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Problem when running SOWFA coupled with OpenFAST #72

Closed wcha533 closed 3 years ago

wcha533 commented 3 years ago

Hi, I compiled OpenFAST using the recommended CMake options (-DBUILD_OPENFAST_CPP_API=ON, DFPE_TRAP_ENABLED=ON). I could compile pisoFoamTurbine.ALMAdvancedOpenFAST and windPlantSolver.ALMAdvancedOpenFAST. But when I run both solvers, I got error as shown below where the error was thrown out from openfastcpp.c that there is no turbine (while SOWFA echo turbine = 1).

Note that I could run the standalone OpenFAST for the NREL5MWRef.0.fst input file.

/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.4.0                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.4.0-dcea1e13ff76
Exec   : /nesi/project/uoa00003/wcha533/SOWFA/applications/bin/linux64GccDPOpt/pisoFoamTurbine.ALMAdvancedOpenFAST -parallel
Date   : Jul 17 2020
Time   : 15:25:59
Host   : "wbn112"
PID    : 186759
Case   : /scale_wlg_nobackup/filesets/nobackup/uoa00003/wcha533/SOWFA/exampleCases/example.NREL5MW.ALMAdvancedFAST8
nProcs : 2
Slaves : 1("wbn112.186760")
Pstream initialized with:
    floatTransfer      : 0
    nProcsSimpleSum    : 0
    commsType          : nonBlocking
    polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

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

Create mesh for time = 0

Reading field, p...
Reading field, U...
Creating vorticity field, omega...
Creating second-invariant of strain-rate tensor field, Q...
Reading/calculating face flux field phi

Selecting incompressible transport model Newtonian
Selecting turbulence model type LESModel
Selecting LES turbulence model oneEqEddy
Selecting LES delta type smooth
Selecting LES delta type cubeRootVol
bounding k, min: 0 max: 0 average: 0
oneEqEddyCoeffs
{
    ce              0.93;
    ck              0.0673;
}

[0] SOWFA nTurbinesGlob: 1
[0] nFASTSubSteps has to be the same for all turbines
[1] SOWFA nTurbinesGlob: 1
[1] nFASTSubSteps has to be the same for all turbines
terminate called after throwing an instance of 'std::runtime_error'
terminate called after throwing an instance of 'std::runtime_error'
  what():  Number of turbines < 0 
  what():  Number of turbines < 0 
srun: error: wbn112: tasks 0-1: Aborted (core dumped)

Thanks for your help WC

ewquon commented 3 years ago

Could you share your constant/turbineArrayProperties?

wcha533 commented 3 years ago

Hi @ewquon

Thank you for your response. Please find the "turbineArrayProperties" file in the attached file. I am using the one provided in the example case.

turbineArrayProperties.txt

Regards,

ewquon commented 3 years ago

How strange. It appears that you've compiled everything correctly and nothing appears out of order in your input file, which has a single turbine defined. Which version of the codes are you using? The current versions don't have the SOWFA nTurbinesGlob output--did you add this to the code?

If you share your inputs I can try to reproduce your error.

wcha533 commented 3 years ago

Hi @ewquon

Thank you very much for your help.

Yes, I added nTurbinesGlob in horizontalAxisWindTurbinesALMOpenFAST.C just to echo the number of turbines in SOWFA since I got an error Number of turbines < 0 from openfastcpp.C.

Please find my input files in the attached .zip file. It consists of setUp, NREL5MWRef.0.fst, controlDict, turbineArrayProperties, 0, preprocess0 and preprocess1 (I did decomposePar for only 2 partitions just for testing). These files are from example.NREL5MW.ALMAdvancedFAST8 and I just used OpenFAST input files instead of FAST8.

Thanks and regards

wcha533.zip

ewquon commented 3 years ago

@wcha533 Did you ever get this issue sorted out?

wcha533 commented 3 years ago

Hi @ewquon I managed to fix some environment modules on the HPC and that eliminates the Number of turbines < 0 problem. However, I still get an error when running the coupled code as shown below.

I successfully run SOWFA coupled with OpenFAST on my desktop machine (Ubuntu 16.04). And I used the same input files to run on the HPC (which shows the error).

I am not sure if OpenFOAM v2.4.x and v2.4.0 are sensitive to the coupled code or not since I installed v2.4.x on my Ubuntu. But on the HPC that I am working on has got OpenFOAM v2.4.0.

Thanks and regards

Running ServoDyn.
Running ServoDyn Interface for Bladed Controllers.
Using legacy Bladed DLL interface.
  Time: 0 of 60 seconds.
[0] #0  Foam::error::printStack(Foam::Ostream&) at ??:?
[0] #1  Foam::sigSegv::sigHandler(int) at ??:?
[0] #2  ? in "/lib64/libpthread.so.0"
[0] #3  Foam::operator<<(Foam::Ostream&, double) at ??:?
[0] #4  Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::printOutputFiles() at ??:?
[0] #5  Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::initialize() at ??:?
[0] #6  Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::horizontalAxisWindTurbinesALMOpenFAST(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) at ??:?
[0] #7  ? at ??:?
[0] #8  __libc_start_main in "/lib64/libc.so.6"
[0] #9  ? at ??:?
HYFOAM commented 3 years ago

@wcha533 Hello I successfully compiled SOWFA and OpenFAST on my desktop computer (Ubuntu 18.04). But when I run /SOWFA/exampleCases/example.NREL5MW.ALMAdvancedFAST8, the following error occurred. Do you have a good solution?

WARNING: Linux kernel CMA support was requested via the btl_vader_single_copy_mechanism MCA variable, but CMA support is not available due to restrictive ptrace settings.

The vader shared memory BTL will fall back on another single-copy mechanism if one is available. This may result in lower performance.

Local host: DESKTOP-MK9U2OS

/---------------------------------------------------------------------------\ | ========= | | | \ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \ / O peration | Version: 2.4.x | | \ / A nd | Web: www.OpenFOAM.org | | \/ M anipulation | | *---------------------------------------------------------------------------*/ Build : 2.4.x Exec : pisoFoamTurbine.ALMAdvancedOpenFAST -parallel Date : Nov 26 2020 Time : 02:13:30 Host : "DESKTOP-MK9U2OS" PID : 22988 Case : /home/luthuyuan1/SOWFA/exampleCases/example.NREL5MW.ALMAdvancedFAST8 nProcs : 4 Slaves : 3 ( "DESKTOP-MK9U2OS.22989" "DESKTOP-MK9U2OS.22990" "DESKTOP-MK9U2OS.22991" )

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

// * // Create time

Create mesh for time = 0

Reading field, p... Reading field, U... Creating vorticity field, omega... Creating second-invariant of strain-rate tensor field, Q... Reading/calculating face flux field phi

Selecting incompressible transport model Newtonian Selecting turbulence model type LESModel Selecting LES turbulence model oneEqEddy Selecting LES delta type smooth Selecting LES delta type cubeRootVol bounding k, min: 0 max: 0 average: 0 oneEqEddyCoeffs { ce 0.93; ck 0.0673; }

[0] nFASTSubSteps has to be the same for all turbines [1] nFASTSubSteps has to be the same for all turbines [2] nFASTSubSteps has to be the same for all turbines [3] nFASTSubSteps has to be the same for all turbines

OpenFAST

Copyright (C) 2020 National Renewable Energy Laboratory Copyright (C) 2020 Envision Energy USA LTD

This program is licensed under Apache License Version 2.0 and comes with ABSOLUTELY NO WARRANTY. See the "LICENSE" file distributed with this software for details.

OpenFAST-HEAD-HASH-NOTFOUND Compile Info:

[0] #0 Foam::error::printStack(Foam::Ostream&) at ??:? [0] #1 Foam::sigSegv::sigHandler(int) at ??:? [0] #2 ? in "/lib/x86_64-linux-gnu/libpthread.so.0" [0] #3 FAST_OpFM_Init[DESKTOP-MK9U2OS:22983] 3 more processes have sent help message help-btl-vader.txt / cma-permission-denied [DESKTOP-MK9U2OS:22983] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages at ??:? [0] #4 fast::OpenFAST::init() at ??:? [0] #5 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::initialize() at ??:? [0] #6 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::horizontalAxisWindTurbinesALMOpenFAST(Foam::GeometricField<Foam::Vector, Foam::fvPatchField, Foam::volMesh> const&) at ??:? [0] #7 ? in "/home/luthuyuan1/OpenFOAM/luthuyuan1-2.4.x/platforms/linux64GccDPOpt/bin/pisoFoamTurbine.ALMAdvancedOpenFAST" [0] #8 libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" [0] #9 ? in "/home/luthuyuan1/OpenFOAM/luthuyuan1-2.4.x/platforms/linux64GccDPOpt/bin/pisoFoamTurbine.ALMAdvancedOpenFAST" [DESKTOP-MK9U2OS:22988] Process received signal [DESKTOP-MK9U2OS:22988] Signal: Segmentation fault (11) [DESKTOP-MK9U2OS:22988] Signal code: (-6) [DESKTOP-MK9U2OS:22988] Failing at address: 0x3e8000059cc [DESKTOP-MK9U2OS:22988] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12980)[0x7f11f88d2980] [DESKTOP-MK9U2OS:22988] [ 1] /lib/x86_64-linux-gnu/libpthread.so.0(raise+0xc7)[0x7f11f88d2817] [DESKTOP-MK9U2OS:22988] [ 2] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12980)[0x7f11f88d2980] [DESKTOP-MK9U2OS:22988] [ 3] /usr/lib/x86_64-linux-gnu/libopenfastlib.so(FAST_OpFM_Init+0x61c)[0x7f11fc3f309c] [DESKTOP-MK9U2OS:22988] [ 4] /usr/lib/x86_64-linux-gnu/libopenfastcpplib.so(_ZN4fast8OpenFAST4initEv+0xbb6)[0x7f11fc7ce486] [DESKTOP-MK9U2OS:22988] [ 5] /home/luthuyuan1/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFAST10initializeEv+0x41)[0x7f1201c091e1] [DESKTOP-MK9U2OS:22988] [ 6] /home/luthuyuan1/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFASTC1ERKNS_14GeometricFieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshEEE+0x1eb1)[0x7f1201c0b3e1] [DESKTOP-MK9U2OS:22988] [ 7] pisoFoamTurbine.ALMAdvancedOpenFAST(+0x2c5e2)[0x7f120302c5e2] [DESKTOP-MK9U2OS:22988] [ 8] /lib/x86_64-linux-gnu/libc.so.6(libc_start_main+0xe7)[0x7f11f84e1bf7] [DESKTOP-MK9U2OS:22988] [ 9] pisoFoamTurbine.ALMAdvancedOpenFAST(+0x32b1a)[0x7f1203032b1a] [DESKTOP-MK9U2OS:22988] End of error message

mpirun noticed that process rank 0 with PID 0 on node DESKTOP-MK9U2OS exited on signal 11 (Segmentation fault).

wcha533 commented 3 years ago

Hi @HYFOAM You may check the setting in the AeroDyn and ElastoDyn input files.

HYFOAM commented 3 years ago

Hi @wcha533 This is my AeroDyn and ElastoDyn input files, and I did not find any errors. I uploaded it in the attachment, can you see it for me? In AeroDyn15.dat, I have deleted lines 26 and 27 according to the method given by others, but this still doesn't work.

AeroDyn and ElastoDyn input files.zip

wcha533 commented 3 years ago

@HYFOAM Are these input files from example.NREL5MW5W.ALMAdvancedFAST8 in SOWFA github? If they are, I suggest you to get all input files from OpenFAST reg_tests. I understand that those input files that you are using are for FAST8 solver.

HYFOAM commented 3 years ago

@wcha533 These input files are indeed from example.NREL5MW5W.ALMAdvancedFAST8 in SOWFA github. Do you mean you need to replace SOWFA\exampleCases\example.NREL5MW.ALMAdvancedFAST8\5MW_Baseline with OpenFAST\reg_tests\r-test\glue-codes\openfast\5MW_Baseline? Can I copy it directly?

wcha533 commented 3 years ago

@HYFOAM Yes, you can copy them directly. Just make sure you point the path to the input files of each solver module in the .fst file correctly. And check that the discon.dll in ServoDyn is compiled properly.

HYFOAM commented 3 years ago

@wcha533 Ok thank you, I will try it. Consult you if you have any questions! thank you very much!!

HYFOAM commented 3 years ago

@wcha533 Hello, I have successfully run example.NREL5MW.ALMAdvancedFAST8 in SOWFA on ubuntu16.04. But when I run in the same way in the server centos, the following error appears. Running the openfast calculation alone is successful, but errors will occur when the two are run together.

libi40iw-i40iw_ucreate_qp: failed to create QP, unsupported QP type: 0x4

Failed to create a queue pair (QP):

Hostname: admin Requested max number of outstanding WRs in the SQ: 1 Requested max number of outstanding WRs in the RQ: 2 Requested max number of SGEs in a WR in the SQ: 511 Requested max number of SGEs in a WR in the RQ: 511 Requested max number of data that can be posted inline to the SQ: 0 Error: Success

Check requested attributes.

Open MPI has detected that there are UD-capable Verbs devices on your system, but none of them were able to be setup properly. This may indicate a problem on this system.

You job will continue, but Open MPI will ignore the "ud" oob component in this run.

Hostname: admin

libi40iw-i40iw_ucreate_qp: failed to create QP, unsupported QP type: 0x4 libi40iw-i40iw_ucreate_qp: failed to create QP, unsupported QP type: 0x4 libi40iw-i40iw_ucreate_qp: failed to create QP, unsupported QP type: 0x4 libi40iw-i40iw_ucreate_qp: failed to create QP, unsupported QP type: 0x4

WARNING: No preset parameters were found for the device that Open MPI detected:

Local host: admin Device name: i40iw1 Device vendor ID: 0x8086 Device vendor part ID: 14289

Default device parameters will be used, which may result in lower performance. You can edit any of the files specified by the btl_openib_device_param_files MCA parameter to set values for your device.

NOTE: You can turn off this warning by setting the MCA parameter btl_openib_warn_no_device_params_found to 0.

No OpenFabrics connection schemes reported that they were able to be used on a specific port. As such, the openib BTL (OpenFabrics support) will be disabled for this port.

Local host: admin Local device: i40iw1 Local port: 1 CPCs attempted: rdmacm, udcm

/---------------------------------------------------------------------------\ | ========= | | | \ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \ / O peration | Version: 2.4.x | | \ / A nd | Web: www.OpenFOAM.org | | \/ M anipulation | | *---------------------------------------------------------------------------*/ Build : 2.4.x Exec : pisoFoamTurbine.ALMAdvancedOpenFAST -parallel Date : Dec 10 2020 Time : 22:23:54 Host : "admin" PID : 211151 Case : /public/home/LUTLiDSh/SOWFA/exampleCases/example.NREL5MW.ALMAdvancedFAST8 nProcs : 4 Slaves : 3 ( "admin.211152" "admin.211153" "admin.211154" )

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

// * // Create time

Create mesh for time = 0

Reading field, p... Reading field, U... Creating vorticity field, omega... Creating second-invariant of strain-rate tensor field, Q... Reading/calculating face flux field phi

Selecting incompressible transport model Newtonian Selecting turbulence model type LESModel Selecting LES turbulence model oneEqEddy Selecting LES delta type smooth Selecting LES delta type cubeRootVol bounding k, min: 0 max: 0 average: 0 oneEqEddyCoeffs { ce 0.93; ck 0.0673; }

[1] nFASTSubSteps has to be the same for all turbines [0] nFASTSubSteps has to be the same for all turbines [2] nFASTSubSteps has to be the same for all turbines [3] nFASTSubSteps has to be the same for all turbines [1] #0 Foam::error::printStack(Foam::Ostream&)[2] #0 Foam::error::printStack(Foam::Ostream&)[0] #0 [3] #0 Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)-------------------------------------------------------------------------- A process has executed an operation involving a call to the "fork()" system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged.

The process that invoked fork was:

Local host: [[35614,1],1] (PID 211152)

If you are absolutely sure that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0.

at ??:? [2] #1 Foam::sigSegv::sigHandler(int) at ??:? at ??:? [0] #1 Foam::sigSegv::sigHandler(int)[1] #1 Foam::sigSegv::sigHandler(int) at ??:? [3] #1 Foam::sigSegv::sigHandler(int) at ??:? [1] #2 ? at ??:? [0] #2 ? at ??:? [2] #2 ? in "/lib64/libpthread.so.0" [1] #3 MPI_Comm_rank in "/ at lib64/libpthread.??:? so.0" [3] #[2] #3 2 MPI_Comm_rank? in "/lib64/libpthread.so.0" [0] #3 MPI_Comm_rank in "/public/home/LUTLiDSh/opt/openmpi/lib/libmpi.so.40" [1] #4 fast::OpenFAST::setInputs(fast::fastInputs const&) in "/lib64/libpthread.so.0" [3] #3 MPI_Comm_rank in "/public/home/LUTLiDSh/opt/openmpi/lib/libmpi.so.40" [2] #4 fast::OpenFAST::setInputs(fast::fastInputs const&) in "/public/home/LUTLiDSh/opt/openmpi/lib/libmpi.so.40" [0] #4 fast::OpenFAST::setInputs(fast::fastInputs const&) in "/public/home/LUTLiDSh/opt/openmpi/lib/libmpi.so.40" [3] #4 fast::OpenFAST::setInputs(fast::fastInputs const&) at ??:? [0] #5 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::sendInput() at ??:? [1] #5 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::sendInput() at ??:? [2] #5 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::sendInput() at ??:? [3] #5 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::sendInput() at ??:? [1] #6 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::initialize() at ??:? [2] #6 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::initialize() at ??:? [0] #6 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::initialize() at ??:? [3] #6 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::initialize() at ??:? [2] #7 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::horizontalAxisWindTurbinesALMOpenFAST(Foam::GeometricField<Foam::Vector, Foam::fvPatchField, Foam::volMesh> const&) at ??:? [0] #7 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::horizontalAxisWindTurbinesALMOpenFAST(Foam::GeometricField<Foam::Vector, Foam::fvPatchField, Foam::volMesh> const&) at ??:? [1] #7 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::horizontalAxisWindTurbinesALMOpenFAST(Foam::GeometricField<Foam::Vector, Foam::fvPatchField, Foam::volMesh> const&) at ??:? [3] #7 Foam::turbineModels::horizontalAxisWindTurbinesALMOpenFAST::horizontalAxisWindTurbinesALMOpenFAST(Foam::GeometricField<Foam::Vector, Foam::fvPatchField, Foam::volMesh> const&) at ??:? [1] #8 at ??:? [0] #8 at ??:? at [2] #8 ??:? [3] #8 ???? at ??:? [1] #9 libc_start_main at ??:? [2] #9 libc_start_main at ??:? [3] #9 libc_start_main at ??:? [0] #9 libc_start_main in "/lib64/libc.so.6" [1] #10 in "/lib64/libc.so.6" [0] #10 ? in "/lib64/libc.so.6" [2] #10 in "/lib64/libc.so.6" [3] #10 ?? at ??:? [admin:211152] Process received signal [admin:211152] Signal: Segmentation fault (11) [admin:211152] Signal code: (-6) [admin:211152] Failing at address: 0x42f000338d0 [admin:211152] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x7ff98c55a5e0] [admin:211152] [ 1] /lib64/libpthread.so.0(raise+0x2b)[0x7ff98c55a4ab] [admin:211152] [ 2] /lib64/libpthread.so.0(+0xf5e0)[0x7ff98c55a5e0] [admin:211152] [ 3] /public/home/LUTLiDSh/opt/openmpi/lib/libmpi.so.40(MPI_Comm_rank+0x4a)[0x7ff98356daca] [admin:211152] [ 4] /public/home/LUTLiDSh/OpenFAST/openfast/lib/libopenfastcpplib.so(_ZN4fast8OpenFAST9setInputsERKNS_10fastInputsE+0x26)[0x7ff9901c73f6] [admin:211152] [ 5] /public/home/LUTLiDSh/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFAST9sendInputEv+0x3ff)[0x7ff9956b244f] [admin:211152] [ 6] ?/public/home/LUTLiDSh/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFAST10initializeEv+0x23)[0x7ff9956baa23] [admin:211152] [ 7] /public/home/LUTLiDSh/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFASTC1ERKNS_14GeometricFieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshEEE+0x1d74)[0x7ff9956bcaa4] [admin:211152] [ 8] pisoFoamTurbine.ALMAdvancedOpenFAST[0x4276af] [admin:211152] [ 9] /lib64/libc.so.6(libc_start_main+0xf5)[0x7ff98c1a9c05] [admin:211152] [10] pisoFoamTurbine.ALMAdvancedOpenFAST[0x42d39a] [admin:211152] End of error message at ??:? [admin:211151] Process received signal [admin:211151] Signal: Segmentation fault (11) [admin:211151] Signal code: (-6) [admin:211151] Failing at address: 0x42f000338cf [admin:211151] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x7fc02f6fe5e0] [admin:211151] [ 1] /lib64/libpthread.so.0(raise+0x2b)[0x7fc02f6fe4ab] [admin:211151] [ 2] /lib64/libpthread.so.0(+0xf5e0)[0x7fc02f6fe5e0] [admin:211151] [ 3] /public/home/LUTLiDSh/opt/openmpi/lib/libmpi.so.40(MPI_Comm_rank+0x4a)[0x7fc026711aca] [admin:211151] [ 4] /public/home/LUTLiDSh/OpenFAST/openfast/lib/libopenfastcpplib.so(_ZN4fast8OpenFAST9setInputsERKNS_10fastInputsE+0x26)[0x7fc03336b3f6] [admin:211151] [ 5] /public/home/LUTLiDSh/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFAST9sendInputEv+0x3ff)[0x7fc03885644f] [admin:211151] [ 6] /public/home/LUTLiDSh/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFAST10initializeEv+0x23)[0x7fc03885ea23] [admin:211151] [ 7] /public/home/LUTLiDSh/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFASTC1ERKNS_14GeometricFieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshEEE+0x1d74)[0x7fc038860aa4] [admin:211151] [ 8] pisoFoamTurbine.ALMAdvancedOpenFAST[0x4276af] [admin:211151] [ 9] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7fc02f34dc05] [admin:211151] [10] pisoFoamTurbine.ALMAdvancedOpenFAST[0x42d39a] [admin:211151] End of error message at ??:? [admin:211154] Process received signal [admin:211154] Signal: Segmentation fault (11) [admin:211154] Signal code: (-6) [admin:211154] Failing at address: 0x42f000338d2 [admin:211154] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x7f83b29505e0] [admin:211154] [ 1] /lib64/libpthread.so.0(raise+0x2b)[0x7f83b29504ab] [admin:211154] [ 2] /lib64/libpthread.so.0(+0xf5e0)[0x7f83b29505e0] [admin:211154] [ 3] /public/home/LUTLiDSh/opt/openmpi/lib/libmpi.so.40(MPI_Comm_rank+0x4a)[0x7f83a9963aca] [admin:211154] [ 4] /public/home/LUTLiDSh/OpenFAST/openfast/lib/libopenfastcpplib.so(_ZN4fast8OpenFAST9setInputsERKNS_10fastInputsE+0x26)[0x7f83b65bd3f6] [admin:211154] [ 5] /public/home/LUTLiDSh/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFAST9sendInputEv+0x3ff)[0x7f83bbaa844f] [admin:211154] [ 6] /public/home/LUTLiDSh/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFAST10initializeEv+0x23)[0x7f83bbab0a23] [admin:211154] [ 7] /public/home/LUTLiDSh/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFASTC1ERKNS_14GeometricFieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshEEE+0x1d74)[0x7f83bbab2aa4] [admin:211154] [ 8] pisoFoamTurbine.ALMAdvancedOpenFAST[0x4276af] [admin:211154] [ 9] /lib64/libc.so.6(libc_start_main+0xf5)[0x7f83b259fc05] [admin:211154] [10] pisoFoamTurbine.ALMAdvancedOpenFAST[0x42d39a] [admin:211154] End of error message at ??:? [admin:211153] Process received signal [admin:211153] Signal: Segmentation fault (11) [admin:211153] Signal code: (-6) [admin:211153] Failing at address: 0x42f000338d1 [admin:211153] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x7fc8fd59c5e0] [admin:211153] [ 1] /lib64/libpthread.so.0(raise+0x2b)[0x7fc8fd59c4ab] [admin:211153] [ 2] /lib64/libpthread.so.0(+0xf5e0)[0x7fc8fd59c5e0] [admin:211153] [ 3] /public/home/LUTLiDSh/opt/openmpi/lib/libmpi.so.40(MPI_Comm_rank+0x4a)[0x7fc8f45afaca] [admin:211153] [ 4] /public/home/LUTLiDSh/OpenFAST/openfast/lib/libopenfastcpplib.so(_ZN4fast8OpenFAST9setInputsERKNS_10fastInputsE+0x26)[0x7fc9012093f6] [admin:211153] [ 5] /public/home/LUTLiDSh/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFAST9sendInputEv+0x3ff)[0x7fc9066f444f] [admin:211153] [ 6] /public/home/LUTLiDSh/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFAST10initializeEv+0x23)[0x7fc9066fca23] [admin:211153] [ 7] /public/home/LUTLiDSh/SOWFA/lib/linux64GccDPOpt/libSOWFATurbineModelsOpenFAST.so(_ZN4Foam13turbineModels37horizontalAxisWindTurbinesALMOpenFASTC1ERKNS_14GeometricFieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshEEE+0x1d74)[0x7fc9066feaa4] [admin:211153] [ 8] pisoFoamTurbine.ALMAdvancedOpenFAST[0x4276af] [admin:211153] [ 9] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7fc8fd1ebc05] [admin:211153] [10] pisoFoamTurbine.ALMAdvancedOpenFAST[0x42d39a] [admin:211153] End of error message

Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted.

mpirun noticed that process rank 1 with PID 0 on node admin exited on signal 11 (Segmentation fault).

[admin:211146] 4 more processes have sent help message help-oob-ud.txt / create-qp-failed [admin:211146] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages [admin:211146] 4 more processes have sent help message help-oob-ud.txt / no-ports-usable [admin:211146] 7 more processes have sent help message help-mpi-btl-openib.txt / no device params found [admin:211146] 7 more processes have sent help message help-mpi-btl-openib-cpc-base.txt / no cpcs for port [admin:211146] 3 more processes have sent help message help-opal-runtime.txt / opal_init:warn-fork

wcha533 commented 3 years ago

Hi @HYFOAM I think you would better discuss with your HPC cluster technical staff since it might be an issue with environment modules on the HPC.

HYFOAM commented 3 years ago

@wcha533 Hi, thank you for answering me. Because I am new to Linux, I would like to ask what HPC environment modules you mentioned? For example what?

Are you Chinese? Can you leave a contact information? For example, QQ or WeChat. thank you! !

pablo-benito commented 3 years ago

On CentOS which version of gcc are you using? Some time ago, I had weird errors (seg faults) when running OpenFoam 2.4.x that was compiled with gcc version > 6. Something changed starting with that version of gcc that produced segfaults on the code.. As you can see here, https://openfoamwiki.net/index.php/Installation/Compatibility_Matrix#GNU_CompilerCollection.28GCC.29 OpenFOAM 2.4.x do not officially support GCC > 6

At that time I had to backport some patches of OpenFoam 3.x back to OpenFoam 2.4.x to properly support that compiler.. You can check it out here: https://github.com/pablo-benito/OpenFOAM-2.4.x

Hope it helps..

HYFOAM commented 3 years ago

@pablo-benito @wcha533 @NRELAdmin Hi, the gcc-4.8.5 and openfoam-2.4.x I use have been successfully compiled and installed on the centos system. However, failures may occur when running calculations related to openfast. If I use ubuntu18.04, this problem will not occur. I have checked my installation environment module and I made sure that the environment module is correct.