diff --git a/config/md.yaml b/config/md.yaml index badf487..799788e 100644 --- a/config/md.yaml +++ b/config/md.yaml @@ -8,3 +8,4 @@ n_inner: 5000 # compiled inner steps sampling_rate: 200 # dump interval buffer_size: 1000 dr_threshold: 0.5 # Neighborlist skin +checkpoint_interval: 200 diff --git a/dvc.lock b/dvc.lock index c3b0669..a3b2ffc 100644 --- a/dvc.lock +++ b/dvc.lock @@ -27264,7 +27264,7 @@ stages: depl_Packmol_1: box: count: - - 16 + - 8 data_ids: density: 900 pbc: true @@ -27272,16 +27272,16 @@ stages: outs: - path: nodes/depl/Packmol_1/atoms.h5 hash: md5 - md5: 7ec77fd6549c61434a9b28b7715027a8 - size: 43328 + md5: 3cd76ae11c9131c8a7f01264bf5946e4 + size: 35776 - path: nodes/depl/Packmol_1/node-meta.json hash: md5 - md5: 4dab86e07acb5e1b620a83587ef489a4 + md5: 003a201fcea1010f61324911d4d48619 size: 48 - path: nodes/depl/Packmol_1/packmol hash: md5 - md5: ac2a1f78e24d4acec487ee8d320e3c86.dir - size: 28854 + md5: 841037c7ba3625d833250e20c6e49d0e.dir + size: 15413 nfiles: 3 depl_ASEGeoOpt: cmd: zntrack run ipsuite.nodes.ASEGeoOpt --name depl_ASEGeoOpt @@ -27313,16 +27313,16 @@ stages: size: 8933596 - path: nodes/depl/Packmol_1/atoms.h5 hash: md5 - md5: 7ec77fd6549c61434a9b28b7715027a8 - size: 43328 + md5: 3cd76ae11c9131c8a7f01264bf5946e4 + size: 35776 - path: nodes/depl/Packmol_1/node-meta.json hash: md5 - md5: 4dab86e07acb5e1b620a83587ef489a4 + md5: 003a201fcea1010f61324911d4d48619 size: 48 - path: nodes/depl/Packmol_1/packmol hash: md5 - md5: ac2a1f78e24d4acec487ee8d320e3c86.dir - size: 28854 + md5: 841037c7ba3625d833250e20c6e49d0e.dir + size: 15413 nfiles: 3 params: params.yaml: @@ -27345,12 +27345,12 @@ stages: nfiles: 1 - path: nodes/depl/ASEGeoOpt/node-meta.json hash: md5 - md5: fe39d4aaaae596691bf44639f50031f0 + md5: b792fe7ae1695af8e65a117401229061 size: 48 - path: nodes/depl/ASEGeoOpt/trajectory.h5 hash: md5 - md5: 983b66b57f7c4f7f7e5d9043e0e0f8e4 - size: 6554344 + md5: ac6bf9748958632f4b4ebe0fb7597a86 + size: 6590696 depl_ASEMD: cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD deps: @@ -27386,12 +27386,12 @@ stages: nfiles: 1 - path: nodes/depl/ASEGeoOpt/node-meta.json hash: md5 - md5: fe39d4aaaae596691bf44639f50031f0 + md5: b792fe7ae1695af8e65a117401229061 size: 48 - path: nodes/depl/ASEGeoOpt/trajectory.h5 hash: md5 - md5: 983b66b57f7c4f7f7e5d9043e0e0f8e4 - size: 6554344 + md5: ac6bf9748958632f4b4ebe0fb7597a86 + size: 6590696 params: params.yaml: depl_ASEMD: @@ -27417,8 +27417,8 @@ stages: outs: - path: nodes/depl/ASEMD/metrics_dict.csv hash: md5 - md5: 9eabeb33f3ffd6fd44e887e438258f81 - size: 42026 + md5: 0691758813e71d9bd9d7321c192e52c8 + size: 41980 - path: nodes/depl/ASEMD/model hash: md5 md5: 64586897446153f477c052dd0e2579ad.dir @@ -27426,7 +27426,7 @@ stages: nfiles: 1 - path: nodes/depl/ASEMD/node-meta.json hash: md5 - md5: 702ac4b90cb94907e6daea3925c92de3 + md5: 92853eb5b2db24b1ad4bc26e4fb2f586 size: 48 - path: nodes/depl/ASEMD/steps_before_stopping.json hash: md5 @@ -27434,8 +27434,8 @@ stages: size: 2 - path: nodes/depl/ASEMD/trajectory.h5 hash: md5 - md5: ed7e9f3b3286701eb4ee6d025a1c72e1 - size: 50790792 + md5: 476eb5dd9ca4ec982f6a62cfbb685f75 + size: 25409160 depl_ASEMD_1: cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD_1 deps: @@ -27466,8 +27466,8 @@ stages: size: 8933596 - path: nodes/depl/ASEMD/metrics_dict.csv hash: md5 - md5: 9eabeb33f3ffd6fd44e887e438258f81 - size: 42026 + md5: 0691758813e71d9bd9d7321c192e52c8 + size: 41980 - path: nodes/depl/ASEMD/model hash: md5 md5: 64586897446153f477c052dd0e2579ad.dir @@ -27475,7 +27475,7 @@ stages: nfiles: 1 - path: nodes/depl/ASEMD/node-meta.json hash: md5 - md5: 702ac4b90cb94907e6daea3925c92de3 + md5: 92853eb5b2db24b1ad4bc26e4fb2f586 size: 48 - path: nodes/depl/ASEMD/steps_before_stopping.json hash: md5 @@ -27483,8 +27483,8 @@ stages: size: 2 - path: nodes/depl/ASEMD/trajectory.h5 hash: md5 - md5: ed7e9f3b3286701eb4ee6d025a1c72e1 - size: 50790792 + md5: 476eb5dd9ca4ec982f6a62cfbb685f75 + size: 25409160 params: params.yaml: depl_ASEMD_1: @@ -27507,8 +27507,8 @@ stages: outs: - path: nodes/depl/ASEMD_1/metrics_dict.csv hash: md5 - md5: 1d7fedd953d3070286a7f7eb3145a04f - size: 41972 + md5: 180d59b898aa5ca11eee252c37769b33 + size: 41946 - path: nodes/depl/ASEMD_1/model hash: md5 md5: 64586897446153f477c052dd0e2579ad.dir @@ -27516,7 +27516,7 @@ stages: nfiles: 1 - path: nodes/depl/ASEMD_1/node-meta.json hash: md5 - md5: b9dc78a7b957ee3fa6edf192a9587642 + md5: 07e0fd3e41ce717e8375a4ab8c2f296c size: 48 - path: nodes/depl/ASEMD_1/steps_before_stopping.json hash: md5 @@ -27524,8 +27524,8 @@ stages: size: 2 - path: nodes/depl/ASEMD_1/trajectory.h5 hash: md5 - md5: 96704554effb815f0a6f29808461916e - size: 50790792 + md5: 005cd53b37325a87bbec0fbaec8bf4ce + size: 25409160 ML17_training_MLModel_4: cmd: zntrack run ipsuite.nodes.Apax --name ML17_training_MLModel_4 deps: @@ -27813,8 +27813,8 @@ stages: size: 8933596 - path: nodes/depl/ASEMD_1/metrics_dict.csv hash: md5 - md5: 1d7fedd953d3070286a7f7eb3145a04f - size: 41972 + md5: 180d59b898aa5ca11eee252c37769b33 + size: 41946 - path: nodes/depl/ASEMD_1/model hash: md5 md5: 64586897446153f477c052dd0e2579ad.dir @@ -27822,7 +27822,7 @@ stages: nfiles: 1 - path: nodes/depl/ASEMD_1/node-meta.json hash: md5 - md5: b9dc78a7b957ee3fa6edf192a9587642 + md5: 07e0fd3e41ce717e8375a4ab8c2f296c size: 48 - path: nodes/depl/ASEMD_1/steps_before_stopping.json hash: md5 @@ -27830,8 +27830,8 @@ stages: size: 2 - path: nodes/depl/ASEMD_1/trajectory.h5 hash: md5 - md5: 96704554effb815f0a6f29808461916e - size: 50790792 + md5: 005cd53b37325a87bbec0fbaec8bf4ce + size: 25409160 params: params.yaml: depl_ApaxJaxMD: @@ -27840,6 +27840,7 @@ stages: repeat: config/md.yaml: buffer_size: 1000 + checkpoint_interval: 200 dr_threshold: 0.5 duration: 20000000 ensemble: @@ -27851,14 +27852,14 @@ stages: outs: - path: nodes/depl/ApaxJaxMD/initial_structure.extxyz hash: md5 - md5: d8e66e3ed64784648957086d9c12796c - size: 50550 + md5: 9a12f22898f77175697adc600bf17e17 + size: 25344 - path: nodes/depl/ApaxJaxMD/md hash: md5 - md5: c90a3eb0c501822a60b483f4bcba4a4a.dir - size: 7914518180 - nfiles: 2 + md5: 0cdc69409922ed8449606e3297224156.dir + size: 4117321789 + nfiles: 6 - path: nodes/depl/ApaxJaxMD/node-meta.json hash: md5 - md5: 449f50cd73381549536365afb653a8ef - size: 65 + md5: 386f7edcfa74df85ab0d1264322eb244 + size: 48 diff --git a/main.py b/main.py index ea11374..e0bdf63 100644 --- a/main.py +++ b/main.py @@ -959,7 +959,7 @@ structure = ips.configuration_generation.Packmol( data=[single_structure.atoms], - count=[16], # 16, 32, 64 + count=[8], # 16, 32, 64 density=900, ) diff --git a/nodes/depl/ASEGeoOpt/node-meta.json b/nodes/depl/ASEGeoOpt/node-meta.json index b49e633..0ad7184 100644 --- a/nodes/depl/ASEGeoOpt/node-meta.json +++ b/nodes/depl/ASEGeoOpt/node-meta.json @@ -1 +1 @@ -{"uuid": "0d584356-51f5-4a5f-ace8-5a4c3eaacc1f"} \ No newline at end of file +{"uuid": "c9925b2d-5f73-4164-b289-a9da5d04f16f"} \ No newline at end of file diff --git a/nodes/depl/ASEMD/node-meta.json b/nodes/depl/ASEMD/node-meta.json index f98b231..a6b51ae 100644 --- a/nodes/depl/ASEMD/node-meta.json +++ b/nodes/depl/ASEMD/node-meta.json @@ -1 +1 @@ -{"uuid": "7762021a-481c-40bc-a25f-268c2bce0a4a"} \ No newline at end of file +{"uuid": "10ac38e8-734f-4413-bd60-cbfb03b000e2"} \ No newline at end of file diff --git a/nodes/depl/ASEMD_1/node-meta.json b/nodes/depl/ASEMD_1/node-meta.json index af6fee2..50cdb18 100644 --- a/nodes/depl/ASEMD_1/node-meta.json +++ b/nodes/depl/ASEMD_1/node-meta.json @@ -1 +1 @@ -{"uuid": "c30fb88b-5e00-49a3-bd12-99d258c289f5"} \ No newline at end of file +{"uuid": "ebc1231a-d151-46d1-b95f-8dce92b2d7e5"} \ No newline at end of file diff --git a/nodes/depl/ApaxJaxMD/node-meta.json b/nodes/depl/ApaxJaxMD/node-meta.json index 20c4ebf..1ae775d 100644 --- a/nodes/depl/ApaxJaxMD/node-meta.json +++ b/nodes/depl/ApaxJaxMD/node-meta.json @@ -1 +1 @@ -{"uuid": "f9c6d9bb-61a2-45fd-9e7a-51ee968fbdd2", "run_count": 1} +{"uuid": "6980bfa0-7655-4bb7-b315-81dd2b24a625"} \ No newline at end of file diff --git a/nodes/depl/Packmol_1/node-meta.json b/nodes/depl/Packmol_1/node-meta.json index b1bd775..ad48912 100644 --- a/nodes/depl/Packmol_1/node-meta.json +++ b/nodes/depl/Packmol_1/node-meta.json @@ -1 +1 @@ -{"uuid": "12b972d9-3c62-4873-a260-c2a25705c182"} \ No newline at end of file +{"uuid": "0248a570-e2cb-4513-9f64-cc86ca028215"} \ No newline at end of file diff --git a/params.yaml b/params.yaml index 5aaf096..8d58f9c 100644 --- a/params.yaml +++ b/params.yaml @@ -1296,7 +1296,7 @@ depl_Packmol: depl_Packmol_1: box: null count: - - 16 + - 8 data_ids: null density: 900 pbc: true diff --git a/submit_cpu.sh b/submit_cpu.sh deleted file mode 100644 index 57aa00b..0000000 --- a/submit_cpu.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/bash -#SBATCH --partition=cpu-multi -#SBATCH --ntasks=32 -#SBATCH --cpus-per-task=8 -#SBATCH --time=16:00:00 -#SBATCH --mem=32gb - -source ~/.bashrc - -export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK} -export IPSUITE_CP2K_SHELL="mpirun -n ${SLURM_NTASKS} cp2k_shell.psmp" - -module load compiler/gnu -module load mpi/openmpi -conda activate ips_jax - -dvc repro diff --git a/submit_ehlers.sh b/submit_ehlers.sh new file mode 100644 index 0000000..c7f781b --- /dev/null +++ b/submit_ehlers.sh @@ -0,0 +1,14 @@ +#!/bin/bash +#SBATCH --partition=dgx +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=8 +#SBATCH --time=12:00:00 +#SBATCH --gres=gpu:1 +#SBATCH --mem=32gb +#SBATCH --job-name=353K-8Pairs + +source ~/.bashrc +conda activate ips + +# dvc repro +zntrack run ipsuite.nodes.ApaxJaxMD --name depl_ApaxJaxMD diff --git a/submit_gpu.sh b/submit_gpu.sh deleted file mode 100644 index 619733a..0000000 --- a/submit_gpu.sh +++ /dev/null @@ -1,18 +0,0 @@ -#!/bin/bash -#SBATCH --partition=single -#SBATCH --ntasks=1 -#SBATCH --cpus-per-task=1 -#SBATCH --time=02:00:00 -#SBATCH --gres=gpu:1 -#SBATCH --mem=8gb - -source ~/.bashrc - -export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK} -export IPSUITE_CP2K_SHELL="mpirun -n ${SLURM_NTASKS} cp2k_shell.psmp" - -module load compiler/gnu -module load mpi/openmpi -conda activate ips_apax - -dvc repro \ No newline at end of file diff --git a/submit_single_multi.sh b/submit_single_multi.sh deleted file mode 100644 index 87a6b1e..0000000 --- a/submit_single_multi.sh +++ /dev/null @@ -1,18 +0,0 @@ -#!/bin/bash -#SBATCH --partition=single -#SBATCH --ntasks=8 -#SBATCH --cpus-per-task=4 -#SBATCH --time=120:00:00 -#SBATCH --gres=gpu:1 -#SBATCH --mem=32gb - -source ~/.bashrc - -export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK} -export IPSUITE_CP2K_SHELL="mpirun -n ${SLURM_NTASKS} cp2k_shell.psmp" - -module load compiler/gnu -module load mpi/openmpi -conda activate ips_apax - -dvc repro