deploy: 3df16ce

_downloads/819e10305ddd6839cd7da05935b17060/mass-inference.txt

@@ -1,17 +1,17 @@
-2024-05-13 17:28:47 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
+2024-05-13 21:57:54 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
 /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/cuda/amp/grad_scaler.py:126: UserWarning: torch.cuda.amp.GradScaler is enabled, but CUDA is not available.  Disabling.
   warnings.warn(
-2024-05-13 17:28:48 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
-2024-05-13 17:28:48 (INFO): amp: true
+2024-05-13 21:57:55 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+2024-05-13 21:57:55 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-05-13-17-29-36
-  commit: db148bb
+  checkpoint_dir: ./checkpoints/2024-05-13-21-58-24
+  commit: 3df16ce
   identifier: ''
-  logs_dir: ./logs/tensorboard/2024-05-13-17-29-36
+  logs_dir: ./logs/tensorboard/2024-05-13-21-58-24
   print_every: 10
-  results_dir: ./results/2024-05-13-17-29-36
+  results_dir: ./results/2024-05-13-21-58-24
   seed: 0
-  timestamp_id: 2024-05-13-17-29-36
+  timestamp_id: 2024-05-13-21-58-24
 dataset:
   a2g_args:
     r_energy: false
@@ -36,6 +36,7 @@ eval_metrics:
     - magnitude_error
     misc:
     - energy_forces_within_threshold
+  primary_metric: forces_mae
 gpus: 0
 logger: tensorboard
 loss_fns:
@@ -121,25 +122,25 @@ test_dataset:
 trainer: ocp
 val_dataset: null
 
-2024-05-13 17:28:48 (INFO): Loading dataset: ase_db
-2024-05-13 17:28:48 (INFO): rank: 0: Sampler created...
-2024-05-13 17:28:48 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-13 17:28:48 (INFO): rank: 0: Sampler created...
-2024-05-13 17:28:48 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-13 17:28:48 (INFO): Loading model: gemnet_t
-2024-05-13 17:28:50 (INFO): Loaded GemNetT with 31671825 parameters.
-2024-05-13 17:28:50 (WARNING): Model gradient logging to tensorboard not yet supported.
-2024-05-13 17:28:50 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
-2024-05-13 17:28:50 (INFO): Overwriting scaling factors with those loaded from checkpoint. If you're generating predictions with a pretrained checkpoint, this is the correct behavior. To disable this, delete `scale_dict` from the checkpoint. 
-2024-05-13 17:28:50 (WARNING): Scale factor comment not found in model
-2024-05-13 17:28:50 (INFO): Predicting on test.
+2024-05-13 21:57:55 (INFO): Loading dataset: ase_db
+2024-05-13 21:57:55 (INFO): rank: 0: Sampler created...
+2024-05-13 21:57:55 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-13 21:57:55 (INFO): rank: 0: Sampler created...
+2024-05-13 21:57:55 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-13 21:57:55 (INFO): Loading model: gemnet_t
+2024-05-13 21:57:57 (INFO): Loaded GemNetT with 31671825 parameters.
+2024-05-13 21:57:57 (WARNING): Model gradient logging to tensorboard not yet supported.
+2024-05-13 21:57:57 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
+2024-05-13 21:57:58 (INFO): Overwriting scaling factors with those loaded from checkpoint. If you're generating predictions with a pretrained checkpoint, this is the correct behavior. To disable this, delete `scale_dict` from the checkpoint. 
+2024-05-13 21:57:58 (WARNING): Scale factor comment not found in model
+2024-05-13 21:57:58 (INFO): Predicting on test.
 device 0:   0%|                                           | 0/3 [00:00<?, ?it/s]/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/amp/autocast_mode.py:250: UserWarning: User provided device_type of 'cuda', but CUDA is not available. Disabling
   warnings.warn(
-device 0:  33%|███████████▋                       | 1/3 [00:05<00:11,  5.83s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:08<00:03,  3.73s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:11<00:00,  3.38s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:11<00:00,  3.69s/it]
-2024-05-13 17:29:02 (INFO): Writing results to ./results/2024-05-13-17-29-36/ocp_predictions.npz
-2024-05-13 17:29:02 (INFO): Total time taken: 11.22813892364502
-Elapsed time = 17.3 seconds
+device 0:  33%|███████████▋                       | 1/3 [00:04<00:08,  4.40s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:06<00:02,  2.91s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.29s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.62s/it]
+2024-05-13 21:58:05 (INFO): Writing results to ./results/2024-05-13-21-58-24/ocp_predictions.npz
+2024-05-13 21:58:05 (INFO): Total time taken: 8.00568413734436
+Elapsed time = 14.4 seconds

_sources/legacy_tutorials/OCP_Tutorial.md

@@ -795,9 +795,9 @@ Lets download it locally,
 
 ```{code-cell} ipython3
 %%bash
-https://github.com/FAIR-Chem/fairchem/blob/main/src/fairchem/core/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc-large.pt
-wget https://github.com/FAIR-Chem/fairchem/blob/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc.pt
-wget https://github.com/FAIR-Chem/fairchem/blob/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-dT.json
+wget https://github.com/FAIR-Chem/fairchem/raw/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc-large.pt
+wget https://github.com/FAIR-Chem/fairchem/raw/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc.pt
+wget https://github.com/FAIR-Chem/fairchem/raw/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-dT.json
 ```
 
 

core/fine-tuning/fine-tuning-oxides.html

@@ -818,7 +818,7 @@ <h1>Fine tuning a model<a class="headerlink" href="#fine-tuning-a-model" title="
   warnings.warn(
 </pre></div>
 </div>
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Elapsed time 67.6 seconds.
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Elapsed time 67.9 seconds.
 </pre></div>
 </div>
 <img alt="../../_images/92bd7f94dd548c8cfc2744eb5890cd23fada1ff98e8dc907657e2eb109af0402.png" src="../../_images/92bd7f94dd548c8cfc2744eb5890cd23fada1ff98e8dc907657e2eb109af0402.png" />
@@ -1036,7 +1036,7 @@ <h2>Setting up the configuration yaml file<a class="headerlink" href="#setting-u
       r_energy: true
       r_forces: true
     src: val.db
-eval_metrics:
+evaluation_metrics:
   metrics:
     energy:
     - mae
@@ -1183,7 +1183,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 <span class="expanded">Hide code cell output</span>
 </summary>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Elapsed time = 38.6 seconds
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Elapsed time = 207.6 seconds
 </pre></div>
 </div>
 </div>
@@ -1199,7 +1199,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&#39;fine-tuning/checkpoints/2024-05-13-17-25-20-ft-oxides&#39;
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&#39;fine-tuning/checkpoints/2024-05-13-21-52-00-ft-oxides&#39;
 </pre></div>
 </div>
 </div>
@@ -1264,7 +1264,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
   warnings.warn(
 </pre></div>
 </div>
-<img alt="../../_images/63a5f1d908808b57026d9a50d0b0ba827fb7ec964f105322b18a0738c5c88c0c.png" src="../../_images/63a5f1d908808b57026d9a50d0b0ba827fb7ec964f105322b18a0738c5c88c0c.png" />
+<img alt="../../_images/a1eb81a787e4c7318422b93c686c36e23de6049d49ca949fea3ebe2f15ea5a68.png" src="../../_images/a1eb81a787e4c7318422b93c686c36e23de6049d49ca949fea3ebe2f15ea5a68.png" />
 </div>
 </div>
 <div class="cell docutils container">
@@ -1275,7 +1275,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>New MAE = 0.686 eV/atom
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>New MAE = 0.215 eV/atom
 </pre></div>
 </div>
 </div>
@@ -1294,7 +1294,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/bf74a5757a49a023060d744464527b5b70bb87f87fbeb750897bc2c22013dc50.png" src="../../_images/bf74a5757a49a023060d744464527b5b70bb87f87fbeb750897bc2c22013dc50.png" />
+<img alt="../../_images/22815deebf21a31b5b0a110c41bf2e418ca25f6aecbd1dc17e3d9990f3848363.png" src="../../_images/22815deebf21a31b5b0a110c41bf2e418ca25f6aecbd1dc17e3d9990f3848363.png" />
 </div>
 </div>
 <p>It is possible to continue refining the fit. The simple things to do are to use more epochs of training. Eventually the MAE will stabilize, and then it may be necessary to adjust other optimization parameters like the learning rate (usually you decrease it).</p>

core/gotchas.html

@@ -987,7 +987,7 @@ <h1>I get wildly different energies from the different models<a class="headerlin
   warnings.warn(
 </pre></div>
 </div>
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1.6787405014038086
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1.675635576248169
 </pre></div>
 </div>
 </div>
@@ -1500,7 +1500,7 @@ <h1>To tag or not?<a class="headerlink" href="#to-tag-or-not" title="Link to thi
   warnings.warn(
 </pre></div>
 </div>
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>-0.429736852645874
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>-0.42973706126213074
 </pre></div>
 </div>
 </div>
@@ -1555,17 +1555,17 @@ <h1>Stochastic simulation results<a class="headerlink" href="#stochastic-simulat
   warnings.warn(
 </pre></div>
 </div>
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1.213986325263977 1.784320568281904e-06
-1.2139856815338135
-1.2139854431152344
-1.2139854431152344
-1.2139906883239746
-1.2139859199523926
-1.2139856815338135
-1.2139880657196045
-1.2139840126037598
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1.2139862775802612 1.2491404435567604e-06
 1.2139852046966553
-1.213987112045288
+1.213986873626709
+1.2139861583709717
+1.2139854431152344
+1.213986873626709
+1.2139849662780762
+1.213986873626709
+1.2139875888824463
+1.2139842510223389
+1.2139885425567627
 </pre></div>
 </div>
 </div>
@@ -1611,7 +1611,7 @@ <h1>The forces don’t sum to zero<a class="headerlink" href="#the-forces-don-t-
   warnings.warn(
 </pre></div>
 </div>
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([ 0.00848023,  0.01409696, -0.05882549], dtype=float32)
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([ 0.00848408,  0.01409468, -0.05882645], dtype=float32)
 </pre></div>
 </div>
 </div>
@@ -1624,7 +1624,7 @@ <h1>The forces don’t sum to zero<a class="headerlink" href="#the-forces-don-t-
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([9.9942554e-08, 7.0082024e-08, 4.7683716e-07], dtype=float32)
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([ 5.9837475e-08,  1.5040860e-07, -1.1920929e-07], dtype=float32)
 </pre></div>
 </div>
 </div>