Merge branch 'gemmi' into dev

Resolve conflicts in CLI and workflow modules: keep gemmi work_dir /
project_root / resolve_artifacts_dir API; drop dev string MDP path
overrides and broken mdmx.main (undefined chimerax_exec).

Co-authored-by: Cursor <[email protected]>

Author: jlee733

.gitignore

@@ -1,5 +1,6 @@
 __pycache__/
 **/__pycache__/
+.nv/
 *.pdb
 *.log
 *.cxc

Dockerfile

@@ -1,6 +1,10 @@
 # Docker Hub image tag: diffuseproject/md:0.0.2
 # ==================== BUILDER ====================
-FROM ubuntu:22.04 AS builder
+# CUDA *devel* image supplies nvcc + headers so GROMACS can configure with -DGMX_GPU=CUDA.
+# Must match the major.minor of the final runtime image (below) for sane libcudart/cufft ABI.
+#   docker build --build-arg CUDA_IMAGE_TAG=12.4.1 -t diffuseproject/md:gemmi .
+ARG CUDA_IMAGE_TAG=12.6.3
+FROM nvidia/cuda:${CUDA_IMAGE_TAG}-devel-ubuntu22.04 AS builder
 
 ENV DEBIAN_FRONTEND=noninteractive
 
@@ -59,6 +63,7 @@ dependencies:
   - cmake =3.31.2
   - awscli
   - gnuplot =5.4.10
+  - gemmi =0.7.4
 YAML
 
 RUN $MAMBA_EXE create -y -f /tmp/lunus.yaml && rm /tmp/lunus.yaml
@@ -80,6 +85,9 @@ RUN set -ex \
     && mkdir build && cd build \
     && cmake .. \
         -DGMX_BUILD_OWN_FFTW=ON \
+        -DGMX_GPU=CUDA \
+        -DCUDAToolkit_ROOT=/usr/local/cuda \
+        -DGMX_CUDA_TARGET_SM=90 \
     && make -j"$(nproc)" \
     && make install \
     && cd / \
@@ -101,27 +109,24 @@ RUN $MAMBA_EXE remove -n lunus -y scons cmake \
     true
 
 # ==================== FINAL ====================
-FROM ubuntu:22.04
+# NVIDIA CUDA runtime: libcudart / cuFFT etc. for CUDA GROMACS at run time.
+# Host still needs the driver + NVIDIA Container Toolkit; use docker run --gpus all ...
+# CUDA_IMAGE_TAG is set by the global ARG at the top of this file.
+FROM nvidia/cuda:${CUDA_IMAGE_TAG}-runtime-ubuntu22.04
+
 
 ENV DEBIAN_FRONTEND=noninteractive
+# Let GPU-requiring processes see the GPU by default (can override at run time).
+ENV NVIDIA_VISIBLE_DEVICES=all
+ENV NVIDIA_DRIVER_CAPABILITIES=compute,utility
 
-ARG CHIMERAX_URL="https://www.cgl.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?file=current/ubuntu-22.04/chimerax-daily.deb"
 RUN apt-get update && apt-get install -y --no-install-recommends \
         ca-certificates \
         coreutils \
         rsync \
         bc \
         bzip2 \
-        curl \
         libgomp1 \
-    && curl -s -c /tmp/cx_cookies -d "choice=Accept" "${CHIMERAX_URL}" \
-       | grep -oP 'url=\K[^"]*' > /tmp/cx_redirect \
-    && curl -s -b /tmp/cx_cookies -o /tmp/chimerax.deb \
-       "https://www.cgl.ucsf.edu$(cat /tmp/cx_redirect)" \
-    && apt-get install -y /tmp/chimerax.deb \
-    && rm -f /tmp/chimerax.deb /tmp/cx_cookies /tmp/cx_redirect \
-    && apt-get purge -y curl \
-    && apt-get autoremove -y \
     && rm -rf /var/lib/apt/lists/*
 
 # ---------- bashrc (inline of bashrc_new) ----------

md_workflows/cli.py

@@ -4,6 +4,7 @@
 
 import argparse
 import sys
+from pathlib import Path
 
 from . import equilibrate
 from . import make_crystal
@@ -20,26 +21,55 @@ def _single_command_cli(command: str) -> None:
 
     if command == "param_prot":
         parser.add_argument("--pdb-id", default="6B8X")
+        parser.add_argument(
+            "--project-root",
+            type=Path,
+            default=None,
+            help="Directory containing artifacts/ and optional <PDB>.pdb (default: cwd)",
+        )
     elif command == "make_crystal":
         parser.add_argument("--ix", type=int, default=1)
         parser.add_argument("--iy", type=int, default=None)
         parser.add_argument("--iz", type=int, default=None)
-        parser.add_argument("--chimerax-exec", default="chimerax")
+        parser.add_argument(
+            "--work-dir",
+            type=Path,
+            default=None,
+            help="Run directory with prot.pdb, pdb_clean.pdb, etc. (default: cwd)",
+        )
     elif command == "make_waterbox":
         parser.add_argument("--ntomp", type=int, default=26)
-        parser.add_argument("--min-water", dest="min_water_mdp", default="artifacts/min_water.mdp", help="Path to min_water.mdp file")
-        parser.add_argument("--equil-water", dest="equil_water_mdp", default="artifacts/equil_water.mdp", help="Path to equil_water.mdp file")
+        parser.add_argument("--work-dir", type=Path, default=None)
+        parser.add_argument(
+            "--artifacts-dir",
+            type=Path,
+            default=None,
+            help="Override MDP directory (default: <project-root>/artifacts)",
+        )
+        parser.add_argument(
+            "--project-root",
+            type=Path,
+            default=None,
+            help="Project root containing artifacts/ (default: cwd; inferred from --work-dir if possible)",
+        )
     elif command == "solvate":
-        pass
+        parser.add_argument("--work-dir", type=Path, default=None)
     elif command == "minimize":
         parser.add_argument("--ntomp", type=int, default=26)
-        parser.add_argument("--min", dest="min_mdp", default="artifacts/min.mdp", help="Path to min.mdp file")
+        parser.add_argument("--work-dir", type=Path, default=None)
+        parser.add_argument("--artifacts-dir", type=Path, default=None)
+        parser.add_argument("--project-root", type=Path, default=None)
     elif command == "equilibrate":
         parser.add_argument("--ntomp", type=int, default=26)
-        parser.add_argument("--equil", dest="equil_mdp", default="artifacts/equil.mdp", help="Path to equil.mdp file")
+        parser.add_argument("--work-dir", type=Path, default=None)
+        parser.add_argument("--artifacts-dir", type=Path, default=None)
+        parser.add_argument("--project-root", type=Path, default=None)
     elif command == "resolvate":
         parser.add_argument("--ntmpi", type=int, default=8)
         parser.add_argument("--ntomp", type=int, default=1)
+        parser.add_argument("--work-dir", type=Path, default=None)
+        parser.add_argument("--artifacts-dir", type=Path, default=None)
+        parser.add_argument("--project-root", type=Path, default=None)
     elif command == "run_params_gaussian":
         parser.add_argument("--g16root", default="/Users/mewall/packages")
         parser.add_argument("--nproc", type=int, default=8)
@@ -49,19 +79,52 @@ def _single_command_cli(command: str) -> None:
     args = parser.parse_args(sys.argv[1:])
 
     if command == "param_prot":
-        param_prot.run(pdb_id=args.pdb_id)
+        root = (args.project_root or Path.cwd()).resolve()
+        wd = param_prot.run(pdb_id=args.pdb_id, project_root=root)
+        print(wd)
     elif command == "make_crystal":
-        make_crystal.run(ix=args.ix, iy=args.iy, iz=args.iz, chimerax_exec=args.chimerax_exec)
+        wd = (args.work_dir or Path.cwd()).resolve()
+        make_crystal.run(ix=args.ix, iy=args.iy, iz=args.iz, work_dir=wd)
     elif command == "make_waterbox":
-        make_waterbox.run(ntomp=args.ntomp, min_water_mdp=args.min_water_mdp, equil_water_mdp=args.equil_water_mdp)
+        wd = (args.work_dir or Path.cwd()).resolve()
+        pr = args.project_root.resolve() if args.project_root else None
+        make_waterbox.run(
+            ntomp=args.ntomp,
+            work_dir=wd,
+            artifacts_dir=args.artifacts_dir,
+            project_root=pr,
+        )
     elif command == "solvate":
-        solvate.run()
+        wd = (args.work_dir or Path.cwd()).resolve()
+        solvate.run(work_dir=wd)
     elif command == "minimize":
-        minimize.run(ntomp=args.ntomp, min_mdp=args.min_mdp)
+        wd = (args.work_dir or Path.cwd()).resolve()
+        pr = args.project_root.resolve() if args.project_root else None
+        minimize.run(
+            ntomp=args.ntomp,
+            work_dir=wd,
+            artifacts_dir=args.artifacts_dir,
+            project_root=pr,
+        )
     elif command == "equilibrate":
-        equilibrate.run(ntomp=args.ntomp, equil_mdp=args.equil_mdp)
+        wd = (args.work_dir or Path.cwd()).resolve()
+        pr = args.project_root.resolve() if args.project_root else None
+        equilibrate.run(
+            ntomp=args.ntomp,
+            work_dir=wd,
+            artifacts_dir=args.artifacts_dir,
+            project_root=pr,
+        )
     elif command == "resolvate":
-        resolvate.run(ntmpi=args.ntmpi, ntomp=args.ntomp)
+        wd = (args.work_dir or Path.cwd()).resolve()
+        pr = args.project_root.resolve() if args.project_root else None
+        resolvate.run(
+            ntmpi=args.ntmpi,
+            ntomp=args.ntomp,
+            work_dir=wd,
+            artifacts_dir=args.artifacts_dir,
+            project_root=pr,
+        )
     elif command == "run_params_gaussian":
         run_params_gaussian.run(
             g16root=args.g16root,