Compiling error

[Emmanuel-324]

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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

[Emmanuel-324]

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

[GiudGiud]

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

[GiudGiud]

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

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

[Emmanuel-324]

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]

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]

Can I clean my moose/app to solve this?

[GiudGiud]

it wont hurt to try
go in moose/ and

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

[milljm]

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]

It worked after cleaning. Thanks

[Emmanuel-324]

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.