Name clashes error in "spack module lmod refresh", Spack Stack 1.9.0 on S4 #1543
Description
Describe the bug
spack module lmod refresh step fails on S4 with Error: Name clashes detected in module files error message;
A couple of packages seem to be installed twice with the same version number
To Reproduce
Steps to reproduce the behavior:
- Clone the branch release/1.9.0
- Navigate to the cloned directory
- Source the setup script
source setup.sh - Create the environment:
spack stack create env --site s4 --template unified-dev --name ue.s4.oneapi --compiler oneapi - Navigate to the newly created environment
cd envs/ue.s4.oneapi - Run the concretize step:
spack concretize --force 2>&1 | tee concretize.log - Run the Install step:
spack install --source --verbose --fail-fast 2>&1 | tee install.log - Run the module refresh step:
spack module lmod refresh
Expected behavior
The module refresh step should run smoothly without error message
System:
What system(s) are you running the code on? S4
Additional context
Below is the whole error message
Error: Name clashes detected in module files:
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel/2021.10.0/bufr/12.1.0.lua
spec: bufr@=12.1.0%intel@=2021.10.0/pqqvn5b ~ipo+python+shared+utils build_system=cmake build_type=Release generator=make test_files=none arch=linux-rocky8-skylake
spec: bufr@=12.1.0%intel@=2021.10.0/3fv3qfa ~ipo+python+shared+utils build_system=cmake build_type=Release generator=make test_files=none arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel-oneapi-mpi/2021.10.0-dazbmdo/intel/2021.10.0/bufr-query/0.0.4.lua
spec: bufr-query@=0.0.4%intel@=2021.10.0/x6mdnvj ~ipo+python build_system=cmake build_type=Release generator=make arch=linux-rocky8-skylake_avx512
spec: bufr-query@=0.0.4%intel@=2021.10.0/fespkhj ~ipo+python build_system=cmake build_type=Release generator=make arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel-oneapi-mpi/2021.10.0-dazbmdo/intel/2021.10.0/esmf/8.6.1.lua
spec: esmf@=8.6.1%intel@=2021.10.0/qntcmd7 ~debug~external-lapack+external-parallelio+mpi+netcdf~pnetcdf+python+shared~xerces build_system=makefile esmf_comm=auto esmf_os=auto esmf_pio=auto patches=f63d405 snapshot=none arch=linux-rocky8-skylake
spec: esmf@=8.6.1%intel@=2021.10.0/oczi5mc ~debug~external-lapack+external-parallelio+mpi+netcdf~pnetcdf+python+shared~xerces build_system=makefile esmf_comm=auto esmf_os=auto esmf_pio=auto patches=f63d405 snapshot=none arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel-oneapi-mpi/2021.10.0-dazbmdo/intel/2021.10.0/jedi-base-env/1.0.0.lua
spec: jedi-base-env@=1.0.0%intel@=2021.10.0/p2vkkkg +bufrquery+fftw+hdf4 build_system=bundle arch=linux-rocky8-skylake_avx512
spec: jedi-base-env@=1.0.0%intel@=2021.10.0/zlz4rft +bufrquery+fftw+hdf4 build_system=bundle arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel-oneapi-mpi/2021.10.0-dazbmdo/intel/2021.10.0/mapl/2.53.0-esmf-8.6.1.lua
spec: mapl@=2.53.0%intel@=2021.10.0/oew7n6v ~debug+extdata2g~f2py+fargparse~ipo+pflogger~pfunit~shared+zstd build_system=cmake build_type=Release generator=make arch=linux-rocky8-skylake
spec: mapl@=2.53.0%intel@=2021.10.0/opuin4t ~debug+extdata2g~f2py+fargparse~ipo+pflogger~pfunit~shared+zstd build_system=cmake build_type=Release generator=make arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel/2021.10.0/py-cftime/1.0.3.4.lua
spec: py-cftime@=1.0.3.4%intel@=2021.10.0/dzvgi7e build_system=python_pip arch=linux-rocky8-skylake
spec: py-cftime@=1.0.3.4%intel@=2021.10.0/lbu7qhl build_system=python_pip arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel/2021.10.0/py-eccodes/1.5.0.lua
spec: py-eccodes@=1.5.0%intel@=2021.10.0/k4demqu build_system=python_pip arch=linux-rocky8-skylake_avx512
spec: py-eccodes@=1.5.0%intel@=2021.10.0/dt2awcj build_system=python_pip arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel-oneapi-mpi/2021.10.0-dazbmdo/intel/2021.10.0/py-h5py/3.12.1.lua
spec: py-h5py@=3.12.1%intel@=2021.10.0/2oh3qnn ~mpi build_system=python_pip arch=linux-rocky8-skylake_avx512
spec: py-h5py@=3.12.1%intel@=2021.10.0/sq7b7jn ~mpi build_system=python_pip arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel-oneapi-mpi/2021.10.0-dazbmdo/intel/2021.10.0/py-netcdf4/1.7.1.post2.lua
spec: py-netcdf4@=1.7.1.post2%intel@=2021.10.0/b7ly3rf ~mpi build_system=python_pip patches=255b5ae,2bce09b arch=linux-rocky8-skylake
spec: py-netcdf4@=1.7.1.post2%intel@=2021.10.0/fanxnys ~mpi build_system=python_pip patches=255b5ae,2bce09b arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel/2021.10.0/py-pandas/2.2.3.lua
spec: py-pandas@=2.2.3%intel@=2021.10.0/hhvvyz2 ~excel~performance build_system=python_pip arch=linux-rocky8-skylake
spec: py-pandas@=2.2.3%intel@=2021.10.0/tnyendm ~excel~performance build_system=python_pip arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel/2021.10.0/py-pyhdf/0.11.4.lua
spec: py-pyhdf@=0.11.4%intel@=2021.10.0/htohkub build_system=python_pip arch=linux-rocky8-skylake_avx512
spec: py-pyhdf@=0.11.4%intel@=2021.10.0/3verqjw build_system=python_pip arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel/2021.10.0/py-pythran/0.16.1.lua
spec: py-pythran@=0.16.1%intel@=2021.10.0/26uogks build_system=python_pip arch=linux-rocky8-skylake_avx512
spec: py-pythran@=0.16.1%intel@=2021.10.0/kb4ydjb build_system=python_pip arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel/2021.10.0/py-scipy/1.13.1.lua
spec: py-scipy@=1.13.1%intel@=2021.10.0/pjglr7i build_system=python_pip patches=3720932 arch=linux-rocky8-skylake_avx512
spec: py-scipy@=1.13.1%intel@=2021.10.0/3v75ekn build_system=python_pip patches=3720932 arch=linux-rocky8-skylake_avx512
file: <PATH_TO_SPACK_STACK>/spack-stack/ss-1.9.0/envs/ue.s4.intel/install/modulefiles/intel/2021.10.0/py-xarray/2024.7.0.lua
spec: py-xarray@=2024.7.0%intel@=2021.10.0/opls6au ~io~parallel~viz build_system=python_pip arch=linux-rocky8-skylake
spec: py-xarray@=2024.7.0%intel@=2021.10.0/bbqedvp ~io~parallel~viz build_system=python_pip arch=linux-rocky8-skylake_avx512
==> Error: Operation aborted