Platforms and engines

Hosts

The pixi environment is solved for linux-64 and linux-aarch64 only. The jammy release tarball is built on ubuntu:22.04 and records arch=amd64 in HOST_RUNTIME.txt. An ARM64 machine uses a pixi checkout rather than that tarball.

Devices

Device strings are auto, cpu, nvidia, and amd. Flags: -device on MojoFq2bamMeth and MojoGiraffe. Environment: METHYLGRAPHER_ALIGN_DEVICE (linear default) and METHYLGRAPHER_GIRAFFE_DEVICE (graph seed path).

gpu-common/src/gpu_kernels.mojo labels kernels as follows.

Request	Label	API passed to DeviceContext
nvidia or cuda	nvidia:sm_90	cuda
amd, hip, or rocm	amdgpu:gfx942	hip
anything else, including cpu	cpu	cpu

For AMD, a non-empty METHYLGRAPHER_AMDGPU_ARCH replaces gfx942 (amdgpu: concatenated with that value).

auto (gpu-common/src/gpu_device.mojo) probes CUDA DeviceContext, then HIP DeviceContext, then nvidia-smi -L, then rocm-smi --showproductname, then rocminfo, and otherwise selects CPU.

METHYLGRAPHER_GPU_REQUIRE empty or 1 fails the NVIDIA/AMD path when DeviceContext cannot be created. 0 allows a host seed extract. The value 1, true, yes, or on also refuses the linear BWA fallback.

Drivers older than 580 need MODULAR_NVPTX_COMPILER_PATH pointing at ptxas before a CUDA DeviceContext is created. The jammy launcher searches $ROOT/cuda/bin/ptxas, /usr/local/cuda/bin/ptxas, and /usr/bin/ptxas when that variable is unset.

Linear engines

MojoFq2bamMeth has two independent switches.

METHYLGRAPHER_LINEAR_MAPPER (fq2bam-meth/python/fq2bam_meth.py):

Value	Behavior
empty, auto, or mojo	Mojo linear mapper, including when -device cpu
bwa	BWA-MEM on the converted reference

METHYLGRAPHER_LINEAR_ENGINE, used when the mapper is mojo:

Value	Module	Index
empty, fm, bwa-mem, bwamem, default	fq2bam-meth/src/linear_gpu_fm.mojo	BWA .bwt, .sa, .pac on the C→T FASTA
parity, science, kmer, k-mer	fq2bam-meth/src/linear_gpu_locate.mojo	Dense k-mer pack (kmers.bin, offsets.bin, postings.bin, meta.json)
speed, fast	fq2bam-meth/src/linear_gpu_speed.mojo	Same dense pack

The fm engine writes a BGZF BAM that is already coordinate-sorted and duplicate-marked. The other engines stream SAM into samtools. Any other string raises RuntimeError.

Graph engines

Align selects a mapper with -align_engine or METHYLGRAPHER_ALIGN_ENGINE. The default when both are unset is cpu_vg.

Value	Also accepted	Mapper
cpu_vg	cpu, vg	vg giraffe -o gaf -M 2 with named coordinates
mojo_giraffe	mojo	Mojo Giraffe. GBZ quartet when those files exist, otherwise GFA
gpu_giraffe	gpu, gh200	Mojo GBZ/GFA. METHYLGRAPHER_GPU_GIRAFFE_FALLBACK is mojo (default), vg, or error

GOLIATH_ALIGN_GIRAFFE_READY defaults to on. 0, false, no, off, or vg keeps align_engine=gpu_giraffe but selects the vg path (mojo_giraffe_ready in giraffe/python/quartet_map.py). MOJO_ALIGN_GIRAFFE_READY and METHYLGRAPHER_MOJO_GIRAFFE_READY are the deprecated names of the same variable.

MojoGiraffe is its own command. It does not consult -align_engine. It takes -device auto|cpu|nvidia|amd and writes the GAF you name with -out_gaf.