Add Kaiju cluster support: pixi env, PETSc build script, and documentation#79
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jcgraciosa wants to merge 10 commits intounderworldcode:developmentfrom
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Add Kaiju cluster support: pixi env, PETSc build script, and documentation#79jcgraciosa wants to merge 10 commits intounderworldcode:developmentfrom
jcgraciosa wants to merge 10 commits intounderworldcode:developmentfrom
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pixi's conda ld (14.3.0) requires explicit transitive shared lib deps. libmmg.so built with SCOTCH caused MMG_WORKS link test to fail in PARMMG's FindMMG.cmake because libscotch.so wasn't explicitly linked. MMG's SCOTCH is only used for mesh renumbering (optional perf feature); PARMMG uses ptscotch separately for parallel partitioning, unaffected. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add shared installation section (admin, Lmod module) - Add troubleshooting entries from install experience: h5py replacing mpi4py, numpy ABI mismatch, PARMMG/pixi ld issue Underworld development team with AI support from Claude Code
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Summary
Background
Kaiju is a Rocky Linux 8.10 HPC cluster (Slurm + spack) used by the Underworld development team. MPI-dependent packages (mpi4py, PETSc+AMR+petsc4py, h5py) must be built from source against spack's OpenMPI to be compatible with Slurm's parallel interconnect.
The architecture is:
pixi kaiju env → Python 3.12, sympy, scipy, pint, ... (conda-forge, no MPI)
spack → openmpi@4.1.6 (cluster MPI)
source build → mpi4py, PETSc+AMR+petsc4py, h5py (linked to spack MPI)
Key fixes included
Test plan
Notes
Install scripts and Slurm job templates are maintained in the kaiju-admin-notes repo (admin/cluster-specific tooling kept separate from the framework).
Underworld development team with AI support from Claude Code