Compiling error #27650

Emmanuel-324 · 2024-05-16T18:52:34Z

Emmanuel-324
May 16, 2024

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Q&A Getting Started is the most appropriate category for my question (trouble installing, beginner user, ...)
I have consulted the posting Guidelines on the Discussions front page
I have searched the Discussions forum and my question has not been asked before
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Issue or question about MOOSE

'''
(python-stack) [emmanuel324@tinkercliffs1 belson]$ make -j6
Creating Unity /home/emmanuel324/projects/moose/modules/solid_mechanics/build/unity_src/materials_Unity.C
Compiling C++ (in opt mode) /home/emmanuel324/projects/moose/modules/solid_mechanics/build/unity_src/materials_Unity.C...
Linking Library /home/emmanuel324/projects/moose/modules/solid_mechanics/lib/libsolid_mechanics-opt.la...
Linking Library /home/emmanuel324/projects/moose/modules/contact/lib/libcontact-opt.la...
Linking Library /home/emmanuel324/projects/moose/modules/fsi/lib/libfsi-opt.la...
Linking Library /home/emmanuel324/projects/moose/modules/peridynamics/lib/libperidynamics-opt.la...
Linking Library /home/emmanuel324/projects/moose/modules/phase_field/lib/libphase_field-opt.la...
Linking Library /home/emmanuel324/projects/moose/modules/porous_flow/lib/libporous_flow-opt.la...
Linking Library /home/emmanuel324/projects/moose/modules/xfem/lib/libxfem-opt.la...
Linking Library /home/emmanuel324/projects/moose/modules/combined/lib/libcombined-opt.la...
Linking Library /home/emmanuel324/projects/moose/modules/module_loader/lib/libmodule_loader_with_cr_em_eps_fp_fet_gc_ls_ray_rdg_rct_rich_st_ht_sp_sm_ns_con_fsi_misc_opt_pd_pf_pflow_th_st_xfem_comb-opt.la...
Linking Library /home/emmanuel324/projects/belson/lib/libbelson-opt.la...
Linking Test Library /home/emmanuel324/projects/belson/test/lib/libbelson_test-opt.la...
Linking Executable /home/emmanuel324/projects/belson/belson-opt...
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/libutil.so when searching for -lutil
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/librt.so when searching for -lrt
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/libdl.so when searching for -ldl
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVElementalKernel::computeResidualAndJacobian()' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::adjustRMGhostLayers(unsigned short) const'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVElementalKernel::computeOffDiagJacobian()' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::computeResidual(FaceInfo const&)'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/modules/porous_flow/lib/libporous_flow-opt.so: undefined reference to FVTimeKernel::FVTimeKernel(InputParameters const&)' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVElementalKernel::computeJacobian()'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/modules/navier_stokes/lib/libnavier_stokes-opt.so: undefined reference to typeinfo for FVFunctorTimeKernel' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to typeinfo for FVScalarLagrangeMultiplierConstraint'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVElementalKernel::computeOffDiagJacobian(unsigned int)' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVElementalKernel::computeResidual()'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVElementalKernel::FVElementalKernel(InputParameters const&)' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::elemArg(bool) const'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVScalarLagrangeMultiplierConstraint::computeOffDiagJacobian()' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::computeJacobian(FaceInfo const&)'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/modules/navier_stokes/lib/libnavier_stokes-opt.so: undefined reference to FVFluxKernel::avoidBoundary(FaceInfo const&) const' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/modules/porous_flow/lib/libporous_flow-opt.so: undefined reference to typeinfo for FVTimeKernel'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to non-virtual thunk to FVFluxKernel::computeResidual(FaceInfo const&)' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVScalarLagrangeMultiplierConstraint::computeResidual()'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to vtable for FVScalarLagrangeMultiplierConstraint' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVScalarLagrangeMultiplierConstraint::computeResidualAndJacobian()'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::computeJacobian()' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::computeResidualAndJacobian()'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/modules/porous_flow/lib/libporous_flow-opt.so: undefined reference to FVFluxKernel::onBoundary(FaceInfo const&) const' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::singleSidedFaceArg(FaceInfo const*, Moose::FV::LimiterType, bool) const'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/modules/navier_stokes/lib/libnavier_stokes-opt.so: undefined reference to vtable for FVFunctorTimeKernel' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to non-virtual thunk to FVFluxKernel::computeResidualAndJacobian(FaceInfo const&)'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::skipForBoundary(FaceInfo const&) const' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVScalarLagrangeMultiplierConstraint::computeJacobian()'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::computeResidual()' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to vtable for FVFluxKernel'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/modules/navier_stokes/lib/libnavier_stokes-opt.so: undefined reference to FVFunctorTimeKernel::validParams()' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVElementalKernel::validParams()'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/modules/porous_flow/lib/libporous_flow-opt.so: undefined reference to vtable for FVTimeKernel' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to non-virtual thunk to FVFluxKernel::computeJacobian(FaceInfo const&)'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::neighborArg(bool) const' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::gradUDotNormal(Moose::StateArg const&) const'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to non-virtual thunk to FVFluxKernel::hasFaceSide(FaceInfo const&, bool) const' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVScalarLagrangeMultiplierConstraint::FVScalarLagrangeMultiplierConstraint(InputParameters const&)'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to typeinfo for FVElementalKernel' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to typeinfo for FVFluxKernel'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to vtable for FVElementalKernel' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/modules/navier_stokes/lib/libnavier_stokes-opt.so: undefined reference to FVTimeKernel::computeQpResidual()'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::hasFaceSide(FaceInfo const&, bool) const' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/modules/porous_flow/lib/libporous_flow-opt.so: undefined reference to FVTimeKernel::validParams()'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::computeResidualAndJacobian(FaceInfo const&)' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVFluxKernel::FVFluxKernel(InputParameters const&)'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to FVScalarLagrangeMultiplierConstraint::validParams()' /apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/modules/navier_stokes/lib/libnavier_stokes-opt.so: undefined reference to FVFunctorTimeKernel::FVFunctorTimeKernel(InputParameters const&)'
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: /home/emmanuel324/projects/moose/framework/libmoose-opt.so: undefined reference to `FVFluxKernel::validParams()'
collect2: error: ld returned 1 exit status
make: *** [/home/emmanuel324/projects/belson/belson-opt] Error 1
'''

Diagnostics for MOOSE installation issues

[Optional] Output of the diagnostics scripts. To run the script: cd ~/projects/moose/scripts; ./diagnostics.sh

Answered by Emmanuel-324

May 16, 2024

Can I clean my moose/app to solve this?

View full answer

Emmanuel-324 · 2024-05-16T18:55:13Z

Emmanuel-324
May 16, 2024
Author

Below is the output of diagnostics script:

(python-stack) [emmanuel324@tinkercliffs1 belson]$ cd ~/projects/moose/scripts; ./diagnostics.sh
##################################################################################################
Influential Environment Variables
CC=mpicc
CONDA_CHANNEL=https://conda.software.inl.gov/public
CONDA_DEFAULT_ENV=python-stack
CONDA_EXE=/home/emmanuel324/mambaforge3/bin/conda
CONDA_PREFIX_1=/home/emmanuel324/mambaforge3
CONDA_PREFIX=/home/emmanuel324/mambaforge3/envs/python-stack
CONDA_PROMPT_MODIFIER=(python-stack) 
CONDA_PYTHON_EXE=/home/emmanuel324/mambaforge3/bin/python
CONDA_SHLVL=2
CURL_CA_BUNDLE=
CXX=mpicxx
F77=mpif77
F90=mpif90
FC=mpif90
LD_LIBRARY_PATH=/apps/easybuild/software/tinkercliffs-rome/libarchive/3.6.2-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/cURL/8.0.1-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/bzip2/1.0.8-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/nc
urses/6.4-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/UCC/1.2.0-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/PMIx/4.2.4-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rom
e/libfabric/1.18.0-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/UCX/1.14.1-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/libevent/2.1.12-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/OpenSSL/1.1/lib:/apps/easybuild/software/tinkercliffs-r
ome/hwloc/2.9.1-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/libpciaccess/0.17-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/libxml2/2.11.4-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/XZ/5.4.2-GCCcore-12.3.0/lib:/apps/easybuild/software
/tinkercliffs-rome/numactl/2.0.16-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/zlib/1.2.13-GCCcore-12.3.0/lib:/apps/easybuild/software/tinkercliffs-rome/GCCcore/12.3.0/lib64:/cm/shared/apps/slur
m/current/lib64/slurm:/cm/shared/apps/slurm/current/lib64:/opt/cray/pe/lib64:/opt/cray/lib64
MODULESHOME=/usr/share/lmod/lmod
MOOSE_JOBS=6
PATH=/apps/easybuild/software/tinkercliffs-rome/CMake/3.26.3-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/libarchive/3.6.2-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/cURL/8.0.1-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/bzip2/1.0.8-
GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/ncurses/6.4-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/UCC/1.2.0-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/PMIx/4.
2.4-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/libfabric/1.18.0-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/UCX/1.14.1-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/libevent/2.1.12-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercli
ffs-rome/OpenSSL/1.1/bin:/apps/easybuild/software/tinkercliffs-rome/hwloc/2.9.1-GCCcore-12.3.0/sbin:/apps/easybuild/software/tinkercliffs-rome/hwloc/2.9.1-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/libxml2/2.11.4-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliff
s-rome/XZ/5.4.2-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/numactl/2.0.16-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin:/apps/easybuild/software/tinkercliffs-rome/GCCcore/12.3.0/bin:/apps/useful_scripts/bin:/cm/shared/a
pps/slurm/current/sbin:/cm/shared/apps/slurm/current/bin:/home/emmanuel324/mambaforge3/envs/python-stack/bin:/home/emmanuel324/mambaforge3/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/share/lmod/lmod/libexec
REQUESTS_CA_BUNDLE=
SLURM_CONF=/cm/shared/apps/slurm/var/etc/slurm/slurm.conf
SSL_CERT_FILE=
##################################################################################################
Compiler(s) (CC CXX FC F77 F90):
CC=/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/bin/mpicc
CC -show:
gcc -I/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/include -L/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/hwloc/2.9.1-GCCcore-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/libevent/2.1.12-GCCcore-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/hwloc/2.9.1-GCCcore-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/libevent/2.1.12-GCCcore-12.3.0/lib -Wl,--enable-new-dtags -lmpi
CC version:     gcc (GCC) 12.3.0

CXX=/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/bin/mpicxx
CXX -show:
g++ -I/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/include -L/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/hwloc/2.9.1-GCCcore-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/libevent/2.1.12-GCCcore-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/hwloc/2.9.1-GCCcore-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/libevent/2.1.12-GCCcore-12.3.0/lib -Wl,--enable-new-dtags -lmpi
CXX version:    g++ (GCC) 12.3.0

FC=/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/bin/mpif90
FC -show:
gfortran -I/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/include -I/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/hwloc/2.9.1-GCCcore-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/libevent/2.1.12-GCCcore-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/hwloc/2.9.1-GCCcore-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/libevent/2.1.12-GCCcore-12.3.0/lib -Wl,--enable-new-dtags -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi
FC version:     GNU Fortran (GCC) 12.3.0

F77=/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/bin/mpif77
F77 -show:
gfortran -I/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/include -I/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/hwloc/2.9.1-GCCcore-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/libevent/2.1.12-GCCcore-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/hwloc/2.9.1-GCCcore-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/libevent/2.1.12-GCCcore-12.3.0/lib -Wl,--enable-new-dtags -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi
F77 version:    GNU Fortran (GCC) 12.3.0

F90=/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/bin/mpif90
F90 -show:
gfortran -I/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/include -I/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/hwloc/2.9.1-GCCcore-12.3.0/lib -L/apps/easybuild/software/tinkercliffs-rome/libevent/2.1.12-GCCcore-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/OpenMPI/4.1.5-GCC-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/hwloc/2.9.1-GCCcore-12.3.0/lib -Wl,-rpath -Wl,/apps/easybuild/software/tinkercliffs-rome/libevent/2.1.12-GCCcore-12.3.0/lib -Wl,--enable-new-dtags -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi
F90 version:    GNU Fortran (GCC) 12.3.0

OK

##################################################################################################
Python Sanity Checks

Verify `/usr/bin/env python3 --version` (reporting as: Python 3.10.13),
matches versions for: `which python3 && which python`

OK

##################################################################################################
Python Modules (TestHarness, run-ability)

OK

##################################################################################################
CONDA MOOSE Packages

WARNING: Not using Conda MOOSE packages, or `conda activate moose` not
performed

0 replies

GiudGiud · 2024-05-16T18:57:00Z

GiudGiud
May 16, 2024
Collaborator

Hello

are you using the conda moose packages?
You have two compilers available in your environment already even without the moose packages
You ll need to get that down to 1 by unloading modules / cleaning your environment.
If you want to use our moose conda packages, then down to 0

Guillaume

21 replies

GiudGiud May 16, 2024
Collaborator

(python-stack) [emmanuel324@tinkercliffs1 belson]$ mamba activate python-stack

is this providing a compiler?
what does mamba list return?

Emmanuel-324 May 16, 2024
Author

Below is the output of mamba list:

 packages in environment at /home/emmanuel324/mambaforge3/envs/python-stack:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
alabaster                 0.7.16                   pypi_0    pypi
asttokens                 2.4.1                    pypi_0    pypi
attrs                     23.2.0                   pypi_0    pypi
babel                     2.14.0                   pypi_0    pypi
beautifulsoup4            4.12.3                   pypi_0    pypi
bleach                    6.1.0                    pypi_0    pypi
bzip2                     1.0.8                hd590300_5    conda-forge
ca-certificates           2023.11.17           hbcca054_0    conda-forge
certifi                   2024.2.2                 pypi_0    pypi
charset-normalizer        3.3.2                    pypi_0    pypi
contourpy                 1.2.0                    pypi_0    pypi
coverage                  7.4.4                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
cython                    3.0.10                   pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
defusedxml                0.7.1                    pypi_0    pypi
docutils                  0.20.1                   pypi_0    pypi
exceptiongroup            1.2.0                    pypi_0    pypi
executing                 2.0.1                    pypi_0    pypi
fastjsonschema            2.19.1                   pypi_0    pypi
fonttools                 4.50.0                   pypi_0    pypi
furo                      2024.1.29                pypi_0    pypi
idna                      3.6                      pypi_0    pypi
imagesize                 1.4.1                    pypi_0    pypi
importlib-resources       6.4.0                    pypi_0    pypi
iniconfig                 2.0.0                    pypi_0    pypi
ipython                   8.23.0                   pypi_0    pypi
jedi                      0.19.1                   pypi_0    pypi
jinja2                    3.1.3                    pypi_0    pypi
jsonschema                4.21.1                   pypi_0    pypi
jsonschema-specifications 2023.12.1                pypi_0    pypi
jupyter-client            8.6.1                    pypi_0    pypi
jupyter-core              5.7.2                    pypi_0    pypi
jupyterlab-pygments       0.3.0                    pypi_0    pypi
kiwisolver                1.4.5                    pypi_0    pypi
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_3    conda-forge
libgomp                   13.2.0               h807b86a_3    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsqlite                 3.44.0               h2797004_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
markupsafe                2.1.5                    pypi_0    pypi
matplotlib                3.8.3                    pypi_0    pypi
matplotlib-inline         0.1.6                    pypi_0    pypi
mistune                   3.0.2                    pypi_0    pypi
nbclient                  0.10.0                   pypi_0    pypi
nbconvert                 7.16.3                   pypi_0    pypi
nbformat                  5.10.3                   pypi_0    pypi
nbsphinx                  0.9.3                    pypi_0    pypi
nbsphinx-link             1.3.0                    pypi_0    pypi
ncurses                   6.4                  h59595ed_2    conda-forge
numpy                     1.26.4                   pypi_0    pypi
oldest-supported-numpy    2023.12.21               pypi_0    pypi
openssl                   3.1.4                hd590300_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pandas                    2.2.1                    pypi_0    pypi
pandocfilters             1.5.1                    pypi_0    pypi
parso                     0.8.3                    pypi_0    pypi
pexpect                   4.9.0                    pypi_0    pypi
pillow                    10.3.0                   pypi_0    pypi
pip                       24.0                     pypi_0    pypi
platformdirs              4.2.0                    pypi_0    pypi
pluggy                    1.4.0                    pypi_0    pypi
prompt-toolkit            3.0.43                   pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.2                    pypi_0    pypi
pycalphad                 0.10.4.post2.dev7+g2116efe          pypi_0    pypi
pygments                  2.17.2                   pypi_0    pypi
pyparsing                 3.1.2                    pypi_0    pypi
pytest                    8.1.1                    pypi_0    pypi
pytest-cov                5.0.0                    pypi_0    pypi
python                    3.10.13         hd12c33a_0_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
python_abi                3.10                    4_cp310    conda-forge
pytz                      2024.1                   pypi_0    pypi
pyyaml                    6.0.1           py310h2372a71_1    conda-forge
pyzmq                     25.1.2                   pypi_0    pypi
readline                  8.2                  h8228510_1    conda-forge
referencing               0.34.0                   pypi_0    pypi
requests                  2.31.0                   pypi_0    pypi
rpds-py                   0.18.0                   pypi_0    pypi
scipy                     1.11.4                   pypi_0    pypi
setuptools                69.2.0                   pypi_0    pypi
setuptools-scm            8.0.4                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
snowballstemmer           2.2.0                    pypi_0    pypi
soupsieve                 2.5                      pypi_0    pypi
sphinx                    7.2.6                    pypi_0    pypi
sphinx-basic-ng           1.0.0b2                  pypi_0    pypi
sphinxcontrib-applehelp   1.0.8                    pypi_0    pypi
sphinxcontrib-devhelp     1.0.6                    pypi_0    pypi
sphinxcontrib-htmlhelp    2.0.5                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-qthelp      1.0.7                    pypi_0    pypi
sphinxcontrib-serializinghtml 1.1.10                   pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
symengine                 0.11.0                   pypi_0    pypi
tinycss2                  1.2.1                    pypi_0    pypi
tinydb                    4.8.0                    pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.0.1                    pypi_0    pypi
tornado                   6.4                      pypi_0    pypi
traitlets                 5.14.2                   pypi_0    pypi
typing-extensions         4.10.0                   pypi_0    pypi
tzdata                    2024.1                   pypi_0    pypi
urllib3                   2.2.1                    pypi_0    pypi
wcwidth                   0.2.13                   pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
wheel                     0.43.0                   pypi_0    pypi
xarray                    2024.3.0                 pypi_0    pypi
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge

GiudGiud May 16, 2024
Collaborator

well there was definitely overlap between your modules and the python environment
xz, bzip2, openssl and ncurses were both provided twice. But those arent the concern I think

maybe libgcc-ng ? and _libgcc_mutex ?
@milljm what do you think?

Emmanuel-324 May 16, 2024
Author

Can I clean my moose/app to solve this?

Answer selected by Emmanuel-324

GiudGiud May 16, 2024
Collaborator

it wont hurt to try
go in moose/ and

git commit -a
git clean -xfd
cd test
make -j 6

milljm May 16, 2024
Maintainer

maybe libgcc-ng ? and _libgcc_mutex ?
@milljm what do you think?

This are part of some low level Conda requirements. I don't think they would affect your build. I think what the build needs is to be cleaned as you suggested in your last message.

Emmanuel-324 May 16, 2024
Author

It worked after cleaning. Thanks

Emmanuel-324 May 16, 2024
Author

Just a quick question. When I submit a job the, 'job submitted' is the feedback I get but it does not solve the problem. I mean I do not get any .out files.

Provide feedback

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Compiling error #27650

Emmanuel-324 May 16, 2024

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Issue or question about MOOSE

Diagnostics for MOOSE installation issues

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