feat: update lammps reaxff to use newer builds

Problem: we want to run apptainer with lammps, and not require any spack or previous software installed. This adds an example, and also a new variable that exposes the version of lammps to download. Signed-off-by: vsoch <[email protected]>
researchapps · Feb 6, 2025 · c986723 · c986723
1 parent 763dacc
commit c986723
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Showing 3 changed files with 55 additions and 5 deletions.
diff --git a/examples/apptainer/lammps-reaxff.yaml b/examples/apptainer/lammps-reaxff.yaml
@@ -0,0 +1,43 @@
+ramble:
+  modifiers:
+  - name: apptainer
+  env_vars:
+    set:
+      OMP_NUM_THREADS: '{n_threads}'
+  variables:
+    mpi_command: ''
+    container_uri: docker://ghcr.io/converged-computing/metric-lammps-cpu:libfabric-zen4-reax
+    container_name: lammps-reax
+    batch_submit: '{execute_experiment}'
+    processes_per_node: 1
+    gpus_per_node: 0
+    # This is how you can add flags
+    # apptainer_run_args: --nv --bind {container_mounts} --writable-tmpfs
+  applications:
+    lammps: # Application name
+      workloads:
+        hns-reaxff: # Workload name from application
+          experiments:
+            strong_scale: # Arbitrary experiment name
+              variables:
+                env_name: apptainer
+                n_nodes: 1
+                lammps_path: /usr
+                # Add other lammps flags
+                lammps_flags: "-nocite"
+                # This is the release that is downloaded
+                input_stage: stable_29Aug2024_update1
+                # The input file used for lammps from the input_path directory
+                input_file: in.reaxff.hns
+                # Problem size dimensions for lammps
+                xx: 2
+                yy: 2
+                zz: 2
+  software:
+    packages:
+      apptainer:
+        pkg_spec: apptainer
+    environments:
+      lammps:
+        packages:
+        - apptainer
diff --git a/lib/ramble/ramble/pipeline.py b/lib/ramble/ramble/pipeline.py
@@ -572,6 +572,7 @@ def _execute(self):
             app_inst.add_expand_vars(self.workspace)
             exec_str = app_inst.expander.expand_var(self.executor)
             exec_parts = shlex.split(exec_str)
+
             exec_name = exec_parts[0]
             exec_args = exec_parts[1:]
 

diff --git a/var/ramble/repos/builtin/applications/lammps/application.py b/var/ramble/repos/builtin/applications/lammps/application.py
@@ -72,12 +72,10 @@ class Lammps(ExecutableApplication):
 
     input_file(
         "lammps-stage",
-        url="https://github.com/lammps/lammps/archive/refs/tags/stable_23Jun2022_update3.tar.gz",
-        target_dir="{application_input_dir}/stable_23Jun2022_update3",
-        description="Stage of lammps source from 20220623.3 release",
-        sha256="8a276a01b50d37eecfe6eb36f420f354cde51936d20aca7944dea60d3c098c89",
+        url="https://github.com/lammps/lammps/archive/refs/tags/{input_stage}.tar.gz",
+        target_dir="{application_input_dir}/lammps-input-stage",
+        description="Stage of lammps source from release",
     )
-
     executable(
         "copy",
         template=["cp {input_path} {experiment_run_dir}/input.txt"],
@@ -275,12 +273,20 @@ class Lammps(ExecutableApplication):
         inputs=["lammps-stage"],
     )
 
+    workload_variable(
+        "input_stage",
+         default="stable_23Jun2022_update3.tar.gz",
+         description="Stage name of LAMMPS input archive",
+         workloads=["hns-reaxff"]
+    )
+
     workload_variable(
         "input_file",
         default="in.reaxc.hns",
         description="hns-reaxff input file name",
         workloads=["hns-reaxff"],
     )
+
     workload_variable(
         "input_path",
         default=os.path.join(f"{intel_test_path}"),