymmetryFactor="1.0">
<SelectedParticle Name="speciesPattern2" />
<SelectedParticle Name="speciesPattern3" />
<MacroscopicRateConstant>P_r0_probabilityRate</MacroscopicRateConstant>
<Effect VarName="speciesPattern2" Operation="destroy" />
<Effect VarName="speciesPattern3" Operation="destroy" />
<Effect VarName="speciesPattern4" Operation="create" />
</LangevinParticleJumpProcess>
<LangevinParticleJumpProcess Name="r0_reverse" Subtype="Binding" BondLength="1.0" ProcessSymmetryFactor="1.0">
<SelectedParticle Name="speciesPattern4" />
<MacroscopicRateConstant>P_r0_reverse_probabilityRate</MacroscopicRateConstant>
<Effect VarName="speciesPattern2" Operation="create" />
<Effect VarName="speciesPattern3" Operation="create" />
<Effect VarName="speciesPattern4" Operation="destroy" />
</LangevinParticleJumpProcess>
<ParticleProperties Name="speciesPattern5">
<ParticleInitialCount>
<ParticleCount>s0_Count_initCount</ParticleCount>
<ParticleLocationX>0.0</ParticleLocationX>
<ParticleLocationY>0.0</ParticleLocationY>
<ParticleLocationZ>0.0</ParticleLocationZ>
</ParticleInitialCount>
<ParticleDiffusion>0.0</ParticleDiffusion>
<ParticleDriftX>0.0</ParticleDriftX>
<ParticleDriftY>0.0</ParticleDriftY>
<ParticleDriftZ>0.0</ParticleDriftZ>
</ParticleProperties>
<ParticleProperties Name="speciesPattern6">
<ParticleInitialCount>
<ParticleCount>s1_Count_initCount</ParticleCount>
<ParticleLocationX>0.0</ParticleLocationX>
<ParticleLocationY>0.0</ParticleLocationY>
<ParticleLocationZ>0.0</ParticleLocationZ>
</ParticleInitialCount>
<ParticleDiffusion>0.0</ParticleDiffusion>
<ParticleDriftX>0.0</ParticleDriftX>
<ParticleDriftY>0.0</ParticleDriftY>
<ParticleDriftZ>0.0</ParticleDriftZ>
</ParticleProperties>
</CompartmentSubDomain>
<CompartmentSubDomain Name="Extracellular">
<BoundaryType Boundary="Xm" Type="Flux" />
<BoundaryType Boundary="Xp" Type="Flux" />
<BoundaryType Boundary="Ym" Type="Flux" />
<BoundaryType Boundary="Yp" Type="Flux" />
<BoundaryType Boundary="Zm" Type="Flux" />
<BoundaryType Boundary="Zp" Type="Flux" />
</CompartmentSubDomain>
<MembraneSubDomain Name="Extracellular_Intracellular_membrane" InsideCompartment="Extracellular" OutsideCompartment="Intracellular">
<BoundaryType Boundary="Xm" Type="Value" />
<BoundaryType Boundary="Xp" Type="Value" />
<BoundaryType Boundary="Ym" Type="Value" />
<BoundaryType Boundary="Yp" Type="Value" />
<BoundaryType Boundary="Zm" Type="Value" />
<BoundaryType Boundary="Zp" Type="Value" />
</MembraneSubDomain>
<Version Name="Application1_generated" KeyValue="274672103" BranchId="264499072" Archived="0" Date="22-Aug-2024 13:46:20" FromVersionable="false">
<Owner Name="schaff" Identifier="17" />
<GroupAccess Type="1" />
</Version>
</MathDescription>
<Simulation Name="Copy of Simulation3">
<SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Langevin">
<TimeBound StartTime="0.0" EndTime="1.0" />
<TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0" />
<ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
<OutputOptions OutputTimeStep="0.05" />
<LangevinSimulationOptions>
<NumOfTrials>1</NumOfTrials>
<IntervalSpring>1.0E-9</IntervalSpring>
<IntervalImage>1.0E-4</IntervalImage>
</LangevinSimulationOptions>
<NumberProcessors>1</NumberProcessors>
</SolverTaskDescription>
<MathOverrides />
<MeshSpecification>
<Size X="51" Y="51" Z="51" />
</MeshSpecification>
<Version Name="Copy of Simulation3" KeyValue="274672135" BranchId="274672136" Archived="0" Date="22-Aug-2024 13:46:20" FromVersionable="false">
<Owner Name="schaff" Identifier="17" />
<GroupAccess Type="1" />
</Version>
</Simulation>
<Geometry Name="Geometry1240938551" Dimension="3">
<Extent X="0.1" Y="0.1" Z="0.1" />
<Origin X="0.0" Y="0.0" Z="0.0" />
<SubVolume Name="Intracellular" Handle="1" Type="Analytical" KeyValue="267873106">
<AnalyticExpression>(z &lt; 0.09)</AnalyticExpression>
</SubVolume>
<SubVolume Name="Extracellular" Handle="0" Type="Analytical" KeyValue="267873107">
<AnalyticExpression>1.0</AnalyticExpression>
</SubVolume>
<SurfaceClass Name="Extracellular_Intracellular_membrane" SubVolume1Ref="Extracellular" SubVolume2Ref="Intracellular" KeyValue="267873108" />
<SurfaceDescription NumSamplesX="101" NumSamplesY="101" NumSamplesZ="101" CutoffFrequency="0.3">
<VolumeRegion Name="Intracellular0" RegionID="0" SubVolume="Intracellular" Size="8.949999999999999E-4" Unit="um3" />
<VolumeRegion Name="Extracellular1" RegionID="1" SubVolume="Extracellular" Size="1.0499999999999999E-4" Unit="um3" />
<MembraneRegion Name="membrane_Intracellular0_Extracellular1" VolumeRegion1="Extracellular1" VolumeRegion2="Intracellular0" Size="0.009999999999999827" Unit="um2" />
</SurfaceDescription>
<Version Name="Geometry1240938551" KeyValue="267873103" BranchId="264499055" Archived="0" Date="07-Feb-2024 14:47:29" FromVersionable="false">
<Owner Name="schaff" Identifier="17" />
<GroupAccess Type="1" />
</Version>
</Geometry>
</SimulationTask>
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