Prepare a machine

Any Linux account can become a simulation machine. verlet installs Spack in your home, finds the compilers, MPI and libraries already there, and builds engine executables from short YAML specs. Keep as many as you like side by side; they share every dependency they can. LAMMPS builds are what is implemented today.

Two rules that never bend

Everything is written under ~/.verlet. No step uses sudo.

1. Set up the environment

1. Open Environments and select the machine, your own computer or a connected remote.
2. In LAMMPS setup, press Set up. On a cluster, first list the modules to load, such as gcc/12.3 openmpi/4.1.
3. verlet checks the machine, installs Spack and records what it found. About a minute after the download.

Before changing anything, verlet checks what a build needs; a failed check stops the setup and says how to fix it.

Check	Needed because
Home writable	Everything goes in ~/.verlet.
Free space	A few GB for Spack, sources and builds; 10 GB recommended.
Python 3.6+	Spack is written in Python.
tar, gzip, patch, make	To unpack and build packages.
bzip2, xz, git	Some sources need them (warnings only).
A C++ compiler	On the PATH or from the modules you listed.
github.com, Spack release	To download Spack and sources.

After setup the card lists the compilers found, what was found on the machine and will be reused instead of built (MPI, CMake, CUDA), the GPUs, and the free space. Re-check repeats discovery after you load modules or install something.

2. Create a build

1. Under Builds, press New build.

2. Pick a template:

   Template	For	Packages
   minimal	first runs	MOLECULE, KSPACE, RIGID, EXTRA-PAIR, with OpenMP
   molecular	force-field systems	adds CLASS2, DPD-BASIC, EXTRA-*, REAXFF, QEQ, REPLICA, MISC
   materials	many-body and ML potentials	MANYBODY, MEAM, ML-SNAP, ML-PACE, ML-IAP, PHONON, REAXFF
   everything-cpu	when in doubt	every package that builds without extra libraries
   gpu-kokkos	NVIDIA GPUs	Kokkos with CUDA; needs the CUDA toolkit on the machine

3. Edit the YAML, or use the selects and the package list, which rewrite it for you. Problems appear with the key they belong to, and the Spack spec it will build is shown underneath.

4. Press Start build.

Every key is in the build spec reference.

name: lmp-minimal              # the executable becomes ~/.verlet/bin/lmp-minimal
lammps: stable                 # a release date like 20250722, stable, or latest
packages: [MOLECULE, KSPACE, RIGID, EXTRA-PAIR]
compiler: gcc                  # gcc, clang, oneapi or nvhpc, optionally with a version: gcc@12
optimization: native           # none, O2, O3 or native (O3 with -march=native)
mpi: system                    # system, spack (build OpenMPI) or none
accelerators: [openmp]         # openmp, kokkos-openmp, kokkos-cuda, gpu-cuda, gpu-opencl, intel
lapack: auto
fft: auto
modules: [gcc/12.3, openmpi/4.1]   # loaded before building and before every run

3. Watch it build

State	What happens
Queued	Waiting; one build at a time per machine.
Concretizing	Spack works out every dependency and version.
Concretized	verlet shows how many packages it will build and how many it reuses.
Installing	Packages compile; the bar shows done / total and the current package.
Verifying	The new executable must list every package you asked for.
Done	The executable is registered and verified.

View log shows everything Spack printed. Cancel keeps what was compiled for the next attempt. Builds continue if verlet closes.

On a two-core workstation the minimal template took about 20 minutes, most of it FFTW and the engine; a second build with materials reused FFTW and the toolchain and compiled only the engine and the ML-PACE libraries.

4. Run with it

A done build appears under Executables marked built from spec, and in the Run sheet for that environment. It is a small wrapper, ~/.verlet/bin/<name>, that loads the build’s modules and starts the real binary, so it also works from your own shell.

Deleting a build

Delete removes the executable, the build directory and the packages no other build uses.

When something goes wrong

• A setup check fails: the card shows the fix. Install the missing tool as your user or load a module that provides it, then Re-check.
• The build fails: the last lines of the Spack log are on the build; View log has the rest. A common cause is a package that needs a library the machine lacks; the spec check warns about these.
• “built without X”: the build finished without package X, usually because a dependency was missing; check the log for that package’s CMake output.