Add files using upload-large-folder tool

.gitattributes

@@ -33,3 +33,9 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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fold_0/logs.models.fold_0.ENCSR739VKY/logfile.modelling.fold_0.ENCSR739VKY.chrombpnet.params.json

@@ -0,0 +1,11 @@
+{
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+    "filters": "512",
+    "n_dil_layers": "8",
+    "bias_model_path": "chrombppnet_model_encsr283tme_bias/bias_model_scaled.h5",
+    "inputlen": "2114",
+    "outputlen": "1000",
+    "max_jitter": "500",
+    "chr_fold_path": "splits/fold_0.json",
+    "negative_sampling_ratio": "0.1"
+}

fold_0/logs.models.fold_0.ENCSR739VKY/logfile.modelling.fold_0.ENCSR739VKY.chrombpnet_model_params.tsv

@@ -0,0 +1,9 @@
+counts_loss_weight	9.4
+filters	512
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+bias_model_path	chrombppnet_model_encsr283tme_bias/bias_model_scaled.h5
+inputlen	2114
+outputlen	1000
+max_jitter	500
+chr_fold_path	splits/fold_0.json
+negative_sampling_ratio	0.1

fold_0/logs.models.fold_0.ENCSR739VKY/logfile.modelling.fold_0.ENCSR739VKY.epoch_loss.csv

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fold_2/logs.models.fold_2.ENCSR739VKY/logfile.modelling.fold_2.ENCSR739VKY.args.json

@@ -0,0 +1,23 @@
+{
+    "genome": "/scratch/groups/akundaje/anusri/chromatin_atlas/reference/hg38.genome.fa",
+    "bigwig": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR739VKY//preprocessing/bigWigs/ENCSR739VKY.bigWig",
+    "peaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR739VKY//chrombppnet_model_encsr283tme_bias_fold_2//filtered.peaks.bed",
+    "nonpeaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR739VKY//chrombppnet_model_encsr283tme_bias_fold_2//filtered.nonpeaks.bed",
+    "output_prefix": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR739VKY//chrombppnet_model_encsr283tme_bias_fold_2//chrombpnet",
+    "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_2.json",
+    "trackables": [
+        "logcount_predictions_loss",
+        "loss",
+        "logits_profile_predictions_loss",
+        "val_logcount_predictions_loss",
+        "val_loss",
+        "val_logits_profile_predictions_loss"
+    ],
+    "epochs": 50,
+    "early_stop": 5,
+    "batch_size": 64,
+    "learning_rate": 0.001,
+    "params": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR739VKY//chrombppnet_model_encsr283tme_bias_fold_2//chrombpnet_model_params.tsv",
+    "seed": 1234,
+    "architecture_from_file": "/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/models/chrombpnet_with_bias_model.py"
+}

fold_2/logs.models.fold_2.ENCSR739VKY/logfile.modelling.fold_2.ENCSR739VKY.bias_formatting.stderr.txt

@@ -0,0 +1,38 @@
+INFO:    underlay of /etc/localtime required more than 50 (88) bind mounts
+INFO:    underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
+2023-07-16 23:32:43.605709: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-16 23:32:47.188019: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-16 23:32:47.193055: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
+2023-07-16 23:32:47.231268: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:03:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-16 23:32:47.231370: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-16 23:32:47.261521: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-16 23:32:47.261717: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-16 23:32:47.277153: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-16 23:32:47.284302: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-16 23:32:47.311050: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-16 23:32:47.317958: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-16 23:32:47.319483: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-16 23:32:47.333515: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-16 23:32:47.333968: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 FMA
+To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
+2023-07-16 23:32:47.335034: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-16 23:32:47.351925: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:03:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-16 23:32:47.352052: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-16 23:32:47.352114: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
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+2023-07-16 23:32:47.352164: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-16 23:32:47.352188: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-16 23:32:47.352211: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-16 23:32:47.352235: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
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+2023-07-16 23:32:47.353356: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-16 23:32:47.355004: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-16 23:32:49.652322: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
+2023-07-16 23:32:49.652405: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267]      0 
+2023-07-16 23:32:49.652426: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0:   N 
+2023-07-16 23:32:49.662291: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 14957 MB memory) -> physical GPU (device: 0, name: Tesla P100-PCIE-16GB, pci bus id: 0000:03:00.0, compute capability: 6.0)
+2023-07-16 23:32:50.722721: W tensorflow/python/util/util.cc:348] Sets are not currently considered sequences, but this may change in the future, so consider avoiding using them.

fold_2/logs.models.fold_2.ENCSR739VKY/logfile.modelling.fold_2.ENCSR739VKY.bias_formatting.stdout.txt

@@ -0,0 +1 @@
+singularity exec --nv /home/groups/akundaje/anusri/simg/tf-atlas_gcp-modeling.sif python get_new_tf_model_format.py -i /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR739VKY//chrombppnet_model_encsr283tme_bias_fold_2/bias_model_scaled.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR739VKY//chrombppnet_model_encsr283tme_bias_fold_2/new_model_formats/bias_model_scaled

fold_2/logs.models.fold_2.ENCSR739VKY/logfile.modelling.fold_2.ENCSR739VKY.chrombpnet.params.json

@@ -0,0 +1,11 @@
+{
+    "counts_loss_weight": "9.4",
+    "filters": "512",
+    "n_dil_layers": "8",
+    "bias_model_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR739VKY//chrombppnet_model_encsr283tme_bias_fold_2/bias_model_scaled.h5",
+    "inputlen": "2114",
+    "outputlen": "1000",
+    "max_jitter": "500",
+    "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_2.json",
+    "negative_sampling_ratio": "0.1"
+}

fold_2/logs.models.fold_2.ENCSR739VKY/logfile.modelling.fold_2.ENCSR739VKY.chrombpnet_data_params.tsv

@@ -0,0 +1,3 @@
+counts_sum_min_thresh	20.0
+counts_sum_max_thresh	3880.44
+trainings_pts_post_thresh	158457

fold_2/logs.models.fold_2.ENCSR739VKY/logfile.modelling.fold_2.ENCSR739VKY.chrombpnet_formatting.stderr.txt

@@ -0,0 +1,40 @@
+INFO:    underlay of /etc/localtime required more than 50 (88) bind mounts
+INFO:    underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
+2023-07-17 12:51:18.770266: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 12:51:21.985589: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-17 12:51:21.989767: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
+2023-07-17 12:51:22.922750: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:45:00.0 name: NVIDIA A100-SXM4-80GB computeCapability: 8.0
+coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.15GiB deviceMemoryBandwidth: 1.85TiB/s
+2023-07-17 12:51:22.922889: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 12:51:22.956521: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-17 12:51:22.956623: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-17 12:51:22.973374: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-17 12:51:22.980696: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-17 12:51:23.003657: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-17 12:51:23.009666: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
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+To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
+2023-07-17 12:51:23.056175: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-17 12:51:23.058923: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:45:00.0 name: NVIDIA A100-SXM4-80GB computeCapability: 8.0
+coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.15GiB deviceMemoryBandwidth: 1.85TiB/s
+2023-07-17 12:51:23.058984: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 12:51:23.059028: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
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+2023-07-17 12:51:23.059067: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-17 12:51:23.059086: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-17 12:51:23.059102: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
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+2023-07-17 12:51:23.107243: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-17 12:51:23.108794: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
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+2023-07-17 12:51:26.236572: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267]      0 
+2023-07-17 12:51:26.236587: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0:   N 
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fold_2/logs.models.fold_2.ENCSR739VKY/logfile.modelling.fold_2.ENCSR739VKY.chrombpnet_formatting.stdout.txt

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