Skip to content

NVT 32 313 #8

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 2 commits into
base: NVT
Choose a base branch
from
Open

NVT 32 313 #8

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
4a9dd64
313K, 32 pairs, 20 ns
PythonFZ Jan 28, 2024
bf52e33
313K, 8 pairs, 20 ns
PythonFZ Jan 30, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
106 changes: 53 additions & 53 deletions dvc.lock
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27232,56 +27232,56 @@ stages:
outs:
- path: nodes/depl/Packmol/atoms.h5
hash: md5
md5: 2400ddfca5ec50ebe880626f190e0797
md5: 39380ec230e5378714d338776da9e790
size: 27968
- path: nodes/depl/Packmol/node-meta.json
hash: md5
md5: 183c2b460f416178653dc0ea9b0a9fdd
md5: 5e0b2cfcda800b14b1e0b713d8909146
size: 48
- path: nodes/depl/Packmol/packmol
hash: md5
md5: 9211f580932fa95a1d122b0e2be6699c.dir
md5: c8b3e52f00edc5172826bf4a3cbc7a42.dir
size: 3841
nfiles: 4
depl_Packmol_1:
cmd: zntrack run ipsuite.nodes.Packmol --name depl_Packmol_1
deps:
- path: nodes/depl/Packmol/atoms.h5
hash: md5
md5: 2400ddfca5ec50ebe880626f190e0797
md5: 39380ec230e5378714d338776da9e790
size: 27968
- path: nodes/depl/Packmol/node-meta.json
hash: md5
md5: 183c2b460f416178653dc0ea9b0a9fdd
md5: 5e0b2cfcda800b14b1e0b713d8909146
size: 48
- path: nodes/depl/Packmol/packmol
hash: md5
md5: 9211f580932fa95a1d122b0e2be6699c.dir
md5: c8b3e52f00edc5172826bf4a3cbc7a42.dir
size: 3841
nfiles: 4
params:
params.yaml:
depl_Packmol_1:
box:
count:
- 16
- 8
data_ids:
density: 900
pbc: true
tolerance: 2.0
outs:
- path: nodes/depl/Packmol_1/atoms.h5
hash: md5
md5: 7ec77fd6549c61434a9b28b7715027a8
size: 43328
md5: 34cf04ddb4032de238ea34596aaa1960
size: 35776
- path: nodes/depl/Packmol_1/node-meta.json
hash: md5
md5: 4dab86e07acb5e1b620a83587ef489a4
md5: fb6ded561e00da1722e0da7c2cba15b0
size: 48
- path: nodes/depl/Packmol_1/packmol
hash: md5
md5: ac2a1f78e24d4acec487ee8d320e3c86.dir
size: 28854
md5: 565b6debcb6531b1fc75a04f6aedc040.dir
size: 15413
nfiles: 3
depl_ASEGeoOpt:
cmd: zntrack run ipsuite.nodes.ASEGeoOpt --name depl_ASEGeoOpt
Expand Down Expand Up @@ -27313,16 +27313,16 @@ stages:
size: 8933596
- path: nodes/depl/Packmol_1/atoms.h5
hash: md5
md5: 7ec77fd6549c61434a9b28b7715027a8
size: 43328
md5: 34cf04ddb4032de238ea34596aaa1960
size: 35776
- path: nodes/depl/Packmol_1/node-meta.json
hash: md5
md5: 4dab86e07acb5e1b620a83587ef489a4
md5: fb6ded561e00da1722e0da7c2cba15b0
size: 48
- path: nodes/depl/Packmol_1/packmol
hash: md5
md5: ac2a1f78e24d4acec487ee8d320e3c86.dir
size: 28854
md5: 565b6debcb6531b1fc75a04f6aedc040.dir
size: 15413
nfiles: 3
params:
params.yaml:
Expand All @@ -27345,12 +27345,12 @@ stages:
nfiles: 1
- path: nodes/depl/ASEGeoOpt/node-meta.json
hash: md5
md5: fe39d4aaaae596691bf44639f50031f0
md5: 4f8d82e5d777b0715c7a4bd0d3cbeffc
size: 48
- path: nodes/depl/ASEGeoOpt/trajectory.h5
hash: md5
md5: 983b66b57f7c4f7f7e5d9043e0e0f8e4
size: 6554344
md5: 67203a958e889ff5f9bae5ab7fcbce2d
size: 9719256
depl_ASEMD:
cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD
deps:
Expand Down Expand Up @@ -27386,12 +27386,12 @@ stages:
nfiles: 1
- path: nodes/depl/ASEGeoOpt/node-meta.json
hash: md5
md5: fe39d4aaaae596691bf44639f50031f0
md5: 4f8d82e5d777b0715c7a4bd0d3cbeffc
size: 48
- path: nodes/depl/ASEGeoOpt/trajectory.h5
hash: md5
md5: 983b66b57f7c4f7f7e5d9043e0e0f8e4
size: 6554344
md5: 67203a958e889ff5f9bae5ab7fcbce2d
size: 9719256
params:
params.yaml:
depl_ASEMD:
Expand All @@ -27417,25 +27417,25 @@ stages:
outs:
- path: nodes/depl/ASEMD/metrics_dict.csv
hash: md5
md5: 983d17a2cde8d650b5cd0dd9f90e59f2
size: 42017
md5: 7667aa5831eafcdc7936f9833270fb6a
size: 41999
- path: nodes/depl/ASEMD/model
hash: md5
md5: 64586897446153f477c052dd0e2579ad.dir
size: 11
nfiles: 1
- path: nodes/depl/ASEMD/node-meta.json
hash: md5
md5: 547a6e5066b6f5faab48d9656cdd68b0
size: 64
md5: 15ce8ca94939f782f3c9a30ada653ce2
size: 48
- path: nodes/depl/ASEMD/steps_before_stopping.json
hash: md5
md5: 6bb61e3b7bce0931da574d19d1d82c88
size: 2
- path: nodes/depl/ASEMD/trajectory.h5
hash: md5
md5: 0486da66cab9852204d102f0209fe6ce
size: 50790792
md5: 3e8975e4bfbf2025a0ac600f10ae3687
size: 25409160
depl_ASEMD_1:
cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD_1
deps:
Expand Down Expand Up @@ -27466,25 +27466,25 @@ stages:
size: 8933596
- path: nodes/depl/ASEMD/metrics_dict.csv
hash: md5
md5: 983d17a2cde8d650b5cd0dd9f90e59f2
size: 42017
md5: 7667aa5831eafcdc7936f9833270fb6a
size: 41999
- path: nodes/depl/ASEMD/model
hash: md5
md5: 64586897446153f477c052dd0e2579ad.dir
size: 11
nfiles: 1
- path: nodes/depl/ASEMD/node-meta.json
hash: md5
md5: 547a6e5066b6f5faab48d9656cdd68b0
size: 64
md5: 15ce8ca94939f782f3c9a30ada653ce2
size: 48
- path: nodes/depl/ASEMD/steps_before_stopping.json
hash: md5
md5: 6bb61e3b7bce0931da574d19d1d82c88
size: 2
- path: nodes/depl/ASEMD/trajectory.h5
hash: md5
md5: 0486da66cab9852204d102f0209fe6ce
size: 50790792
md5: 3e8975e4bfbf2025a0ac600f10ae3687
size: 25409160
params:
params.yaml:
depl_ASEMD_1:
Expand All @@ -27507,25 +27507,25 @@ stages:
outs:
- path: nodes/depl/ASEMD_1/metrics_dict.csv
hash: md5
md5: 35ad797b779589a3b5078a59bbfdaa97
size: 41989
md5: 38f06330fa7f29646f302d94fad17d75
size: 41969
- path: nodes/depl/ASEMD_1/model
hash: md5
md5: 64586897446153f477c052dd0e2579ad.dir
size: 11
nfiles: 1
- path: nodes/depl/ASEMD_1/node-meta.json
hash: md5
md5: 1726952160edcfcd21c10afce4e9838c
size: 64
md5: 21952312416e2f30cc7836cc7011934b
size: 48
- path: nodes/depl/ASEMD_1/steps_before_stopping.json
hash: md5
md5: 6bb61e3b7bce0931da574d19d1d82c88
size: 2
- path: nodes/depl/ASEMD_1/trajectory.h5
hash: md5
md5: 7ae71e49129b96fce45aef46689fc2af
size: 50790792
md5: fed9ed12c153338ed91e19e139f585c8
size: 25409160
ML17_training_MLModel_4:
cmd: zntrack run ipsuite.nodes.Apax --name ML17_training_MLModel_4
deps:
Expand Down Expand Up @@ -27813,25 +27813,25 @@ stages:
size: 8933596
- path: nodes/depl/ASEMD_1/metrics_dict.csv
hash: md5
md5: 35ad797b779589a3b5078a59bbfdaa97
size: 41989
md5: 38f06330fa7f29646f302d94fad17d75
size: 41969
- path: nodes/depl/ASEMD_1/model
hash: md5
md5: 64586897446153f477c052dd0e2579ad.dir
size: 11
nfiles: 1
- path: nodes/depl/ASEMD_1/node-meta.json
hash: md5
md5: 1726952160edcfcd21c10afce4e9838c
size: 64
md5: 21952312416e2f30cc7836cc7011934b
size: 48
- path: nodes/depl/ASEMD_1/steps_before_stopping.json
hash: md5
md5: 6bb61e3b7bce0931da574d19d1d82c88
size: 2
- path: nodes/depl/ASEMD_1/trajectory.h5
hash: md5
md5: 7ae71e49129b96fce45aef46689fc2af
size: 50790792
md5: fed9ed12c153338ed91e19e139f585c8
size: 25409160
params:
params.yaml:
depl_ApaxJaxMD:
Expand All @@ -27852,14 +27852,14 @@ stages:
outs:
- path: nodes/depl/ApaxJaxMD/initial_structure.extxyz
hash: md5
md5: fc771cb638ca56a79d07ce3218ce0f0a
size: 50547
md5: 16b46396e82c8f39bd6006d4524e1252
size: 25347
- path: nodes/depl/ApaxJaxMD/md
hash: md5
md5: ea658d6fc6eb15b4dfd04b05014e1623.dir
size: 7722462227
md5: 0fc8c0fe53570ae252197552e148dacc.dir
size: 4239550354
nfiles: 6
- path: nodes/depl/ApaxJaxMD/node-meta.json
hash: md5
md5: 22a73482bec976bda5099f57c3daa1ce
size: 64
md5: bb623661d4a74a71202f4ef5e532dab9
size: 48
4 changes: 2 additions & 2 deletions main.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,
)

Expand Down Expand Up @@ -1002,4 +1002,4 @@

project.build(nodes=[depl])

# pip uninstall jax jaxlib nvidia-nvtx-cu12 nvidia-nccl-cu12 nvidia-nvjitlink-cu12 nvidia-cusparse-cu12 nvidia-cublas-cu12 nvidia-cuda-cupti-cu12 nvidia-cuda-nvcc-cu12 nvidia-cuda-nvrtc-cu12 nvidia-cuda-runtime-cu12 nvidia-cudnn-cu12 nvidia-cufft-cu12 nvidia-curand-cu12 nvidia-cusolver-cu12
# pip uninstall jax jaxlib nvidia-nvtx-cu12 nvidia-nccl-cu12 nvidia-nvjitlink-cu12 nvidia-cusparse-cu12 nvidia-cublas-cu12 nvidia-cuda-cupti-cu12 nvidia-cuda-nvcc-cu12 nvidia-cuda-nvrtc-cu12 nvidia-cuda-runtime-cu12 nvidia-cudnn-cu12 nvidia-cufft-cu12 nvidia-curand-cu12 nvidia-cusolver-cu12
2 changes: 1 addition & 1 deletion nodes/depl/ASEGeoOpt/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"uuid": "0d584356-51f5-4a5f-ace8-5a4c3eaacc1f"}
{"uuid": "9839dd5f-732e-4533-aed7-a467dc0d6aaa"}
2 changes: 1 addition & 1 deletion nodes/depl/ASEMD/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"uuid": "6718a1e1-ffcd-4291-b487-436f21b3e9f4", "run_count": 1}
{"uuid": "43e7a5e2-cf35-4b8c-b78f-0b6f7a6ebd02"}
2 changes: 1 addition & 1 deletion nodes/depl/ASEMD_1/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"uuid": "6cb887a6-6c62-4edc-8471-edaa963ffaf4", "run_count": 1}
{"uuid": "0536ba9f-2984-4ccf-8b71-afcce80bd8f5"}
2 changes: 1 addition & 1 deletion nodes/depl/ApaxJaxMD/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"uuid": "43998d26-aec1-481d-9cd6-55bf6c0515d3", "run_count": 1}
{"uuid": "f44d518d-6b07-4262-991f-8a70f5c961c8"}
2 changes: 1 addition & 1 deletion nodes/depl/Packmol/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"uuid": "c1b8c707-89b9-444f-892d-2f173a8bad8d"}
{"uuid": "701891fe-faeb-4b38-b3bf-547af9ad7754"}
2 changes: 1 addition & 1 deletion nodes/depl/Packmol_1/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"uuid": "12b972d9-3c62-4873-a260-c2a25705c182"}
{"uuid": "8b9c1ff8-161e-4a6f-b0fd-b437101eed86"}
2 changes: 1 addition & 1 deletion params.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1296,7 +1296,7 @@ depl_Packmol:
depl_Packmol_1:
box: null
count:
- 16
- 8
data_ids: null
density: 900
pbc: true
Expand Down
17 changes: 0 additions & 17 deletions submit_cpu.sh
View file
Open in desktop

This file was deleted.

14 changes: 14 additions & 0 deletions submit_ehlers.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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=313K-8Pairs

source ~/.bashrc
conda activate ips

# dvc repro
zntrack run ipsuite.nodes.ApaxJaxMD --name depl_ApaxJaxMD
18 changes: 0 additions & 18 deletions submit_gpu.sh
View file
Open in desktop

This file was deleted.

18 changes: 0 additions & 18 deletions submit_single_multi.sh
View file
Open in desktop

This file was deleted.