Issue with SLEPc installation during MOOSE setup on old HPC system

[hityyds]

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Issue or question about MOOSE

Hello everyone,

I’m currently trying to install MOOSE on an HPC platform with an outdated system, and I'm unable to update the system, which is why I cannot use conda for installation. A while ago, I managed to install some of MOOSE’s dependencies (specifically the Python environment) using conda, and then followed the ‘Offline Installation’ guide to successfully install MOOSE by running the following command:

./update_and_rebuild_petsc.sh --skip-submodule-update --with-packages-download-dir=~/projects/downloads || return
./update_and_rebuild_libmesh.sh --skip-submodule-update || return
./update_and_rebuild_wasp.sh --skip-submodule-update || return

However, when I try to install PETSc on a new account using the same method, I encounter the following error:

*** Building SLEPc ***
Checking environment... done
Checking PETSc installation... Traceback (most recent call last):
  File "/public3/home/a0s000425/ZhangHu-MOOSE/projects/moose/petsc/arch-moose/externalpackages/slepc-2e87c100eacb3466e83737e0fd6f542957174390/./configure", line 12, in <module>
    exec(f.read())
  File "<string>", line 263, in <module>
  File "/public3/home/a0s000425/ZhangHu-MOOSE/projects/moose/petsc/arch-moose/externalpackages/slepc-2e87c100eacb3466e83737e0fd6f542957174390/config/packages/petsc.py", line 226, in Process
    slepcdate = dateutil.parser.parse(slepc.gitdate)
  File "/public3/home/a0s000425/ZhangHu-MOOSE/minforge/envs/moose-py/lib/python3.9/site-packages/dateutil/parser/_parser.py", line 1368, in parse
    return DEFAULTPARSER.parse(timestr, **kwargs)
  File "/public3/home/a0s000425/ZhangHu-MOOSE/minforge/envs/moose-py/lib/python3.9/site-packages/dateutil/parser/_parser.py", line 643, in parse
    raise ParserError("Unknown string format: %s", timestr)
dateutil.parser._parser.ParserError: Unknown string format: unknown
**************************ERROR*************************************
Error building SLEPc.
********************************************************************
gmake[2]: *** [slepcbuild] Error 1
**************************ERROR*************************************
  Error during compile, check arch-moose/lib/petsc/conf/make.log
  Send it and arch-moose/lib/petsc/conf/configure.log to petsc-maint@mcs.anl.gov
  Having Conda in your shell may have caused this problem, consider turning off Conda.
********************************************************************
make[1]: *** [all] Error 1
make: *** [all] Error 2
There was an error. Exiting...
-bash: return: can only `return' from a function or sourced script

I have tried turning off conda and also added the conda environment paths to PATH, LD_LIBRARY_PATH, and CPATH (thinking that this would allow me to use the libraries even when conda is deactivated). Unfortunately, this only removed the warning about needing to turn off conda, but the error persists.

Does anyone have suggestions on how to resolve this issue?

(Optional) code in question / simulation log / errors

No response

Encountering Errors? Please include diagnostic output

No response

[GiudGiud]

Hello

If I understand properly, you installed it once, and are now trying to install from a user account (rather than as an admin)

Do you have permission over the folders where petsc was initially installed?

[GiudGiud]

Additionally, the GCC and MPI module versions are slightly different,

no part of the install can be shared then.
You must make sure that the two installs are completely separate. When installing the second one, check the environment to make sure there's no contamination.

you can use the diagnostics script in moose/scripts to look at the relevant environment variables

[hityyds]

The two installations were done under different accounts, so their home directories are completely separate. Therefore, the installation directories for both MOOSE installations are also completely different, with no sharing between them.

[GiudGiud]

I'd like to check though
what is the output of the diagnostics script?

[hityyds]

Here’s the output from running diagnostics.sh

####################################################################################################
Influential Environment Variables

CC=mpicc
CONDA_CHANNEL=https://conda.software.inl.gov/public
CONDA_DEFAULT_ENV=moose-py
CONDA_EXE=/public3/home/a0s000425/ZhangHu-MOOSE/minforge/bin/conda
CONDA_PREFIX=/public3/home/a0s000425/ZhangHu-MOOSE/minforge/envs/moose-py
CONDA_PROMPT_MODIFIER=(moose-py) 
CONDA_PYTHON_EXE=/public3/home/a0s000425/ZhangHu-MOOSE/minforge/bin/python
CONDA_SHLVL=1
CURL_CA_BUNDLE=
CXX=mpicxx
F77=mpif77
F90=mpif90
FC=mpif90
FI_PROVIDER_PATH=/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/libfabric/lib/prov:/usr/lib64/libfabric
LD_LIBRARY_PATH_modshare=/public3/soft/intel/2020u4/debugger_2020/libipt/intel64/lib:1::1:/public3/soft/gcc/12.2/lib:1:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/mic/lib:2:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/ipp/lib/intel64:1:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/libfabric/lib:1:/opt/slurm/slurm/lib:1:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64:1:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/daal/lib/intel64_lin:1:/public3/soft/gcc/12.2/libexec:1:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64_lin:1:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64_lin:1:/public3/soft/gcc/12.2/lib64:1:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/daal/../tbb/lib/intel64_lin/gcc4.8:1:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release:1:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib:2:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/tbb/lib/intel64/gcc4.8:1
LD_LIBRARY_PATH=/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/libfabric/lib:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release:/public3/soft/intel/2020u4/debugger_2020/libipt/intel64/lib:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/daal/../tbb/lib/intel64_lin/gcc4.8:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/daal/lib/intel64_lin:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/tbb/lib/intel64/gcc4.8:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64_lin:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/ipp/lib/intel64:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/mic/lib:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64_lin:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64:/public3/soft/gcc/12.2/lib64:/public3/soft/gcc/12.2/lib:/public3/soft/gcc/12.2/libexec:/opt/slurm/slurm/lib:
MODULES_CMD=/public3/soft/modules/4.1.2-public3/libexec/modulecmd.tcl
MODULESHOME=/public3/soft/modules/4.1.2-public3
MOOSE_JOBS=6
PATH_modshare=/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin:1:/usr/bin:1:/public3/soft/gcc/12.2/bin:1:/usr/local/bin:1:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/bin/intel64:1:/public3/home/a0s000425/ZhangHu-MOOSE/minforge/envs/moose-py/bin:1:/public3/soft/modules/4.1.2-public3/bin:1:/opt/ibutils/bin:1:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/libfabric/bin:1:/opt/slurm/slurm/bin:1:/opt/slurm/slurm/sbin:1:/public3/clurm/bin:1:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/debugger/gdb/intel64_mic/bin:1:/usr/sbin:1:/usr/lib64/qt-3.3/bin:1:/usr/local/sbin:1:/public3/home/a0s000425/ZhangHu-MOOSE/minforge/condabin:1:/public3/home/a0s000425/.local/bin:1:/public3/home/a0s000425/bin:1
PATH=/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/libfabric/bin:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/debugger/gdb/intel64_mic/bin:/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/bin/intel64:/public3/soft/gcc/12.2/bin:/public3/home/a0s000425/ZhangHu-MOOSE/minforge/envs/moose-py/bin:/public3/soft/modules/4.1.2-public3/bin:/public3/home/a0s000425/ZhangHu-MOOSE/minforge/condabin:/public3/clurm/bin:/usr/lib64/qt-3.3/bin:/opt/slurm/slurm/sbin:/opt/slurm/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/public3/home/a0s000425/.local/bin:/public3/home/a0s000425/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
####################################################################################################
Compiler(s) (CC CXX FC F77 F90):

which $CC; /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin/mpicc
$CC --version; gcc (GCC) 12.2.0
$CC -show; gcc -I/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/include -L/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release -L/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release -Xlinker -rpath -Xlinker /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -Wl,-z,now -Wl,-z,relro -Wl,-z,noexecstack -Xlinker --enable-new-dtags -ldl

which $CXX; /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin/mpicxx
$CXX --version; g++ (GCC) 12.2.0
$CXX -show; g++ -I/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/include -L/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release -L/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release -Xlinker -rpath -Xlinker /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -lmpicxx -lmpifort -lmpi -lrt -lpthread -Wl,-z,now -Wl,-z,relro -Wl,-z,noexecstack -Xlinker --enable-new-dtags -ldl

which $FC; /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin/mpif90
$FC --version; GNU Fortran (GCC) 12.2.0
$FC -show; gfortran -fallow-argument-mismatch -I/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/include/gfortran -I/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/include -L/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release -L/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release -Xlinker -rpath -Xlinker /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -Wl,-z,now -Wl,-z,relro -Wl,-z,noexecstack -Xlinker --enable-new-dtags -ldl

which $F77; /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin/mpif77
$F77 --version; GNU Fortran (GCC) 12.2.0
$F77 -show; gfortran -I/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/include -L/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release -L/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release -Xlinker -rpath -Xlinker /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -Wl,-z,now -Wl,-z,relro -Wl,-z,noexecstack -Xlinker --enable-new-dtags -ldl

which $F90; /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin/mpif90
$F90 --version; GNU Fortran (GCC) 12.2.0
$F90 -show; gfortran -fallow-argument-mismatch -I/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/include/gfortran -I/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/include -L/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release -L/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release -Xlinker -rpath -Xlinker /public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -Wl,-z,now -Wl,-z,relro -Wl,-z,noexecstack -Xlinker --enable-new-dtags -ldl

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

/usr/bin/env python3 --version; (reporting as: Python 3.9.21) matches
which python3 python;

/public3/home/a0s000425/ZhangHu-MOOSE/minforge/envs/moose-py/bin/python3 --version; == Python 3.9.21
/public3/home/a0s000425/ZhangHu-MOOSE/minforge/envs/moose-py/bin/python --version; == Python 3.9.21

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

OK
####################################################################################################
MOOSE Repository/Conda Version Checks

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


checks PASSED

[GiudGiud]

This makes me uneasy

/public3/soft/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/libfabric/lib

we dont support the intel compilers. It looks like the environment variables for the compilers are set up for GCC/Gfortran, but LD_LIBRARY_PATH is not clearly setup for GCC/Gfortran