Loading BaseGPU/2021
Loading requirement: nvhpc/21.3 cuda/11.2 openmpi/4.0.3cu11.2.v2
WARNING:tensorflow:From /sqfs/work/G14979/u6b368/bin/deepmd_kit_gpu_2.1.5_cuda11.6/lib/python3.10/site-packages/tensorflow/python/compat/v2_compat.py:107: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
WARNING:root:To get the best performance, it is recommended to adjust the number of threads by setting the environment variables OMP_NUM_THREADS, TF_INTRA_OP_PARALLELISM_THREADS, and TF_INTER_OP_PARALLELISM_THREADS.
WARNING:root:Environment variable KMP_BLOCKTIME is empty. Use the default value 0
WARNING:root:Environment variable KMP_AFFINITY is empty. Use the default value granularity=fine,verbose,compact,1,0
/sqfs/work/G14979/u6b368/bin/deepmd_kit_gpu_2.1.5_cuda11.6/lib/python3.10/importlib/__init__.py:169: UserWarning: The NumPy module was reloaded (imported a second time). This can in some cases result in small but subtle issues and is discouraged.
_bootstrap._exec(spec, module)
DEEPMD INFO
DEEPMD INFO stage 1: compress the model
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DEEPMD INFO Please read and cite:
DEEPMD INFO Wang, Zhang, Han and E, Comput.Phys.Comm. 228, 178-184 (2018)
DEEPMD INFO installed to: /home/conda/feedstock_root/build_artifacts/deepmd-kit_1663923590539/work/_skbuild/linux-x86_64-3.10/cmake-install
DEEPMD INFO source : v2.1.5
DEEPMD INFO source brach: HEAD
DEEPMD INFO source commit: 6e3d4a62
DEEPMD INFO source commit at: 2022-09-23 16:10:28 +0800
DEEPMD INFO build float prec: double
DEEPMD INFO build variant: cuda
DEEPMD INFO build with tf inc: /sqfs/work/G14979/u6b368/bin/deepmd_kit_gpu_2.1.5_cuda11.6/lib/python3.10/site-packages/tensorflow/include;/sqfs/work/G14979/u6b368/bin/deepmd_kit_gpu_2.1.5_cuda11.6/include
DEEPMD INFO build with tf lib:
DEEPMD INFO ---Summary of the training---------------------------------------
DEEPMD INFO running on: gpu0501
DEEPMD INFO computing device: gpu:0
DEEPMD INFO CUDA_VISIBLE_DEVICES: 0,1
DEEPMD INFO Count of visible GPU: 2
DEEPMD INFO num_intra_threads: 0
DEEPMD INFO num_inter_threads: 0
DEEPMD INFO -----------------------------------------------------------------
DEEPMD INFO training without frame parameter
DEEPMD INFO training data with lower boundary: [-0.22680075 -0.29381635]
DEEPMD INFO training data with upper boundary: [30.16753829 41.82551879]
OMP: Info #155: KMP_AFFINITY: Initial OS proc set respected: 0
OMP: Info #216: KMP_AFFINITY: decoding x2APIC ids.
OMP: Info #157: KMP_AFFINITY: 1 available OS procs
OMP: Info #158: KMP_AFFINITY: Uniform topology
OMP: Info #287: KMP_AFFINITY: topology layer "LL cache" is equivalent to "socket".
OMP: Info #287: KMP_AFFINITY: topology layer "L3 cache" is equivalent to "socket".
OMP: Info #287: KMP_AFFINITY: topology layer "L2 cache" is equivalent to "core".
OMP: Info #287: KMP_AFFINITY: topology layer "L1 cache" is equivalent to "core".
OMP: Info #192: KMP_AFFINITY: 1 socket x 1 core/socket x 1 thread/core (1 total cores)
OMP: Info #218: KMP_AFFINITY: OS proc to physical thread map:
OMP: Info #172: KMP_AFFINITY: OS proc 0 maps to socket 0 core 0 thread 0
OMP: Info #254: KMP_AFFINITY: pid 449229 tid 449422 thread 0 bound to OS proc set 0
OMP: Info #254: KMP_AFFINITY: pid 449229 tid 449421 thread 1 bound to OS proc set 0
DEEPMD INFO training data with lower boundary: [-1505.35165116 -4165.88651941]
DEEPMD INFO training data with upper boundary: [1505.35165116 4165.88651941]
DEEPMD INFO built lr
DEEPMD INFO built network
DEEPMD INFO built training
DEEPMD INFO initialize model from scratch
INFO:tensorflow:/sqfs2/cmc/0/work/G14979/u6b368/bbb0/model-compression/model.ckpt.index
DEEPMD INFO /sqfs2/cmc/0/work/G14979/u6b368/bbb0/model-compression/model.ckpt.index
INFO:tensorflow:0
DEEPMD INFO 0
INFO:tensorflow:/sqfs2/cmc/0/work/G14979/u6b368/bbb0/model-compression/model.ckpt.data-00000-of-00001
DEEPMD INFO /sqfs2/cmc/0/work/G14979/u6b368/bbb0/model-compression/model.ckpt.data-00000-of-00001
INFO:tensorflow:69300
DEEPMD INFO 69300
INFO:tensorflow:/sqfs2/cmc/0/work/G14979/u6b368/bbb0/model-compression/model.ckpt.meta
DEEPMD INFO /sqfs2/cmc/0/work/G14979/u6b368/bbb0/model-compression/model.ckpt.meta
INFO:tensorflow:1659000
DEEPMD INFO 1659000
DEEPMD INFO finished compressing
DEEPMD INFO
DEEPMD INFO stage 2: freeze the model
INFO:tensorflow:Restoring parameters from model-compression/model.ckpt
DEEPMD INFO Restoring parameters from model-compression/model.ckpt
DEEPMD INFO The following nodes will be frozen: ['model_type', 'descrpt_attr/rcut', 'descrpt_attr/ntypes', 'model_attr/tmap', 'model_attr/model_type', 'model_attr/model_version', 'train_attr/min_nbor_dist', 'train_attr/training_script', 'o_energy', 'o_force', 'o_virial', 'o_atom_energy', 'o_atom_virial', 'fitting_attr/dfparam', 'fitting_attr/daparam']
WARNING:tensorflow:From /sqfs/work/G14979/u6b368/bin/deepmd_kit_gpu_2.1.5_cuda11.6/lib/python3.10/site-packages/deepmd/entrypoints/freeze.py:246: convert_variables_to_constants (from tensorflow.python.framework.graph_util_impl) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.compat.v1.graph_util.convert_variables_to_constants`
DEEPMD WARNING From /sqfs/work/G14979/u6b368/bin/deepmd_kit_gpu_2.1.5_cuda11.6/lib/python3.10/site-packages/deepmd/entrypoints/freeze.py:246: convert_variables_to_constants (from tensorflow.python.framework.graph_util_impl) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.compat.v1.graph_util.convert_variables_to_constants`
WARNING:tensorflow:From /sqfs/work/G14979/u6b368/bin/deepmd_kit_gpu_2.1.5_cuda11.6/lib/python3.10/site-packages/tensorflow/python/framework/convert_to_constants.py:925: extract_sub_graph (from tensorflow.python.framework.graph_util_impl) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.compat.v1.graph_util.extract_sub_graph`
DEEPMD WARNING From /sqfs/work/G14979/u6b368/bin/deepmd_kit_gpu_2.1.5_cuda11.6/lib/python3.10/site-packages/tensorflow/python/framework/convert_to_constants.py:925: extract_sub_graph (from tensorflow.python.framework.graph_util_impl) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.compat.v1.graph_util.extract_sub_graph`
DEEPMD INFO 1258 ops in the final graph.
"descriptor": {
"type": "hybrid",
"list": [
{
"type": "se_e2_a",
"sel": "auto",
"rcut_smth": 0.5,
"activation_function": "tanh",
"rcut": 6.5,
"neuron": [
30,
60,
120
],
"resnet_dt": false,
"axis_neuron": 32,
"seed": 13290,
"_comment": " that's all"
},
{
"type": "se_e3",
"sel": "auto",
"rcut_smth": 0.5,
"activation_function": "tanh",
"rcut": 5.0,
"neuron": [
5,
10,
20
],
"resnet_dt": false,
"seed": 1327,
"_comment": " that's all"
}
]
},
"fitting_net": {
"neuron": [
320,
320,
320
],
"resnet_dt": true,
"seed": 6374,
"_comment": " that's all"
},
Discussed in #2182
Originally posted by shihao-code December 15, 2022
When I used a hybrid descriptor of se_e2_a and se_e3, the RMSE of deep potential is very small (3 meV/atom for energy and 59 meV/Ang for atomic force), however, after compressing the potential, the RMSE change very large (16 meV/atom for energy and 64 meV/Ang for atomic force). But if I only used se_e2_a descriptor with keepind other parameter in input.json file unchanged, there is no change before and after compression. And if only se_e3 descriptor was used, there is also a large error induced by compression.
Verison of deepmd-kit: 2.1.5_cuda11.6
Command I used: dp compress -i FeH.pb -o FeH-compress.pb --step 0.002
The output of compression:
My input.json file