diff --git a/src/base/labels_nebius.config b/src/base/labels_nebius.config index fa7cfe90e..c5edf9719 100644 --- a/src/base/labels_nebius.config +++ b/src/base/labels_nebius.config @@ -132,6 +132,17 @@ process { containerOptions = { workflow.containerEngine == "singularity" ? '--nv': ( workflow.containerEngine == "docker" ? '--gpus all': null ) } } + withLabel: gpuh100 { + // Nebius H100 gpu-node-group: NVIDIA H100 SXM, 1 GPU, 16 CPUs, 196 GiB RAM + // ~195 GiB / ~15.9 vCPU allocatable — cap well below node max to leave headroom + cpus = 12 + accelerator = 1 + memory = { [ 120.GB * task.attempt, 180.GB ].min() } + disk = 200.GB + pod = [[nodeSelector: 'nebius.com/node-group-id=mk8snodegroup-e00jp7hyqr094tmy35']] + containerOptions = { workflow.containerEngine == "singularity" ? '--nv': + ( workflow.containerEngine == "docker" ? '--gpus all': null ) } + } withLabel: hightime { time = 12.h } withLabel: veryhightime { time = 24.h } diff --git a/src/methods_calculate_cell_volume/alpha_shapes/script.py b/src/methods_calculate_cell_volume/alpha_shapes/script.py index 087a0f1b9..f54c8fdf5 100644 --- a/src/methods_calculate_cell_volume/alpha_shapes/script.py +++ b/src/methods_calculate_cell_volume/alpha_shapes/script.py @@ -15,7 +15,7 @@ sdata = sd.read_zarr(par['input']) print('Determine cell ids', flush=True) -cell_ids = sorted(sdata["transcripts"]["cell_id"].unique()) +cell_ids = sorted(sdata["transcripts"]["cell_id"].unique().compute()) if cell_ids[0] == 0: cell_ids = cell_ids[1:] diff --git a/src/methods_cell_type_annotation/moscot/config.vsh.yaml b/src/methods_cell_type_annotation/moscot/config.vsh.yaml index 57d041245..ea79aa1b5 100644 --- a/src/methods_cell_type_annotation/moscot/config.vsh.yaml +++ b/src/methods_cell_type_annotation/moscot/config.vsh.yaml @@ -57,4 +57,4 @@ runners: - type: executable - type: nextflow directives: - label: [ hightime, midcpu, veryhighmem, gpuhighmem ] + label: [ hightime, midcpu, veryhighmem, gpuh100 ] diff --git a/src/methods_cell_type_annotation/tangram/config.vsh.yaml b/src/methods_cell_type_annotation/tangram/config.vsh.yaml index 714f7a2d2..903c82c52 100644 --- a/src/methods_cell_type_annotation/tangram/config.vsh.yaml +++ b/src/methods_cell_type_annotation/tangram/config.vsh.yaml @@ -40,4 +40,4 @@ runners: - type: executable - type: nextflow directives: - label: [ midtime, midcpu, midmem, gpuhighmem ] + label: [ midtime, midcpu, midmem, gpuh100 ]