update pymatgen dependency to fix CP2K input parsing bug; update configs

Author: svandenhaute

configs/hortense.yaml

@@ -1,7 +1,7 @@
 ---
 container:
   engine: "apptainer"
-  uri: "oras://ghcr.io/molmod/psiflow:2.0.0-cuda"
+  uri: "oras://ghcr.io/molmod/psiflow:3.0.0-python3.9-cuda"
 ModelEvaluation:
   cores_per_worker: 1
   simulation_engine: 'openmm'
@@ -30,6 +30,7 @@ ModelTraining:
     scheduler_options: "#SBATCH --clusters=dodrio\n#SBATCH --gpus=1\n"
 ReferenceEvaluation:
   max_walltime: 20
+  cpu_affinity: 'alternating'
   SlurmProvider:
     partition: "cpu_rome"
     account: "2022_069"

configs/htex.yaml

@@ -1,10 +1,6 @@
 ---
-container:
-  engine: "apptainer"
-  uri: "/home/sandervandenhaute/doctorate/source/psiflow/psiflow_python3.10_cuda_latest.sif"
 ModelEvaluation:
   cores_per_worker: 2
-  max_walltime: 0.3
   simulation_engine: 'openmm'
   gpu: false
 ModelTraining:
@@ -13,7 +9,4 @@ ModelTraining:
   gpu: true
 ReferenceEvaluation:
   cores_per_worker: 1
-  max_walltime: 0.3
-  cpu_affinity: 'block'
-  #mpi_command: 'mpirun -np {}'
 ...

configs/mahti.yaml

@@ -1,7 +1,7 @@
 ---
 container:
   engine: "apptainer"
-  uri: "oras://ghcr.io/molmod/psiflow:3.0.0-cuda"
+  uri: "oras://ghcr.io/molmod/psiflow:3.0.0-python3.10-cuda" # use python3.9 depending on installation
 ModelEvaluation:
   cores_per_worker: 1
   simulation_engine: 'openmm'

configs/puhti.yaml

@@ -1,7 +1,7 @@
 ---
 container:
   engine: "apptainer"
-  uri: "oras://ghcr.io/molmod/psiflow:3.0.0-cuda"
+  uri: "oras://ghcr.io/molmod/psiflow:3.0.0-python3.10-cuda" # use python3.9 depending on installation
 ModelEvaluation:
   cores_per_worker: 1
   simulation_engine: 'openmm'

configs/threadpool.yaml

@@ -10,6 +10,6 @@ ModelTraining:
   use_threadpool: true
 ReferenceEvaluation:
   max_walltime: 0.3
-  mpi_command: 'mpirun -np {}'
+  mpi_command: 'mpirun -np {}' # cp2k on conda-forge comes with OpenMPI (not MPICH as in container)
   use_threadpool: true
 ...

pyproject.toml

@@ -14,7 +14,7 @@ dependencies = [
     "pyyaml>=6.0",
     "numpy>=1.22.3",
     "wandb>=0.14.0",
-    "pymatgen>=2023.3.23",
+    "pymatgen>=2023.11.12",
     "parsl",
     "prettytable",
     "psutil",