feat: add configs for GPU optimizations

.gitignore

@@ -7,3 +7,5 @@ testing/
 testing*
 *.pyc
 null/
+*output*/
+**/*output*/

assets/bindcraft/fast_4stage_multimer.json

@@ -0,0 +1,67 @@
+{
+    "omit_AAs": "C",
+    "force_reject_AA": false,
+    "use_multimer_design": true,
+    "design_algorithm": "4stage",
+    "sample_models": true,
+    "rm_template_seq_design": false,
+    "rm_template_seq_predict": false,
+    "rm_template_sc_design": false,
+    "rm_template_sc_predict": false,
+    "predict_initial_guess": false,
+    "predict_bigbang": false,
+    "soft_iterations": 40,
+    "temporary_iterations": 20,
+    "hard_iterations": 3,
+    "greedy_iterations": 8,
+    "greedy_percentage": 5,
+    "save_design_animations": false,
+    "save_design_trajectory_plots": false,
+    "weights_plddt": 0.1,
+    "weights_pae_intra": 0.4,
+    "weights_pae_inter": 0.1,
+    "weights_con_intra": 1.0,
+    "weights_con_inter": 1.0,
+    "intra_contact_distance": 14.0,
+    "inter_contact_distance": 20.0,
+    "intra_contact_number": 2,
+    "inter_contact_number": 2,
+    "weights_helicity": -0.3,
+    "random_helicity": false,
+    "use_i_ptm_loss": true,
+    "weights_iptm": 0.05,
+    "use_rg_loss": true,
+    "weights_rg": 0.3,
+    "use_termini_distance_loss": false,
+    "weights_termini_loss": 0.1,
+    "cyclize_peptide": false,
+    "enable_mpnn": true,
+    "mpnn_fix_interface": true,
+    "num_seqs": 10,
+    "max_mpnn_sequences": 1,
+    "sampling_temp": 0.1,
+    "backbone_noise": 0.00,
+    "model_path": "v_48_020",
+    "mpnn_weights": "soluble",
+    "save_mpnn_fasta": false,
+    "num_recycles_design": 1,
+    "num_recycles_validation": 2,
+    "optimise_beta": true,
+    "optimise_beta_extra_soft": 0,
+    "optimise_beta_extra_temp": 0,
+    "optimise_beta_recycles_design": 2,
+    "optimise_beta_recycles_valid": 2,
+    "remove_unrelaxed_trajectory": true,
+    "remove_unrelaxed_complex": true,
+    "remove_binder_monomer": true,
+    "zip_animations": false,
+    "zip_plots": false,
+    "save_trajectory_pickle": false,
+    "max_trajectories": false,
+    "enable_rejection_check": true,
+    "acceptance_rate": 0.01,
+    "start_monitoring": 600,
+    "af_params_dir": "",
+    "dssp_path": "",
+    "dalphaball_path": ""
+}

assets/samplesheet.csv

@@ -1,2 +1,2 @@
 id,binder_name,starting_pdb,chains,target_hotspot_residues,min_length,max_length,number_of_final_designs,settings_filters,settings_advanced
-s1,PDL1,https://raw.githubusercontent.com/Australian-Structural-Biology-Computing/bindflow/refs/heads/main/assets/bindcraft/PDL1.pdb,A,56,65,150,4,https://raw.githubusercontent.com/Australian-Structural-Biology-Computing/bindflow/refs/heads/main/assets/bindcraft/default_filters.json,https://raw.githubusercontent.com/Australian-Structural-Biology-Computing/bindflow/refs/heads/main/assets/bindcraft/default_4stage_multimer.json
+s1,PDL1,https://raw.githubusercontent.com/Australian-Structural-Biology-Computing/bindflow/refs/heads/main/assets/bindcraft/PDL1.pdb,A,56,65,150,4,https://raw.githubusercontent.com/Australian-Structural-Biology-Computing/bindflow/refs/heads/main/assets/bindcraft/default_filters.json,assets/bindcraft/fast_4stage_multimer.json

bindflow-launcher.yaml

@@ -0,0 +1,52 @@
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  name: nextflow-runner
+  namespace: default
+---
+apiVersion: rbac.authorization.k8s.io/v1
+kind: Role
+metadata:
+  name: nextflow-runner
+  namespace: default
+rules:
+- apiGroups: [""]
+  resources: ["pods", "pods/log", "events"]
+  verbs: ["get", "list", "watch", "create", "delete"]
+---
+apiVersion: rbac.authorization.k8s.io/v1
+kind: RoleBinding
+metadata:
+  name: nextflow-runner
+  namespace: default
+subjects:
+- kind: ServiceAccount
+  name: nextflow-runner
+  namespace: default
+roleRef:
+  apiGroup: rbac.authorization.k8s.io
+  kind: Role
+  name: nextflow-runner
+---
+apiVersion: v1
+kind: Pod
+metadata:
+  name: bindflow-launcher
+  namespace: default
+spec:
+  serviceAccountName: nextflow-runner
+  restartPolicy: Never
+  containers:
+  - name: launcher
+    image: nextflow/nextflow:25.10.4
+    command: ["/bin/bash", "-lc", "sleep infinity"]
+    env:
+    - name: NXF_HOME
+      value: /workspace/.nextflow
+    volumeMounts:
+    - name: work
+      mountPath: /workspace
+  volumes:
+  - name: work
+    persistentVolumeClaim:
+      claimName: bindflow-rwo

conf/k8s_gpu.config

@@ -0,0 +1,64 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Kubernetes + GPU profile for bindflow
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Notes:
+    - This profile is intended for Kubernetes clusters with NVIDIA device plugin enabled.
+    - Use an OCI image tag for --bindcraft_container when running on k8s.
+    - Set --k8s_storage_claim to a RWX PVC shared by all pods.
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Kubernetes + GPU'
+    config_profile_description = 'Kubernetes executor tuned for GPU-backed BINDCRAFT tasks'
+}
+
+k8s {
+    namespace      = params.k8s_namespace
+    serviceAccount = params.k8s_service_account
+    pullPolicy     = params.k8s_pull_policy
+    runAsUser      = 1000
+}
+
+if( params.k8s_storage_claim ) {
+    k8s.storageClaimName = params.k8s_storage_claim
+    k8s.storageMountPath = params.k8s_storage_mount
+}
+
+if( params.k8s_workdir ) {
+    workDir = params.k8s_workdir
+}
+
+process {
+    executor = 'k8s'
+    queueSize = params.gpu_parallel_tasks as int
+
+    withName: 'JSONMANAGER' {
+        cpus   = 1
+        memory = 2.GB
+        time   = 1.h
+    }
+
+    withName: 'RANKER' {
+        cpus   = 1
+        memory = 2.GB
+        time   = 1.h
+    }
+
+    withName: 'BINDCRAFT' {
+        cpus   = 8
+        memory = 32.GB
+        time   = 24.h
+        accelerator = params.gpu_per_task as int
+        maxForks = params.gpu_parallel_tasks as int
+    }
+}
+
+docker.enabled       = false
+apptainer.enabled    = false
+singularity.enabled  = false
+podman.enabled       = false
+conda.enabled        = false
+charliecloud.enabled = false
+shifter.enabled      = false

conf/local_gpu.config

@@ -0,0 +1,38 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Local GPU profile (no OCI push required)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Uses Singularity + local .img container with NVIDIA passthrough.
+    Tune parallelism with --gpu_parallel_tasks (recommended: 1 per physical GPU).
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Local GPU (Singularity)'
+    config_profile_description = 'Run on local host GPUs using Singularity .img containers'
+}
+
+singularity {
+    enabled    = true
+    autoMounts = true
+    runOptions = '--nv'
+}
+
+apptainer.enabled    = false
+docker.enabled       = false
+podman.enabled       = false
+conda.enabled        = false
+charliecloud.enabled = false
+shifter.enabled      = false
+
+process {
+    executor  = 'local'
+    queueSize = params.gpu_parallel_tasks as int
+
+    withName: 'BINDCRAFT' {
+        cpus     = 8
+        memory   = 32.GB
+        time     = 24.h
+        maxForks = params.gpu_parallel_tasks as int
+    }
+}

modules/local/bindcraft/main.nf

@@ -20,8 +20,17 @@ process BINDCRAFT {
     script:
     def version = "1.2.0"
     def args = task.ext.args ?: ''
+    def gpuCount = (params.gpu_device_count ?: 1) as Integer
+    def gpuId = ((task.index ?: 1) - 1) % gpuCount
 
     """
+    export CUDA_VISIBLE_DEVICES=${gpuId}
+    export XLA_PYTHON_CLIENT_PREALLOCATE=false
+    export XLA_PYTHON_CLIENT_ALLOCATOR=platform
+    export XLA_PYTHON_CLIENT_MEM_FRACTION=0.60
+    export TF_FORCE_GPU_ALLOW_GROWTH=true
+    echo "BINDCRAFT task ${task.index ?: 1} using CUDA_VISIBLE_DEVICES=\$CUDA_VISIBLE_DEVICES"
+
     /app/run_bindcraft.sh \\
         --settings ${target_file} \\
         --filters ${filters} \\

nextflow.config

@@ -18,6 +18,15 @@ params {
     batches = 1
     quote_char = "\""
     bindcraft_container = null
+    gpu_device_count = 1
+    gpu_per_task = 1
+    gpu_parallel_tasks = 1
+    k8s_namespace = null
+    k8s_service_account = null
+    k8s_storage_claim = null
+    k8s_storage_mount = '/workspace'
+    k8s_workdir = null
+    k8s_pull_policy = 'IfNotPresent'
 
     // MultiQC options
     multiqc_config             = null
@@ -99,6 +108,7 @@ profiles {
     singularity {
         singularity.enabled     = true
         singularity.autoMounts  = true
+        singularity.runOptions  = '--nv'
         conda.enabled           = false
         docker.enabled          = false
         podman.enabled          = false
@@ -136,6 +146,7 @@ profiles {
     apptainer {
         apptainer.enabled       = true
         apptainer.autoMounts    = true
+        apptainer.runOptions    = '--nv'
         conda.enabled           = false
         docker.enabled          = false
         singularity.enabled     = false
@@ -154,6 +165,8 @@ profiles {
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
     gadi      { includeConfig 'conf/gadi.config'      }
+    local_gpu { includeConfig 'conf/local_gpu.config' }
+    k8s_gpu   { includeConfig 'conf/k8s_gpu.config'   }
 }
 
 // Load nf-core custom profiles from different Institutions
@@ -185,15 +198,8 @@ env {
     JULIA_DEPOT_PATH = "/usr/local/share/julia"
 }
 
-// Set bash options
-process.shell = """\
-bash
-
-set -e # Exit if a tool returns a non-zero status/exit code
-set -u # Treat unset variables and parameters as an error
-set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
-set -C # No clobber - prevent output redirection from overwriting files.
-"""
+// Set bash options as argv tokens (Nextflow does not accept newlines here)
+process.shell = ['/bin/bash', '-euo', 'pipefail', '-C']
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false

nextflow_schema.json

@@ -52,9 +52,7 @@
             "properties": {
                 "bindcraft_container": {
                     "type": "string",
-                    "format": "file-path",
-                    "exists": true,
-                    "description": "Path to bindcraft container to be used during execution.",
+                    "description": "Bindcraft container reference. Use a local image path for Singularity/Apptainer or an OCI image URI (e.g. ghcr.io/org/image:tag) for Docker/Kubernetes.",
                     "help_text": "",
                     "fa_icon": "fas fa-file-csv"
                 },
@@ -98,6 +96,52 @@
                     "description": ".",
                     "help_text": "",
                     "fa_icon": "fas fa-file-json"
+                },
+                "gpu_per_task": {
+                    "type": "integer",
+                    "default": 1,
+                    "description": "Number of GPUs requested per BINDCRAFT task in k8s_gpu profile.",
+                    "help_text": ""
+                },
+                "gpu_device_count": {
+                    "type": "integer",
+                    "default": 1,
+                    "description": "Number of visible GPUs used for local task-to-GPU mapping (CUDA_VISIBLE_DEVICES).",
+                    "help_text": ""
+                },
+                "gpu_parallel_tasks": {
+                    "type": "integer",
+                    "default": 1,
+                    "description": "Maximum number of concurrent BINDCRAFT GPU tasks in k8s_gpu profile.",
+                    "help_text": ""
+                },
+                "k8s_namespace": {
+                    "type": ["string", "null"],
+                    "description": "Kubernetes namespace for workflow pods.",
+                    "help_text": ""
+                },
+                "k8s_service_account": {
+                    "type": ["string", "null"],
+                    "description": "Kubernetes service account used by workflow pods.",
+                    "help_text": ""
+                },
+                "k8s_storage_claim": {
+                    "type": ["string", "null"],
+                    "description": "RWX PVC claim name to mount as shared pipeline storage in k8s_gpu profile.",
+                    "help_text": ""
+                },
+                "k8s_storage_mount": {
+                    "type": "string",
+                    "default": "/workspace",
+                    "description": "Mount path inside pods for the shared PVC.",
+                    "help_text": ""
+                },
+                "k8s_pull_policy": {
+                    "type": "string",
+                    "default": "IfNotPresent",
+                    "description": "Image pull policy for Kubernetes pods.",
+                    "enum": ["Always", "IfNotPresent", "Never"],
+                    "help_text": ""
                 }
 
             }