DWARF error while linking smilei

Goo-JZhang commented 2 years ago

Need help regarding installation? Read this doc first: https://smileipic.github.io/Smilei/installation.html
Issues installing C++, MPI, HDF5 or python? Please refer to your system administrator first.
If you are still in trouble, please provide the result of these commands in the issue: git describe --all --long make config=verbose make env echo $LD_LIBRARY_PATH # on mac: echo $DYLD_LIBRARY_PATH python -m sysconfig ldd smilei

I tried to run smilei in WSL2 but met some problem in the make process.

here is my dependencies information (I've follow the installing step provided for Linux): gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 Python 3.9.7 HDF5-1.12.1 MPICH-4.0.2

here is the error info: Linking smilei /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 3319 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 3377 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 740e /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 741a /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7a81 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7ac8 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7b0f /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7b56 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7b85 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7bc0 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7bcc /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7c07 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7c13 build/src/Tools/H5.o: in function H5::init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, int*, bool)': /home/zjlwsl/smilei/Smilei/src/Tools/H5.cpp:41: undefined reference toH5Pset_fapl_mpio' /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/zjlwsl/smilei/Smilei/src/Tools/H5.cpp:65: undefined reference to `H5Pset_dxpl_mpio' collect2: error: ld returned 1 exit status make: *** [makefile:298: smilei] Error 1

I don't know how to deal with it, does anyone could help me? With my great appreciation.

iltommi commented 2 years ago

This probably means that you have HDF5 serial version. Smilei uses the MPI version.

Since WSL2 is basically a linux, follow the linux installation written in the Smilei doc

Sorry I can't help more, you should provide some answers to these questions:

git describe --all --long make config=verbose make env echo $LD_LIBRARY_PATH # on mac: echo $DYLD_LIBRARY_PATH python -m sysconfig ldd smilei

Goo-JZhang commented 2 years ago

git describe --all --long heads/master-0-gd021d9e08

make config=verbose Linking smilei mpicxx build/src/Checkpoint/Checkpoint.o build/src/Collisions/CollisionsSingle.o build/src/Collisions/Collisions.o build/src/Collisions/CollisionalFusionDD.o build/src/Collisions/CollisionalIonization.o build/src/Collisions/CollisionalNuclearReaction.o build/src/Diagnostic/DiagnosticFields.o build/src/Diagnostic/DiagnosticProbes.o build/src/Diagnostic/TimeSelection.o build/src/Diagnostic/DiagnosticFields1D.o build/src/Diagnostic/Histogram.o build/src/Diagnostic/DiagnosticRadiationSpectrum.o build/src/Diagnostic/DiagnosticFields3D.o build/src/Diagnostic/DiagnosticTrack.o build/src/Diagnostic/DiagnosticScalar.o build/src/Diagnostic/DiagnosticParticleBinningBase.o build/src/Diagnostic/DiagnosticScreen.o build/src/Diagnostic/DiagnosticPerformances.o build/src/Diagnostic/DiagnosticFields2D.o build/src/Diagnostic/DiagnosticParticleBinning.o build/src/Diagnostic/DiagnosticFieldsAM.o build/src/DomainDecomposition/GlobalDomainDecomposition.o build/src/DomainDecomposition/Hilbert_functions.o build/src/DomainDecomposition/HilbertDomainDecomposition.o build/src/DomainDecomposition/RegionDomainDecomposition.o build/src/DomainDecomposition/LinearizedDomainDecomposition.o build/src/ElectroMagn/LaserEnvelope1D.o build/src/ElectroMagn/LaserPropagator.o build/src/ElectroMagn/LaserEnvelope2D.o build/src/ElectroMagn/ElectroMagn2D.o build/src/ElectroMagn/ElectroMagn.o build/src/ElectroMagn/ElectroMagnAM.o build/src/ElectroMagn/Laser.o build/src/ElectroMagn/ElectroMagn3D.o build/src/ElectroMagn/LaserEnvelope.o build/src/ElectroMagn/LaserEnvelopeAM.o build/src/ElectroMagn/LaserEnvelope3D.o build/src/ElectroMagn/ElectroMagn1D.o build/src/ElectroMagnBC/EnvelopeBCAM_refl.o build/src/ElectroMagnBC/ElectroMagnBC2D_refl.o build/src/ElectroMagnBC/ElectroMagnBCAM_ramp.o build/src/ElectroMagnBC/EnvelopeBC1D_refl.o build/src/ElectroMagnBC/EnvelopeBC.o build/src/ElectroMagnBC/ElectroMagnBCAM_BM.o build/src/ElectroMagnBC/ElectroMagnBC2D.o build/src/ElectroMagnBC/ElectroMagnBC.o build/src/ElectroMagnBC/ElectroMagnBCAM.o build/src/ElectroMagnBC/EnvelopeBCAM_Axis.o build/src/ElectroMagnBC/ElectroMagnBC2D_Trans_Damping.o build/src/ElectroMagnBC/ElectroMagnBCAM_SM.o build/src/ElectroMagnBC/ElectroMagnBC3D_SM.o build/src/ElectroMagnBC/ElectroMagnBC3D_refl.o build/src/ElectroMagnBC/ElectroMagnBC1D_SM.o build/src/ElectroMagnBC/EnvelopeBC2D_refl.o build/src/ElectroMagnBC/ElectroMagnBCAM_PML.o build/src/ElectroMagnBC/EnvelopeBC3D_refl.o build/src/ElectroMagnBC/ElectroMagnBC2D_PML.o build/src/ElectroMagnBC/ElectroMagnBC2D_SM.o build/src/ElectroMagnBC/ElectroMagnBC1D_refl.o build/src/ElectroMagnBC/ElectroMagnBC3D.o build/src/ElectroMagnBC/ElectroMagnBC3D_BM.o build/src/ElectroMagnBC/ElectroMagnBC1D.o build/src/ElectroMagnBC/ElectroMagnBC3D_PML.o build/src/ElectroMagnSolver/MA_Solver2D_norm.o build/src/ElectroMagnSolver/MF_Solver2D_GrassiSpL.o build/src/ElectroMagnSolver/PML_SolverAM.o build/src/ElectroMagnSolver/MF_Solver1D_Yee.o build/src/ElectroMagnSolver/MA_Solver3D_norm.o build/src/ElectroMagnSolver/PXR_Solver2D_GPSTD.o build/src/ElectroMagnSolver/PML_Solver2D_Bouchard.o build/src/ElectroMagnSolver/MA_Solver1D_norm.o build/src/ElectroMagnSolver/MF_Solver3D_Bouchard.o build/src/ElectroMagnSolver/MF_Solver3D_Lehe.o build/src/ElectroMagnSolver/MF_Solver2D_Bouchard.o build/src/ElectroMagnSolver/MF_Solver2D_Lehe.o build/src/ElectroMagnSolver/MF_Solver2D_Grassi.o build/src/ElectroMagnSolver/MA_Solver2D_Friedman.o build/src/ElectroMagnSolver/PML_Solver3D_Bouchard.o build/src/ElectroMagnSolver/MF_SolverAM_Yee.o build/src/ElectroMagnSolver/MF_Solver3D_M4.o build/src/ElectroMagnSolver/PML_Solver2D_Yee.o build/src/ElectroMagnSolver/PXR_Solver3D_FDTD.o build/src/ElectroMagnSolver/MA_SolverAM_norm.o build/src/ElectroMagnSolver/MF_Solver2D_Yee.o build/src/ElectroMagnSolver/MF_Solver3D_Yee.o build/src/ElectroMagnSolver/MF_Solver1D_M4.o build/src/ElectroMagnSolver/MF_Solver2D_M4.o build/src/ElectroMagnSolver/PML_Solver3D_Yee.o build/src/ElectroMagnSolver/PXR_SolverAM_GPSTD.o build/src/ElectroMagnSolver/MF_Solver2D_Cowan.o build/src/ElectroMagnSolver/PXR_Solver3D_GPSTD.o build/src/Field/cField1D.o build/src/Field/Field1D.o build/src/Field/Field2D.o build/src/Field/cField2D.o build/src/Field/Field3D.o build/src/Field/cField3D.o build/src/Interpolator/Interpolator1D2OrderV.o build/src/Interpolator/Interpolator2DWT2OrderV.o build/src/Interpolator/Interpolator2D2OrderV.o build/src/Interpolator/Interpolator2D4Order.o build/src/Interpolator/Interpolator3DWT4Order.o build/src/Interpolator/Interpolator2D2Order.o build/src/Interpolator/Interpolator1D3Order.o build/src/Interpolator/Interpolator1DWT2OrderV.o build/src/Interpolator/Interpolator.o build/src/Interpolator/Interpolator2DWT4OrderV.o build/src/Interpolator/Interpolator3D2OrderV.o build/src/Interpolator/Interpolator1DWT4Order.o build/src/Interpolator/Interpolator2DWT2Order.o build/src/Interpolator/Interpolator3D4OrderV.o build/src/Interpolator/Interpolator1D2Order.o build/src/Interpolator/InterpolatorAM2Order.o build/src/Interpolator/Interpolator3D2Order.o build/src/Interpolator/Interpolator2DWT4Order.o build/src/Interpolator/Interpolator1DWT2Order.o build/src/Interpolator/InterpolatorAM1Order.o build/src/Interpolator/InterpolatorAM.o build/src/Interpolator/Interpolator3DWT2Order.o build/src/Interpolator/Interpolator3DWT2OrderV.o build/src/Interpolator/Interpolator1D.o build/src/Interpolator/Interpolator2D.o build/src/Interpolator/Interpolator3D.o build/src/Interpolator/Interpolator3DWT4OrderV.o build/src/Interpolator/Interpolator2D4OrderV.o build/src/Interpolator/Interpolator1D4Order.o build/src/Interpolator/Interpolator3D4Order.o build/src/Ionization/IonizationFromRate.o build/src/Ionization/IonizationTunnelEnvelopeAveraged.o build/src/Ionization/IonizationTunnel.o build/src/Ionization/Ionization.o build/src/Ionization/IonizationTables.o build/src/Merging/Merging.o build/src/Merging/MergingVranicSpherical.o build/src/Merging/MergingVranicCartesian.o build/src/MovWindow/SimWindow.o build/src/MultiphotonBreitWheeler/MultiphotonBreitWheelerTablesDefault.o build/src/MultiphotonBreitWheeler/MultiphotonBreitWheelerTables.o build/src/MultiphotonBreitWheeler/MultiphotonBreitWheeler.o build/src/Params/PeekAtSpecies.o build/src/Params/Params.o build/src/Params/OpenPMDparams.o build/src/ParticleBC/PartWall.o build/src/ParticleBC/PartBoundCond.o build/src/ParticleBC/BoundaryConditionType.o build/src/ParticleInjector/ParticleInjector.o build/src/Particles/Particle.o build/src/Particles/Particles.o build/src/Particles/ParticleCreator.o build/src/Patch/Patch.o build/src/Patch/VectorPatch.o build/src/Patch/SyncVectorPatch.o build/src/Patch/Patch2D.o build/src/Patch/Region.o build/src/Patch/DoubleGrids.o build/src/Patch/Patch3D.o build/src/Patch/PatchAM.o build/src/Patch/Patch1D.o build/src/Patch/DoubleGridsAM.o build/src/Profiles/Profile.o build/src/Profiles/Function.o build/src/Projector/Projector2D2OrderV.o build/src/Projector/ProjectorAM2Order.o build/src/Projector/Projector3D2Order.o build/src/Projector/Projector3D2OrderV.o build/src/Projector/ProjectorAM.o build/src/Projector/Projector3D4OrderV.o build/src/Projector/Projector3D.o build/src/Projector/Projector3D4Order.o build/src/Projector/Projector1D2Order.o build/src/Projector/ProjectorAM1Order.o build/src/Projector/Projector2D2Order.o build/src/Projector/Projector.o build/src/Projector/Projector1D.o build/src/Projector/Projector1D4Order.o build/src/Projector/Projector2D4OrderV.o build/src/Projector/Projector3D2OrderGPU.o build/src/Projector/Projector2D4Order.o build/src/Projector/Projector2D.o build/src/Pusher/PusherPonderomotivePositionBoris.o build/src/Pusher/PusherBorisNR.o build/src/Pusher/PusherVay.o build/src/Pusher/Pusher.o build/src/Pusher/PusherHigueraCary.o build/src/Pusher/PusherPhoton.o build/src/Pusher/PusherBoris.o build/src/Pusher/PusherPonderomotiveBoris.o build/src/Radiation/RadiationDiagRadiationSpectrum.o build/src/Radiation/RadiationCorrLandauLifshitz.o build/src/Radiation/Radiation.o build/src/Radiation/RadiationNiel.o build/src/Radiation/RadiationTablesDefault.o build/src/Radiation/RadiationLandauLifshitz.o build/src/Radiation/RadiationTables.o build/src/Radiation/RadiationMonteCarlo.o build/src/Radiation/RadiationTools.o build/src/Smilei.o build/src/SmileiMPI/SmileiMPI.o build/src/SmileiMPI/SmileiMPI_test.o build/src/SmileiMPI/AsyncMPIbuffers.o build/src/Species/SpeciesVAdaptiveMixedSort.o build/src/Species/Species.o build/src/Species/SpeciesMetrics.o build/src/Species/SpeciesVAdaptive.o build/src/Species/SpeciesV.o build/src/Tools/Tools.o build/src/Tools/H5.o build/src/Tools/userFunctions.o build/src/Tools/Timer.o build/src/Tools/PyTools.o build/src/Tools/backward.o build/src/Tools/Timers.o build/src/Tools/tabulatedFunctions.o build/src/picsar_interface/interface.o -o build/smilei -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -lhdf5 -L/home/zjlwsl/anaconda3/lib/python3.9/config-3.9-x86_64-linux-gnu -lpython3.9 -lcrypt -lpthread -ldl -lutil -lm -lm -Xlinker -export-dynamic -lm -fopenmp -D_OMP /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 3319 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 3377 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 740e /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 741a /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7a81 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7ac8 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7b0f /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7b56 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7b85 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7bc0 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7bcc /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7c07 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7c13 build/src/Tools/H5.o: in function H5::init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, int*, bool)': /home/zjlwsl/smilei/Smilei/src/Tools/H5.cpp:41: undefined reference toH5Pset_fapl_mpio' /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/zjlwsl/smilei/Smilei/src/Tools/H5.cpp:65: undefined reference to `H5Pset_dxpl_mpio' collect2: error: ld returned 1 exit status make: *** [makefile:298: smilei] Error 1

make env VERSION : 4.7-5-gd021d9e08-master SMILEICXX : mpicxx OPENMP_FLAG : -fopenmp -D_OMP HDF5_ROOT_DIR : FFTW3_LIB_DIR : SITEDIR : /home/zjlwsl/.local/lib/python3.9/site-packages PYTHONEXE : python PY_CXXFLAGS : -I/home/zjlwsl/anaconda3/include/python3.9 -I/home/zjlwsl/anaconda3/include/python3.9 -I/home/zjlwsl/anaconda3/lib/python3.9/site-packages/numpy/core/include -DSMILEI_USE_NUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION PY_LDFLAGS : -L/home/zjlwsl/anaconda3/lib/python3.9/config-3.9-x86_64-linux-gnu -lpython3.9 -lcrypt -lpthread -ldl -lutil -lm -lm -Xlinker -export-dynamic CXXFLAGS : -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -D__VERSION=\"4.7-5-gd021d9e08-master\" -D_VECTO -std=c++11 -Wall -Isrc -Isrc/SmileiMPI -Isrc/MovWindow -Isrc/Ionization -Isrc/Field -Isrc/Collisions -Isrc/Params -Isrc/ElectroMagnSolver -Isrc/MultiphotonBreitWheeler -Isrc/ElectroMagn -Isrc/DomainDecomposition -Isrc/Merging -Isrc/picsar_interface -Isrc/Interpolator -Isrc/Projector -Isrc/ParticleBC -Isrc/Diagnostic -Isrc/Radiation -Isrc/Tools -Isrc/Patch -Isrc/Python -Isrc/Profiles -Isrc/ElectroMagnBC -Isrc/Particles -Isrc/Species -Isrc/Checkpoint -Isrc/ParticleInjector -Isrc/Pusher -Ibuild/src/Python -I/home/zjlwsl/anaconda3/include/python3.9 -I/home/zjlwsl/anaconda3/include/python3.9 -I/home/zjlwsl/anaconda3/lib/python3.9/site-packages/numpy/core/include -DSMILEI_USE_NUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -O3 -g -fopenmp -D_OMP LDFLAGS : -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -lhdf5 -L/home/zjlwsl/anaconda3/lib/python3.9/config-3.9-x86_64-linux-gnu -lpython3.9 -lcrypt -lpthread -ldl -lutil -lm -lm -Xlinker -export-dynamic -lm -fopenmp -D_OMP

echo $LD_LIBRARY_PATH :/home/zjlwsl/hdf5/lib:/home/zjlwsl/hdf5/lib:/home/zjlwsl/hdf5/lib:/home/zjlwsl/hdf5/lib

python -m sysconfig Platform: "linux-x86_64" Python version: "3.9" Current installation scheme: "posix_prefix"

Paths: data = "/home/zjlwsl/anaconda3" include = "/home/zjlwsl/anaconda3/include/python3.9" platinclude = "/home/zjlwsl/anaconda3/include/python3.9" platlib = "/home/zjlwsl/anaconda3/lib/python3.9/site-packages" platstdlib = "/home/zjlwsl/anaconda3/lib/python3.9" purelib = "/home/zjlwsl/anaconda3/lib/python3.9/site-packages" scripts = "/home/zjlwsl/anaconda3/bin" stdlib = "/home/zjlwsl/anaconda3/lib/python3.9"

Variables: ABIFLAGS = "" AC_APPLE_UNIVERSAL_BUILD = "0" AIX_BUILDDATE = "0" AIX_GENUINE_CPLUSPLUS = "0" ALT_SOABI = "0" ANDROID_API_LEVEL = "0" AR = "x86_64-conda-linux-gnu-ar" ARFLAGS = "rcs" BASECFLAGS = "-Wno-unused-result -Wsign-compare" BASECPPFLAGS = "-IObjects -IInclude -IPython" BASEMODLIBS = "" BINDIR = "/home/zjlwsl/anaconda3/bin" BINLIBDEST = "/home/zjlwsl/anaconda3/lib/python3.9" BLDLIBRARY = "libpython3.9.a" BLDSHARED = " x86_64-conda-linux-gnu-gcc -pthread -shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib" BUILDEXE = "" BUILDPYTHON = "python" BUILD_GNU_TYPE 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-L/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib" LDLIBRARY = "libpython3.9.a" LDLIBRARYDIR = "" LDSHARED = " x86_64-conda-linux-gnu-gcc -pthread -shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib" LDVERSION = "3.9" LIBC = "" LIBDEST = "/home/zjlwsl/anaconda3/lib/python3.9" LIBDIR = "/home/zjlwsl/anaconda3/lib" LIBFFI_INCLUDEDIR = "/home/zjlwsl/anaconda3/include" LIBM = "-lm" LIBOBJDIR = "Python/" LIBOBJS = "" LIBPC = "/home/zjlwsl/anaconda3/lib/pkgconfig" LIBPL = "/home/zjlwsl/anaconda3/lib/python3.9/config-3.9-x86_64-linux-gnu" LIBPYTHON = "" LIBRARY = "libpython3.9.a" LIBRARY_OBJS = "\" LIBRARY_OBJS_OMIT_FROZEN = "\" LIBS = "-lcrypt -lpthread -ldl -lutil -lm" LIBSUBDIRS = "tkinter tkinter/test tkinter/test/test_tkinter \" LINKCC = " x86_64-conda-linux-gnu-gcc -pthread" LINKFORSHARED = "-Xlinker -export-dynamic" LIPO_32BIT_FLAGS = "" LIPO_INTEL64_FLAGS = "" LLVM_PROF_ERR = "no" LLVM_PROF_FILE = "" LLVM_PROF_MERGER = "true" LN = "ln" LOCALMODLIBS = "" MACHDEP = "linux" MACHDEP_OBJS = "" MACHDESTLIB = "/home/zjlwsl/anaconda3/lib/python3.9" MACOSX_DEPLOYMENT_TARGET = "" MAINCC = " x86_64-conda-linux-gnu-gcc -pthread" MAJOR_IN_MKDEV = "0" MAJOR_IN_SYSMACROS = "0" MAKESETUP = "/tmp/build/80754af9/python-split_1631797238431/work/Modules/makesetup" MANDIR = "/home/zjlwsl/anaconda3/share/man" MKDIR_P = "/usr/bin/mkdir -p" MODBUILT_NAMES = "posix errno pwd _sre _codecs _weakref _functools _operator _collections _abc itertools atexit _signal _stat time _thread _locale _io faulthandler _tracemalloc _peg_parser _symtable xxsubtype" MODDISABLED_NAMES = "" MODLIBS = "" MODOBJS = "Modules/posixmodule.o Modules/errnomodule.o Modules/pwdmodule.o Modules/_sre.o Modules/_codecsmodule.o Modules/_weakref.o Modules/_functoolsmodule.o Modules/_operator.o Modules/_collectionsmodule.o Modules/_abc.o Modules/itertoolsmodule.o Modules/atexitmodule.o Modules/signalmodule.o Modules/_stat.o Modules/timemodule.o Modules/_threadmodule.o Modules/_localemodule.o Modules/_iomodule.o Modules/iobase.o Modules/fileio.o Modules/bytesio.o Modules/bufferedio.o Modules/textio.o Modules/stringio.o Modules/faulthandler.o Modules/_tracemalloc.o Modules/_peg_parser.o Modules/symtablemodule.o Modules/xxsubtype.o" MODULE_OBJS = "\" MULTIARCH = "x86_64-linux-gnu" MULTIARCH_CPPFLAGS = "-DMULTIARCH=\"x86_64-linux-gnu\"" MVWDELCH_IS_EXPRESSION = "1" NO_AS_NEEDED = "-Wl,--no-as-needed" OBJECT_OBJS = "\" OPENSSL_INCLUDES = "-I/home/zjlwsl/anaconda3/include" OPENSSL_LDFLAGS = "-L/home/zjlwsl/anaconda3/lib" OPENSSL_LIBS = "-lssl -lcrypto" OPT = "-DNDEBUG -O2 -Wall" OTHER_LIBTOOL_OPT = "" PACKAGE_BUGREPORT = "0" PACKAGE_NAME = "0" PACKAGE_STRING = "0" PACKAGE_TARNAME = "0" PACKAGE_URL = "0" PACKAGE_VERSION = "0" PARSER_HEADERS = "\" PARSER_OBJS = "\ \ Parser/myreadline.o Parser/parsetok.o Parser/tokenizer.o" PEGEN_HEADERS = "\" PEGEN_OBJS = "\" PGO_PROF_GEN_FLAG = "-fprofile-generate" PGO_PROF_USE_FLAG = " " PLATLIBDIR = "lib" POBJS = "\" POSIX_SEMAPHORES_NOT_ENABLED = "0" PROFILE_TASK = "-m test --pgo" PTHREAD_KEY_T_IS_COMPATIBLE_WITH_INT = "1" PTHREAD_SYSTEM_SCHED_SUPPORTED = "1" PURIFY = "" PY3LIBRARY = "" PYLONG_BITS_IN_DIGIT = "0" PYTHON = "python" PYTHONFRAMEWORK = "" PYTHONFRAMEWORKDIR = "no-framework" PYTHONFRAMEWORKINSTALLDIR = "" PYTHONFRAMEWORKPREFIX = "" PYTHONPATH = "" PYTHON_FOR_BUILD = "./python -E" PYTHON_HEADERS = "\" PYTHON_OBJS = "\" PY_BUILD_ENVIRON = "" PY_BUILTIN_HASHLIB_HASHES = ""md5,sha1,sha256,sha512,sha3,blake2"" PY_BUILTIN_MODULE_CFLAGS = "-Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -g -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -fvisibility=hidden -I/tmp/build/80754af9/python-split_1631797238431/work/Include/internal -IObjects -IInclude -IPython -I. -I/tmp/build/80754af9/python-split_1631797238431/work/Include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -DPy_BUILD_CORE_BUILTIN" PY_CFLAGS = "-Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include " PY_CFLAGS_NODIST = " -g -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -fvisibility=hidden -I/tmp/build/80754af9/python-split_1631797238431/work/Include/internal" PY_COERCE_C_LOCALE = "1" PY_CORE_CFLAGS = "-Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -g -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -fvisibility=hidden -I/tmp/build/80754af9/python-split_1631797238431/work/Include/internal -IObjects -IInclude -IPython -I. -I/tmp/build/80754af9/python-split_1631797238431/work/Include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -DPy_BUILD_CORE" PY_CORE_LDFLAGS = "-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -g" PY_CPPFLAGS = "-IObjects -IInclude -IPython -I. -I/tmp/build/80754af9/python-split_1631797238431/work/Include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include" PY_FORMAT_SIZE_T = ""z"" PY_LDFLAGS = "-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib" PY_LDFLAGS_NODIST = " -g" PY_SSL_DEFAULT_CIPHERS = "1" PY_SSL_DEFAULT_CIPHER_STRING = "0" PY_STDMODULE_CFLAGS = "-Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -g -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -fvisibility=hidden -I/tmp/build/80754af9/python-split_1631797238431/work/Include/internal -IObjects -IInclude -IPython -I. -I/tmp/build/80754af9/python-split_1631797238431/work/Include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include" Py_DEBUG = "0" Py_ENABLE_SHARED = "0" Py_HASH_ALGORITHM = "0" Py_TRACE_REFS = "0" QUICKTESTOPTS = "-x test_subprocess test_io test_lib2to3 \" READELF = "x86_64-conda-linux-gnu-readelf" RESSRCDIR = "Mac/Resources/framework" RETSIGTYPE = "void" RUNSHARED = "" SCRIPTDIR = "/home/zjlwsl/anaconda3/lib" SETPGRP_HAVE_ARG = "0" SGI_ABI = "" SHELL = "/bin/sh" SHLIBS = "-lcrypt -lpthread -ldl -lutil -lm" SHLIB_SUFFIX = ".so" SHM_NEEDS_LIBRT = "1" SIGNED_RIGHT_SHIFT_ZERO_FILLS = "0" SITEPATH = "" SIZEOF_DOUBLE = "8" SIZEOF_FLOAT = "4" SIZEOF_FPOS_T = "16" SIZEOF_INT = "4" SIZEOF_LONG = "8" SIZEOF_LONG_DOUBLE = "16" SIZEOF_LONG_LONG = "8" SIZEOF_OFF_T = "8" SIZEOF_PID_T = "4" SIZEOF_PTHREAD_KEY_T = "4" SIZEOF_PTHREAD_T = "8" SIZEOF_SHORT = "2" SIZEOF_SIZE_T = "8" SIZEOF_TIME_T = "8" SIZEOF_UINTPTR_T = "8" SIZEOF_VOID_P = "8" SIZEOF_WCHAR_T = "4" SIZEOF__BOOL = "1" SO = ".cpython-39-x86_64-linux-gnu.so" SOABI = "cpython-39-x86_64-linux-gnu" SRCDIRS = "Parser Parser/pegen Objects Python Modules Modules/_io Programs" SRC_GDB_HOOKS = "/tmp/build/80754af9/python-split_1631797238431/work/Tools/gdb/libpython.py" STDC_HEADERS = "1" STRICT_SYSV_CURSES = "/ Don't use ncurses extensions /" STRIPFLAG = "-s" SUBDIRS = "" SUBDIRSTOO = "Include Lib Misc" SYSLIBS = "-lm" SYS_SELECT_WITH_SYS_TIME = "1" TCLTK_INCLUDES = "-I/home/zjlwsl/anaconda3/include" TCLTK_LIBS = "-L/home/zjlwsl/anaconda3/lib -ltcl8.6 -ltk8.6" TESTOPTS = "" TESTPATH = "" TESTPYTHON = "./python" TESTPYTHONOPTS = "" TESTRUNNER = "./python /tmp/build/80754af9/python-split_1631797238431/work/Tools/scripts/run_tests.py" TESTTIMEOUT = "1200" TIMEMODULE_LIB = "0" TIME_WITH_SYS_TIME = "1" TM_IN_SYS_TIME = "0" TZPATH = "/home/zjlwsl/anaconda3/share/zoneinfo:/home/zjlwsl/anaconda3/share/tzinfo" UNICODE_DEPS = "\" UNIVERSALSDK = "" UPDATE_FILE = "python3 /tmp/build/80754af9/python-split_1631797238431/work/Tools/scripts/update_file.py" USE_COMPUTED_GOTOS = "1" VERSION = "3.9" VPATH = "/tmp/build/80754af9/python-split_1631797238431/work" WINDOW_HAS_FLAGS = "1" WITH_DECIMAL_CONTEXTVAR = "1" WITH_DOC_STRINGS = "1" WITH_DTRACE = "0" WITH_DYLD = "0" WITH_LIBINTL = "0" WITH_NEXT_FRAMEWORK = "0" WITH_PYMALLOC = "1" WITH_VALGRIND = "0" X87_DOUBLE_ROUNDING = "0" XMLLIBSUBDIRS = "xml xml/dom xml/etree xml/parsers xml/sax" abiflags = "" abs_builddir = "/tmp/build/80754af9/python-split_1631797238431/work/build-static" abs_srcdir = "/tmp/build/80754af9/python-split_1631797238431/work" base = "/home/zjlwsl/anaconda3" datarootdir = "/home/zjlwsl/anaconda3/share" exec_prefix = "/home/zjlwsl/anaconda3" installed_base = "/home/zjlwsl/anaconda3" installed_platbase = "/home/zjlwsl/anaconda3" platbase = "/home/zjlwsl/anaconda3" platlibdir = "lib" prefix = "/home/zjlwsl/anaconda3" projectbase = "/home/zjlwsl/anaconda3/bin" py_version = "3.9.7" py_version_nodot = "39" py_version_short = "3.9" srcdir = "/home/zjlwsl/anaconda3/lib/python3.9/config-3.9-x86_64-linux-gnu" userbase = "/home/zjlwsl/.local"

ldd smilei ldd: ./smilei: No such file or directory

iltommi commented 2 years ago

How did you install hdf5?

mccoys commented 2 years ago

the hdf5 path is not set in HDF5_ROOT_DIR

Goo-JZhang commented 2 years ago

the hdf5 path is not set in HDF5_ROOT_DIR

Is that 'export HDF5_ROOT_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi' not enough?

Goo-JZhang commented 2 years ago

How did you install hdf5?

First, download the hdf5-1.12.1.tar from https://www.hdfgroup.org/downloads/hdf5/source-code/ Then unpack the file and configure it by ./configure --prefix=MYPATH --enable-fortran --enable-parallel After that make and make install Finally add hdf5 path to bash.

here are what I add to .bashrc

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/zjlwsl/hdf5/lib

export PATH=$PATH:/home/zjlwsl/hdf5/bin

export CPATH=:$CPATH:/home/zjlwsl/hdf5/include

export HDF5_MPI="ON"

iltommi commented 2 years ago

Is that 'export HDF5_ROOT_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi' not enough?

That should the same as MYPATH (maybe /home/zjlwsl/hdf5?), but in the above command I asked to print (make env) HDF5_ROOT_DIR is empty

HDF5_ROOT_DIR is the directory in which you have 2 subdirectories :

include with the file hdf5.h among others inside
lib with the file libhdf5.so among others inside

mccoys commented 2 years ago

There must be something wrong when you set the variable HDF5_ROOT_DIR. It appears empty. Maybe you set it in the wrong environment?

Goo-JZhang commented 2 years ago

I've reset my WSL2 and reconfigured my dependencies, following the provided manual installation steps for Linux. But the problem still exists.

git describe --all --long heads/master-0-gd021d9e08

make config=verbose Linking smilei mpicxx build/src/Checkpoint/Checkpoint.o build/src/Collisions/CollisionsSingle.o build/src/Collisions/Collisions.o build/src/Collisions/CollisionalFusionDD.o build/src/Collisions/CollisionalIonization.o build/src/Collisions/CollisionalNuclearReaction.o build/src/Diagnostic/DiagnosticFields.o build/src/Diagnostic/DiagnosticProbes.o build/src/Diagnostic/TimeSelection.o build/src/Diagnostic/DiagnosticFields1D.o build/src/Diagnostic/Histogram.o build/src/Diagnostic/DiagnosticRadiationSpectrum.o build/src/Diagnostic/DiagnosticFields3D.o build/src/Diagnostic/DiagnosticTrack.o build/src/Diagnostic/DiagnosticScalar.o build/src/Diagnostic/DiagnosticParticleBinningBase.o build/src/Diagnostic/DiagnosticScreen.o build/src/Diagnostic/DiagnosticPerformances.o build/src/Diagnostic/DiagnosticFields2D.o build/src/Diagnostic/DiagnosticParticleBinning.o build/src/Diagnostic/DiagnosticFieldsAM.o build/src/DomainDecomposition/GlobalDomainDecomposition.o build/src/DomainDecomposition/Hilbert_functions.o build/src/DomainDecomposition/HilbertDomainDecomposition.o build/src/DomainDecomposition/RegionDomainDecomposition.o build/src/DomainDecomposition/LinearizedDomainDecomposition.o build/src/ElectroMagn/LaserEnvelope1D.o build/src/ElectroMagn/LaserPropagator.o build/src/ElectroMagn/LaserEnvelope2D.o build/src/ElectroMagn/ElectroMagn2D.o build/src/ElectroMagn/ElectroMagn.o build/src/ElectroMagn/ElectroMagnAM.o build/src/ElectroMagn/Laser.o build/src/ElectroMagn/ElectroMagn3D.o build/src/ElectroMagn/LaserEnvelope.o build/src/ElectroMagn/LaserEnvelopeAM.o build/src/ElectroMagn/LaserEnvelope3D.o build/src/ElectroMagn/ElectroMagn1D.o build/src/ElectroMagnBC/EnvelopeBCAM_refl.o build/src/ElectroMagnBC/ElectroMagnBC2D_refl.o build/src/ElectroMagnBC/ElectroMagnBCAM_ramp.o build/src/ElectroMagnBC/EnvelopeBC1D_refl.o build/src/ElectroMagnBC/EnvelopeBC.o build/src/ElectroMagnBC/ElectroMagnBCAM_BM.o build/src/ElectroMagnBC/ElectroMagnBC2D.o build/src/ElectroMagnBC/ElectroMagnBC.o build/src/ElectroMagnBC/ElectroMagnBCAM.o build/src/ElectroMagnBC/EnvelopeBCAM_Axis.o build/src/ElectroMagnBC/ElectroMagnBC2D_Trans_Damping.o build/src/ElectroMagnBC/ElectroMagnBCAM_SM.o build/src/ElectroMagnBC/ElectroMagnBC3D_SM.o build/src/ElectroMagnBC/ElectroMagnBC3D_refl.o build/src/ElectroMagnBC/ElectroMagnBC1D_SM.o build/src/ElectroMagnBC/EnvelopeBC2D_refl.o build/src/ElectroMagnBC/ElectroMagnBCAM_PML.o build/src/ElectroMagnBC/EnvelopeBC3D_refl.o build/src/ElectroMagnBC/ElectroMagnBC2D_PML.o build/src/ElectroMagnBC/ElectroMagnBC2D_SM.o build/src/ElectroMagnBC/ElectroMagnBC1D_refl.o build/src/ElectroMagnBC/ElectroMagnBC3D.o build/src/ElectroMagnBC/ElectroMagnBC3D_BM.o build/src/ElectroMagnBC/ElectroMagnBC1D.o build/src/ElectroMagnBC/ElectroMagnBC3D_PML.o build/src/ElectroMagnSolver/MA_Solver2D_norm.o build/src/ElectroMagnSolver/MF_Solver2D_GrassiSpL.o build/src/ElectroMagnSolver/PML_SolverAM.o build/src/ElectroMagnSolver/MF_Solver1D_Yee.o build/src/ElectroMagnSolver/MA_Solver3D_norm.o build/src/ElectroMagnSolver/PXR_Solver2D_GPSTD.o build/src/ElectroMagnSolver/PML_Solver2D_Bouchard.o build/src/ElectroMagnSolver/MA_Solver1D_norm.o build/src/ElectroMagnSolver/MF_Solver3D_Bouchard.o build/src/ElectroMagnSolver/MF_Solver3D_Lehe.o build/src/ElectroMagnSolver/MF_Solver2D_Bouchard.o build/src/ElectroMagnSolver/MF_Solver2D_Lehe.o build/src/ElectroMagnSolver/MF_Solver2D_Grassi.o build/src/ElectroMagnSolver/MA_Solver2D_Friedman.o build/src/ElectroMagnSolver/PML_Solver3D_Bouchard.o build/src/ElectroMagnSolver/MF_SolverAM_Yee.o build/src/ElectroMagnSolver/MF_Solver3D_M4.o build/src/ElectroMagnSolver/PML_Solver2D_Yee.o build/src/ElectroMagnSolver/PXR_Solver3D_FDTD.o build/src/ElectroMagnSolver/MA_SolverAM_norm.o build/src/ElectroMagnSolver/MF_Solver2D_Yee.o build/src/ElectroMagnSolver/MF_Solver3D_Yee.o build/src/ElectroMagnSolver/MF_Solver1D_M4.o build/src/ElectroMagnSolver/MF_Solver2D_M4.o build/src/ElectroMagnSolver/PML_Solver3D_Yee.o build/src/ElectroMagnSolver/PXR_SolverAM_GPSTD.o build/src/ElectroMagnSolver/MF_Solver2D_Cowan.o build/src/ElectroMagnSolver/PXR_Solver3D_GPSTD.o build/src/Field/cField1D.o build/src/Field/Field1D.o build/src/Field/Field2D.o build/src/Field/cField2D.o build/src/Field/Field3D.o build/src/Field/cField3D.o build/src/Interpolator/Interpolator1D2OrderV.o build/src/Interpolator/Interpolator2DWT2OrderV.o build/src/Interpolator/Interpolator2D2OrderV.o build/src/Interpolator/Interpolator2D4Order.o build/src/Interpolator/Interpolator3DWT4Order.o build/src/Interpolator/Interpolator2D2Order.o build/src/Interpolator/Interpolator1D3Order.o build/src/Interpolator/Interpolator1DWT2OrderV.o build/src/Interpolator/Interpolator.o build/src/Interpolator/Interpolator2DWT4OrderV.o build/src/Interpolator/Interpolator3D2OrderV.o build/src/Interpolator/Interpolator1DWT4Order.o build/src/Interpolator/Interpolator2DWT2Order.o build/src/Interpolator/Interpolator3D4OrderV.o build/src/Interpolator/Interpolator1D2Order.o build/src/Interpolator/InterpolatorAM2Order.o build/src/Interpolator/Interpolator3D2Order.o build/src/Interpolator/Interpolator2DWT4Order.o build/src/Interpolator/Interpolator1DWT2Order.o build/src/Interpolator/InterpolatorAM1Order.o build/src/Interpolator/InterpolatorAM.o build/src/Interpolator/Interpolator3DWT2Order.o build/src/Interpolator/Interpolator3DWT2OrderV.o build/src/Interpolator/Interpolator1D.o build/src/Interpolator/Interpolator2D.o build/src/Interpolator/Interpolator3D.o build/src/Interpolator/Interpolator3DWT4OrderV.o build/src/Interpolator/Interpolator2D4OrderV.o build/src/Interpolator/Interpolator1D4Order.o build/src/Interpolator/Interpolator3D4Order.o build/src/Ionization/IonizationFromRate.o build/src/Ionization/IonizationTunnelEnvelopeAveraged.o build/src/Ionization/IonizationTunnel.o build/src/Ionization/Ionization.o build/src/Ionization/IonizationTables.o build/src/Merging/Merging.o build/src/Merging/MergingVranicSpherical.o build/src/Merging/MergingVranicCartesian.o build/src/MovWindow/SimWindow.o build/src/MultiphotonBreitWheeler/MultiphotonBreitWheelerTablesDefault.o build/src/MultiphotonBreitWheeler/MultiphotonBreitWheelerTables.o build/src/MultiphotonBreitWheeler/MultiphotonBreitWheeler.o build/src/Params/PeekAtSpecies.o build/src/Params/Params.o build/src/Params/OpenPMDparams.o build/src/ParticleBC/PartWall.o build/src/ParticleBC/PartBoundCond.o build/src/ParticleBC/BoundaryConditionType.o build/src/ParticleInjector/ParticleInjector.o build/src/Particles/Particle.o build/src/Particles/Particles.o build/src/Particles/ParticleCreator.o build/src/Patch/Patch.o build/src/Patch/VectorPatch.o build/src/Patch/SyncVectorPatch.o build/src/Patch/Patch2D.o build/src/Patch/Region.o build/src/Patch/DoubleGrids.o build/src/Patch/Patch3D.o build/src/Patch/PatchAM.o build/src/Patch/Patch1D.o build/src/Patch/DoubleGridsAM.o build/src/Profiles/Profile.o build/src/Profiles/Function.o build/src/Projector/Projector2D2OrderV.o build/src/Projector/ProjectorAM2Order.o build/src/Projector/Projector3D2Order.o build/src/Projector/Projector3D2OrderV.o build/src/Projector/ProjectorAM.o build/src/Projector/Projector3D4OrderV.o build/src/Projector/Projector3D.o build/src/Projector/Projector3D4Order.o build/src/Projector/Projector1D2Order.o build/src/Projector/ProjectorAM1Order.o build/src/Projector/Projector2D2Order.o build/src/Projector/Projector.o build/src/Projector/Projector1D.o build/src/Projector/Projector1D4Order.o build/src/Projector/Projector2D4OrderV.o build/src/Projector/Projector3D2OrderGPU.o build/src/Projector/Projector2D4Order.o build/src/Projector/Projector2D.o build/src/Pusher/PusherPonderomotivePositionBoris.o build/src/Pusher/PusherBorisNR.o build/src/Pusher/PusherVay.o build/src/Pusher/Pusher.o build/src/Pusher/PusherHigueraCary.o build/src/Pusher/PusherPhoton.o build/src/Pusher/PusherBoris.o build/src/Pusher/PusherPonderomotiveBoris.o build/src/Radiation/RadiationDiagRadiationSpectrum.o build/src/Radiation/RadiationCorrLandauLifshitz.o build/src/Radiation/Radiation.o build/src/Radiation/RadiationNiel.o build/src/Radiation/RadiationTablesDefault.o build/src/Radiation/RadiationLandauLifshitz.o build/src/Radiation/RadiationTables.o build/src/Radiation/RadiationMonteCarlo.o build/src/Radiation/RadiationTools.o build/src/Smilei.o build/src/SmileiMPI/SmileiMPI.o build/src/SmileiMPI/SmileiMPI_test.o build/src/SmileiMPI/AsyncMPIbuffers.o build/src/Species/SpeciesVAdaptiveMixedSort.o build/src/Species/Species.o build/src/Species/SpeciesMetrics.o build/src/Species/SpeciesVAdaptive.o build/src/Species/SpeciesV.o build/src/Tools/Tools.o build/src/Tools/H5.o build/src/Tools/userFunctions.o build/src/Tools/Timer.o build/src/Tools/PyTools.o build/src/Tools/backward.o build/src/Tools/Timers.o build/src/Tools/tabulatedFunctions.o build/src/picsar_interface/interface.o -o build/smilei -L/home/zjlwsl/hdf5/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -lhdf5 -L/home/zjlwsl/anaconda3/lib/python3.9/config-3.9-x86_64-linux-gnu -lpython3.9 -lcrypt -lpthread -ldl -lutil -lm -lm -Xlinker -export-dynamic -lm -fopenmp -D_OMP /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 30a5 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 3100 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 6ad2 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 6add /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 70f4 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7136 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7178 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 71ba /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 71e6 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 721d /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 7228 /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 725f /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: DWARF error: could not find variable specification at offset 726a build/src/Tools/H5.o: in function H5::init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, int*, bool)': /home/zjlwsl/smilei/Smilei/src/Tools/H5.cpp:41: undefined reference toH5Pset_fapl_mpio' /home/zjlwsl/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/zjlwsl/smilei/Smilei/src/Tools/H5.cpp:65: undefined reference to `H5Pset_dxpl_mpio' collect2: error: ld returned 1 exit status make: *** [makefile:298: smilei] Error 1

make env VERSION : 4.7-5-gd021d9e08-master SMILEICXX : mpicxx OPENMP_FLAG : -fopenmp -D_OMP HDF5_ROOT_DIR : /home/zjlwsl/hdf5 FFTW3_LIB_DIR : SITEDIR : /home/zjlwsl/.local/lib/python3.9/site-packages PYTHONEXE : python3 PY_CXXFLAGS : -I/home/zjlwsl/anaconda3/include/python3.9 -I/home/zjlwsl/anaconda3/include/python3.9 -I/home/zjlwsl/anaconda3/lib/python3.9/site-packages/numpy/core/include -DSMILEI_USE_NUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION PY_LDFLAGS : -L/home/zjlwsl/anaconda3/lib/python3.9/config-3.9-x86_64-linux-gnu -lpython3.9 -lcrypt -lpthread -ldl -lutil -lm -lm -Xlinker -export-dynamic CXXFLAGS : -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -D__VERSION=\"4.7-5-gd021d9e08-master\" -D_VECTO -std=c++11 -Wall -I/home/zjlwsl/hdf5/include -Isrc -Isrc/SmileiMPI -Isrc/MovWindow -Isrc/Ionization -Isrc/Field -Isrc/Collisions -Isrc/Params -Isrc/ElectroMagnSolver -Isrc/MultiphotonBreitWheeler -Isrc/ElectroMagn -Isrc/DomainDecomposition -Isrc/Merging -Isrc/picsar_interface -Isrc/Interpolator -Isrc/Projector -Isrc/ParticleBC -Isrc/Diagnostic -Isrc/Radiation -Isrc/Tools -Isrc/Patch -Isrc/Python -Isrc/Profiles -Isrc/ElectroMagnBC -Isrc/Particles -Isrc/Species -Isrc/Checkpoint -Isrc/ParticleInjector -Isrc/Pusher -Ibuild/src/Python -I/home/zjlwsl/anaconda3/include/python3.9 -I/home/zjlwsl/anaconda3/include/python3.9 -I/home/zjlwsl/anaconda3/lib/python3.9/site-packages/numpy/core/include -DSMILEI_USE_NUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -O3 -g -fopenmp -D_OMP LDFLAGS : -L/home/zjlwsl/hdf5/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -lhdf5 -L/home/zjlwsl/anaconda3/lib/python3.9/config-3.9-x86_64-linux-gnu -lpython3.9 -lcrypt -lpthread -ldl -lutil -lm -lm -Xlinker -export-dynamic -lm -fopenmp -D_OMP

echo $LD_LIBRARY_PATH /home/zjlwsl/hdf5/lib:/home/zjlwsl/openmpi/lib:/home/zjlwsl/hdf5/lib:/home/zjlwsl/openmpi/lib:

python -m sysconfig Platform: "linux-x86_64" Python version: "3.9" Current installation scheme: "posix_prefix"

Paths: data = "/home/zjlwsl/anaconda3" include = "/home/zjlwsl/anaconda3/include/python3.9" platinclude = "/home/zjlwsl/anaconda3/include/python3.9" platlib = "/home/zjlwsl/anaconda3/lib/python3.9/site-packages" platstdlib = "/home/zjlwsl/anaconda3/lib/python3.9" purelib = "/home/zjlwsl/anaconda3/lib/python3.9/site-packages" scripts = "/home/zjlwsl/anaconda3/bin" stdlib = "/home/zjlwsl/anaconda3/lib/python3.9"

Variables: ABIFLAGS = "" AC_APPLE_UNIVERSAL_BUILD = "0" AIX_BUILDDATE = "0" AIX_GENUINE_CPLUSPLUS = "0" ALT_SOABI = "0" ANDROID_API_LEVEL = "0" AR = "x86_64-conda-linux-gnu-ar" ARFLAGS = "rcs" BASECFLAGS = "-Wno-unused-result -Wsign-compare" BASECPPFLAGS = "-IObjects -IInclude -IPython" BASEMODLIBS = "" BINDIR = "/home/zjlwsl/anaconda3/bin" BINLIBDEST = "/home/zjlwsl/anaconda3/lib/python3.9" BLDLIBRARY = "libpython3.9.a" BLDSHARED = " x86_64-conda-linux-gnu-gcc -pthread -shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib" BUILDEXE = "" BUILDPYTHON = "python" BUILD_GNU_TYPE = "x86_64-conda-linux-gnu" BYTESTR_DEPS = "\" CC = " x86_64-conda-linux-gnu-gcc -pthread" CCSHARED = "-fPIC" CFLAGS = "-Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include " CFLAGSFORSHARED = "" CFLAGS_ALIASING = "" CONFIGFILES = "configure configure.ac acconfig.h pyconfig.h.in Makefile.pre.in" CONFIGURE_CFLAGS = "-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include" CONFIGURE_CFLAGS_NODIST = " -g -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -fvisibility=hidden" CONFIGURE_CPPFLAGS = "-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include" CONFIGURE_LDFLAGS = "-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib" CONFIGURE_LDFLAGS_NODIST = " -g" CONFIG_ARGS = "'--prefix=/home/zjlwsl/anaconda3' '--build=x86_64-conda-linux-gnu' '--host=x86_64-conda-linux-gnu' '--enable-ipv6' '--with-ensurepip=no' '--with-tzpath=/home/zjlwsl/anaconda3/share/zoneinfo:/home/zjlwsl/anaconda3/share/tzinfo' '--with-computed-gotos' '--with-system-ffi' '--enable-loadable-sqlite-extensions' '--with-tcltk-includes=-I/home/zjlwsl/anaconda3/include' '--with-tcltk-libs=-L/home/zjlwsl/anaconda3/lib -ltcl8.6 -ltk8.6' '--with-platlibdir=lib' '--with-openssl=/home/zjlwsl/anaconda3' 'PKG_CONFIG_LIBDIR=/home/zjlwsl/anaconda3/lib' 'PKG_CONFIG_PATH=/home/zjlwsl/anaconda3/lib' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include' 'CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include' 'CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/zjlwsl/anaconda3/lib -Wl,-rpath-link,/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib -L/home/zjlwsl/anaconda3/lib' 'CC= x86_64-conda-linux-gnu-gcc' 'CXX=x86_64-conda-linux-gnu-c++' '--with-lto' '--enable-optimizations' '-oldincludedir=/usr/include' '--disable-shared' 'PROFILE_TASK=-m test --pgo' 'build_alias=x86_64-conda-linux-gnu' 'host_alias=x86_64-conda-linux-gnu' 'MACHDEP=linux' 'CPP=/tmp/build/80754af9/python-split_1631797238431/_build_env/bin/x86_64-conda-linux-gnu-cpp'" CONFINCLUDEDIR = "/home/zjlwsl/anaconda3/include" CONFINCLUDEPY = "/home/zjlwsl/anaconda3/include/python3.9" COREPYTHONPATH = "" COVERAGE_INFO = "/tmp/build/80754af9/python-split_1631797238431/work/build-static/coverage.info" COVERAGE_REPORT = "/tmp/build/80754af9/python-split_1631797238431/work/build-static/lcov-report" COVERAGE_REPORT_OPTIONS = "--no-branch-coverage --title "CPython lcov report"" CPPFLAGS = "-IObjects -IInclude -IPython -I. -I/tmp/build/80754af9/python-split_1631797238431/work/Include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/zjlwsl/anaconda3/include -I/home/zjlwsl/anaconda3/include" CXX = "x86_64-conda-linux-gnu-c++ -pthread" DESTDIRS = "/home/zjlwsl/anaconda3 /home/zjlwsl/anaconda3/lib /home/zjlwsl/anaconda3/lib/python3.9 /home/zjlwsl/anaconda3/lib/python3.9/lib-dynload" DESTLIB = "/home/zjlwsl/anaconda3/lib/python3.9" DESTPATH = "" DESTSHARED = "/home/zjlwsl/anaconda3/lib/python3.9/lib-dynload" DFLAGS = "" DIRMODE = "755" DIST = "README.rst ChangeLog configure configure.ac acconfig.h pyconfig.h.in Makefile.pre.in Include Lib Misc Ext-dummy" DISTDIRS = "Include Lib Misc Ext-dummy" DISTFILES = "README.rst ChangeLog configure configure.ac acconfig.h pyconfig.h.in Makefile.pre.in" DLINCLDIR = "." 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ldd smilei ldd: ./smilei: No such file or directory

iltommi commented 2 years ago

I'm really sorry it still does not link the executable. In my opinion there is another libhdf5.so (compiled without mpi support) somewhere in your path that is picked before the one you compiled (I don't understand why hdf5 is providing basically two incompatible versions of the library with the same name). I suspect:

/home/zjlwsl/anaconda3/lib

less likely this:

/home/zjlwsl/anaconda3/lib/python3.9/config-3.9-x86_64-linux-gnu

or one of the default search paths that you can check with ld (here is an explanation https://stackoverflow.com/questions/9922949/how-to-print-the-ldlinker-search-path )

There is something else I was thinking about (and that might be our fault). Could you try to replace the line of the makefile https://github.com/SmileiPIC/Smilei/blob/master/makefile#L97

LDFLAGS := -L$(HDF5_ROOT_DIR)/lib  $(LDFLAGS)

with

LDFLAGS := $(LDFLAGS) -L$(HDF5_ROOT_DIR)/lib

and check if it works?

It's however strange because on my mac I have both sequential and parallel versions of the hdf5 library (libhdf5.dylib on mac) in my DYLD_LIBRARY_PATH (equivalent of LD_LYBRARY_PATH on linux) and the makefile picks up the right one.

mccoys commented 2 years ago

Also, it could be that you need to clean your compilation

make clean

And recompile

Goo-JZhang commented 2 years ago

I'm really sorry it still does not link the executable. In my opinion there is another libhdf5.so (compiled without mpi support) somewhere in your path that is picked before the one you compiled (I don't understand why hdf5 is providing basically two incompatible versions of the library with the same name). I suspect:
/home/zjlwsl/anaconda3/lib
less likely this:
/home/zjlwsl/anaconda3/lib/python3.9/config-3.9-x86_64-linux-gnu
or one of the default search paths that you can check with ld (here is an explanation https://stackoverflow.com/questions/9922949/how-to-print-the-ldlinker-search-path )

There is something else I was thinking about (and that might be our fault). Could you try to replace the line of the makefile https://github.com/SmileiPIC/Smilei/blob/master/makefile#L97
LDFLAGS := -L$(HDF5_ROOT_DIR)/lib  $(LDFLAGS)
with
LDFLAGS := $(LDFLAGS) -L$(HDF5_ROOT_DIR)/lib
and check if it works?

yeah, hdf5lib.so is both in ~/hdf5/lib and ~/anaconda3/lib

the latter replacing method doesn't work.

Goo-JZhang commented 2 years ago

Referring to https://github.com/NCAR/ParallelIO/issues/1281 , I tried to export LD_LIBRARY_PATH=~/anaconda3/lib:$LD_LIBRARY_PATH. But then there outputs "no version information available" after make.

iltommi commented 2 years ago

Some options (seems that anaconda is too much invasive): 1) You could try to uninstall the other libhdf5, compile smilei and reinstall the libhdf5 serial (but that might break other thing like h5py in the meantime) 2) there are some conda packages with parallel hdf5 https://anaconda.org/clawpack/hdf5-parallel 3) based on this there should be a way to have h5py (I suppose that package instlaled the serial version of libhdf5). Look at the answer here: https://stackoverflow.com/questions/58345261/configuring-h5py-with-mpio-using-anaconda-on-windows

Goo-JZhang commented 2 years ago

Some options (seems that anaconda is too much invasive):

You could try to uninstall the other libhdf5, compile smilei and reinstall the libhdf5 serial (but that might break other thing like h5py in the meantime)

there are some conda packages with parallel hdf5 https://anaconda.org/clawpack/hdf5-parallel

based on this there should be a way to have h5py (I suppose that package instlaled the serial version of libhdf5). Look at the answer here: https://stackoverflow.com/questions/58345261/configuring-h5py-with-mpio-using-anaconda-on-windows

YEAH, I also wondering whether is the anaconda the problem, on my other machine, I installed anaconda after smilei was installed, with another python interpreter, mpich and hdf5. And with conda installed, openmpi could not be installed due to some unknown problem.

mccoys commented 2 years ago

Have you tried make clean?

Goo-JZhang commented 2 years ago

Have you tried make clean?

yes, after every change I do make clean.

Goo-JZhang commented 2 years ago

After removing conda, make process could go on. But in the end there are 2 warnings: Linking smilei /usr/bin/ld: warning: libmpi.so.40, needed by /home/zjlwsl/hdf5/lib/libhdf5.so, may conflict with libmpi.so.12 Compiling src/Smilei.cpp for test mode Linking smilei_test for test mode /usr/bin/ld: warning: libmpi.so.40, needed by /home/zjlwsl/hdf5/lib/libhdf5.so, may conflict with libmpi.so.12

And I tried to run the 1st benchmark but fail. The error info is below:

Abort(469325317) on node 0 (rank 0 in comm 0): Fatal error in MPII_Comm_set_attr: Invalid communicator, error stack: MPII_Comm_set_attr(90): MPI_Comm_set_attr(comm=0x663e6cc0, keyval=0xa4400000, attribute_val=(nil)) failed MPII_Comm_set_attr(47): Invalid communicator

Is there any conflict between mpich and openmpi?

mccoys commented 2 years ago

It seems the hdf5 lib was compiled with a different version of MPI. You cannot indeed combine openMPI and MPICH.

Goo-JZhang commented 2 years ago

Problem solved. DWARF error occurs due to the invasion of anaconda, and the latter problem is due to the miscompilation of hdf5 with different versions of MPI. But I still wonder whether MPICH could replace openmpi, if I export the corresponding PATH instead of openmpi's.

iltommi commented 2 years ago

Glad to hear you sorted it out! Yes, you can use mpich to compile Smilei. This has already been done several times.

SmileiPIC / Smilei

DWARF error while linking smilei #526