Features/gromacs

experiments/gromacs/experiment.py

@@ -18,14 +18,14 @@ class Gromacs(
 ):
     variant(
         "workload",
-        default="water_gmx50_adac",
+        default="water_gmx50",
         description="workload name",
     )
 
     variant(
         "version",
-        default="2024",
-        values=("2024", "2023.3"),
+        default="2025.2",
+        values=("2025.2", "2024", "2023.3"),
         description="app version",
     )
 
@@ -41,6 +41,14 @@ class Gromacs(
         description="Use GPU-aware MPI",
     )
 
+    variant(
+        "sycl",
+        default=True,
+        values=(True, False),
+        when=("+rocm"),
+        description="Enable GPU-aware MPI",
+    )
+
     def compute_applications_section(self):
         if self.spec.satisfies("+openmp"):
             self.set_environment_variable("OMP_PROC_BIND", "close")
@@ -79,6 +87,7 @@ def compute_applications_section(self):
             "pme": "auto",
             "bonded": f"{bonded_target}",
             "update": f"{target}",
+            "additional_args": " -pin {pin} -nb {nb} -pme {pme} -bonded {bonded} -update {update} -maxh {maxh} -nstlist {nstlist} -npme {npme} ",
         }
 
         for k, v in input_variables.items():
@@ -97,7 +106,7 @@ def compute_package_section(self):
         app_version = self.spec.variants["version"][0]
 
         spack_specs = "+mpi~hwloc"
-        spack_specs += "+sycl" if self.spec.satisfies("+rocm") else "~sycl"
+        spack_specs += "+sycl" if self.spec.satisfies("+sycl") else "~sycl"
 
         if self.spec.satisfies("+cuda") or self.spec.satisfies("+rocm"):
             spack_specs += f" gpu-aware-mpi={self.spec.variants['gpu-aware-mpi'][0]} "

modifiers/allocation/modifier.py

@@ -322,6 +322,7 @@ def slurm_instructions(self, v):
         sbatch_directives = list(f"#SBATCH {x}" for x in (srun_opts + sbatch_opts))
 
         v.mpi_command = f"srun {' '.join(srun_opts)}"
+        v.single_rank_mpi_command = "srun -n 1 -N 1"
         v.batch_submit = "sbatch {execute_experiment}"
         v.allocation_directives = "\n".join(sbatch_directives)
 
@@ -390,6 +391,7 @@ def flux_instructions(self, v):
         batch_directives = list(f"# flux: {x}" for x in (cmd_opts + batch_opts))
 
         v.mpi_command = f"flux run {' '.join([cmd_ranks] + cmd_opts)}"
+        v.single_rank_mpi_command = "flux run -n 1 -N 1"
         v.batch_submit = "flux batch {execute_experiment}"
         v.allocation_directives = "\n".join(batch_directives)
 
@@ -398,6 +400,7 @@ def mpi_instructions(self, v):
         cmd_opts.extend([f"-n {v.n_ranks}"])
 
         v.mpi_command = "mpirun " + " ".join(cmd_opts)
+        v.single_rank_mpi_command = "mpirun -n 1"
         v.batch_submit = "{execute_experiment}"
         v.allocation_directives = ""
 
@@ -428,6 +431,7 @@ def lsf_instructions(self, v):
         batch_directives = list(f"#BSUB {x}" for x in batch_opts)
 
         v.mpi_command = f"lrun {' '.join(cmd_opts)}"
+        v.single_rank_mpi_command = "lrun -n 1"
         v.batch_submit = "bsub {execute_experiment}"
         v.allocation_directives = "\n".join(batch_directives)
 
@@ -444,6 +448,7 @@ def pjm_instructions(self, v):
         batch_directives = list(f"#PJM {x}" for x in batch_opts)
 
         v.mpi_command = "mpiexec " + " ".join(cmd_opts)
+        v.single_rank_mpi_command = "mpiexec --mpi proc=1"
         v.batch_submit = "pjsub {execute_experiment}"
         v.allocation_directives = "\n".join(batch_directives)