VMD: 1.9.4a57 (GH200)

config.yaml

@@ -347,3 +347,10 @@ uenvs:
         todi: [gh200]
         daint: [gh200]
       develop: False
+  vmd:
+    "1.9.4a57":
+      recipes:
+        gh200: 1.9.4a57/gh200
+      deploy:
+        daint: [gh200]
+      develop: False

recipes/vmd/1.9.4a57/gh200/compilers.yaml

@@ -0,0 +1,5 @@
+bootstrap:
+  spec: gcc@13
+gcc:
+  specs:
+  - gcc@13

recipes/vmd/1.9.4a57/gh200/config.yaml

@@ -0,0 +1,7 @@
+name: vmd
+description: VMD Visual Molecular Dynamics 1.9.4 alpha 57
+store: /user-environment
+spack:
+  repo: https://github.com/spack/spack.git
+  commit: v0.23.1
+modules: false

recipes/vmd/1.9.4a57/gh200/environments.yaml

@@ -0,0 +1,29 @@
+vmd-env:
+  compiler:
+  - toolchain: gcc
+    spec: gcc@13
+  unify: true
+  specs:
+  - [email protected] ~xss
+  - [email protected]
+  - fltk
+  - libpng
+  - zlib
+  - [email protected]
+  - vmd
+  variants:
+    - +cuda
+    - cuda_arch=90a
+  views:
+    default:
+      link: roots
+      uenv:
+        add_compilers: false
+        LD_LIBRARY_PATH: [lib, lib64]
+    develop:
+      link: roots
+      exclude: ["vmd"]
+      uenv:
+        prefix_paths:
+          CPATH: [include]
+          LIBRARY_PATH: [lib, lib64]

recipes/vmd/1.9.4a57/gh200/pre-install

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+set -u
+
+vmd_version="1.9.4a57"
+vmd_tarball="vmd-${vmd_version}.src.tar.gz"
+vmd_tarball_filepath={{ env.build }}/environments/${vmd_tarball}
+
+curl --user $CSCS_REGISTRY_USERNAME:$CSCS_REGISTRY_PASSWORD https://jfrog.svc.cscs.ch/artifactory/uenv-sources/vmd/${vmd_tarball} --output ${vmd_tarball_filepath}
+
+tar xf ${vmd_tarball_filepath}

recipes/vmd/1.9.4a57/gh200/repo/packages/vmd/configure-cuda.patch

@@ -0,0 +1,15 @@
+--- spack.src/configure   2025-02-21 12:14:19.000000000 +0100
++++ spack.src.patched/configure   2025-02-21 12:15:38.000000000 +0100
+@@ -2629,10 +2629,9 @@
+   if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }
+   $vmd_libs          = "$tcl_libs -lz";
+
+-  $arch_nvcc     = "/usr/local/cuda/bin/nvcc";
++  $arch_nvcc     = "nvcc";
+   $arch_nvccflags   = "--ptxas-options=-v " .
+-                    "-gencode arch=compute_30,code=compute_30 " .
+-                    "-gencode arch=compute_70,code=compute_70 " .
++                    "-gencode arch=compute_90,code=compute_90 " .
+                     "--ftz=true ";
+   $cuda_library     = "-L/usr/local/cuda/lib64";
+   $arch_cc       = "cc";

recipes/vmd/1.9.4a57/gh200/repo/packages/vmd/package.py

@@ -0,0 +1,121 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+
+from spack.package import *
+
+
+class Vmd(MakefilePackage, CudaPackage):
+    """VMD provides user-editable materials which can be applied
+    to molecular geometry.
+
+    These material properties control the details of how VMD shades
+    the molecular geometry, and how transparent or opaque the displayed
+    molecular geometry is. With this feature, one can easily create nice
+    looking transparent surfaces which allow inner structural details to
+    be seen within a large molecular structure. The material controls can
+    be particularly helpful when rendering molecular scenes using external
+    ray tracers, each of which typically differ slightly.
+    """
+
+    homepage = "https://www.ks.uiuc.edu/Research/vmd/"
+    version(
+        "1.9.4a57",
+        sha256="de278d0c5d969336d89068e0806fb50aaa0cb0f546ba985d840b279357860679",
+    )
+
+    url = "file://{0}/vmd-1.9.4a57.src.tar.gz".format(os.getcwd())
+    manual_download = True
+    redistribute(source=False, binary=False)
+
+    requires("%gcc", msg="Currently GCC is hard-coded.")
+    requires("target=aarch64", msg="Currently LINUXARM64 is hard-coded.")
+
+    depends_on("[email protected]")
+    depends_on("[email protected]")
+    depends_on("fltk")
+
+    depends_on("libx11", type=("run", "link"))
+    depends_on("gl@3:", type=("run", "link"))
+
+    depends_on("patchelf", type="build")
+    depends_on("gmake", type="build")
+
+    patch(
+        "configure-cuda.patch",
+        sha256="a1954e289c80f520aaf9086b6fa41de64d78cc8d895ef7c54fb3e8c509da7fdf",
+        working_dir="vmd-1.9.4a57",
+    )
+
+    def setup_build_environment(self, env):
+        env.set("VMDINSTALLBINDIR", self.prefix.bin)
+        env.set("VMDINSTALLLIBRARYDIR", self.prefix.lib64)
+        env.set("PLUGINDIR", self.prefix.lib64.plugins)
+
+    def build(self, spec, prefix):
+        with working_dir(join_path(self.stage.source_path, "plugins")):
+            gmake = Executable("gmake")
+            gmake("LINUXARM64")
+            gmake("distrib")
+
+        VMD_SOURCE_DIR = join_path(self.stage.source_path, "vmd-1.9.4a57")
+        with working_dir(VMD_SOURCE_DIR):
+            os.symlink(join_path(self.prefix.lib64, "plugins"), "plugins")
+
+            configure_opts = [
+                "LINUXARM64",
+                "GCC",
+                "TCL",
+                "FLTK",
+                "FLTKOPENGL",
+                "EGLPBUFFER",
+                "PTHREADS",
+                "SHARED",
+                "NOSTATICPLUGINS",
+                "LIBPNG",
+                "ZLIB",
+            ]
+
+            if "+cuda" in spec:
+                configure_opts.append("CUDA")
+
+            configure(*configure_opts)
+
+        with working_dir(join_path(VMD_SOURCE_DIR, "src")):
+            make()
+
+    def install(self, spec, prefix):
+        with working_dir(join_path(self.stage.source_path, "vmd-1.9.4a57/src")):
+            make("install")
+            os.symlink(
+                join_path(prefix.lib64, "vmd.so"),
+                join_path(prefix.lib64, "vmd_LINUXARM64"),
+            )
+
+    # @run_after("install")
+    # def ensure_rpaths(self):
+    #     # make sure the executable finds and uses the Spack-provided
+    #     # libraries, otherwise the executable may or may not run depending
+    #     # on what is installed on the host
+    #     patchelf = which("patchelf")
+    #     rpath = ":".join(
+    #         self.spec[dep].libs.directories[0]
+    #         for dep in [
+    #             "libx11",
+    #             "libxi",
+    #             "libxinerama",
+    #             "gl",
+    #             "fltk",
+    #             "tcl",
+    #             "tk",
+    #             "cuda",
+    #         ]
+    #     )
+    #     patchelf(
+    #         "--set-rpath", rpath, join_path(self.prefix, "lib64", "vmd_LINUXAMD64")
+    #     )
+
+    def setup_run_environment(self, env):
+        env.set("PLUGINDIR", self.spec.prefix.lib64.plugins)

recipes/vmd/1.9.4a57/gh200/repo/repo.yaml

@@ -0,0 +1,2 @@
+repo:
+  namespace: 'spack-repo'