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IDProjectCategoryView StatusDate SubmittedLast Update
0004255OpenFOAMBugpublic2025-07-10 08:202025-07-15 17:50
Reporterotaolafr Assigned Towill  
PriorityhighSeveritymajorReproducibilityalways
Status resolvedResolutionfixed 
PlatformGNU/LinuxOSOtherOS Version(please specify)
Product Version12 
Fixed in Version13 
Summary0004255: foamRun crashing when first time run in new terminal, when run it again runs correctly
DescriptionHello,
It took me some time to find out the culprid of this strange behavior. I have recently moved to fondation version, and with it migrated my scripts Allrun scripts.
I am sourcing only the v12 no ESI or extend version in my bashrc.
when I open a *new* terminal window (so OFv12 is loaded as it is in the bashrc the sourcing) in the case folder, and I run my ./Allrun script which uses the following function and commands:
```
#!/bin/bash
cd "${0%/*}" || exit # Run from this directory
. ${WM_PROJECT_DIR:?}/bin/tools/RunFunctions # Tutorial run functions
runApp() {
    # Example usage:
    # runApp $nbProcs "myApp" "-flag1" "-flag2" "-flag3" ... "-flagN"
    local nbProc="$1"
    local application="$2"
    shift 2 # Shift to remove the first two arguments (application and nbProc)
    
    # Join the remaining arguments as flags
    local flagsOptional=("$@")

    # Build the command
    local command="$application ${flagsOptional[*]}"

    message="- Running $application"
    if [[ -n "$flagsOptional" ]]; then
        message="$message ${flagsOptional[*]}"
    fi
    if (( nbProc > 1 )); then
        message="$message in parallel"
    else
        message="$message in serial"
    fi
    # echo ' '"$message"
    if (( nbProc > 1 )); then
        command="mpirun -np $nbProc $command -parallel"
    fi
    # Execute the command and handle errors
    { rm -f "log.$application" && eval "$command" > "log.$application" 2>&1; } || { echo "!!!!!!!!Error in $application!!!!!!!!"; exit 1; }
}
nProcs=44
rm -fr processor*
echo "using decomposePar"
runApp 1 "decomposePar" "-copyZero"
echo "using setFields"
runApp $nProcs "setFields"
echo "using topoSet"
runApp $nProcs "topoSet"
echo "using $(getApplication)"
runApp $nProcs "$(getApplication)"

```
the decomposePar, setFields and topoSet work properly (the logs shows that the tool was run correctly. on the contrary the log of foamRun when I run it i get the following error:
```

Starting time loop

[calcul2-Precision-7960-Tower:2220822] *** An error occurred in MPI_Recv
[calcul2-Precision-7960-Tower:2220822] *** reported by process [21299201,4]
[calcul2-Precision-7960-Tower:2220822] *** on communicator MPI COMMUNICATOR 3 SPLIT FROM 0
[calcul2-Precision-7960-Tower:2220822] *** MPI_ERR_TRUNCATE: message truncated
[calcul2-Precision-7960-Tower:2220822] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[calcul2-Precision-7960-Tower:2220822] *** and potentially your MPI job)
[calcul2-Precision-7960-Tower:2220811] 5 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal
[calcul2-Precision-7960-Tower:2220811] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

```
if in that same terminal, i run again ./Allrun without changing anything. then the foamRun runs as expected and the simulation begings without issues.
Steps To Reproduceopen a new terminal
cd $casePath
./Allrun #->foamRun will crash but other applications (such as topoSet) work
./Allrun #->foamRun and other applications (such as topoSet) work
TagsNo tags attached.

Activities

otaolafr

2025-07-10 08:37

reporter   ~0013597

if in the script before `rm -fr processor*` I add `foamRun > /dev/null 2>&1` so simply a dummy command that will crash. then the second one `runApp $nProcs "$(getApplication)"` will run correctly.

otaolafr

2025-07-10 08:54

reporter   ~0013598

tested in two different pcs in the two it gives me the same issue when running the first time. this only happens when i run it in parallel, in serial even first time it still runs correctly.

otaolafr

2025-07-10 08:57

reporter   ~0013599

for the version of the operating system it is ubuntu 24.04.02LTS also might be helpful, `mpirun --version` prompts `mpirun (Open MPI) 4.1.6`

otaolafr

2025-07-10 09:09

reporter   ~0013600

lastly, another thing that is super strange is that if I add `echo "$(mpirun --version)"` before and after the first dummy `foamRun > /dev/null 2>&1` , the second foamRun in parallel, that when the foamRun dummy was added was running, now it does not run anymore. and goes back to the error cited.

otaolafr

2025-07-11 13:09

reporter   ~0013603

for more info,
```
which foamRun
/opt/openfoam13/platforms/linux64GccDPInt32Opt/bin/foamRun
ldd `which foamRun`
linux-vdso.so.1 (0x00007fef09899000)
libfiniteVolume.so => /opt/openfoam13/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so (0x00007fef07800000)
libOpenFOAM.so => /opt/openfoam13/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so (0x00007fef06c00000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fef06800000)
libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007fef06b17000)
libgcc_s.so.1 => /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fef0985a000)
libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007fef06400000)
libtriSurface.so => /opt/openfoam13/platforms/linux64GccDPInt32Opt/lib/libtriSurface.so (0x00007fef06764000)
libmeshTools.so => /opt/openfoam13/platforms/linux64GccDPInt32Opt/lib/libmeshTools.so (0x00007fef05e00000)
libPstream.so => /opt/openfoam13/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so (0x00007fef0984a000)
libz.so.1 => /usr/lib/x86_64-linux-gnu/libz.so.1 (0x00007fef077e4000)
/lib64/ld-linux-x86-64.so.2 (0x00007fef0989b000)
libfileFormats.so => /opt/openfoam13/platforms/linux64GccDPInt32Opt/lib/libfileFormats.so (0x00007fef077b4000)
libsurfMesh.so => /opt/openfoam13/platforms/linux64GccDPInt32Opt/lib/libsurfMesh.so (0x00007fef0665f000)
libmpi.so.40 => /usr/lib/x86_64-linux-gnu/libmpi.so.40 (0x00007fef05cce000)
libopen-rte.so.40 => /usr/lib/x86_64-linux-gnu/libopen-rte.so.40 (0x00007fef05c12000)
libopen-pal.so.40 => /usr/lib/x86_64-linux-gnu/libopen-pal.so.40 (0x00007fef05b5e000)
libhwloc.so.15 => /usr/lib/x86_64-linux-gnu/libhwloc.so.15 (0x00007fef06ab6000)
libevent_core-2.1.so.7 => /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7 (0x00007fef06a81000)
libevent_pthreads-2.1.so.7 => /usr/lib/x86_64-linux-gnu/libevent_pthreads-2.1.so.7 (0x00007fef09841000)
libudev.so.1 => /usr/lib/x86_64-linux-gnu/libudev.so.1 (0x00007fef0662c000)
libcap.so.2 => /usr/lib/x86_64-linux-gnu/libcap.so.2 (0x00007fef077a7000)

which mpirun
/usr/bin/mpirun
ldd `which mpirun`
  linux-vdso.so.1 (0x00007fa4a6c6f000)
    libopen-rte.so.40 => /usr/lib/x86_64-linux-gnu/libopen-rte.so.40 (0x00007fa4a6ba8000)
    libopen-pal.so.40 => /usr/lib/x86_64-linux-gnu/libopen-pal.so.40 (0x00007fa4a6af4000)
    libevent_core-2.1.so.7 => /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7 (0x00007fa4a6abf000)
    libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007fa4a6800000)
    libz.so.1 => /usr/lib/x86_64-linux-gnu/libz.so.1 (0x00007fa4a6aa1000)
    libhwloc.so.15 => /usr/lib/x86_64-linux-gnu/libhwloc.so.15 (0x00007fa4a6a40000)
    libevent_pthreads-2.1.so.7 => /usr/lib/x86_64-linux-gnu/libevent_pthreads-2.1.so.7 (0x00007fa4a6a3b000)
    /lib64/ld-linux-x86-64.so.2 (0x00007fa4a6c71000)
    libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007fa4a6717000)
    libudev.so.1 => /usr/lib/x86_64-linux-gnu/libudev.so.1 (0x00007fa4a66e4000)
    libcap.so.2 => /usr/lib/x86_64-linux-gnu/libcap.so.2 (0x00007fa4a6a2c000)
```
I can reproduce this behavior each time.

wyldckat

2025-07-11 13:46

updater   ~0013604

@otaolafr: The issue seems to be mostly due to something in Open-MPI and not OpenFOAM. And very likely related to the hardware you are using.
If this issue didn't use to happen with other versions/variants of OpenFOAM, then it might have used different Open-MPI versions as well and not with Open-MPI 4.1.6.

I don't remember by heart what can be done to diagnose Open-MPI, so I suggest you try the Open-MPI "Getting Help" page: https://docs.open-mpi.org/en/main/getting-help.html

Either way, it's not clear how to reproduce the errors you're reporting. Everything seems specific to your case and not to one or more tutorial cases in OpenFOAM.

otaolafr

2025-07-11 13:57

reporter   ~0013605

Hello,
sorry for the lack of information, I am pretty confident that it is not hardware issue as I tested in two different pcs with clear different cpus:
 11th Gen Intel(R) Core(TM) i7-11850H @ 2.50GHz
Intel(R) Xeon(R) w9-3495X
so quite different the two (i will test at home and report as i have a AMD pc also). maybe is in the linux version? here is the output of etc/os-release
```
PRETTY_NAME="Ubuntu 24.04.2 LTS"
NAME="Ubuntu"
VERSION_ID="24.04"
VERSION="24.04.2 LTS (Noble Numbat)"
VERSION_CODENAME=noble
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=noble
LOGO=ubuntu-logo
```
the thing is this ONLY happens with foamRun and in version 13, before it was not happening. for other applications, such as topoSet, setFields etc, i am not facing this issue even in version 13.

wyldckat

2025-07-11 14:16

updater   ~0013606

Can you reproduce the same issue with OpenFOAM's own tutorial cases?
If yes, then please indicate which tutorial cases, how you ran them and the error messages you get with them.

otaolafr

2025-07-11 15:20

reporter   ~0013607

hello @wyldckat
so i tried to reproduce the problem with a tutorial, and when i did not succed, i began the past hour and a half to test <what was wrong> with the case (as this did not gave any problem in previous versions) (and belive me when i say it was quite hard to find.)
my simulation has a function file with 3 function objects (i copy paste at the end of the note) the last 2 of them are type coded; when I have the two function, and run foamRun in parallel in a new terminal (in V13) it crashes with the mpi error but if I automaticly run it after again, it will run without issues, where in v12 runs from 'first time'. if I have 1 commented one of them (whichever of the two coded ones) then when i run foamRun in parallel in a new terminal (in V13) it DOES NOT crash.
here are the functions:
```
/*--------------------------------*- C++ -*----------------------------------*\
  ========= |
  \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
   \\ / O peration | Website: https://openfoam.org
    \\ / A nd | Version: 12
     \\/ M anipulation |
\*---------------------------------------------------------------------------*/
FoamFile
{
    format ascii;
    class dictionary;
    location "system";
    object functions;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //


#includeFunc fieldAverage(U.gas, U.liquid, alpha.gas, p)


updateO2liquid
{
    type coded;
    libs ("libutilityFunctionObjects.so"); // already included in OpenFOAM
    name updateO2liquid;
    
    codeExecute
    #{

        // const volScalarField& alphagas = mesh().lookupObject<volScalarField>("alpha.gas"); //[-]
        const volScalarField& rholiquid = mesh().lookupObject<volScalarField>("rho.liquid"); //[kgT/m3]
        const scalar factor = 1 ; // [-]
        const scalar OURMax = 1.2345e-3; // OURMax-> 50 [g/L] chlorella
        const scalar Yo2Ref = 1.3E-07 ; // [-]

        volScalarField& Yo2 = const_cast<volScalarField&>(mesh().lookupObject<volScalarField>("O2.liquid")); //[kgO2/kgT]
        volScalarField& YH2O = const_cast<volScalarField&>(mesh().lookupObject<volScalarField>("H2O.liquid")); //[kgO2/kgT]

        scalar dt = mesh().time().deltaTValue();



        forAll(Yo2, i)
        {
            scalar OUR = factor*OURMax * Yo2[i]/max(Yo2Ref+Yo2[i],SMALL); // [kgO2/(m3*s)]
            scalar denom = rholiquid[i]; // [kgT/m3]
            scalar deltaYo2 = dt * OUR / max(denom, 1e-6); // [kgO2/kgT] == [s]* [kgO2/(m3*s)] / [kgT/m3]
            Yo2[i] = max(0.0, min(Yo2[i] - deltaYo2, 1.0)); // [kgO2/kgT] == [s]*[kgO2/(m3*s)] / [kgT/m3]
        }
        Yo2.correctBoundaryConditions();

        forAll(YH2O, i)
        {
            YH2O[i] = 1-Yo2[i];
        }
        YH2O.correctBoundaryConditions();

    #};
    
}


alphaSpecie
{
    type coded;
    libs ("libutilityFunctionObjects.so");

    // Name of on-the-fly generated functionObject
    name alphaSpecie;
    writeControl writeTime;
    codeInclude
    #{
        #include "fvcGrad.H"
        #include "volFields.H"
        #include "symmTensorField.H"
    #};

    codeWrite
    #{
        const volScalarField& alphagas = mesh().lookupObject<volScalarField>("alpha.gas");
        const volScalarField& alphaliquid = mesh().lookupObject<volScalarField>("alpha.liquid");
        const volScalarField& O2gas = mesh().lookupObject<volScalarField>("O2.gas");
        const volScalarField& N2gas = mesh().lookupObject<volScalarField>("N2.gas");
        const volScalarField& H2Ogas = mesh().lookupObject<volScalarField>("H2O.gas");
        const volScalarField& O2liquid = mesh().lookupObject<volScalarField>("O2.liquid");
        const volScalarField& N2liquid = mesh().lookupObject<volScalarField>("N2.liquid");
        const volScalarField& H2Oliquid = mesh().lookupObject<volScalarField>("H2O.liquid");
        const volScalarField& rholiquid = mesh().lookupObject<volScalarField>("rho.liquid"); //[kgT/m3]
        const volScalarField& rhogas = mesh().lookupObject<volScalarField>("rho.gas"); //[kgT/m3]

        volScalarField
        (
            IOobject
            (
                "alphagas*O2gas",
                mesh().time().name(),
                mesh()
            ),
            alphagas*O2gas
        ).write();
        volScalarField
        (
            IOobject
            (
                "alphagas*N2gas",
                mesh().time().name(),
                mesh()
            ),
            alphagas*N2gas
        ).write();
        volScalarField
        (
            IOobject
            (
                "alphagas*H2Ogas",
                mesh().time().name(),
                mesh()
            ),
            alphagas*H2Ogas
        ).write();
        volScalarField
        (
            IOobject
            (
                "alphaliquid*O2liquid",
                mesh().time().name(),
                mesh()
            ),
            alphaliquid*O2liquid
        ).write();
        volScalarField
        (
            IOobject
            (
                "alphaliquid*N2liquid",
                mesh().time().name(),
                mesh()
            ),
            alphaliquid*N2liquid
        ).write();
        volScalarField
        (
            IOobject
            (
                "alphaliquid*H2Oliquid",
                mesh().time().name(),
                mesh()
            ),
            alphaliquid*H2Oliquid
        ).write();
        rholiquid().write();
        rhogas().write();
    #};
}

                        // ************************************************************************* //
                        
```
so there IS something that changed in behavior in V13 that brings a problem.

wyldckat

2025-07-11 15:33

updater   ~0013608

It's not clear what the issue is, but from what your describing, the actual issue has been pointed out by foamRun several times already... but whatever it pointed out, it wasn't looked at.
The _complete_ output from foamRun when it fails to run, is what should be describing the actual issue.

otaolafr

2025-07-11 15:40

reporter   ~0013609

sorry, and what would that be? the dynamicCode folder? you can find each folder created inside dynamicCode in the tars here:
platforms.tar.gz (1,337,420 bytes)
alphaSpecie.tar.gz (819,829 bytes)
updateO2liquid.tar.gz (836,274 bytes)

wyldckat

2025-07-11 15:51

updater   ~0013610

foamRun outputs information to the screen (unless it's redirected into a log file, maybe "log.foamRun"?).
Based on what you've shared, I don't know what appears above the line "Starting time loop".
Therefore, the complete output from foamRun is what is needed, including error messages.

otaolafr

2025-07-11 16:12

reporter   ~0013611

Hello here you can find the complete log. hope it helps
log.foamRun (8,414 bytes)    
Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     | Website:  https://openfoam.org
    \\  /    A nd           | Version:  13
     \\/     M anipulation  |
\*---------------------------------------------------------------------------*/
Build  : 13-65eda17ad4ca
Exec   : foamRun -parallel
Date   : Jul 11 2025
Time   : 16:38:47
Host   : "franco-work"
PID    : 2770839
I/O    : uncollated
Case   : /home/franco/Downloads/bubbleColumn2kV13
nProcs : 8
Slaves : 
7
(
"franco-work.2770840"
"franco-work.2770841"
"franco-work.2770842"
"franco-work.2770843"
"franco-work.2770844"
"franco-work.2770845"
"franco-work.2770846"
)

Pstream initialised with:
    floatTransfer      : false
    nProcsSimpleSum    : 0
    commsType          : nonBlocking
    polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Selecting solver multiphaseEuler
No MRF models present

Selecting phaseModel for gas: multicomponentIsothermalPhaseModel
Selecting diameterModel for phase gas: velocityGroup
Selecting thermodynamics package 
{
    type            heRhoThermo;
    mixture         multicomponentMixture;
    transport       const;
    thermo          eConst;
    equationOfState perfectGas;
    specie          specie;
    energy          sensibleInternalEnergy;
}

Calculating face flux field phi.gas
Selecting turbulence model type laminar
    Selecting laminar stress model Stokes
Selecting thermophysical transport type laminar
Selecting default laminar thermophysical transport model unityLewisFourier
Selecting phaseModel for liquid: multicomponentIsothermalPhaseModel
Selecting diameterModel for phase liquid: constant
Selecting thermodynamics package 
{
    type            heRhoThermo;
    mixture         multicomponentMixture;
    transport       const;
    thermo          eConst;
    equationOfState rPolynomial;
    specie          specie;
    energy          sensibleInternalEnergy;
}

Calculating face flux field phi.liquid
Selecting turbulence model type laminar
    Selecting laminar stress model Stokes
Selecting thermophysical transport type laminar
Selecting default laminar thermophysical transport model unityLewisFourier
Selecting surfaceTensionCoefficientModel for gas_liquid: constant
Selecting dragModel blending method for gas_liquid: linear
Selecting dragModel for gas_dispersedIn_liquid: TomiyamaCorrelatedOrlando
Selecting dragModel for liquid_dispersedIn_gas: SchillerNaumann
Selecting virtualMassModel blending method for gas_liquid: linear
Selecting virtualMassModel for gas_dispersedIn_liquid: constantCoefficient
Selecting virtualMassModel for liquid_dispersedIn_gas: constantCoefficient
Selecting SidedInterfacialModel<heatTransferModel> blending method for gas_liquid: linear
Selecting heatTransferModel for gas_dispersedIn_liquid_inThe_gas: RanzMarshall
Selecting heatTransferModel for gas_dispersedIn_liquid_inThe_liquid: RanzMarshall
Selecting heatTransferModel for liquid_dispersedIn_gas_inThe_gas: RanzMarshall
Selecting heatTransferModel for liquid_dispersedIn_gas_inThe_liquid: RanzMarshall
Setting up population balance: bubbles
Selecting coalescence model for bubbles: Luo
Selecting binary breakup model for bubbles: powerLawUniformBinary
Courant Number mean: 6.01596e-07 max: 0.00692706
Creating fvModels from "constant/fvModels"

Selecting finite volume model type massDiffusionLimitedPhaseChange
    Name: phaseChange
Selecting interfaceCompositionModel for gas_liquid_inThe_gas: saturated
Selecting saturationPressureModel ArdenBuck
Selecting interfaceCompositionModel for gas_liquid_inThe_liquid: Henry
Selecting SidedInterfacialModel<diffusiveMassTransferModel> blending method for gas_liquid: linear
Selecting diffusiveMassTransferModel for gas_dispersedIn_liquid_inThe_gas: spherical
Selecting diffusiveMassTransferModel for gas_dispersedIn_liquid_inThe_liquid: Frossling
Selecting diffusiveMassTransferModel for liquid_dispersedIn_gas_inThe_gas: Frossling
Selecting diffusiveMassTransferModel for liquid_dispersedIn_gas_inThe_liquid: spherical
Selecting finite volume model type porosityForce
    Name: filter1
Porosity region filter1:
    selecting model: DarcyForchheimer
    creating porous zone: filter
Creating fvConstraints from "system/fvConstraints"

Selecting finite volume constraint type limitPressure
    Name: limitp
    min 10000


PIMPLE: No convergence criteria found


PIMPLE: No corrector convergence criteria found
        Calculations will do 3 corrections


PIMPLE: Operating solver in transient mode with 3 outer correctors


Using dynamicCode for coded updateO2liquid at line 21 in "/home/franco/Downloads/bubbleColumn2kV13/system/functions/updateO2liquid"
Creating new library in "dynamicCode/updateO2liquid/platforms/linux64GccDPInt32Opt/lib/libupdateO2liquid_c17dcb57373e4b2172a83a2f7ecc9882db24442e.so"
"/opt/openfoam13/etc/codeTemplates/dynamicCode/codedFunctionObjectTemplate.C" "/home/franco/Downloads/bubbleColumn2kV13/dynamicCode/updateO2liquid/codedFunctionObjectTemplate.C"
"/opt/openfoam13/etc/codeTemplates/dynamicCode/codedFunctionObjectTemplate.H" "/home/franco/Downloads/bubbleColumn2kV13/dynamicCode/updateO2liquid/codedFunctionObjectTemplate.H"
Invoking "wmake -s libso /home/franco/Downloads/bubbleColumn2kV13/dynamicCode/updateO2liquid"
wmake libso /home/franco/Downloads/bubbleColumn2kV13/dynamicCode/updateO2liquid
    ln: ./lnInclude
    wmkdep: codedFunctionObjectTemplate.C
    Ctoo: codedFunctionObjectTemplate.C
    ld: /home/franco/Downloads/bubbleColumn2kV13/dynamicCode/updateO2liquid/../platforms/linux64GccDPInt32Opt/lib/libupdateO2liquid_c17dcb57373e4b2172a83a2f7ecc9882db24442e.so
Using dynamicCode for coded alphaSpecie at line 63 in "/home/franco/Downloads/bubbleColumn2kV13/system/functions/alphaSpecie"
Creating new library in "dynamicCode/alphaSpecie/platforms/linux64GccDPInt32Opt/lib/libalphaSpecie_be4922a4fbb586e4fbf5878a3cca29e3c7f0506e.so"
"/opt/openfoam13/etc/codeTemplates/dynamicCode/codedFunctionObjectTemplate.C" "/home/franco/Downloads/bubbleColumn2kV13/dynamicCode/alphaSpecie/codedFunctionObjectTemplate.C"
"/opt/openfoam13/etc/codeTemplates/dynamicCode/codedFunctionObjectTemplate.H" "/home/franco/Downloads/bubbleColumn2kV13/dynamicCode/alphaSpecie/codedFunctionObjectTemplate.H"
Invoking "wmake -s libso /home/franco/Downloads/bubbleColumn2kV13/dynamicCode/alphaSpecie"
wmake libso /home/franco/Downloads/bubbleColumn2kV13/dynamicCode/alphaSpecie
    ln: ./lnInclude
    wmkdep: codedFunctionObjectTemplate.C
    Ctoo: codedFunctionObjectTemplate.C
    ld: /home/franco/Downloads/bubbleColumn2kV13/dynamicCode/alphaSpecie/../platforms/linux64GccDPInt32Opt/lib/libalphaSpecie_be4922a4fbb586e4fbf5878a3cca29e3c7f0506e.so

Starting time loop

[franco-work:2770840] *** An error occurred in MPI_Recv
[franco-work:2770840] *** reported by process [3799580673,1]
[franco-work:2770840] *** on communicator MPI COMMUNICATOR 3 SPLIT FROM 0
[franco-work:2770840] *** MPI_ERR_TRUNCATE: message truncated
[franco-work:2770840] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[franco-work:2770840] ***    and potentially your MPI job)
[franco-work:2770825] 2 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal
[franco-work:2770825] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
log.foamRun (8,414 bytes)   

wyldckat

2025-07-11 16:22

updater   ~0013612

The messages right at the top of the log file:

   Authorization required, but no authorization protocol specified

This should not happen. It might not be the reason why this is failing, but it is very suspicious that this might be what is leading to the crash.

will

2025-07-11 16:45

manager   ~0013613

Last edited: 2025-07-11 16:45

 The log.foamRun isn't as helpful as it might be as there is no stack trace from the error. Could you try sourcing the OpenFOAM bashrc like this:

. /opt/openfoam13/etc/bashrc FOAM_SIGFPE=1 FOAM_SETNAN=1 FOAM_VERBOSE=1 FOAM_ABORT=1

And then try running again and upload the log.foamRun again.

otaolafr

2025-07-15 07:58

reporter   ~0013617

Hello will, sorry for the late replay, i was away from my pc, with the new sourcing, i am getting this ouput at the begining and i am attaching the two logs of foamRun, same behavior as before first time does not run, second it does.
```
export FOAM_ABORT=1
Sourcing: /opt/openfoam13/etc/config.sh/settings
Sourcing: /opt/openfoam13/etc/config.sh/compiler
Sourcing: /opt/openfoam13/etc/config.sh/aliases
Sourcing: /opt/openfoam13/etc/config.sh/mpi
Sourcing: /opt/openfoam13/etc/config.sh/paraview
Using paraview
    ParaView_DIR : /usr
    ParaView_LIB_DIR : /usr/bin/../lib/x86_64-linux-gnu
    ParaView_INCLUDE_DIR : /usr/include/paraview-5.11
    PV_PLUGIN_PATH : /opt/openfoam13/platforms/linux64GccDPInt32Opt/lib/paraview-5.11
Sourcing: /opt/openfoam13/etc/config.sh/ensight
Sourcing: /opt/openfoam13/etc/config.sh/gperftools
```
hope it helps.
log.foamRun_firstTime (8,443 bytes)    
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Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     | Website:  https://openfoam.org
    \\  /    A nd           | Version:  13
     \\/     M anipulation  |
\*---------------------------------------------------------------------------*/
Build  : 13-65eda17ad4ca
Exec   : foamRun -parallel
Date   : Jul 15 2025
Time   : 08:55:43
Host   : "franco-work"
PID    : 10538
I/O    : uncollated
Case   : /home/franco/Downloads/bubbleColumn2kV13
nProcs : 8
Slaves : 
7
(
"franco-work.10540"
"franco-work.10545"
"franco-work.10546"
"franco-work.10547"
"franco-work.10548"
"franco-work.10549"
"franco-work.10550"
)

Pstream initialised with:
    floatTransfer      : false
    nProcsSimpleSum    : 0
    commsType          : nonBlocking
    polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
SetNaN : Initialising allocated memory to NaN (FOAM_SETNAN).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Selecting solver multiphaseEuler
No MRF models present

Selecting phaseModel for gas: multicomponentIsothermalPhaseModel
Selecting diameterModel for phase gas: velocityGroup
Selecting thermodynamics package 
{
    type            heRhoThermo;
    mixture         multicomponentMixture;
    transport       const;
    thermo          eConst;
    equationOfState perfectGas;
    specie          specie;
    energy          sensibleInternalEnergy;
}

Calculating face flux field phi.gas
Selecting turbulence model type laminar
    Selecting laminar stress model Stokes
Selecting thermophysical transport type laminar
Selecting default laminar thermophysical transport model unityLewisFourier
Selecting phaseModel for liquid: multicomponentIsothermalPhaseModel
Selecting diameterModel for phase liquid: constant
Selecting thermodynamics package 
{
    type            heRhoThermo;
    mixture         multicomponentMixture;
    transport       const;
    thermo          eConst;
    equationOfState rPolynomial;
    specie          specie;
    energy          sensibleInternalEnergy;
}

Calculating face flux field phi.liquid
Selecting turbulence model type laminar
    Selecting laminar stress model Stokes
Selecting thermophysical transport type laminar
Selecting default laminar thermophysical transport model unityLewisFourier
Selecting surfaceTensionCoefficientModel for gas_liquid: constant
Selecting dragModel blending method for gas_liquid: linear
Selecting dragModel for gas_dispersedIn_liquid: TomiyamaCorrelatedOrlando
Selecting dragModel for liquid_dispersedIn_gas: SchillerNaumann
Selecting virtualMassModel blending method for gas_liquid: linear
Selecting virtualMassModel for gas_dispersedIn_liquid: constantCoefficient
Selecting virtualMassModel for liquid_dispersedIn_gas: constantCoefficient
Selecting SidedInterfacialModel<heatTransferModel> blending method for gas_liquid: linear
Selecting heatTransferModel for gas_dispersedIn_liquid_inThe_gas: RanzMarshall
Selecting heatTransferModel for gas_dispersedIn_liquid_inThe_liquid: RanzMarshall
Selecting heatTransferModel for liquid_dispersedIn_gas_inThe_gas: RanzMarshall
Selecting heatTransferModel for liquid_dispersedIn_gas_inThe_liquid: RanzMarshall
Setting up population balance: bubbles
Selecting coalescence model for bubbles: Luo
Selecting binary breakup model for bubbles: powerLawUniformBinary
Courant Number mean: 6.01596e-07 max: 0.00692706
Creating fvModels from "constant/fvModels"

Selecting finite volume model type massDiffusionLimitedPhaseChange
    Name: phaseChange
Selecting interfaceCompositionModel for gas_liquid_inThe_gas: saturated
Selecting saturationPressureModel ArdenBuck
Selecting interfaceCompositionModel for gas_liquid_inThe_liquid: Henry
Selecting SidedInterfacialModel<diffusiveMassTransferModel> blending method for gas_liquid: linear
Selecting diffusiveMassTransferModel for gas_dispersedIn_liquid_inThe_gas: spherical
Selecting diffusiveMassTransferModel for gas_dispersedIn_liquid_inThe_liquid: Frossling
Selecting diffusiveMassTransferModel for liquid_dispersedIn_gas_inThe_gas: Frossling
Selecting diffusiveMassTransferModel for liquid_dispersedIn_gas_inThe_liquid: spherical
Selecting finite volume model type porosityForce
    Name: filter1
Porosity region filter1:
    selecting model: DarcyForchheimer
    creating porous zone: filter
Creating fvConstraints from "system/fvConstraints"

Selecting finite volume constraint type limitPressure
    Name: limitp
    min 10000


PIMPLE: No convergence criteria found


PIMPLE: No corrector convergence criteria found
        Calculations will do 3 corrections


PIMPLE: Operating solver in transient mode with 3 outer correctors


Using dynamicCode for coded updateO2liquid at line 21 in "/home/franco/Downloads/bubbleColumn2kV13/system/functions/updateO2liquid"
Creating new library in "dynamicCode/updateO2liquid/platforms/linux64GccDPInt32Opt/lib/libupdateO2liquid_c17dcb57373e4b2172a83a2f7ecc9882db24442e.so"
"/opt/openfoam13/etc/codeTemplates/dynamicCode/codedFunctionObjectTemplate.C" "/home/franco/Downloads/bubbleColumn2kV13/dynamicCode/updateO2liquid/codedFunctionObjectTemplate.C"
"/opt/openfoam13/etc/codeTemplates/dynamicCode/codedFunctionObjectTemplate.H" "/home/franco/Downloads/bubbleColumn2kV13/dynamicCode/updateO2liquid/codedFunctionObjectTemplate.H"
Invoking "wmake -s libso /home/franco/Downloads/bubbleColumn2kV13/dynamicCode/updateO2liquid"
wmake libso /home/franco/Downloads/bubbleColumn2kV13/dynamicCode/updateO2liquid
    ln: ./lnInclude
    wmkdep: codedFunctionObjectTemplate.C
    Ctoo: codedFunctionObjectTemplate.C
    ld: /home/franco/Downloads/bubbleColumn2kV13/dynamicCode/updateO2liquid/../platforms/linux64GccDPInt32Opt/lib/libupdateO2liquid_c17dcb57373e4b2172a83a2f7ecc9882db24442e.so
Using dynamicCode for coded alphaSpecie at line 63 in "/home/franco/Downloads/bubbleColumn2kV13/system/functions/alphaSpecie"
Creating new library in "dynamicCode/alphaSpecie/platforms/linux64GccDPInt32Opt/lib/libalphaSpecie_be4922a4fbb586e4fbf5878a3cca29e3c7f0506e.so"
"/opt/openfoam13/etc/codeTemplates/dynamicCode/codedFunctionObjectTemplate.C" "/home/franco/Downloads/bubbleColumn2kV13/dynamicCode/alphaSpecie/codedFunctionObjectTemplate.C"
"/opt/openfoam13/etc/codeTemplates/dynamicCode/codedFunctionObjectTemplate.H" "/home/franco/Downloads/bubbleColumn2kV13/dynamicCode/alphaSpecie/codedFunctionObjectTemplate.H"
Invoking "wmake -s libso /home/franco/Downloads/bubbleColumn2kV13/dynamicCode/alphaSpecie"
wmake libso /home/franco/Downloads/bubbleColumn2kV13/dynamicCode/alphaSpecie
    ln: ./lnInclude
    wmkdep: codedFunctionObjectTemplate.C
    Ctoo: codedFunctionObjectTemplate.C
    ld: /home/franco/Downloads/bubbleColumn2kV13/dynamicCode/alphaSpecie/../platforms/linux64GccDPInt32Opt/lib/libalphaSpecie_be4922a4fbb586e4fbf5878a3cca29e3c7f0506e.so

Starting time loop

[franco-work:10540] *** An error occurred in MPI_Recv
[franco-work:10540] *** reported by process [2361786369,1]
[franco-work:10540] *** on communicator MPI COMMUNICATOR 3 SPLIT FROM 0
[franco-work:10540] *** MPI_ERR_TRUNCATE: message truncated
[franco-work:10540] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[franco-work:10540] ***    and potentially your MPI job)
[franco-work:10524] 2 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal
[franco-work:10524] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
log.foamRun_firstTime (8,443 bytes)   
log.foamRun_secondTime (13,639 bytes)    
Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     | Website:  https://openfoam.org
    \\  /    A nd           | Version:  13
     \\/     M anipulation  |
\*---------------------------------------------------------------------------*/
Build  : 13-65eda17ad4ca
Exec   : foamRun -parallel
Date   : Jul 15 2025
Time   : 08:56:52
Host   : "franco-work"
PID    : 11420
I/O    : uncollated
Case   : /home/franco/Downloads/bubbleColumn2kV13
nProcs : 8
Slaves : 
7
(
"franco-work.11421"
"franco-work.11422"
"franco-work.11423"
"franco-work.11424"
"franco-work.11425"
"franco-work.11426"
"franco-work.11427"
)

Pstream initialised with:
    floatTransfer      : false
    nProcsSimpleSum    : 0
    commsType          : nonBlocking
    polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
SetNaN : Initialising allocated memory to NaN (FOAM_SETNAN).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Selecting solver multiphaseEuler
No MRF models present

Selecting phaseModel for gas: multicomponentIsothermalPhaseModel
Selecting diameterModel for phase gas: velocityGroup
Selecting thermodynamics package 
{
    type            heRhoThermo;
    mixture         multicomponentMixture;
    transport       const;
    thermo          eConst;
    equationOfState perfectGas;
    specie          specie;
    energy          sensibleInternalEnergy;
}

Calculating face flux field phi.gas
Selecting turbulence model type laminar
    Selecting laminar stress model Stokes
Selecting thermophysical transport type laminar
Selecting default laminar thermophysical transport model unityLewisFourier
Selecting phaseModel for liquid: multicomponentIsothermalPhaseModel
Selecting diameterModel for phase liquid: constant
Selecting thermodynamics package 
{
    type            heRhoThermo;
    mixture         multicomponentMixture;
    transport       const;
    thermo          eConst;
    equationOfState rPolynomial;
    specie          specie;
    energy          sensibleInternalEnergy;
}

Calculating face flux field phi.liquid
Selecting turbulence model type laminar
    Selecting laminar stress model Stokes
Selecting thermophysical transport type laminar
Selecting default laminar thermophysical transport model unityLewisFourier
Selecting surfaceTensionCoefficientModel for gas_liquid: constant
Selecting dragModel blending method for gas_liquid: linear
Selecting dragModel for gas_dispersedIn_liquid: TomiyamaCorrelatedOrlando
Selecting dragModel for liquid_dispersedIn_gas: SchillerNaumann
Selecting virtualMassModel blending method for gas_liquid: linear
Selecting virtualMassModel for gas_dispersedIn_liquid: constantCoefficient
Selecting virtualMassModel for liquid_dispersedIn_gas: constantCoefficient
Selecting SidedInterfacialModel<heatTransferModel> blending method for gas_liquid: linear
Selecting heatTransferModel for gas_dispersedIn_liquid_inThe_gas: RanzMarshall
Selecting heatTransferModel for gas_dispersedIn_liquid_inThe_liquid: RanzMarshall
Selecting heatTransferModel for liquid_dispersedIn_gas_inThe_gas: RanzMarshall
Selecting heatTransferModel for liquid_dispersedIn_gas_inThe_liquid: RanzMarshall
Setting up population balance: bubbles
Selecting coalescence model for bubbles: Luo
Selecting binary breakup model for bubbles: powerLawUniformBinary
Courant Number mean: 6.01596e-07 max: 0.00692706
Creating fvModels from "constant/fvModels"

Selecting finite volume model type massDiffusionLimitedPhaseChange
    Name: phaseChange
Selecting interfaceCompositionModel for gas_liquid_inThe_gas: saturated
Selecting saturationPressureModel ArdenBuck
Selecting interfaceCompositionModel for gas_liquid_inThe_liquid: Henry
Selecting SidedInterfacialModel<diffusiveMassTransferModel> blending method for gas_liquid: linear
Selecting diffusiveMassTransferModel for gas_dispersedIn_liquid_inThe_gas: spherical
Selecting diffusiveMassTransferModel for gas_dispersedIn_liquid_inThe_liquid: Frossling
Selecting diffusiveMassTransferModel for liquid_dispersedIn_gas_inThe_gas: Frossling
Selecting diffusiveMassTransferModel for liquid_dispersedIn_gas_inThe_liquid: spherical
Selecting finite volume model type porosityForce
    Name: filter1
Porosity region filter1:
    selecting model: DarcyForchheimer
    creating porous zone: filter
Creating fvConstraints from "system/fvConstraints"

Selecting finite volume constraint type limitPressure
    Name: limitp
    min 10000


PIMPLE: No convergence criteria found


PIMPLE: No corrector convergence criteria found
        Calculations will do 3 corrections


PIMPLE: Operating solver in transient mode with 3 outer correctors


Using dynamicCode for coded updateO2liquid at line 21 in "/home/franco/Downloads/bubbleColumn2kV13/system/functions/updateO2liquid"
Using dynamicCode for coded alphaSpecie at line 63 in "/home/franco/Downloads/bubbleColumn2kV13/system/functions/alphaSpecie"

Starting time loop

Courant Number mean: 6.01596e-07 max: 0.00692706
deltaT = 0.000239981
Time = 0.000239981s

PIMPLE: Iteration 1
massDiffusionLimitedPhaseChange: phaseChange
    min/mean/max Ts = 303/303/303
    min/mean/max mDot = 0/0/0
MULES: Solving for alpha.gas
MULES: Solving for alpha.liquid
MULES: Correcting alpha.gas
MULES: Correcting alpha.liquid
gas fraction, min, max = 0.147216 0 1
liquid fraction, min, max = 0.852784 0 1
Phase-sum volume fraction, min, max = 1 1 1
MULES: Solving for alpha.gas
MULES: Solving for alpha.liquid
MULES: Correcting alpha.gas
MULES: Correcting alpha.liquid
gas fraction, min, max = 0.147217 0 1
liquid fraction, min, max = 0.852783 0 1
Phase-sum volume fraction, min, max = 1 1 1
Constructing momentum equations
DILUPBiCGStab:  Solving for O2.gas, Initial residual = 1, Final residual = 1.16097e-14, No Iterations 1
DILUPBiCGStab:  Solving for H2O.gas, Initial residual = 0, Final residual = 0, No Iterations 0
DILUPBiCGStab:  Solving for O2.liquid, Initial residual = 0, Final residual = 0, No Iterations 0
DILUPBiCGStab:  Solving for N2.liquid, Initial residual = 0, Final residual = 0, No Iterations 0
GAMG:  Solving for p_rgh, Initial residual = 0.122152, Final residual = 7.91206e-09, No Iterations 35
GAMG:  Solving for p_rgh, Initial residual = 5.63566e-06, Final residual = 8.13023e-09, No Iterations 8
PIMPLE: Iteration 2
massDiffusionLimitedPhaseChange: phaseChange
    min/mean/max Ts = 298.992/303/303
    min/mean/max mDot = -3.63426/-0.000396911/0
MULES: Solving for alpha.gas
MULES: Solving for alpha.liquid
MULES: Correcting alpha.gas
MULES: Correcting alpha.liquid
gas fraction, min, max = 0.147216 0 1
liquid fraction, min, max = 0.852784 0 1
Phase-sum volume fraction, min, max = 1 1 1
MULES: Solving for alpha.gas
MULES: Solving for alpha.liquid
MULES: Correcting alpha.gas
MULES: Correcting alpha.liquid
gas fraction, min, max = 0.147217 -1.85872e-21 1
liquid fraction, min, max = 0.852783 0 1
Phase-sum volume fraction, min, max = 1 1 1
Constructing momentum equations
DILUPBiCGStab:  Solving for O2.gas, Initial residual = 0.0106276, Final residual = 7.48352e-13, No Iterations 1
DILUPBiCGStab:  Solving for H2O.gas, Initial residual = 1, Final residual = 6.77365e-15, No Iterations 2
DILUPBiCGStab:  Solving for O2.liquid, Initial residual = 1, Final residual = 3.86207e-13, No Iterations 2
DILUPBiCGStab:  Solving for N2.liquid, Initial residual = 0, Final residual = 0, No Iterations 0
GAMG:  Solving for p_rgh, Initial residual = 0.0194645, Final residual = 8.32797e-09, No Iterations 29
GAMG:  Solving for p_rgh, Initial residual = 1.56321e-06, Final residual = 5.90464e-09, No Iterations 5
PIMPLE: Iteration 3
massDiffusionLimitedPhaseChange: phaseChange
    min/mean/max Ts = 288.402/302.952/303
    min/mean/max mDot = -0.840112/-0.000108195/0
MULES: Solving for alpha.gas
MULES: Solving for alpha.liquid
MULES: Correcting alpha.gas
MULES: Correcting alpha.liquid
gas fraction, min, max = 0.147216 -2.41776e-21 1
liquid fraction, min, max = 0.852784 0 1
Phase-sum volume fraction, min, max = 1 1 1
MULES: Solving for alpha.gas
MULES: Solving for alpha.liquid
MULES: Correcting alpha.gas
MULES: Correcting alpha.liquid
gas fraction, min, max = 0.147216 -2.142e-17 1
liquid fraction, min, max = 0.852784 0 1
Phase-sum volume fraction, min, max = 1 1 1
populationBalance bubbles: Iteration 1
DILUPBiCGStab:  Solving for f0.gas, Initial residual = 1, Final residual = 1.03867e-07, No Iterations 1
DILUPBiCGStab:  Solving for f1.gas, Initial residual = 1, Final residual = 1.02729e-07, No Iterations 1
DILUPBiCGStab:  Solving for f2.gas, Initial residual = 1, Final residual = 9.67382e-08, No Iterations 1
DILUPBiCGStab:  Solving for f3.gas, Initial residual = 1, Final residual = 9.64042e-08, No Iterations 1
DILUPBiCGStab:  Solving for f4.gas, Initial residual = 1, Final residual = 9.24984e-08, No Iterations 1
DILUPBiCGStab:  Solving for f5.gas, Initial residual = 1, Final residual = 8.65749e-08, No Iterations 1
DILUPBiCGStab:  Solving for f6.gas, Initial residual = 1, Final residual = 8.6644e-08, No Iterations 1
DILUPBiCGStab:  Solving for f7.gas, Initial residual = 1, Final residual = 8.30426e-08, No Iterations 1
bubbles sizeGroup phase fraction first, last = 0.00202632 0.00195257
Scaling sizeGroups for velocityGroup gas
gas sizeGroups-sum volume fraction, min, max = 1 1 1
gas Sauter mean diameter, min, max = 0.00397376 0.0038808 0.00411469
Constructing momentum equations
DILUPBiCGStab:  Solving for O2.gas, Initial residual = 0.00355364, Final residual = 3.69437e-14, No Iterations 2
DILUPBiCGStab:  Solving for H2O.gas, Initial residual = 0.0030202, Final residual = 9.21234e-16, No Iterations 1
DILUPBiCGStab:  Solving for O2.liquid, Initial residual = 0.037639, Final residual = 2.59602e-13, No Iterations 2
DILUPBiCGStab:  Solving for N2.liquid, Initial residual = 0, Final residual = 0, No Iterations 0
GAMG:  Solving for p_rgh, Initial residual = 0.011965, Final residual = 7.79725e-09, No Iterations 22
GAMG:  Solving for p_rgh, Initial residual = 1.60755e-07, Final residual = 4.22874e-09, No Iterations 2
ExecutionTime = 36.0118 s  ClockTime = 37 s

Courant Number mean: 0.0308413 max: 2.10693
deltaT = 8.54204e-05
Time = 0.000325401s

PIMPLE: Iteration 1
massDiffusionLimitedPhaseChange: phaseChange
    min/mean/max Ts = 287.006/302.903/303
    min/mean/max mDot = -0.737385/-8.69935e-05/0
MULES: Solving for alpha.gas
MULES: Solving for alpha.liquid
MULES: Correcting alpha.gas
MULES: Correcting alpha.liquid
gas fraction, min, max = 0.147217 -2.3223e-22 1
liquid fraction, min, max = 0.852783 0 1
Phase-sum volume fraction, min, max = 1 1 1
MULES: Solving for alpha.gas
MULES: Solving for alpha.liquid
MULES: Correcting alpha.gas
MULES: Correcting alpha.liquid
gas fraction, min, max = 0.147217 -1.59173e-22 1
liquid fraction, min, max = 0.852783 0 1
Phase-sum volume fraction, min, max = 1 1 1
Constructing momentum equations
DILUPBiCGStab:  Solving for O2.gas, Initial residual = 0.000232988, Final residual = 1.42623e-14, No Iterations 1
DILUPBiCGStab:  Solving for H2O.gas, Initial residual = 0.000141745, Final residual = 2.79718e-15, No Iterations 1
DILUPBiCGStab:  Solving for O2.liquid, Initial residual = 0.0543119, Final residual = 8.55811e-14, No Iterations 2
DILUPBiCGStab:  Solving for N2.liquid, Initial residual = 0, Final residual = 0, No Iterations 0
GAMG:  Solving for p_rgh, Initial residual = 0.0206263, Final residual = 5.84343e-09, No Iterations 9
GAMG:  Solving for p_rgh, Initial residual = 7.58675e-07, Final residual = 8.16415e-09, No Iterations 3
PIMPLE: Iteration 2
massDiffusionLimitedPhaseChange: phaseChange
    min/mean/max Ts = 287.613/302.88/303
    min/mean/max mDot = -1.13394/-0.000132882/0
MULES: Solving for alpha.gas
MULES: Solving for alpha.liquid
MULES: Correcting alpha.gas
MULES: Correcting alpha.liquid
gas fraction, min, max = 0.147217 -2.341e-20 1
liquid fraction, min, max = 0.852783 0 1
Phase-sum volume fraction, min, max = 1 1 1
MULES: Solving for alpha.gas
MULES: Solving for alpha.liquid
MULES: Correcting alpha.gas
MULES: Correcting alpha.liquid
gas fraction, min, max = 0.147217 -1.09916e-21 1
liquid fraction, min, max = 0.852783 0 1
Phase-sum volume fraction, min, max = 1 1 1
Constructing momentum equations
DILUPBiCGStab:  Solving for O2.gas, Initial residual = 0.000123402, Final residual = 2.24357e-14, No Iterations 1
DILUPBiCGStab:  Solving for H2O.gas, Initial residual = 0.000394485, Final residual = 5.24147e-15, No Iterations 1
DILUPBiCGStab:  Solving for O2.liquid, Initial residual = 0.0196331, Final residual = 3.5455e-14, No Iterations 2
DILUPBiCGStab:  Solving for N2.liquid, Initial residual = 0, Final residual = 0, No Iterations 0
log.foamRun_secondTime (13,639 bytes)   

will

2025-07-15 12:01

manager   ~0013618

There's nothing more in that log that helps. You can try uploading the whole case to see if we can reproduce it. Failing that you'd need to get the coredump and/or run it in gdb to figure out where its failing.

cgoessni

2025-07-15 12:12

reporter   ~0013619

Since first time it doesn't work, second time it works, and the only difference is the compilation: It might be that your dynamic code library was written incompletely, so rank0 compiles, all other ranks use the library. If it is always like that (first, or compilation, run fails, all other runs work), try increasing e.g. fileModificationSkew.

otaolafr

2025-07-15 12:19

reporter   ~0013620

Hello will,
here you have the modified bubbleColumnEvaporatingDissolving tutorial, with really slight modifications for testing (moved to parallel run and changed the var names on the functions)

Hello cgoessnl,
could you give me a more insight in how to increase this fileModificationSkew? in any case you are right, when compiling, foamRun will crash (ie, first time) but the second time (as it can be seen in the log.foamRun_secondTime) it is already compiled and therefore it runs correctly.
bubbleColumnEvaporatingDissolvingTest.tar.gz (88,681 bytes)

cgoessni

2025-07-15 12:20

reporter   ~0013621

https://github.com/OpenFOAM/OpenFOAM-dev/blob/17ffc27f6f81eaaf937c328dfbc5f2a45dd52f42/etc/controlDict#L49

cgoessni

2025-07-15 12:25

reporter   ~0013622

Your case crashes here as well, and increasing fileModificationSkew didn't help here neither.

will

2025-07-15 12:55

manager   ~0013623

Yes, crashes for me too. It's something to do with the fact there are calls to `correctBoundaryConditions` within the execute of the `updateairliquid` function. These are doing communication and that's somehow not compatible with the communication performed by the initial build process.

otaolafr

2025-07-15 13:54

reporter   ~0013624

hello will,
not sure that it is the correctBoundaryConditions, as if you leave only that funciton it works in first try, furthermore if you put the writeCode section of the second function inside the first (ie., merge the two functions into one) it also compiles correctly.

will

2025-07-15 17:50

manager   ~0013628

Fixed in dev and v13 here:

https://github.com/OpenFOAM/OpenFOAM-dev/commit/362c3d3da4f0d72e158df73e19083835f5907b93
https://github.com/OpenFOAM/OpenFOAM-13/commit/8a1ca5e148f5948a88bb06a1de93a4412b57b19b

Issue History

Date Modified Username Field Change
2025-07-10 08:20 otaolafr New Issue
2025-07-10 08:37 otaolafr Note Added: 0013597
2025-07-10 08:54 otaolafr Note Added: 0013598
2025-07-10 08:57 otaolafr Note Added: 0013599
2025-07-10 09:09 otaolafr Note Added: 0013600
2025-07-11 13:09 otaolafr Note Added: 0013603
2025-07-11 13:46 wyldckat Note Added: 0013604
2025-07-11 13:57 otaolafr Note Added: 0013605
2025-07-11 14:16 wyldckat Note Added: 0013606
2025-07-11 15:20 otaolafr Note Added: 0013607
2025-07-11 15:33 wyldckat Note Added: 0013608
2025-07-11 15:40 otaolafr Note Added: 0013609
2025-07-11 15:40 otaolafr File Added: platforms.tar.gz
2025-07-11 15:40 otaolafr File Added: alphaSpecie.tar.gz
2025-07-11 15:40 otaolafr File Added: updateO2liquid.tar.gz
2025-07-11 15:51 wyldckat Note Added: 0013610
2025-07-11 16:12 otaolafr Note Added: 0013611
2025-07-11 16:12 otaolafr File Added: log.foamRun
2025-07-11 16:22 wyldckat Note Added: 0013612
2025-07-11 16:45 will Note Added: 0013613
2025-07-11 16:45 will Note Edited: 0013613
2025-07-15 07:58 otaolafr Note Added: 0013617
2025-07-15 07:58 otaolafr File Added: log.foamRun_firstTime
2025-07-15 07:58 otaolafr File Added: log.foamRun_secondTime
2025-07-15 12:01 will Note Added: 0013618
2025-07-15 12:12 cgoessni Note Added: 0013619
2025-07-15 12:19 otaolafr Note Added: 0013620
2025-07-15 12:19 otaolafr File Added: bubbleColumnEvaporatingDissolvingTest.tar.gz
2025-07-15 12:20 cgoessni Note Added: 0013621
2025-07-15 12:25 cgoessni Note Added: 0013622
2025-07-15 12:55 will Note Added: 0013623
2025-07-15 13:54 otaolafr Note Added: 0013624
2025-07-15 17:50 will Assigned To => will
2025-07-15 17:50 will Status new => resolved
2025-07-15 17:50 will Resolution open => fixed
2025-07-15 17:50 will Fixed in Version => 13
2025-07-15 17:50 will Note Added: 0013628