install script

lawsonfulton · Oct 19, 2018 · a3c0f57 · a3c0f57
1 parent de961ca
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diff --git a/README.md b/README.md
@@ -7,29 +7,7 @@ Install MKL? (make optional)
 ```
 git clone --recursive git@github.com:zero-impact/AutoDef.git
 cd AutoDef
-./installDependencies.sh
-
-# Build GAUSS
-cd extern/GAUSS
-mkdir build
-cd build
-cmake -DCMAKE_BUILD_TYPE=Release ..
-make
-cd ../../../
-
-# Build Cubacode
-cd src/Cubacode
-mkdir build
-cd build
-cmake ..
-make
-cd ../../../
-
-# Build Main app
-cd src/AutoDefRuntime
-mkdir build
-cd build
-cmake ..
-make
+sudo ./installDependencies.sh
+./build.sh
 
 ```
diff --git a/build.sh b/build.sh
@@ -0,0 +1,29 @@
+# Build GAUSS
+cd extern/GAUSS
+mkdir build
+cd build
+cmake -DCMAKE_BUILD_TYPE=Release ..
+make -j8
+cd ../../../
+
+# Build Libigl Python bindings
+cd extern/libigl/python
+mkdir build
+cd build; cmake ..; make -j8;
+cd ../../../../
+
+# Build Cubacode
+cd src/cubacode
+mkdir build
+cd build
+cmake ..
+make -j8
+cd ../../../
+
+# Build Main app
+cd src/AutoDefRuntime
+mkdir build
+cd build
+cmake ..
+make -j8
+cd ../../../
diff --git a/configs/X.json b/configs/X.json
@@ -38,10 +38,10 @@
         "ae_encoded_dim_min": 6,
         "ae_encoded_dim_max": 6,
 
-        "activation": "relu",
+        "activation": "elu",
         "learning_rate": 0.001,
         "batch_size": 800,
-        "training_epochs": 3000,
+        "training_epochs": 1000,
         "batch_size_increase": false,
 
         "cubature_type": "an08",

diff --git a/installDependencies.sh b/installDependencies.sh
@@ -0,0 +1,26 @@
+
+### install Anaconda
+CONTREPO=https://repo.continuum.io/archive/
+# Stepwise filtering of the html at $CONTREPO
+# Get the topmost line that matches our requirements, extract the file name.
+ANACONDAURL=$(wget -q -O - $CONTREPO index.html | grep "Anaconda3-" | grep "Linux" | grep "86_64" | head -n 1 | cut -d \" -f 2)
+mkdir deps/
+wget -O deps/anaconda.sh $CONTREPO$ANACONDAURL
+bash deps/anaconda.sh
+
+
+# Keras stuff? Libigl python bindinggsss
+
+
+
+### For tensorflow cc
+sudo apt-get install build-essential curl git cmake unzip autoconf autogen automake libtool mlocate \
+                     zlib1g-dev g++-7 python python3-numpy python3-dev python3-pip python3-wheel wget
+sudo updatedb
+
+cd extern/tensorflow_cc/tensorflow_cc
+mkdir build && cd build
+# for static library only:
+cmake ..
+make -j8 && sudo make install
+
diff --git a/models/X/energy_model/an08/pca_dim_6/0000003_samples/details.txt b/models/X/energy_model/an08/pca_dim_6/0000003_samples/details.txt
@@ -0,0 +1,8 @@
+n_tets: 3
+relErr: 0.184437
+Selected tets: 6184, 24829, 21277, 
+Weights: 47103.4, 2973.29, 12403.3, 
+n_nonzero: 3
+
+Running time so far: 0.420346s
+
diff --git a/models/X/energy_model/an08/pca_dim_6/0000005_samples/details.txt b/models/X/energy_model/an08/pca_dim_6/0000005_samples/details.txt
@@ -0,0 +1,8 @@
+n_tets: 6
+relErr: 0.0472099
+Selected tets: 6184, 24829, 21277, 5536, 17749, 20527, 
+Weights: 26518.5, 4509.76, 12668.7, 4274.13, 0, 5331.39, 
+n_nonzero: 5
+
+Running time so far: 0.57504s
+
diff --git a/models/X/keras_models/autoencoder.json b/models/X/keras_models/autoencoder.json
@@ -0,0 +1 @@
+{"class_name": "Model", "config": {"name": "model_1", "layers": [{"name": "encoder_input", "class_name": "InputLayer", "config": {"batch_input_shape": [null, 1], "dtype": "float64", "sparse": false, "name": "encoder_input"}, "inbound_nodes": []}, {"name": "dense_encode_layer_0", "class_name": "Dense", "config": {"name": "dense_encode_layer_0", "trainable": true, "units": 200, "activation": "elu", "use_bias": true, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["encoder_input", 0, 0, {}]]]}, {"name": "dense_encode_layer_1", "class_name": "Dense", "config": {"name": "dense_encode_layer_1", "trainable": true, "units": 200, "activation": "elu", "use_bias": true, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense_encode_layer_0", 0, 0, {}]]]}, {"name": "encoded_layer", "class_name": "Dense", "config": {"name": "encoded_layer", "trainable": true, "units": 6, "activation": "elu", "use_bias": true, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense_encode_layer_1", 0, 0, {}]]]}, {"name": "dense_decode_layer_0", "class_name": "Dense", "config": {"name": "dense_decode_layer_0", "trainable": true, "units": 200, "activation": "elu", "use_bias": true, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["encoded_layer", 0, 0, {}]]]}, {"name": "dense_decode_layer_1", "class_name": "Dense", "config": {"name": "dense_decode_layer_1", "trainable": true, "units": 200, "activation": "elu", "use_bias": true, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense_decode_layer_0", 0, 0, {}]]]}, {"name": "decoder_output_layer", "class_name": "Dense", "config": {"name": "decoder_output_layer", "trainable": true, "units": 1, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense_decode_layer_1", 0, 0, {}]]]}], "input_layers": [["encoder_input", 0, 0]], "output_layers": [["decoder_output_layer", 0, 0]]}, "keras_version": "2.0.8", "backend": "tensorflow"}
diff --git a/models/X/keras_models/decoder.json b/models/X/keras_models/decoder.json
@@ -0,0 +1 @@
+{"class_name": "Model", "config": {"name": "model_3", "layers": [{"name": "decoder_input", "class_name": "InputLayer", "config": {"batch_input_shape": [null, 6], "dtype": "float64", "sparse": false, "name": "decoder_input"}, "inbound_nodes": []}, {"name": "dense_decode_layer_0", "class_name": "Dense", "config": {"name": "dense_decode_layer_0", "trainable": true, "units": 200, "activation": "elu", "use_bias": true, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["decoder_input", 0, 0, {}]]]}, {"name": "dense_decode_layer_1", "class_name": "Dense", "config": {"name": "dense_decode_layer_1", "trainable": true, "units": 200, "activation": "elu", "use_bias": true, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense_decode_layer_0", 0, 0, {}]]]}, {"name": "decoder_output_layer", "class_name": "Dense", "config": {"name": "decoder_output_layer", "trainable": true, "units": 1, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense_decode_layer_1", 0, 0, {}]]]}], "input_layers": [["decoder_input", 0, 0]], "output_layers": [["decoder_output_layer", 0, 0]]}, "keras_version": "2.0.8", "backend": "tensorflow"}
diff --git a/models/X/keras_models/encoder.json b/models/X/keras_models/encoder.json
@@ -0,0 +1 @@
+{"class_name": "Model", "config": {"name": "model_2", "layers": [{"name": "encoder_input", "class_name": "InputLayer", "config": {"batch_input_shape": [null, 1], "dtype": "float64", "sparse": false, "name": "encoder_input"}, "inbound_nodes": []}, {"name": "dense_encode_layer_0", "class_name": "Dense", "config": {"name": "dense_encode_layer_0", "trainable": true, "units": 200, "activation": "elu", "use_bias": true, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["encoder_input", 0, 0, {}]]]}, {"name": "dense_encode_layer_1", "class_name": "Dense", "config": {"name": "dense_encode_layer_1", "trainable": true, "units": 200, "activation": "elu", "use_bias": true, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense_encode_layer_0", 0, 0, {}]]]}, {"name": "encoded_layer", "class_name": "Dense", "config": {"name": "encoded_layer", "trainable": true, "units": 6, "activation": "elu", "use_bias": true, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense_encode_layer_1", 0, 0, {}]]]}], "input_layers": [["encoder_input", 0, 0]], "output_layers": [["encoded_layer", 0, 0]]}, "keras_version": "2.0.8", "backend": "tensorflow"}
diff --git a/models/X/model_config.json b/models/X/model_config.json
@@ -0,0 +1,40 @@
+{
+  "training_dataset": "models/X/unified_generate/high_res/training_data/training/",
+  "validation_dataset": "",
+  "learning_config": {
+    "save_objs": false,
+    "skip_training": false,
+    "skip_jacobian": false,
+    "use_mass_pca": false,
+    "record_full_loss": false,
+    "autoencoder_config": {
+      "search_for_dims": true,
+      "outer_dim_max_vert_error": 0.018,
+      "inner_dim_max_vert_error": 0.006,
+      "non_pca_layer_sizes": [
+        200,
+        200
+      ],
+      "ae_encoded_dim_min": 6,
+      "ae_encoded_dim_max": 6,
+      "train_in_full_space": false,
+      "pca_init": true,
+      "activation": "elu",
+      "learning_rate": 0.001,
+      "batch_size": 800,
+      "batch_size_increase": false,
+      "training_epochs": 1000,
+      "do_fine_tuning": false,
+      "loss_weight": 1.0
+    },
+    "energy_model_config": {
+      "type": "an08",
+      "enabled": true,
+      "pca_dim": 40,
+      "num_sample_tets": 500,
+      "brute_force_iterations": 100,
+      "target_anneal_mins": 5,
+      "rel_error_tol": 0.05
+    }
+  }
+}
diff --git a/models/X/sim_config.json b/models/X/sim_config.json
@@ -0,0 +1,57 @@
+{
+  "mesh": "models/X/tets.mesh",
+  "logging_enabled": false,
+  "save_objs": false,
+  "save_pngs": false,
+  "save_training_data": false,
+  "save_training_data_path": "",
+  "alternative_full_space_mesh": "",
+  "material_config": {
+    "density": 1000,
+    "youngs_modulus": 60000,
+    "poissons_ratio": 0.47
+  },
+  "integrator_config": {
+    "reduced_space_type": "autoencoder",
+    "use_reduced_energy": true,
+    "use_partial_decode": true,
+    "reduced_energy_method": "an08",
+    "use_preconditioner": true,
+    "pca_dim": 1,
+    "ae_encoded_dim": 6,
+    "ae_decoded_dim": 1,
+    "timestep": 0.005,
+    "lbfgs_config": {
+      "lbfgs_max_iterations": 1000,
+      "lbfgs_epsilon": 1e-08,
+      "lbfgs_delta": 1e-08,
+      "lbfgs_delta_past": 0,
+      "lbfgs_m": 8
+    },
+    "gravity": -9.8,
+    "gravity_axis": 1,
+    "start_pose_from_training_data": -1,
+    "quasi_static": false,
+    "save_obj_every_iteration": false
+  },
+  "visualization_config": {
+    "gpu_decode": true,
+    "show_stress": false,
+    "show_energy": false,
+    "show_lines": false,
+    "interaction_spring_stiffness": 30,
+    "spring_grab_radius": 0.03,
+    "use_spring_grab_radius_for_reduced": false,
+    "full_space_constrained_axis": 1,
+    "constrained_axis_eps": 0.001,
+    "flip_constrained_axis": false,
+    "fixed_point_constraint": [
+      0,
+      0.124,
+      -0.1
+    ],
+    "fixed_point_radius": -1,
+    "print_every_n_frames": 10,
+    "max_frames": 0
+  }
+}