[MC] NAMD (#204)

Author: RMeli

config.yaml

@@ -247,8 +247,10 @@ uenvs:
     "3.0":
       recipes:
         gh200: 3.0/gh200
+        zen2: 3.0/mc
       deploy:
         daint: [gh200]
+        eiger: [zen2]
       develop: False
   netcdf-tools:
     "2024":

recipes/namd/3.0/gh200/compilers.yaml

@@ -2,4 +2,4 @@ bootstrap:
   spec: gcc@12
 gcc:
   specs:
-  - gcc@12.3
+  - gcc@13

recipes/namd/3.0/gh200/config.yaml

@@ -3,5 +3,5 @@ description: "NAMD: Scalable Molecular Dynamics"
 store: /user-environment
 spack:
   repo: https://github.com/spack/spack.git
-  commit: v0.22.0
+  commit: v0.23.1
 modules: True

recipes/namd/3.0/gh200/environments.yaml

@@ -1,10 +1,10 @@
 namd-single-node:
   compiler:
   - toolchain: gcc
-    spec: gcc@12.3
+    spec: gcc@13
   unify: true
   specs:
-  - cuda@12.4
+  - cuda@12.8
   - [email protected] +openmp ~mpi
   - [email protected]
   - charmpp@=8.0.0 backend=multicore +production +tracing
@@ -24,10 +24,10 @@ namd-single-node:
 namd:
   compiler:
   - toolchain: gcc
-    spec: gcc@12.3
+    spec: gcc@13
   unify: true
   specs:
-  - cuda@12.4
+  - cuda@12.8
   - [email protected] +openmp
   - [email protected]
   - charmpp@=8.0.0 backend=mpi +production +tracing ^cray-mpich

recipes/namd/3.0/gh200/repo/packages/charmpp/ofi-crayshasta-arm-8.0.0.patch

@@ -1,3 +1,5 @@
+diff --git a/src/arch/ofi-crayshasta/conv-mach.h b/src/arch/ofi-crayshasta/conv-mach.h
+index 61d295df3..9e15fd2a9 100644
 --- a/src/arch/ofi-crayshasta/conv-mach.h
 +++ b/src/arch/ofi-crayshasta/conv-mach.h
 @@ -74,7 +74,7 @@

recipes/namd/3.0/gh200/repo/packages/charmpp/ofi-crayshasta-arm-7.0.0.patch renamed to recipes/namd/3.0/gh200/repo/packages/charmpp/ofi-crayshasta-arm.patch

@@ -27,9 +27,9 @@ class Charmpp(Package):
     version("main", branch="main")
 
     version(
-            "8.0.0",
-            sha256="e30fc1e921e5cbf3406e792d5b0ca5f211c5d8ffbfc56e56d5501d8118abcaf6",
-            url="https://github.com/charmplusplus/charm/archive/refs/tags/v8.0.0.tar.gz"
+        "8.0.0",
+        sha256="e30fc1e921e5cbf3406e792d5b0ca5f211c5d8ffbfc56e56d5501d8118abcaf6",
+        url="https://github.com/charmplusplus/charm/archive/refs/tags/v8.0.0.tar.gz",
     )
     version("7.0.0", sha256="9c247b421bb157bdf9bc0ced3e25738c7a1dc1f7ec57b7943a7faf97f7e4fb2e")
     version("6.10.2", sha256="7abb4cace8aebdfbb8006eac03eb766897c009cfb919da0d0a33f74c3b4e6deb")
@@ -45,6 +45,10 @@ class Charmpp(Package):
     version("6.6.0", sha256="c916010f2d4cc2c6bd30ea19764839d0298fb56d1696d8ff08d9fa9a61dfb1c9")
     version("6.5.1", sha256="68aa43e2a6e476e116a7e80e385c25c6ac6497807348025505ba8bfa256ed34a")
 
+    depends_on("c", type="build")  # generated
+    depends_on("cxx", type="build")  # generated
+    depends_on("fortran", type="build")  # generated
+
     # Support OpenMPI; see
     # <https://github.com/UIUC-PPL/charm/issues/1206>
     # Patch is no longer needed in versions 6.8.0+
@@ -64,8 +68,7 @@ class Charmpp(Package):
     patch("strictpass.patch", when="@:6.8.2")
 
     # Support Cray Shasta with ARM
-    patch("ofi-crayshasta-arm-7.0.0.patch", when="backend=ofi pmi=cray-pmi target=aarch64: @=7.0.0")
-    patch("ofi-crayshasta-arm-8.0.0.patch", when="backend=ofi pmi=cray-pmi target=aarch64: @=8.0.0")
+    patch("ofi-crayshasta-arm.patch", when="backend=ofi pmi=cray-pmi target=aarch64:")
 
     # Build targets
     # "target" is reserved, so we have to use something else.
@@ -274,7 +277,7 @@ def charmarch(self):
 
     def install(self, spec, prefix):
         if not ("backend=mpi" in self.spec) or not ("backend=netlrts" in self.spec):
-            if "+pthreads" in self.spec:
+            if self.spec.satisfies("+pthreads"):
                 raise InstallError(
                     "The pthreads option is only\
                                     available on the Netlrts and MPI \
@@ -286,7 +289,7 @@ def install(self, spec, prefix):
             or ("backend=ofi" in self.spec)
             or ("backend=gni" in self.spec)
         ):
-            if "pmi=none" in self.spec:
+            if self.spec.satisfies("pmi=none"):
                 raise InstallError(
                     "The UCX/OFI/GNI backends need \
                                     PMI to run. Please add pmi=... \
@@ -299,7 +302,7 @@ def install(self, spec, prefix):
             or ("pmi=slurmpmi" in self.spec)
             or ("pmi=slurmpmi2" in self.spec)
         ):
-            if "^openmpi" in self.spec:
+            if self.spec.satisfies("^openmpi"):
                 raise InstallError(
                     "To use any process management \
                                     interface other than PMIx, \
@@ -321,15 +324,15 @@ def install(self, spec, prefix):
         options.append("-j%d" % make_jobs)
         options.append("--destination=%s" % builddir)
 
-        if "pmi=slurmpmi" in spec:
+        if spec.satisfies("pmi=slurmpmi"):
             options.append("slurmpmi")
-        if "pmi=slurmpmi2" in spec:
+        if spec.satisfies("pmi=slurmpmi2"):
             options.append("slurmpmi2")
-        if "pmi=pmix" in spec:
+        if spec.satisfies("pmi=pmix"):
             options.append("ompipmix")
             options.extend(["--basedir=%s" % spec["openmpi"].prefix])
 
-        if "backend=mpi" in spec:
+        if spec.satisfies("backend=mpi"):
             # in intelmpi <prefix>/include and <prefix>/lib fails so --basedir
             # cannot be used
             options.extend(
@@ -339,38 +342,45 @@ def install(self, spec, prefix):
                 ["--libdir={0}".format(libdir) for libdir in spec["mpi"].libs.directories]
             )
 
-        if "backend=ucx" in spec:
+        if spec.satisfies("backend=ucx"):
             options.extend(["--basedir=%s" % spec["ucx"].prefix])
-        if "+papi" in spec:
+        if spec.satisfies("+papi"):
             options.extend(["papi", "--basedir=%s" % spec["papi"].prefix])
         if "+smp" in spec and "backend=multicore" not in spec:
             # The 'multicore' backend always uses SMP, so we don't have to
             # append the 'smp' option when the 'multicore' backend is active. As
             # of Charm++ v7.0.0 it is actually a build error to append 'smp'
             # with the 'multicore' backend.
             options.append("smp")
-        if "+tcp" in spec:
+        if spec.satisfies("+tcp"):
             if "backend=netlrts" not in spec:
                 # This is a Charm++ limitation; it would lead to a
                 # build error
                 raise InstallError(
                     "The +tcp variant requires " "the backend=netlrts communication mechanism"
                 )
             options.append("tcp")
-        if "+omp" in spec:
+        if spec.satisfies("+omp"):
             options.append("omp")
-        if "+pthreads" in spec:
+        if spec.satisfies("+pthreads"):
             options.append("pthreads")
-        if "+cuda" in spec:
+        if spec.satisfies("+cuda"):
             options.append("cuda")
 
-        if "+shared" in spec:
+        if spec.satisfies("+shared"):
             options.append("--build-shared")
-        if "+production" in spec:
+        if spec.satisfies("+production"):
             options.append("--with-production")
-        if "+tracing" in spec:
+        if spec.satisfies("+tracing"):
             options.append("--enable-tracing")
 
+        # charmpp build was failing with clang based compilers for -DNETWORK=mpi as discussed in
+        # https://github.com/charmplusplus/charm/issues/3645
+        # Fix was suggested in https://github.com/charmplusplus/charm/pull/3646 and the same has
+        # been implemented in v8.0.0
+        if self.spec.satisfies("@8.0.0: %aocc"):
+            options.append("--disable-fortran")
+
         # Call "make" via the build script
         # Note: This builds Charm++ in the "tmp" subdirectory of the
         # install directory. Maybe we could set up a symbolic link

recipes/namd/3.0/gh200/repo/packages/charmpp/package.py

@@ -9,10 +9,11 @@
 
 import llnl.util.tty as tty
 
+from spack.build_environment import optimization_flags
 from spack.package import *
 
 
-class Namd(MakefilePackage, CudaPackage):
+class Namd(MakefilePackage, CudaPackage, ROCmPackage):
     """NAMD is a parallel molecular dynamics code designed for
     high-performance simulation of large biomolecular systems."""
 
@@ -26,14 +27,32 @@ class Namd(MakefilePackage, CudaPackage):
 
     version("master", branch="master")
     version("3.0", sha256="301c64f0f1db860f7336efdb26223ccf66b5ab42bfc9141df8d81ec1e20bf472")
-    version("3.0b7", sha256="b18ff43b0f55ec59e137c62eba1812589dd88b2122c3a05ea652781667f438b4", deprecated=True)
-    version("3.0b6", sha256="8b5fb1dc8d5b5666c6a45d20ee7e8c9d1f5c186578e2cf148b68ba421d43b850", deprecated=True)
-    version("3.0b3", sha256="20c32b6161f9c376536e3cb97c3bfe5367e1baaaace3c716ff79831fc2eb8199", deprecated=True)
-    version("2.15a2", sha256="8748cbaa93fc480f92fc263d9323e55bce6623fc693dbfd4a40f59b92669713e", deprecated=True)
+    version(
+        "3.0b7",
+        sha256="b18ff43b0f55ec59e137c62eba1812589dd88b2122c3a05ea652781667f438b4",
+        deprecated=True,
+    )
+    version(
+        "3.0b6",
+        sha256="8b5fb1dc8d5b5666c6a45d20ee7e8c9d1f5c186578e2cf148b68ba421d43b850",
+        deprecated=True,
+    )
+    version(
+        "3.0b3",
+        sha256="20c32b6161f9c376536e3cb97c3bfe5367e1baaaace3c716ff79831fc2eb8199",
+        deprecated=True,
+    )
+    version(
+        "2.15a2",
+        sha256="8748cbaa93fc480f92fc263d9323e55bce6623fc693dbfd4a40f59b92669713e",
+        deprecated=True,
+    )
     version("2.15a1", branch="master", tag="release-2-15-alpha-1", deprecated=True)
     # Same as above, but lets you use a local file instead of git
     version(
-        "2.15a1.manual", sha256="474006e98e32dddae59616b3b75f13a2bb149deaf7a0d617ce7fb9fd5a56a33a", deprecated=True
+        "2.15a1.manual",
+        sha256="474006e98e32dddae59616b3b75f13a2bb149deaf7a0d617ce7fb9fd5a56a33a",
+        deprecated=True,
     )
     version(
         "2.14",
@@ -57,9 +76,24 @@ class Namd(MakefilePackage, CudaPackage):
         description="Enables Tcl and/or python interface",
     )
 
-    variant("avxtiles", when="target=x86_64_v4:", default=False, description="Enable avxtiles")
+    variant(
+        "avxtiles",
+        when="target=x86_64_v4: @2.15:",
+        default=False,
+        description="Enable avxtiles supported with NAMD 2.15+",
+    )
     variant("single_node_gpu", default=False, description="Single node GPU")
 
+    # Adding memopt variant to build memory-optimized mode that utilizes a compressed
+    # version of the molecular structure and also supports parallel I/O.
+    # Refer: https://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction
+    variant(
+        "memopt",
+        when="@2.8:",
+        default=False,
+        description="Enable memory-optimized build supported with NAMD 2.8+",
+    )
+
     # init_tcl_pointers() declaration and implementation are inconsistent
     # "src/colvarproxy_namd.C", line 482: error: inherited member is not
     # allowed
@@ -85,7 +119,13 @@ class Namd(MakefilePackage, CudaPackage):
     depends_on("tcl", when="interface=python")
     depends_on("python", when="interface=python")
 
-    conflicts("+avxtiles", when="@:2.14,3:", msg="AVXTiles algorithm requires NAMD 2.15")
+    conflicts("+rocm", when="+cuda", msg="NAMD supports only one GPU backend at a time")
+    conflicts("+single_node_gpu", when="~cuda~rocm")
+    conflicts(
+        "+memopt",
+        when="+single_node_gpu",
+        msg="memopt mode is not compatible with GPU-resident builds",
+    )
 
     # https://www.ks.uiuc.edu/Research/namd/2.12/features.html
     # https://www.ks.uiuc.edu/Research/namd/2.13/features.html
@@ -136,7 +176,7 @@ def _edit_arch_generic(self, spec, prefix):
                 # this options are take from the default provided
                 # configuration files
                 # https://github.com/UIUC-PPL/charm/pull/2778
-                archopt = spec.architecture.target.optimization_flags(spec.compiler)
+                archopt = optimization_flags(self.compiler, spec.target)
 
                 if self.spec.satisfies("^charmpp@:6.10.1"):
                     optims_opts = {
@@ -276,6 +316,17 @@ def edit(self, spec, prefix):
             if "+single_node_gpu" in spec:
                 opts.extend(["--with-single-node-cuda"])
 
+        if "+rocm" in spec:
+            self._copy_arch_file("hip")
+            opts.append("--with-hip")
+            opts.extend(["--rocm-prefix", os.environ["ROCM_PATH"]])
+
+            if "+single_node_gpu" in spec:
+                opts.extend(["--with-single-node-hip"])
+
+        if spec.satisfies("+memopt"):
+            opts.append("--with-memopt")
+
         config = Executable("./config")
 
         config(self.build_directory, *opts)

recipes/namd/3.0/gh200/repo/packages/namd/package.py

@@ -0,0 +1,5 @@
+bootstrap:
+  spec: gcc@12
+gcc:
+  specs:
+  - gcc@13

recipes/namd/3.0/mc/compilers.yaml

@@ -0,0 +1,7 @@
+name: namd
+description: "NAMD: Scalable Molecular Dynamics" 
+store: /user-environment
+spack:
+  repo: https://github.com/spack/spack.git
+  commit: v0.23.1
+modules: True

recipes/namd/3.0/mc/config.yaml

@@ -0,0 +1,24 @@
+namd:
+  compiler:
+  - toolchain: gcc
+    spec: gcc@13
+  unify: true
+  specs:
+  - [email protected] +openmp +mpi
+  - [email protected]
+  - charmpp@=8.0.0 backend=mpi +production +tracing
+  - namd@=3.0
+  mpi:
+    spec: [email protected]
+  views:
+    develop:
+      link: roots
+      exclude: ["namd"]
+      uenv:
+        prefix_paths:
+          LD_LIBRARY_PATH: [lib, lib64]
+    namd:
+      link: roots
+      uenv:
+        prefix_paths:
+          LD_LIBRARY_PATH: [lib, lib64]