Compile libMesh failed using HPC Cluster

[PengWei97]

Dear MOOSE experts,

Recently I wanted to link libmesh directly to moose, and completed the installation of PESTs according to HPC Cluster, the results are as follows,

But when compiling libmesh, ./scripts/update_and_rebuild_libmesh.sh, the following error occurs,

-- Done configuring core library features ---
---------------------------------------------
---------------------------------------------
----- Configuring for optional packages -----
---------------------------------------------
checking for built-in XDR support... yes
checking for boostlib >= 1.57.0... configure: We could not detect the boost libraries (version 1.57 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option.  If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.
<<< External boost installation *not* found... will try to configure for libmesh's internal boost >>>
checking for boostlib >= 1.57.0... yes
<<< Using libmesh-provided boost in ./contrib >>>
checking for boost::movelib::unique_ptr support... yes
note: Checking /lib and /include for MPI
note: Could not find /lib/libmpi(.a/.so/.dylib)
mpicxx -std=gnu++17 Compiler Supports MPI 
<<< Found PETSc 3.16.5 installation in /home/pengwei/projects/libmesh/moose/petsc ... >>>
checking whether we can compile a trivial PETSc program... yes
checking for TAO support via PETSc... yes
configure: error: *** PETSc with Hypre was not found, but --enable-petsc-hypre-required was specified.
Running make -j 1...
make: *** No targets specified and no makefile found.  Stop.

Any suggestions or recommendations to fix the problem would be greatly appreciated.

Thank you
Wei

[milljm]

MOOSE requires libMesh and PETSc. But also that PETSc to be built with HYPRE support (--download-hypre=1 during PETSc configure). You can see the options MOOSE requires or recommends in the moose/scripts/configure_petsc.sh script:

cat moose/scripts/configure_petsc.sh
<trimmed>
  python ./configure --download-hypre=1 \
      --with-shared-libraries=$SHARED \
      "$HDF5_STR" \
      "$HDF5_FORTRAN_STR" \
      "$MAKE_NP_STR" \
      --with-debugging=no \
      --download-fblaslapack=1 \
      --download-metis=1 \
      --download-ptscotch=1 \
      --download-parmetis=1 \
      --download-superlu_dist=1 \
      --download-mumps=1 \
      --download-strumpack=1 \
      --download-scalapack=1 \
      --download-slepc=1 \
      --with-mpi=1 \
      --with-openmp=1 \
      --with-cxx-dialect=C++11 \
      --with-fortran-bindings=0 \
      --with-sowing=0 \
      --with-64-bit-indices \
      "$@"

[PengWei97]

Yes, I used https://mooseframework.inl.gov/getting_started/installation/conda.html first, then created a folder ./projects/libmesh/moose to clone the moose repository, and then based on https:/ /mooseframework.inl.gov/getting_started/installation/hpc_install_moose.html to install.

[milljm]

I think you followed one too many instructions, based on what I am seeing in the libmesh_diagnostic.log. Was there a reason to try and perform the HPC instructions? The Conda instructions are best used for single workstations/laptops (which I think you have).

The HPC instructions are for those wishing to use a high performance job scheduling capable environment. Where typically you need optimized binaries designed to work specifically with that system's MPI infrastructure.

If following the HPC instructions was an accident, I believe the only steps left for you to do is:

mamba activate moose
mamba install moose-libmesh moose-tools
mamba deactivate
mamba activate moose
cd ~/projects/libmesh/moose/test
make clobber all       # to clean up any previous build
make -j 6
./run_tests -j 6

[PengWei97]

Was there a reason to try and perform the HPC instructions?

My purpose is to be able to link libmesh directly, so that I can have a deeper understanding of moose, considering that I need to create my own model, this is related to mesh data.

I think my libmesh has been installed, but when I execute the following code,

cd ~/projects/moose/test
make -j4

It shows make: python-config: Command not found, how to solve this?

Compiling C++ (in opt mode) /home/pengwei/projects/moose/framework/build/unity_src/mesh_Unity.C...
Building and linking /home/pengwei/projects/moose/framework/contrib/hit/hit.so...
/home/pengwei/projects/moose/framework/contrib/hit/hit.cpp:4:10: fatal error: Python.h: No such file or directory
    4 | #include "Python.h"
      |          ^~~~~~~~~~
compilation terminated.
Compiling C++ (in opt mode) /home/pengwei/projects/moose/framework/contrib/exodiff/exodiff.C...
make: *** [/home/pengwei/projects/moose/framework/moose.mk:124: /home/pengwei/projects/moose/framework/contrib/hit/hit.so] Error 1
make: *** Waiting for unfinished jobs....

[PengWei97]

Woohoo!! It works using sudo apt-get install python3-dev

[milljm]

🎉 Nice! Looks like you got it sorted!

FYI, you can still use Conda instead of the manual install (if you choose). You simply install only the things that moose-libmesh requires. Which I admit, is not documented. But that package install would look something like:

mamba create -n just-petsc moose-petsc
mamba activate just-petsc
cd moose/scripts
export METHODS=oprof MOOSE_JOBS=6   # build profile method, using 6 cores
./update_and_rebuild_libmesh.sh
export METHOD=oprof                 # build moose using same method as libMesh
cd ../test
make -j 6
./run_tests --oprof                 # run tests using the moose_test-oprof binary

There are several 'METHOD(S)' available, FYI; oprof, opt, devel, dbg
The description of what each means can be found here: https://mooseframework.inl.gov/moose/application_development/build_system.html