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SmileiPIC / Smilei

Particle-in-cell code for plasma simulation
https://smileipic.github.io/Smilei
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Difficulties with running simulation on EXPLOR cluster #116

Closed HomamBetar closed 5 years ago

HomamBetar commented 5 years ago

Dears,

I have tried to run the simulation (Smilei-4.1) on EXPLOR cluster . With first 1) intelmpi/2018.0.128 2) python/2.7/intel.2017-3 3) hdf5/1.10.1/intelmpi/intel17 4) intel/2018.3 In makefile file, I made the following modifications 

SMILEICXX ?= mpicc
HDF5_ROOT_DIR ?= /opt/modulefiles/libraries/hdf5/1.10.1/intelmpi
BUILD_DIR ?= build
PYTHONEXE ?= python
PYTHONCONFIG := $(PYTHONEXE) scripts/CompileTools/python-config.py

the main problems were

  1. problem in openmp work, such as 

    src/ElectroMagn/ElectroMagn2D.cpp:1031:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
^

  2. Linking smilei /usr/bin/ld: ne peut trouver -lhdf5 collect2: erreur: ld a retourné 1 code d'état d'exécution

The Resutls of the Compiling

Unknown smilei version
Checking dependencies for src/Tools/userFunctions.cpp
Checking dependencies for src/Tools/Tools.cpp
Checking dependencies for src/Tools/Timers.cpp
Checking dependencies for src/Tools/Timer.cpp
Checking dependencies for src/Tools/tabulatedFunctions.cpp
Checking dependencies for src/Tools/backward.cpp
Checking dependencies for src/Species/SpeciesV.cpp
Checking dependencies for src/Species/SpeciesNormV.cpp
Checking dependencies for src/Species/SpeciesNorm.cpp
Checking dependencies for src/Species/SpeciesMetrics.cpp
Checking dependencies for src/Species/SpeciesAdaptiveV2.cpp
Checking dependencies for src/Species/SpeciesAdaptiveV.cpp
Checking dependencies for src/Species/Species.cpp
Checking dependencies for src/Species/PartWall.cpp
Checking dependencies for src/Species/Particles.cpp
Checking dependencies for src/Species/Particle.cpp
Checking dependencies for src/Species/PartBoundCond.cpp
Checking dependencies for src/SmileiMPI/SmileiMPI_test.cpp
Checking dependencies for src/SmileiMPI/SmileiMPI.cpp
Checking dependencies for src/SmileiMPI/AsyncMPIbuffers.cpp
Checking dependencies for src/Smilei.cpp
Checking dependencies for src/Radiation/RadiationTables.cpp
Checking dependencies for src/Radiation/RadiationNiel.cpp
Checking dependencies for src/Radiation/RadiationMonteCarlo.cpp
Checking dependencies for src/Radiation/RadiationLandauLifshitz.cpp
Checking dependencies for src/Radiation/RadiationCorrLandauLifshitz.cpp
Checking dependencies for src/Radiation/Radiation.cpp
Checking dependencies for src/Pusher/PusherVay.cpp
Checking dependencies for src/Pusher/PusherRRLL.cpp
Checking dependencies for src/Pusher/PusherPonderomotivePositionBorisV.cpp
Checking dependencies for src/Pusher/PusherPonderomotivePositionBoris.cpp
Checking dependencies for src/Pusher/PusherPonderomotiveBorisV.cpp
Checking dependencies for src/Pusher/PusherPonderomotiveBoris.cpp
Checking dependencies for src/Pusher/PusherPhoton.cpp
Checking dependencies for src/Pusher/PusherHigueraCary.cpp
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Checking dependencies for src/Pusher/PusherBorisNR.cpp
Checking dependencies for src/Pusher/PusherBoris.cpp
Checking dependencies for src/Pusher/Pusher.cpp
Checking dependencies for src/Projector/ProjectorAM2Order.cpp
Checking dependencies for src/Projector/ProjectorAM.cpp
Checking dependencies for src/Projector/Projector3D4OrderV.cpp
Checking dependencies for src/Projector/Projector3D4Order.cpp
Checking dependencies for src/Projector/Projector3D2OrderV.cpp
Checking dependencies for src/Projector/Projector3D2Order.cpp
Checking dependencies for src/Projector/Projector3D.cpp
Checking dependencies for src/Projector/Projector2D4Order.cpp
Checking dependencies for src/Projector/Projector2D2OrderV.cpp
Checking dependencies for src/Projector/Projector2D2Order.cpp
Checking dependencies for src/Projector/Projector2D.cpp
Checking dependencies for src/Projector/Projector1D4Order.cpp
Checking dependencies for src/Projector/Projector1D2Order.cpp
Checking dependencies for src/Projector/Projector1D.cpp
Checking dependencies for src/Projector/Projector.cpp
Checking dependencies for src/Profiles/Profile.cpp
Checking dependencies for src/Profiles/Function.cpp
Checking dependencies for src/picsar_interface/interface.cpp
Checking dependencies for src/Patch/VectorPatch.cpp
Checking dependencies for src/Patch/SyncVectorPatch.cpp
Checking dependencies for src/Patch/SyncCartesianPatch.cpp
Checking dependencies for src/Patch/PatchAM.cpp
Checking dependencies for src/Patch/Patch3D.cpp
Checking dependencies for src/Patch/Patch2D.cpp
Checking dependencies for src/Patch/Patch1D.cpp
Checking dependencies for src/Patch/Patch.cpp
Checking dependencies for src/Patch/Domain.cpp
Checking dependencies for src/Params/PeekAtSpecies.cpp
Checking dependencies for src/Params/Params.cpp
Checking dependencies for src/Params/OpenPMDparams.cpp
Checking dependencies for src/MultiphotonBreitWheeler/MultiphotonBreitWheelerTables.cpp
Checking dependencies for src/MultiphotonBreitWheeler/MultiphotonBreitWheeler.cpp
Checking dependencies for src/MovWindow/SimWindow.cpp
Checking dependencies for src/Ionization/IonizationTunnel.cpp
Checking dependencies for src/Ionization/IonizationTables.cpp
Checking dependencies for src/Ionization/IonizationFromRate.cpp
Checking dependencies for src/Ionization/Ionization.cpp
Checking dependencies for src/Interpolator/InterpolatorAM2Order.cpp
Checking dependencies for src/Interpolator/InterpolatorAM.cpp
Checking dependencies for src/Interpolator/Interpolator3D4OrderV.cpp
Checking dependencies for src/Interpolator/Interpolator3D4Order.cpp
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Checking dependencies for src/Interpolator/Interpolator3D2Order.cpp
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Checking dependencies for src/Field/Field3D.cpp
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Checking dependencies for src/Field/cField3D.cpp
Checking dependencies for src/Field/cField2D.cpp
Checking dependencies for src/ElectroMagnSolver/PXR_Solver3D_GPSTD.cpp
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Checking dependencies for src/ElectroMagnSolver/PXR_Solver2D_GPSTD.cpp
Checking dependencies for src/ElectroMagnSolver/MF_SolverAM_Yee.cpp
Checking dependencies for src/ElectroMagnSolver/MF_Solver3D_Yee.cpp
Checking dependencies for src/ElectroMagnSolver/MF_Solver3D_Lehe.cpp
Checking dependencies for src/ElectroMagnSolver/MF_Solver2D_Yee.cpp
Checking dependencies for src/ElectroMagnSolver/MF_Solver2D_Lehe.cpp
Checking dependencies for src/ElectroMagnSolver/MF_Solver2D_GrassiSpL.cpp
Checking dependencies for src/ElectroMagnSolver/MF_Solver2D_Grassi.cpp
Checking dependencies for src/ElectroMagnSolver/MF_Solver2D_Cowan.cpp
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Checking dependencies for src/ElectroMagnSolver/MA_SolverAM_norm.cpp
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Checking dependencies for src/ElectroMagnSolver/MA_Solver2D_norm.cpp
Checking dependencies for src/ElectroMagnSolver/MA_Solver2D_Friedman.cpp
Checking dependencies for src/ElectroMagnSolver/MA_Solver1D_norm.cpp
Checking dependencies for src/ElectroMagnBC/EnvelopeBC3D_refl.cpp
Checking dependencies for src/ElectroMagnBC/EnvelopeBC.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBCAM_SM.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBCAM_BM.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBCAM_Axis.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBC3D_SM.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBC3D_refl.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBC3D_BM.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBC3D.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBC2D_Trans_Damping.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBC2D_SM.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBC2D_refl.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBC2D.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBC1D_SM.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBC1D_refl.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBC1D.cpp
Checking dependencies for src/ElectroMagnBC/ElectroMagnBC.cpp
Checking dependencies for src/ElectroMagn/LaserPropagator.cpp
Checking dependencies for src/ElectroMagn/LaserEnvelope.cpp
Checking dependencies for src/ElectroMagn/Laser.cpp
Checking dependencies for src/ElectroMagn/ElectroMagnAM.cpp
Checking dependencies for src/ElectroMagn/ElectroMagn3D.cpp
Checking dependencies for src/ElectroMagn/ElectroMagn2D.cpp
Checking dependencies for src/ElectroMagn/ElectroMagn1D.cpp
Checking dependencies for src/ElectroMagn/ElectroMagn.cpp
Checking dependencies for src/DomainDecomposition/HilbertDomainDecomposition.cpp
Checking dependencies for src/DomainDecomposition/Hilbert_functions.cpp
Checking dependencies for src/DomainDecomposition/GlobalDomainDecomposition.cpp
Checking dependencies for src/DomainDecomposition/CartesianDomainDecomposition.cpp
Checking dependencies for src/Diagnostic/TimeSelection.cpp
Checking dependencies for src/Diagnostic/Histogram.cpp
Checking dependencies for src/Diagnostic/DiagnosticTrack.cpp
Checking dependencies for src/Diagnostic/DiagnosticScreen.cpp
Checking dependencies for src/Diagnostic/DiagnosticScalar.cpp
Checking dependencies for src/Diagnostic/DiagnosticProbes.cpp
Checking dependencies for src/Diagnostic/DiagnosticPerformances.cpp
Checking dependencies for src/Diagnostic/DiagnosticParticleBinning.cpp
Checking dependencies for src/Diagnostic/DiagnosticFieldsAM.cpp
Checking dependencies for src/Diagnostic/DiagnosticFields3D.cpp
Checking dependencies for src/Diagnostic/DiagnosticFields2D.cpp
Checking dependencies for src/Diagnostic/DiagnosticFields1D.cpp
Checking dependencies for src/Diagnostic/DiagnosticFields.cpp
Checking dependencies for src/Diagnostic/DiagnosticCartFields3D.cpp
Checking dependencies for src/Diagnostic/DiagnosticCartFields2D.cpp
Checking dependencies for src/Diagnostic/DiagnosticCartFields.cpp
Checking dependencies for src/Collisions/CollisionsSingle.cpp
Checking dependencies for src/Collisions/Collisions.cpp
Checking dependencies for src/Collisions/CollisionalIonization.cpp
Checking dependencies for src/Checkpoint/Checkpoint.cpp
Unknown smilei version
Compiling src/Checkpoint/Checkpoint.cpp
Compiling src/Collisions/CollisionalIonization.cpp
Compiling src/Collisions/Collisions.cpp
Compiling src/Collisions/CollisionsSingle.cpp
Compiling src/Diagnostic/DiagnosticCartFields.cpp
Compiling src/Diagnostic/DiagnosticCartFields2D.cpp
Compiling src/Diagnostic/DiagnosticCartFields3D.cpp
Compiling src/Diagnostic/DiagnosticFields.cpp
Compiling src/Diagnostic/DiagnosticFields1D.cpp
Compiling src/Diagnostic/DiagnosticFields2D.cpp
Compiling src/Diagnostic/DiagnosticFields3D.cpp
Compiling src/Diagnostic/DiagnosticFieldsAM.cpp
Compiling src/Diagnostic/DiagnosticParticleBinning.cpp
Compiling src/Diagnostic/DiagnosticPerformances.cpp
Compiling src/Diagnostic/DiagnosticProbes.cpp
SPECIAL COMPILATION FOR src/Diagnostic/DiagnosticScalar.cpp
Compiling src/Diagnostic/DiagnosticScreen.cpp
Compiling src/Diagnostic/DiagnosticTrack.cpp
Compiling src/Diagnostic/Histogram.cpp
Compiling src/Diagnostic/TimeSelection.cpp
Compiling src/DomainDecomposition/CartesianDomainDecomposition.cpp
Compiling src/DomainDecomposition/GlobalDomainDecomposition.cpp
Compiling src/DomainDecomposition/Hilbert_functions.cpp
Compiling src/DomainDecomposition/HilbertDomainDecomposition.cpp
Compiling src/ElectroMagn/ElectroMagn.cpp
Compiling src/ElectroMagn/ElectroMagn1D.cpp
Compiling src/ElectroMagn/ElectroMagn2D.cpp
src/ElectroMagn/ElectroMagn2D.cpp:1010:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/ElectroMagn/ElectroMagn2D.cpp:1018:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/ElectroMagn/ElectroMagn2D.cpp:1026:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/ElectroMagn/ElectroMagn2D.cpp:1031:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/ElectroMagn/ElectroMagn2D.cpp:1035:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
Compiling src/ElectroMagn/ElectroMagn3D.cpp
Compiling src/ElectroMagn/ElectroMagnAM.cpp
Compiling src/ElectroMagn/Laser.cpp
Compiling src/ElectroMagn/LaserEnvelope.cpp
Compiling src/ElectroMagn/LaserPropagator.cpp
Compiling src/ElectroMagnBC/ElectroMagnBC.cpp
Compiling src/ElectroMagnBC/ElectroMagnBC1D.cpp
Compiling src/ElectroMagnBC/ElectroMagnBC1D_refl.cpp
Compiling src/ElectroMagnBC/ElectroMagnBC1D_SM.cpp
Compiling src/ElectroMagnBC/ElectroMagnBC2D.cpp
Compiling src/ElectroMagnBC/ElectroMagnBC2D_refl.cpp
Compiling src/ElectroMagnBC/ElectroMagnBC2D_SM.cpp
Compiling src/ElectroMagnBC/ElectroMagnBC2D_Trans_Damping.cpp
Compiling src/ElectroMagnBC/ElectroMagnBC3D.cpp
Compiling src/ElectroMagnBC/ElectroMagnBC3D_BM.cpp
Compiling src/ElectroMagnBC/ElectroMagnBC3D_refl.cpp
Compiling src/ElectroMagnBC/ElectroMagnBC3D_SM.cpp
Compiling src/ElectroMagnBC/ElectroMagnBCAM_Axis.cpp
Compiling src/ElectroMagnBC/ElectroMagnBCAM_BM.cpp
Compiling src/ElectroMagnBC/ElectroMagnBCAM_SM.cpp
Compiling src/ElectroMagnBC/EnvelopeBC.cpp
Compiling src/ElectroMagnBC/EnvelopeBC3D_refl.cpp
Compiling src/ElectroMagnSolver/MA_Solver1D_norm.cpp
Compiling src/ElectroMagnSolver/MA_Solver2D_Friedman.cpp
Compiling src/ElectroMagnSolver/MA_Solver2D_norm.cpp
Compiling src/ElectroMagnSolver/MA_Solver3D_norm.cpp
Compiling src/ElectroMagnSolver/MA_SolverAM_norm.cpp
Compiling src/ElectroMagnSolver/MF_Solver1D_Yee.cpp
Compiling src/ElectroMagnSolver/MF_Solver2D_Cowan.cpp
Compiling src/ElectroMagnSolver/MF_Solver2D_Grassi.cpp
Compiling src/ElectroMagnSolver/MF_Solver2D_GrassiSpL.cpp
Compiling src/ElectroMagnSolver/MF_Solver2D_Lehe.cpp
Compiling src/ElectroMagnSolver/MF_Solver2D_Yee.cpp
src/ElectroMagnSolver/MF_Solver2D_Yee.cpp:40:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/ElectroMagnSolver/MF_Solver2D_Yee.cpp:47:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/ElectroMagnSolver/MF_Solver2D_Yee.cpp:55:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/ElectroMagnSolver/MF_Solver2D_Yee.cpp:63:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
Compiling src/ElectroMagnSolver/MF_Solver3D_Lehe.cpp
Compiling src/ElectroMagnSolver/MF_Solver3D_Yee.cpp
Compiling src/ElectroMagnSolver/MF_SolverAM_Yee.cpp
src/ElectroMagnSolver/MF_SolverAM_Yee.cpp:42:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/ElectroMagnSolver/MF_SolverAM_Yee.cpp:50:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/ElectroMagnSolver/MF_SolverAM_Yee.cpp:58:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
Compiling src/ElectroMagnSolver/PXR_Solver2D_GPSTD.cpp
Compiling src/ElectroMagnSolver/PXR_Solver3D_FDTD.cpp
Compiling src/ElectroMagnSolver/PXR_Solver3D_GPSTD.cpp
Compiling src/Field/cField2D.cpp
Compiling src/Field/cField3D.cpp
Compiling src/Field/Field1D.cpp
Compiling src/Field/Field2D.cpp
Compiling src/Field/Field3D.cpp
Compiling src/Interpolator/Interpolator.cpp
Compiling src/Interpolator/Interpolator1D.cpp
Compiling src/Interpolator/Interpolator1D2Order.cpp
Compiling src/Interpolator/Interpolator1D3Order.cpp
Compiling src/Interpolator/Interpolator1D4Order.cpp
Compiling src/Interpolator/Interpolator2D.cpp
Compiling src/Interpolator/Interpolator2D2Order.cpp
Compiling src/Interpolator/Interpolator2D2OrderV.cpp
src/Interpolator/Interpolator2D2OrderV.cpp:87:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Interpolator/Interpolator2D2OrderV.cpp:112:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
Compiling src/Interpolator/Interpolator2D4Order.cpp
Compiling src/Interpolator/Interpolator3D.cpp
Compiling src/Interpolator/Interpolator3D2Order.cpp
Compiling src/Interpolator/Interpolator3D2OrderV.cpp
src/Interpolator/Interpolator3D2OrderV.cpp:92:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Interpolator/Interpolator3D2OrderV.cpp:119:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Interpolator/Interpolator3D2OrderV.cpp:476:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Interpolator/Interpolator3D2OrderV.cpp:501:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Interpolator/Interpolator3D2OrderV.cpp:712:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Interpolator/Interpolator3D2OrderV.cpp:737:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
Compiling src/Interpolator/Interpolator3D4Order.cpp
Compiling src/Interpolator/Interpolator3D4OrderV.cpp
src/Interpolator/Interpolator3D4OrderV.cpp:104:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Interpolator/Interpolator3D4OrderV.cpp:133:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
Compiling src/Interpolator/InterpolatorAM.cpp
Compiling src/Interpolator/InterpolatorAM2Order.cpp
Compiling src/Ionization/Ionization.cpp
Compiling src/Ionization/IonizationFromRate.cpp
Compiling src/Ionization/IonizationTables.cpp
Compiling src/Ionization/IonizationTunnel.cpp
Compiling src/MovWindow/SimWindow.cpp
Compiling src/MultiphotonBreitWheeler/MultiphotonBreitWheeler.cpp
src/MultiphotonBreitWheeler/MultiphotonBreitWheeler.cpp:95:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/MultiphotonBreitWheeler/MultiphotonBreitWheeler.cpp:187:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
Compiling src/MultiphotonBreitWheeler/MultiphotonBreitWheelerTables.cpp
Compiling src/Params/OpenPMDparams.cpp
Compiling src/Params/Params.cpp
src/Params/Params.cpp: In member function ‘bool Params::isSpeciesField(std::string)’:
src/Params/Params.cpp:1107:17: attention : suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
                 && (field_name.substr(2,6)!="_mode_" || field_name.find("mode_") != field_name.rfind("mode_"))
                 ^
Compiling src/Params/PeekAtSpecies.cpp
Compiling src/Patch/Domain.cpp
Compiling src/Patch/Patch.cpp
Compiling src/Patch/Patch1D.cpp
Compiling src/Patch/Patch2D.cpp
src/Patch/Patch2D.cpp:242:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
                 #pragma omp simd
 ^
Compiling src/Patch/Patch3D.cpp
Compiling src/Patch/PatchAM.cpp
Compiling src/Patch/SyncCartesianPatch.cpp
Compiling src/Patch/SyncVectorPatch.cpp
Compiling src/Patch/VectorPatch.cpp
Compiling src/picsar_interface/interface.cpp
Compiling src/Profiles/Function.cpp
Compiling src/Profiles/Profile.cpp
Compiling src/Projector/Projector.cpp
Compiling src/Projector/Projector1D.cpp
Compiling src/Projector/Projector1D2Order.cpp
Compiling src/Projector/Projector1D4Order.cpp
Compiling src/Projector/Projector2D.cpp
Compiling src/Projector/Projector2D2Order.cpp
Compiling src/Projector/Projector2D2OrderV.cpp
src/Projector/Projector2D2OrderV.cpp:375:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector2D2OrderV.cpp:386:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector2D2OrderV.cpp:417:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
             #pragma unroll
 ^
src/Projector/Projector2D2OrderV.cpp:448:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
             #pragma unroll
 ^
src/Projector/Projector2D2OrderV.cpp:455:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector2D2OrderV.cpp:484:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector2D2OrderV.cpp:488:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
             #pragma unroll
 ^
src/Projector/Projector2D2OrderV.cpp:496:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector2D2OrderV.cpp:504:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector2D2OrderV.cpp:535:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
             #pragma unroll
 ^
src/Projector/Projector2D2OrderV.cpp:566:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
             #pragma unroll
 ^
src/Projector/Projector2D2OrderV.cpp:573:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector2D2OrderV.cpp:600:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector2D2OrderV.cpp:604:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
             #pragma unroll
 ^
src/Projector/Projector2D2OrderV.cpp:613:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
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src/Projector/Projector2D2OrderV.cpp:621:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector2D2OrderV.cpp:652:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
             #pragma unroll
 ^
src/Projector/Projector2D2OrderV.cpp:683:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
             #pragma unroll
 ^
src/Projector/Projector2D2OrderV.cpp:691:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector2D2OrderV.cpp:717:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector2D2OrderV.cpp:721:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
             #pragma unroll
 ^
Compiling src/Projector/Projector2D4Order.cpp
Compiling src/Projector/Projector3D.cpp
Compiling src/Projector/Projector3D2Order.cpp
Compiling src/Projector/Projector3D2OrderV.cpp
src/Projector/Projector3D2OrderV.cpp:98:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:107:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:113:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:133:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:137:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
                 #pragma unroll(8)
 ^
src/Projector/Projector3D2OrderV.cpp:398:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:407:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:413:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:426:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:430:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
                 #pragma unroll(8)
 ^
src/Projector/Projector3D2OrderV.cpp:441:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:452:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:458:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:467:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:471:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
                 #pragma unroll(8)
 ^
src/Projector/Projector3D2OrderV.cpp:484:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:493:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:499:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:509:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:513:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
                 #pragma unroll(8)
 ^
src/Projector/Projector3D2OrderV.cpp:621:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:631:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:711:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:740:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Projector/Projector3D2OrderV.cpp:744:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
                 #pragma unroll(8)
 ^
Compiling src/Projector/Projector3D4Order.cpp
Compiling src/Projector/Projector3D4OrderV.cpp
src/Projector/Projector3D4OrderV.cpp:90:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:98:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:217:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:275:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:279:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
                 #pragma unroll(8)
 ^
src/Projector/Projector3D4OrderV.cpp:291:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:301:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:419:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:469:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:473:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
                 #pragma unroll(8)
 ^
src/Projector/Projector3D4OrderV.cpp:484:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:494:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:612:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:662:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:666:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
                 #pragma unroll(8)
 ^
src/Projector/Projector3D4OrderV.cpp:679:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:687:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:764:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:785:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:789:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
                 #pragma unroll(8)
 ^
src/Projector/Projector3D4OrderV.cpp:958:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:966:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:1085:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:1143:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:1147:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
                 #pragma unroll(8)
 ^
src/Projector/Projector3D4OrderV.cpp:1160:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:1174:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:1292:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:1342:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:1346:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
                 #pragma unroll(8)
 ^
src/Projector/Projector3D4OrderV.cpp:1357:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:1375:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:1493:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:1543:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Projector/Projector3D4OrderV.cpp:1547:0: attention : #pragma unroll  ignoré [-Wunknown-pragmas]
                 #pragma unroll(8)
 ^
Compiling src/Projector/ProjectorAM.cpp
Compiling src/Projector/ProjectorAM2Order.cpp
src/Projector/ProjectorAM2Order.cpp: In member function ‘void ProjectorAM2Order::currents_mode0(std::complex<double>*, std::complex<double>*, std::complex<double>*, Particles&, unsigned int, double, int*, double*)’:
src/Projector/ProjectorAM2Order.cpp:161:50: attention : array subscript is above array bounds [-Warray-bounds]
                 Wl[i][j-nfold] += Wl[i][-j-nfold]; 
                                                  ^
src/Projector/ProjectorAM2Order.cpp:161:50: attention : array subscript is above array bounds [-Warray-bounds]
src/Projector/ProjectorAM2Order.cpp:162:50: attention : array subscript is above array bounds [-Warray-bounds]
                 Wr[i][j-nfold] += Wr[i][-j-nfold]; 
                                                  ^
src/Projector/ProjectorAM2Order.cpp:162:50: attention : array subscript is above array bounds [-Warray-bounds]
src/Projector/ProjectorAM2Order.cpp:163:50: attention : array subscript is above array bounds [-Warray-bounds]
                 Wt[i][j-nfold] += Wt[i][-j-nfold]; 
                                                  ^
src/Projector/ProjectorAM2Order.cpp:163:50: attention : array subscript is above array bounds [-Warray-bounds]
src/Projector/ProjectorAM2Order.cpp:161:50: attention : array subscript is above array bounds [-Warray-bounds]
                 Wl[i][j-nfold] += Wl[i][-j-nfold]; 
                                                  ^
src/Projector/ProjectorAM2Order.cpp:161:50: attention : array subscript is above array bounds [-Warray-bounds]
src/Projector/ProjectorAM2Order.cpp:162:50: attention : array subscript is above array bounds [-Warray-bounds]
                 Wr[i][j-nfold] += Wr[i][-j-nfold]; 
                                                  ^
src/Projector/ProjectorAM2Order.cpp:162:50: attention : array subscript is above array bounds [-Warray-bounds]
src/Projector/ProjectorAM2Order.cpp:163:50: attention : array subscript is above array bounds [-Warray-bounds]
                 Wt[i][j-nfold] += Wt[i][-j-nfold]; 
                                                  ^
src/Projector/ProjectorAM2Order.cpp:163:50: attention : array subscript is above array bounds [-Warray-bounds]
src/Projector/ProjectorAM2Order.cpp: In member function ‘void ProjectorAM2Order::currentsAndDensity_mode0(std::complex<double>*, std::complex<double>*, std::complex<double>*, std::complex<double>*, Particles&, unsigned int, double, int*, double*)’:
src/Projector/ProjectorAM2Order.cpp:543:50: attention : array subscript is above array bounds [-Warray-bounds]
                 Wl[i][j-nfold] += Wl[i][-j-nfold]; 
                                                  ^
src/Projector/ProjectorAM2Order.cpp:543:50: attention : array subscript is above array bounds [-Warray-bounds]
src/Projector/ProjectorAM2Order.cpp:544:50: attention : array subscript is above array bounds [-Warray-bounds]
                 Wr[i][j-nfold] += Wr[i][-j-nfold]; 
                                                  ^
src/Projector/ProjectorAM2Order.cpp:544:50: attention : array subscript is above array bounds [-Warray-bounds]
src/Projector/ProjectorAM2Order.cpp:545:50: attention : array subscript is above array bounds [-Warray-bounds]
                 Wt[i][j-nfold] += Wt[i][-j-nfold]; 
                                                  ^
src/Projector/ProjectorAM2Order.cpp:545:50: attention : array subscript is above array bounds [-Warray-bounds]
src/Projector/ProjectorAM2Order.cpp:543:50: attention : array subscript is above array bounds [-Warray-bounds]
                 Wl[i][j-nfold] += Wl[i][-j-nfold]; 
                                                  ^
src/Projector/ProjectorAM2Order.cpp:543:50: attention : array subscript is above array bounds [-Warray-bounds]
src/Projector/ProjectorAM2Order.cpp:544:50: attention : array subscript is above array bounds [-Warray-bounds]
                 Wr[i][j-nfold] += Wr[i][-j-nfold]; 
                                                  ^
src/Projector/ProjectorAM2Order.cpp:544:50: attention : array subscript is above array bounds [-Warray-bounds]
src/Projector/ProjectorAM2Order.cpp:545:50: attention : array subscript is above array bounds [-Warray-bounds]
                 Wt[i][j-nfold] += Wt[i][-j-nfold]; 
                                                  ^
src/Projector/ProjectorAM2Order.cpp:545:50: attention : array subscript is above array bounds [-Warray-bounds]
Compiling src/Pusher/Pusher.cpp
Compiling src/Pusher/PusherBoris.cpp
src/Pusher/PusherBoris.cpp:59:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
Compiling src/Pusher/PusherBorisNR.cpp
src/Pusher/PusherBorisNR.cpp:90:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
Compiling src/Pusher/PusherBorisV.cpp
src/Pusher/PusherBorisV.cpp:63:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Pusher/PusherBorisV.cpp:67:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
Compiling src/Pusher/PusherHigueraCary.cpp
src/Pusher/PusherHigueraCary.cpp:68:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
 #pragma omp simd
 ^
src/Pusher/PusherHigueraCary.cpp:141:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
Compiling src/Pusher/PusherPhoton.cpp
src/Pusher/PusherPhoton.cpp:50:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Pusher/PusherPhoton.cpp:72:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
Compiling src/Pusher/PusherPonderomotiveBoris.cpp
src/Pusher/PusherPonderomotiveBoris.cpp:61:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
Compiling src/Pusher/PusherPonderomotiveBorisV.cpp
src/Pusher/PusherPonderomotiveBorisV.cpp:58:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Pusher/PusherPonderomotiveBorisV.cpp:62:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
Compiling src/Pusher/PusherPonderomotivePositionBoris.cpp
src/Pusher/PusherPonderomotivePositionBoris.cpp:61:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
Compiling src/Pusher/PusherPonderomotivePositionBorisV.cpp
src/Pusher/PusherPonderomotivePositionBorisV.cpp:67:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
Compiling src/Pusher/PusherRRLL.cpp
src/Pusher/PusherRRLL.cpp:157:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
Compiling src/Pusher/PusherVay.cpp
src/Pusher/PusherVay.cpp:70:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Pusher/PusherVay.cpp:156:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
Compiling src/Radiation/Radiation.cpp
src/Radiation/Radiation.cpp:97:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
Compiling src/Radiation/RadiationCorrLandauLifshitz.cpp
src/Radiation/RadiationCorrLandauLifshitz.cpp:110:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Radiation/RadiationCorrLandauLifshitz.cpp:157:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd reduction(+:radiated_energy_loc)
 ^
Compiling src/Radiation/RadiationLandauLifshitz.cpp
src/Radiation/RadiationLandauLifshitz.cpp:107:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Radiation/RadiationLandauLifshitz.cpp:153:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd reduction(+:radiated_energy_loc)
 ^
Compiling src/Radiation/RadiationMonteCarlo.cpp
Compiling src/Radiation/RadiationNiel.cpp
src/Radiation/RadiationNiel.cpp:128:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Radiation/RadiationNiel.cpp:164:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Radiation/RadiationNiel.cpp:181:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd private(p,temp)
 ^
src/Radiation/RadiationNiel.cpp:244:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd private(temp)
 ^
src/Radiation/RadiationNiel.cpp:261:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd private(temp)
 ^
src/Radiation/RadiationNiel.cpp:279:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd private(temp)
 ^
src/Radiation/RadiationNiel.cpp:296:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd private(temp,rad_energy)
 ^
src/Radiation/RadiationNiel.cpp:325:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd reduction(+:radiated_energy_loc)
 ^
Compiling src/Radiation/RadiationTables.cpp
Compiling src/Smilei.cpp
Compiling src/SmileiMPI/AsyncMPIbuffers.cpp
Compiling src/SmileiMPI/SmileiMPI.cpp
Compiling src/SmileiMPI/SmileiMPI_test.cpp
Compiling src/Species/PartBoundCond.cpp
Compiling src/Species/Particle.cpp
Compiling src/Species/Particles.cpp
Compiling src/Species/PartWall.cpp
Compiling src/Species/Species.cpp
src/Species/Species.cpp: In member function ‘virtual void Species::computeCharge(unsigned int, ElectroMagn*)’:
src/Species/Species.cpp:981:50: attention : comparaison entre des expressions entières signée et non signée [-Wsign-compare]
                 for (unsigned int imode=0; imode<Nmode;imode++){
                                                  ^
Compiling src/Species/SpeciesAdaptiveV.cpp
src/Species/SpeciesAdaptiveV.cpp:121:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
Compiling src/Species/SpeciesAdaptiveV2.cpp
Compiling src/Species/SpeciesMetrics.cpp
src/Species/SpeciesMetrics.cpp:31:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd reduction(+:number_of_vecto_cells,number_of_non_zero_cells)
 ^
src/Species/SpeciesMetrics.cpp:67:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd reduction(+:vecto_time_loc,scalar_time_loc) private(particle_number,log_particle_number)
 ^
src/Species/SpeciesMetrics.cpp:101:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd reduction(+:vecto_time_loc,scalar_time_loc) private(particle_number,log_particle_number)
 ^
Compiling src/Species/SpeciesNorm.cpp
Compiling src/Species/SpeciesNormV.cpp
Compiling src/Species/SpeciesV.cpp
src/Species/SpeciesV.cpp:455:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
             #pragma omp simd
 ^
src/Species/SpeciesV.cpp:584:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
src/Species/SpeciesV.cpp:611:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
     #pragma omp simd
 ^
Compiling src/Tools/backward.cpp
Compiling src/Tools/tabulatedFunctions.cpp
Compiling src/Tools/Timer.cpp
Compiling src/Tools/Timers.cpp
Compiling src/Tools/Tools.cpp
Compiling src/Tools/userFunctions.cpp
src/Tools/userFunctions.cpp:578:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Tools/userFunctions.cpp:584:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Tools/userFunctions.cpp:603:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
src/Tools/userFunctions.cpp:609:0: attention : #pragma omp simd ignoré [-Wunknown-pragmas]
         #pragma omp simd
 ^
Linking smilei
/usr/bin/ld: ne peut trouver -lhdf5
collect2: erreur: ld a retourné 1 code d'état d'exécution
make: *** [smilei] Erreur 1

Thanks very much Cheers

jderouillat commented 5 years ago

Hi, Two comments before looking forward :

Julien

HomamBetar commented 5 years ago

Hi, mpiicpc --version icpc (ICC) 18.0.3 20180410 Copyright (C) 1985-2018 Intel Corporation. All rights reserved. [bzu91@vm-zmc46 Smilei-4.1]$ mpiicc --version icc (ICC) 18.0.3 20180410 Copyright (C) 1985-2018 Intel Corporation. All rights reserved. [bzu91@vm-zmc46 bzu91]$ ls /opt/modulefiles/libraries/hdf5/1.10.1/intelmpi/lib ls: impossible d'accéder à /opt/modulefiles/libraries/hdf5/1.10.1/intelmpi/lib: Aucun fichier ou dossier de ce type It seems it does not find "lib" directory?

Now I am trying to compile with intel 2017. Thanks a lot for your help

mccoys commented 5 years ago

It looks like your HDF5 directory is incorrect. There should be a lib folder and an include folder inside.

HomamBetar commented 5 years ago

I will send an email to the cluster administrator. I compiled now the simulation with the following

1) intelmpi/2017.1.132 2) intel/2017.1.132 3) python/2.7/intel.2017-3 4) hdf5/1.10.1/intelmpi/intel17

I still have Linking smilei ld: ne peut trouver -lhdf5 ll wait for the answer from cluster team, and then come back with the feedback.

Thank you very much

HomamBetar commented 5 years ago

I have compiled the code with the following modules, and an executable smilei has been generated.
1]- Currently Loaded Modules:

1) intel/2017.1.132 2) intelmpi/2017.1.132 3) python/2.7/intel.2017-3 4) hdf5/1.10.1/intelmpi/intel17

2]- I ran the simulation by submitting the follwoing submission file on the cluster (with two stream instability)

#!/bin/bash
#SBATCH -N 2
#SBATCH -p std
#SBATCH -J mpiSmilei
#SBATCH -n 64
#SBATCH --ntasks-per-node=32
#SBATCH -t 24:00:00
module purge
module load intel/2017.1.132 intelmpi/2017.1.132 python/2.7/intel.2017-3 hdf5/1.10.1/intelmpi/intel17
srun smilei < tst1d_02_two_str_instability.py

3]- The output file contain a segmentation fault as following:

more slurm-122042.out
srun: error: cna60: tasks 0-9,11-31: Segmentation fault
srun: Terminating job step 122042.0
slurmstepd: error: *** STEP 122042.0 ON cna60 CANCELLED AT 2019-05-31T15:54:22 ***
srun: error: cna62: tasks 32-63: Terminated
srun: error: cna60: task 10: Terminated
srun: Force Terminated job step 122042.0

I tried my best to figure out what is the problem, and until now I do not know.

2]- ldd smilei gives

    linux-vdso.so.1 =>  (0x00007ffde1eb3000)
    libhdf5.so.101 => /opt/soft/hf/hdf5-1.10.1-intelmpi-intel/lib/libhdf5.so.101 (0x00002adfd4c4f000)
    libpython2.7.so.1.0 => /opt/soft/all/intel/intelpython2/lib/libpython2.7.so.1.0 (0x00002adfd5316000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00002adfd5748000)
    libdl.so.2 => /lib64/libdl.so.2 (0x00002adfd5965000)
    libutil.so.1 => /lib64/libutil.so.1 (0x00002adfd5b69000)
    libm.so.6 => /lib64/libm.so.6 (0x00002adfd5d6c000)
    libmpicxx.so.12 => /opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/mpi/intel64/lib/libmpicxx.so.12 (0x00002adfd606f000)
    libmpifort.so.12 => /opt/soft/all/intel/intelpython2/lib/libmpifort.so.12 (0x00002adfd628f000)
    libmpi.so.12 => /opt/soft/all/intel/intelpython2/lib/libmpi.so.12 (0x00002adfd664e000)
    librt.so.1 => /lib64/librt.so.1 (0x00002adfd737d000)
    libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00002adfd7585000)
    libiomp5.so => /opt/soft/all/intel/intelpython2/lib/libiomp5.so (0x00002adfd788d000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002adfd7c30000)
    libc.so.6 => /lib64/libc.so.6 (0x00002adfd7e46000)
    libz.so.1 => /opt/soft/all/intel/intelpython2/lib/libz.so.1 (0x00002adfd8209000)
    libimf.so => /opt/soft/all/intel/intelpython2/lib/libimf.so (0x00002adfd8425000)
    libsvml.so => /opt/soft/all/intel/intelpython2/lib/libsvml.so (0x00002adfd8923000)
    libirng.so => /opt/soft/all/intel/intelpython2/lib/libirng.so (0x00002adfd982f000)
    libintlc.so.5 => /opt/soft/all/intel/intelpython2/lib/libintlc.so.5 (0x00002adfd9ba2000)
    /lib64/ld-linux-x86-64.so.2 (0x000055e9e554e000)

3]- make env gives

SMILEICXX : mpiicpc
PYTHONEXE : python
MPIVERSION : 
VERSION : ??-??
OPENMP_FLAG : -fopenmp -D_OMP
HDF5_ROOT_DIR : /opt/soft/std/hdf5-1.10.1-intelmpi-intel
SITEDIR : /home/zmc46/bzu91/.local/lib/python2.7/site-packages
PY_CXXFLAGS : -I/opt/soft/all/intel/intelpython2/include/python2.7 -I/opt/soft/all/intel/intelpython2/include/python2.7 -I/opt/soft/all/intel/intelpython2/lib/python2.7/site-packages/numpy/core/include -DSMILEI_USE_NUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
PY_LDFLAGS : -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic
CXXFLAGS : -D__VERSION=\"??-??\" -D_VECTO -std=c++11 -Wall -I/opt/soft/std/hdf5-1.10.1-intelmpi-intel/include -Isrc -Isrc/Checkpoint -Isrc/Collisions -Isrc/Diagnostic -Isrc/DomainDecomposition -Isrc/ElectroMagn -Isrc/ElectroMagnBC -Isrc/ElectroMagnSolver -Isrc/Field -Isrc/Interpolator -Isrc/Ionization -Isrc/MovWindow -Isrc/MultiphotonBreitWheeler -Isrc/Params -Isrc/Patch -Isrc/picsar_interface -Isrc/Profiles -Isrc/Projector -Isrc/Pusher -Isrc/Python -Isrc/Radiation -Isrc/SmileiMPI -Isrc/Species -Isrc/Tools -Ibuild/src/Python -I/opt/soft/all/intel/intelpython2/include/python2.7 -I/opt/soft/all/intel/intelpython2/include/python2.7 -I/opt/soft/all/intel/intelpython2/lib/python2.7/site-packages/numpy/core/include -DSMILEI_USE_NUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -D_VECTO -O3 -g  -fopenmp -D_OMP
LDFLAGS : -L/opt/soft/std/hdf5-1.10.1-intelmpi-intel/lib  -lhdf5 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lm -fopenmp -D_OMP

4]- make config=verbose gives

Unknown smilei version
make: Rien à faire pour « default ».

5]- echo $LD_LIBRARY_PATH gives

/opt/soft/hf/hdf5-1.10.1-intelmpi-intel/lib:/opt/soft/all/intel/intelpython2/lib:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/mpi/intel64/lib:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/mpi/mic/lib:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/compiler/lib/intel64:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/compiler/lib/intel64_lin:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/ipp/lib/intel64:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/compiler/lib/intel64_lin:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/tbb/lib/intel64/gcc4.7:/opt/soft/all/intel/debugger_2017/iga/lib:/opt/soft/all/intel/debugger_2017/libipt/intel64/lib:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/daal/lib/intel64_lin:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/tbb/lib/intel64_lin/gcc4.4

@jderouillat @mccoys any help? I really appreciate your help as I'm not an expert with clusters.
Thanks a lot

MickaelGrechX commented 5 years ago

Dear Homam,

This input file (tst1d_02_two_str_instabilitity) uses 16 patches. This means that you can use up to 16 cores to run it. It seems to me that you try to use way to much resources for this (light) simulation. Can you have a try using eg. 2MPI et 8openMP threads?

Cheers, M

On Fri, May 31, 2019 at 4:25 PM HomamBetar notifications@github.com wrote:

I have compiled the code with the following modules, and an executable smilei has been generated. 1]- Currently Loaded Modules:

1) intel/2017.1.132 2) intelmpi/2017.1.132 3) python/2.7/intel.2017-3 4) hdf5/1.10.1/intelmpi/intel17

2]- I ran the simulation by submitting the follwoing submission file on the cluster (with two stream instability)

!/bin/bash #SBATCH -N 2 #SBATCH -p std #SBATCH -J mpiSmilei #SBATCH -n 64

SBATCH --ntasks-per-node=32 #SBATCH -t 24:00:00 module purge module load

intel/2017.1.132 intelmpi/2017.1.132 python/2.7/intel.2017-3 hdf5/1.10.1/intelmpi/intel17 srun smilei < tst1d_02_two_str_instability.py

3]- The output file contain a segmentation fault as following: more slurm-122042.out srun: error: cna60: tasks 0-9,11-31: Segmentation fault srun: Terminating job step 122042.0 slurmstepd: error: STEP 122042.0 ON cna60 CANCELLED AT 2019-05-31T15:54:22 srun: error: cna62: tasks 32-63: Terminated srun: error: cna60: task 10: Terminated srun: Force Terminated job step 122042.0

I tried my best to figure out what is the problem, and until now I do not know.

2]- ldd smilei gives linux-vdso.so.1 => (0x00007ffde1eb3000) libhdf5.so.101 => /opt/soft/hf/hdf5-1.10.1-intelmpi-intel/lib/libhdf5.so.101 (0x00002adfd4c4f000) libpython2.7.so.1.0 => /opt/soft/all/intel/intelpython2/lib/libpython2.7.so.1.0 (0x00002adfd5316000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002adfd5748000) libdl.so.2 => /lib64/libdl.so.2 (0x00002adfd5965000) libutil.so.1 => /lib64/libutil.so.1 (0x00002adfd5b69000) libm.so.6 => /lib64/libm.so.6 (0x00002adfd5d6c000) libmpicxx.so.12 => /opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/mpi/intel64/lib/libmpicxx.so.12 (0x00002adfd606f000) libmpifort.so.12 => /opt/soft/all/intel/intelpython2/lib/libmpifort.so.12 (0x00002adfd628f000) libmpi.so.12 => /opt/soft/all/intel/intelpython2/lib/libmpi.so.12 (0x00002adfd664e000) librt.so.1 => /lib64/librt.so.1 (0x00002adfd737d000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00002adfd7585000) libiomp5.so => /opt/soft/all/intel/intelpython2/lib/libiomp5.so (0x00002adfd788d000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002adfd7c30000) libc.so.6 => /lib64/libc.so.6 (0x00002adfd7e46000) libz.so.1 => /opt/soft/all/intel/intelpython2/lib/libz.so.1 (0x00002adfd8209000) libimf.so => /opt/soft/all/intel/intelpython2/lib/libimf.so (0x00002adfd8425000) libsvml.so => /opt/soft/all/intel/intelpython2/lib/libsvml.so (0x00002adfd8923000) libirng.so => /opt/soft/all/intel/intelpython2/lib/libirng.so (0x00002adfd982f000) libintlc.so.5 => /opt/soft/all/intel/intelpython2/lib/libintlc.so.5 (0x00002adfd9ba2000) /lib64/ld-linux-x86-64.so.2 (0x000055e9e554e000)

3]- make env gives SMILEICXX : mpiicpc PYTHONEXE : python MPIVERSION : VERSION : ??-?? OPENMP_FLAG : -fopenmp -D_OMP HDF5_ROOT_DIR : /opt/soft/std/hdf5-1.10.1-intelmpi-intel SITEDIR : /home/zmc46/bzu91/.local/lib/python2.7/site-packages PY_CXXFLAGS : -I/opt/soft/all/intel/intelpython2/include/python2.7 -I/opt/soft/all/intel/intelpython2/include/python2.7 -I/opt/soft/all/intel/intelpython2/lib/python2.7/site-packages/numpy/core/include -DSMILEI_USE_NUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION PY_LDFLAGS : -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic CXXFLAGS : -D__VERSION=\"??-??\" -D_VECTO -std=c++11 -Wall -I/opt/soft/std/hdf5-1.10.1-intelmpi-intel/include -Isrc -Isrc/Checkpoint -Isrc/Collisions -Isrc/Diagnostic -Isrc/DomainDecomposition -Isrc/ElectroMagn -Isrc/ElectroMagnBC -Isrc/ElectroMagnSolver -Isrc/Field -Isrc/Interpolator -Isrc/Ionization -Isrc/MovWindow -Isrc/MultiphotonBreitWheeler -Isrc/Params -Isrc/Patch -Isrc/picsar_interface -Isrc/Profiles -Isrc/Projector -Isrc/Pusher -Isrc/Python -Isrc/Radiation -Isrc/SmileiMPI -Isrc/Species -Isrc/Tools -Ibuild/src/Python -I/opt/soft/all/intel/intelpython2/include/python2.7 -I/opt/soft/all/intel/intelpython2/include/python2.7 -I/opt/soft/all/intel/intelpython2/lib/python2.7/site-packages/numpy/core/include -DSMILEI_USE_NUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -D_VECTO -O3 -g -fopenmp -D_OMP LDFLAGS : -L/opt/soft/std/hdf5-1.10.1-intelmpi-intel/lib -lhdf5 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lm -fopenmp -D_OMP

4]- make config=verbose gives

Unknown smilei version make: Rien à faire pour « default ».

5]- echo $LD_LIBRARY_PATH gives

/opt/soft/hf/hdf5-1.10.1-intelmpi-intel/lib:/opt/soft/all/intel/intelpython2/lib:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/mpi/intel64/lib:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/mpi/mic/lib:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/compiler/lib/intel64:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/compiler/lib/intel64_lin:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/ipp/lib/intel64:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/compiler/lib/intel64_lin:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/tbb/lib/intel64/gcc4.7:/opt/soft/all/intel/debugger_2017/iga/lib:/opt/soft/all/intel/debugger_2017/libipt/intel64/lib:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/daal/lib/intel64_lin:/opt/soft/all/intel/compilers_and_libraries_2017.1.132/linux/tbb/lib/intel64_lin/gcc4.4

@jderouillat https://github.com/jderouillat @mccoys https://github.com/mccoys any help? I really appreciate your help as I'm not an expert with clusters. Thanks a lot

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mccoys commented 5 years ago

Also, please indicate at what point the simulation crash. For example, submit the full output log.

mccoys commented 5 years ago

And you could also try smilei_test in your login node (not submitting a job) to see if this works. Just type smilei_test path/to/simulation.py

HomamBetar commented 5 years ago

I tried smilei_test, but always segfault [bzu91@vm-zmc46 Smilei-4.1]$ ls benchmarks happi scripts slurm-122407.out src validation build License slurm-122042.out smilei subSmilei.slurm databases makefile slurm-122404.out smilei.sh tst1d_02_two_str_instability.py doc README.md slurm-122405.out smilei_test tst1d_07_cir_plane_wave_rela.py

[bzu91@vm-zmc46 Smilei-4.1]$ ./smilei_test tst1d_02_two_str_instability.py Erreur de segmentation [bzu91@vm-zmc46 Smilei-4.1]$

output file is attached to this comment. [slurm-122042.txt](https://github.com/SmileiPIC/Smilei/files/3247825/slurm-122042.txt

mccoys commented 5 years ago

The program does not even start it seems. There must be something wrong in your setup.

First things first: have you cleaned your build after you made changes in your environment? make clean and make again.

HomamBetar commented 5 years ago

@mccoys @MickaelGrechX @jderouillat Thanks a lot for your help. Everything is working fine now and the simulation has performed successfully. Should I submit submit the submission file on EXPLOR cluster here? or send it by email?

mccoys commented 5 years ago

As you wish. You can propose a pull request with your new file, or send it to one of us.