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- .gitattributes +8 -0
- fold_0/logs.models.fold_0.ENCSR038POV/logfile.modelling.fold_0.ENCSR038POV.bias_formatting.stderr.txt +38 -0
- fold_0/logs.models.fold_0.ENCSR038POV/logfile.modelling.fold_0.ENCSR038POV.chrombpnet_formatting.stdout.txt +1 -0
- fold_0/logs.models.fold_0.ENCSR038POV/logfile.modelling.fold_0.ENCSR038POV.chrombpnet_model_params.tsv +9 -0
- fold_0/logs.models.fold_0.ENCSR038POV/logfile.modelling.fold_0.ENCSR038POV.stdout_v1.txt +3 -0
- fold_0/model.bias_scaled.fold_0.ENCSR038POV.h5 +3 -0
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- fold_1/model.chrombpnet.fold_1.ENCSR038POV.h5 +3 -0
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- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.args.json +23 -0
- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.batch_loss.tsv +0 -0
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- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.bias_formatting.stdout.txt +1 -0
- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet.params.json +11 -0
- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet_data_params.tsv +3 -0
- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet_formatting.stderr.txt +40 -0
- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet_formatting.stdout.txt +1 -0
- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet_model_params.tsv +9 -0
- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet_no_bias_formatting.stderr.txt +1 -0
- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet_no_bias_formatting.stdout.txt +1 -0
- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.epoch_loss.csv +16 -0
- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.stderr.txt +328 -0
- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.stdout.txt +3 -0
- fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.stdout_v1.txt +3 -0
- fold_2/model.bias_scaled.fold_2.ENCSR038POV.h5 +3 -0
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- fold_2/model.chrombpnet.fold_2.ENCSR038POV.h5 +3 -0
- fold_2/model.chrombpnet.fold_2.ENCSR038POV.tar +3 -0
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- fold_3/model.bias_scaled.fold_3.ENCSR038POV.h5 +3 -0
- fold_3/model.bias_scaled.fold_3.ENCSR038POV.tar +3 -0
- fold_3/model.chrombpnet.fold_3.ENCSR038POV.h5 +3 -0
- fold_3/model.chrombpnet.fold_3.ENCSR038POV.tar +3 -0
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- fold_4/model.bias_scaled.fold_4.ENCSR038POV.h5 +3 -0
.gitattributes
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INFO: underlay of /etc/localtime required more than 50 (88) bind mounts
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2023-07-16 23:36:40.240538: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
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pciBusID: 0000:03:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
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coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
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2023-07-16 23:36:43.995872: 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
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To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
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2023-07-16 23:36:43.996926: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
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2023-07-16 23:36:43.997846: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
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coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
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2023-07-16 23:36:46.268116: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
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2023-07-16 23:36:46.268261: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
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2023-07-16 23:36:46.271915: 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)
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2023-07-16 23:36:47.282555: 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.
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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//ENCSR038POV//chrombppnet_model_encsr283tme_bias/chrombpnet.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR038POV//chrombppnet_model_encsr283tme_bias/new_model_formats/chrombpnet
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counts_loss_weight 8.0
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oid sha256:f58c9389bd9fa3481d02e508a92ba69d32fa99830a2945f2fe1271bbfef7402c
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+
size 1198080
|
fold_1/model.chrombpnet.fold_1.ENCSR038POV.h5
ADDED
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+
version https://git-lfs.github.com/spec/v1
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+
oid sha256:59e5d3ca5b0ee0343fa2e320f5eb8af4396e50c1ef7477b6b340e6f59edcc537
|
| 3 |
+
size 26447928
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fold_1/model.chrombpnet.fold_1.ENCSR038POV.tar
ADDED
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+
version https://git-lfs.github.com/spec/v1
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oid sha256:ae54264bdace1fe8c7d2c0f936d3beb048c8a5039ef724266d46223c2b802ce7
|
| 3 |
+
size 27607040
|
fold_1/model.chrombpnet_nobias.fold_1.ENCSR038POV.h5
ADDED
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+
version https://git-lfs.github.com/spec/v1
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oid sha256:0f699c7edf77bd96c149e924be95a037db8f5e9e32c24709d8b4074f4e429f5b
|
| 3 |
+
size 25583536
|
fold_1/model.chrombpnet_nobias.fold_1.ENCSR038POV.tar
ADDED
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+
version https://git-lfs.github.com/spec/v1
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+
oid sha256:f48090fe0ba80aefbf7180e4172c3a4d05bd0bce8b93de37334fdedfbce5f78b
|
| 3 |
+
size 26081280
|
fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.args.json
ADDED
|
@@ -0,0 +1,23 @@
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|
|
|
|
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|
|
|
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|
| 1 |
+
{
|
| 2 |
+
"genome": "/scratch/groups/akundaje/anusri/chromatin_atlas/reference/hg38.genome.fa",
|
| 3 |
+
"bigwig": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR038POV//preprocessing/bigWigs/ENCSR038POV.bigWig",
|
| 4 |
+
"peaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2//filtered.peaks.bed",
|
| 5 |
+
"nonpeaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2//filtered.nonpeaks.bed",
|
| 6 |
+
"output_prefix": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2//chrombpnet",
|
| 7 |
+
"chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_2.json",
|
| 8 |
+
"trackables": [
|
| 9 |
+
"logcount_predictions_loss",
|
| 10 |
+
"loss",
|
| 11 |
+
"logits_profile_predictions_loss",
|
| 12 |
+
"val_logcount_predictions_loss",
|
| 13 |
+
"val_loss",
|
| 14 |
+
"val_logits_profile_predictions_loss"
|
| 15 |
+
],
|
| 16 |
+
"epochs": 50,
|
| 17 |
+
"early_stop": 5,
|
| 18 |
+
"batch_size": 64,
|
| 19 |
+
"learning_rate": 0.001,
|
| 20 |
+
"params": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2//chrombpnet_model_params.tsv",
|
| 21 |
+
"seed": 1234,
|
| 22 |
+
"architecture_from_file": "/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/models/chrombpnet_with_bias_model.py"
|
| 23 |
+
}
|
fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.batch_loss.tsv
ADDED
|
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|
|
|
fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.bias_formatting.stderr.txt
ADDED
|
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|
|
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|
|
|
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|
|
|
| 1 |
+
INFO: underlay of /etc/localtime required more than 50 (88) bind mounts
|
| 2 |
+
INFO: underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
|
| 3 |
+
2023-07-16 23:36:40.259180: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 4 |
+
2023-07-16 23:36:43.915241: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 5 |
+
2023-07-16 23:36:43.921078: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
|
| 6 |
+
2023-07-16 23:36:43.969832: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 7 |
+
pciBusID: 0000:04:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
|
| 8 |
+
coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
|
| 9 |
+
2023-07-16 23:36:43.969957: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 10 |
+
2023-07-16 23:36:44.001416: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 11 |
+
2023-07-16 23:36:44.001561: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 12 |
+
2023-07-16 23:36:44.018345: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 13 |
+
2023-07-16 23:36:44.025441: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 14 |
+
2023-07-16 23:36:44.053425: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 15 |
+
2023-07-16 23:36:44.060300: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 16 |
+
2023-07-16 23:36:44.061746: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 17 |
+
2023-07-16 23:36:44.076966: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 18 |
+
2023-07-16 23:36:44.077395: 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
|
| 19 |
+
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
|
| 20 |
+
2023-07-16 23:36:44.078527: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 21 |
+
2023-07-16 23:36:44.079056: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 22 |
+
pciBusID: 0000:04:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
|
| 23 |
+
coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
|
| 24 |
+
2023-07-16 23:36:44.079097: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 25 |
+
2023-07-16 23:36:44.079138: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 26 |
+
2023-07-16 23:36:44.079164: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 27 |
+
2023-07-16 23:36:44.079190: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 28 |
+
2023-07-16 23:36:44.079215: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 29 |
+
2023-07-16 23:36:44.079240: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 30 |
+
2023-07-16 23:36:44.079265: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 31 |
+
2023-07-16 23:36:44.079313: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 32 |
+
2023-07-16 23:36:44.080497: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 33 |
+
2023-07-16 23:36:44.082099: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 34 |
+
2023-07-16 23:36:46.273826: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
|
| 35 |
+
2023-07-16 23:36:46.273888: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
|
| 36 |
+
2023-07-16 23:36:46.273909: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
|
| 37 |
+
2023-07-16 23:36:46.277428: 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: 0000:04:00.0, compute capability: 6.0)
|
| 38 |
+
2023-07-16 23:36:47.299446: 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.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.bias_formatting.stdout.txt
ADDED
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| 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//ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2/bias_model_scaled.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2/new_model_formats/bias_model_scaled
|
fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet.params.json
ADDED
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@@ -0,0 +1,11 @@
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| 1 |
+
{
|
| 2 |
+
"counts_loss_weight": "8.0",
|
| 3 |
+
"filters": "512",
|
| 4 |
+
"n_dil_layers": "8",
|
| 5 |
+
"bias_model_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2/bias_model_scaled.h5",
|
| 6 |
+
"inputlen": "2114",
|
| 7 |
+
"outputlen": "1000",
|
| 8 |
+
"max_jitter": "500",
|
| 9 |
+
"chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_2.json",
|
| 10 |
+
"negative_sampling_ratio": "0.1"
|
| 11 |
+
}
|
fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet_data_params.tsv
ADDED
|
@@ -0,0 +1,3 @@
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|
| 1 |
+
counts_sum_min_thresh 8.0
|
| 2 |
+
counts_sum_max_thresh 4573.19
|
| 3 |
+
trainings_pts_post_thresh 178966
|
fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet_formatting.stderr.txt
ADDED
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|
|
| 1 |
+
INFO: underlay of /etc/localtime required more than 50 (88) bind mounts
|
| 2 |
+
INFO: underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
|
| 3 |
+
2023-07-17 12:58:41.623933: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 4 |
+
2023-07-17 12:58:44.613057: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 5 |
+
2023-07-17 12:58:44.616736: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
|
| 6 |
+
2023-07-17 12:58:45.451802: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 7 |
+
pciBusID: 0000:c3:00.0 name: NVIDIA A100-SXM4-80GB computeCapability: 8.0
|
| 8 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.15GiB deviceMemoryBandwidth: 1.85TiB/s
|
| 9 |
+
2023-07-17 12:58:45.451909: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 10 |
+
2023-07-17 12:58:45.474616: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 11 |
+
2023-07-17 12:58:45.474682: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 12 |
+
2023-07-17 12:58:45.487526: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 13 |
+
2023-07-17 12:58:45.493676: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 14 |
+
2023-07-17 12:58:45.512131: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 15 |
+
2023-07-17 12:58:45.516864: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 16 |
+
2023-07-17 12:58:45.517870: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 17 |
+
2023-07-17 12:58:45.617419: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 18 |
+
2023-07-17 12:58:45.617841: 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
|
| 19 |
+
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
|
| 20 |
+
2023-07-17 12:58:45.618824: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 21 |
+
2023-07-17 12:58:45.664013: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 22 |
+
pciBusID: 0000:c3:00.0 name: NVIDIA A100-SXM4-80GB computeCapability: 8.0
|
| 23 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.15GiB deviceMemoryBandwidth: 1.85TiB/s
|
| 24 |
+
2023-07-17 12:58:45.664058: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 25 |
+
2023-07-17 12:58:45.664089: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 26 |
+
2023-07-17 12:58:45.664107: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 27 |
+
2023-07-17 12:58:45.664125: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 28 |
+
2023-07-17 12:58:45.664141: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 29 |
+
2023-07-17 12:58:45.664156: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 30 |
+
2023-07-17 12:58:45.664172: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 31 |
+
2023-07-17 12:58:45.664188: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 32 |
+
2023-07-17 12:58:45.713150: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 33 |
+
2023-07-17 12:58:45.715079: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 34 |
+
2023-07-17 12:58:48.086487: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
|
| 35 |
+
2023-07-17 12:58:48.086603: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
|
| 36 |
+
2023-07-17 12:58:48.086618: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
|
| 37 |
+
2023-07-17 12:58:48.093649: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 75650 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-SXM4-80GB, pci bus id: 0000:c3:00.0, compute capability: 8.0)
|
| 38 |
+
2023-07-17 12:58:51.037565: 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.
|
| 39 |
+
/opt/conda/lib/python3.7/site-packages/tensorflow/python/keras/layers/core.py:1059: UserWarning: is not loaded, but a Lambda layer uses it. It may cause errors.
|
| 40 |
+
, UserWarning)
|
fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet_formatting.stdout.txt
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 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//ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2/chrombpnet.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2/new_model_formats/chrombpnet
|
fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet_model_params.tsv
ADDED
|
@@ -0,0 +1,9 @@
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|
|
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|
|
|
|
|
|
| 1 |
+
counts_loss_weight 8.0
|
| 2 |
+
filters 512
|
| 3 |
+
n_dil_layers 8
|
| 4 |
+
bias_model_path /scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2/bias_model_scaled.h5
|
| 5 |
+
inputlen 2114
|
| 6 |
+
outputlen 1000
|
| 7 |
+
max_jitter 500
|
| 8 |
+
chr_fold_path /scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_2.json
|
| 9 |
+
negative_sampling_ratio 0.1
|
fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet_no_bias_formatting.stderr.txt
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 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//ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2/new_model_formats/chrombpnet_wo_bias
|
fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.chrombpnet_no_bias_formatting.stdout.txt
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 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//ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2/new_model_formats/chrombpnet_wo_bias
|
fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.epoch_loss.csv
ADDED
|
@@ -0,0 +1,16 @@
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|
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|
|
|
| 1 |
+
epoch,logcount_predictions_loss,logits_profile_predictions_loss,loss,val_logcount_predictions_loss,val_logits_profile_predictions_loss,val_loss
|
| 2 |
+
0,2.702136278152466,487.5805358886719,509.19769287109375,0.8965531587600708,477.45458984375,484.62713623046875
|
| 3 |
+
1,0.7884988784790039,455.6800537109375,461.9881896972656,0.5868847370147705,463.36993408203125,468.06500244140625
|
| 4 |
+
2,0.662825345993042,446.10430908203125,451.4070129394531,0.5590391755104065,455.93572998046875,460.4077453613281
|
| 5 |
+
3,0.6043997406959534,439.7535705566406,444.5887145996094,0.48553359508514404,455.86761474609375,459.75189208984375
|
| 6 |
+
4,0.5626344680786133,435.02874755859375,439.5299072265625,0.4902230203151703,447.43463134765625,451.3565673828125
|
| 7 |
+
5,0.5412852764129639,431.811279296875,436.1412048339844,0.4616963267326355,455.8392639160156,459.5330810546875
|
| 8 |
+
6,0.5188483595848083,428.0033874511719,432.1546325683594,0.45085909962654114,453.6055908203125,457.2122802734375
|
| 9 |
+
7,0.5024115443229675,426.5348205566406,430.5535583496094,0.4474053382873535,451.1673583984375,454.7466125488281
|
| 10 |
+
8,0.4539332985877991,417.40704345703125,421.0393371582031,0.47847387194633484,446.71295166015625,450.5406494140625
|
| 11 |
+
9,0.43969783186912537,413.9564514160156,417.47406005859375,0.4300617277622223,444.5404968261719,447.9809875488281
|
| 12 |
+
10,0.42329514026641846,409.94818115234375,413.3346862792969,0.46827706694602966,446.64642333984375,450.3924255371094
|
| 13 |
+
11,0.41152581572532654,406.7900695800781,410.08197021484375,0.43047213554382324,448.91497802734375,452.3586120605469
|
| 14 |
+
12,0.4007745683193207,404.9291076660156,408.13543701171875,0.42071616649627686,449.4823913574219,452.8480224609375
|
| 15 |
+
13,0.3794959783554077,399.10906982421875,402.1450500488281,0.4211646318435669,446.58953857421875,449.95904541015625
|
| 16 |
+
14,0.3663191497325897,397.19268798828125,400.1235046386719,0.42077991366386414,450.8209228515625,454.1870422363281
|
fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.stderr.txt
ADDED
|
@@ -0,0 +1,328 @@
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|
| 1 |
+
2022-10-06 06:39:16.514393: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 2 |
+
2022-10-06 06:45:23.326776: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 3 |
+
2022-10-06 06:45:23.328902: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
|
| 4 |
+
2022-10-06 06:45:23.777256: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 5 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 6 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 7 |
+
2022-10-06 06:45:23.777387: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 8 |
+
2022-10-06 06:45:23.802581: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 9 |
+
2022-10-06 06:45:23.802693: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 10 |
+
2022-10-06 06:45:23.816499: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 11 |
+
2022-10-06 06:45:23.822871: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 12 |
+
2022-10-06 06:45:23.845193: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 13 |
+
2022-10-06 06:45:23.851483: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 14 |
+
2022-10-06 06:45:23.852969: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 15 |
+
2022-10-06 06:45:23.857503: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 16 |
+
2022-10-06 06:45:23.857850: 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
|
| 17 |
+
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
|
| 18 |
+
2022-10-06 06:45:23.857932: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 19 |
+
2022-10-06 06:45:23.859336: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 20 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 21 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 22 |
+
2022-10-06 06:45:23.859366: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 23 |
+
2022-10-06 06:45:23.859385: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 24 |
+
2022-10-06 06:45:23.859401: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 25 |
+
2022-10-06 06:45:23.859416: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 26 |
+
2022-10-06 06:45:23.859431: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 27 |
+
2022-10-06 06:45:23.859446: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 28 |
+
2022-10-06 06:45:23.859462: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 29 |
+
2022-10-06 06:45:23.859476: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 30 |
+
2022-10-06 06:45:23.862135: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 31 |
+
2022-10-06 06:45:23.863753: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 32 |
+
2022-10-06 06:45:25.559234: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
|
| 33 |
+
2022-10-06 06:45:25.559379: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
|
| 34 |
+
2022-10-06 06:45:25.559392: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
|
| 35 |
+
2022-10-06 06:45:25.566786: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 37440 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-SXM4-40GB, pci bus id: 0000:47:00.0, compute capability: 8.0)
|
| 36 |
+
2022-10-06 06:45:26.949222: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
|
| 37 |
+
2022-10-06 06:45:26.958309: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2000015000 Hz
|
| 38 |
+
2022-10-06 06:45:27.138914: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 39 |
+
2022-10-06 06:45:28.725393: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 40 |
+
2022-10-06 06:45:28.733881: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 41 |
+
2022-10-06 06:46:01.332912: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 42 |
+
2022-10-06 06:46:02.965894: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 43 |
+
2022-10-06 06:46:02.966741: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
|
| 44 |
+
2022-10-06 06:46:03.266199: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 45 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 46 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 47 |
+
2022-10-06 06:46:03.266329: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 48 |
+
2022-10-06 06:46:03.268608: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 49 |
+
2022-10-06 06:46:03.268663: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 50 |
+
2022-10-06 06:46:03.269696: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 51 |
+
2022-10-06 06:46:03.269879: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 52 |
+
2022-10-06 06:46:03.272224: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 53 |
+
2022-10-06 06:46:03.272731: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 54 |
+
2022-10-06 06:46:03.272861: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 55 |
+
2022-10-06 06:46:03.275853: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 56 |
+
2022-10-06 06:46:03.276176: 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
|
| 57 |
+
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
|
| 58 |
+
2022-10-06 06:46:03.276259: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 59 |
+
2022-10-06 06:46:03.277151: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 60 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 61 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 62 |
+
2022-10-06 06:46:03.277202: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 63 |
+
2022-10-06 06:46:03.277221: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 64 |
+
2022-10-06 06:46:03.277237: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 65 |
+
2022-10-06 06:46:03.277252: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 66 |
+
2022-10-06 06:46:03.277266: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 67 |
+
2022-10-06 06:46:03.277280: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 68 |
+
2022-10-06 06:46:03.277295: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 69 |
+
2022-10-06 06:46:03.277309: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 70 |
+
2022-10-06 06:46:03.278950: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 71 |
+
2022-10-06 06:46:03.278982: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 72 |
+
2022-10-06 06:46:03.757711: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
|
| 73 |
+
2022-10-06 06:46:03.757856: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
|
| 74 |
+
2022-10-06 06:46:03.757868: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
|
| 75 |
+
2022-10-06 06:46:03.760714: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 37440 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-SXM4-40GB, pci bus id: 0000:47:00.0, compute capability: 8.0)
|
| 76 |
+
2022-10-06 06:52:08.536405: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
|
| 77 |
+
2022-10-06 06:52:08.536873: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2000015000 Hz
|
| 78 |
+
2022-10-06 06:52:09.935549: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 79 |
+
2022-10-06 06:52:10.431012: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 80 |
+
2022-10-06 06:52:10.446834: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 81 |
+
2022-10-06 06:52:13.812812: I tensorflow/stream_executor/cuda/cuda_blas.cc:1838] TensorFloat-32 will be used for the matrix multiplication. This will only be logged once.
|
| 82 |
+
2022-10-06 08:37:04.335172: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 83 |
+
2022-10-06 08:37:06.949755: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 84 |
+
2022-10-06 08:37:06.950680: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
|
| 85 |
+
2022-10-06 08:37:07.382276: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 86 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 87 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 88 |
+
2022-10-06 08:37:07.382431: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 89 |
+
2022-10-06 08:37:07.385237: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 90 |
+
2022-10-06 08:37:07.385297: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 91 |
+
2022-10-06 08:37:07.386299: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 92 |
+
2022-10-06 08:37:07.386489: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 93 |
+
2022-10-06 08:37:07.388751: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 94 |
+
2022-10-06 08:37:07.389254: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 95 |
+
2022-10-06 08:37:07.389390: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 96 |
+
2022-10-06 08:37:07.392446: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 97 |
+
2022-10-06 08:37:07.392784: 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
|
| 98 |
+
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
|
| 99 |
+
2022-10-06 08:37:07.392862: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 100 |
+
2022-10-06 08:37:07.394814: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 101 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 102 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 103 |
+
2022-10-06 08:37:07.394841: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 104 |
+
2022-10-06 08:37:07.394859: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 105 |
+
2022-10-06 08:37:07.394874: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 106 |
+
2022-10-06 08:37:07.394888: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 107 |
+
2022-10-06 08:37:07.394902: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 108 |
+
2022-10-06 08:37:07.394916: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 109 |
+
2022-10-06 08:37:07.394929: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 110 |
+
2022-10-06 08:37:07.394943: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 111 |
+
2022-10-06 08:37:07.397859: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 112 |
+
2022-10-06 08:37:07.397891: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 113 |
+
2022-10-06 08:37:07.918127: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
|
| 114 |
+
2022-10-06 08:37:07.918293: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
|
| 115 |
+
2022-10-06 08:37:07.918306: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
|
| 116 |
+
2022-10-06 08:37:07.921815: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 37440 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-SXM4-40GB, pci bus id: 0000:47:00.0, compute capability: 8.0)
|
| 117 |
+
2022-10-06 08:38:16.302211: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
|
| 118 |
+
2022-10-06 08:38:16.305862: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2000015000 Hz
|
| 119 |
+
2022-10-06 08:38:16.393096: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 120 |
+
2022-10-06 08:38:16.877370: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 121 |
+
2022-10-06 08:38:16.879604: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 122 |
+
/opt/conda/lib/python3.7/site-packages/tensorflow/python/keras/layers/core.py:1059: UserWarning: is not loaded, but a Lambda layer uses it. It may cause errors.
|
| 123 |
+
, UserWarning)
|
| 124 |
+
/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/metrics.py:69: RuntimeWarning: invalid value encountered in true_divide
|
| 125 |
+
cur_jsd=jensenshannon(true_counts[idx,:]/np.nansum(true_counts[idx,:]),pred_probs[idx,:])
|
| 126 |
+
/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/utils/metrics_utils.py:196: RuntimeWarning: invalid value encountered in true_divide
|
| 127 |
+
profile_prob = profile / np.sum(profile)
|
| 128 |
+
/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/metrics.py:78: RuntimeWarning: invalid value encountered in true_divide
|
| 129 |
+
shuffled_labels_prob=shuffled_labels/np.nansum(shuffled_labels)
|
| 130 |
+
/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/metrics.py:88: RuntimeWarning: invalid value encountered in true_divide
|
| 131 |
+
curr_jsd_rnd=jensenshannon(true_counts[idx,:]/np.nansum(true_counts[idx,:]),shuffled_labels_prob)
|
| 132 |
+
No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
|
| 133 |
+
findfont: Font family ['normal'] not found. Falling back to DejaVu Sans.
|
| 134 |
+
findfont: Font family ['normal'] not found. Falling back to DejaVu Sans.
|
| 135 |
+
findfont: Font family ['normal'] not found. Falling back to DejaVu Sans.
|
| 136 |
+
No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
|
| 137 |
+
No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
|
| 138 |
+
2022-10-06 08:40:18.894114: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 139 |
+
2022-10-06 08:40:21.266707: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 140 |
+
2022-10-06 08:40:21.267696: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
|
| 141 |
+
2022-10-06 08:40:21.541397: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 142 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 143 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 144 |
+
2022-10-06 08:40:21.541529: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 145 |
+
2022-10-06 08:40:21.543882: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 146 |
+
2022-10-06 08:40:21.543941: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 147 |
+
2022-10-06 08:40:21.544969: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 148 |
+
2022-10-06 08:40:21.545175: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 149 |
+
2022-10-06 08:40:21.547560: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 150 |
+
2022-10-06 08:40:21.548070: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 151 |
+
2022-10-06 08:40:21.548210: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 152 |
+
2022-10-06 08:40:21.550116: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 153 |
+
2022-10-06 08:40:21.550453: 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
|
| 154 |
+
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
|
| 155 |
+
2022-10-06 08:40:21.550563: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 156 |
+
2022-10-06 08:40:21.551868: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 157 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 158 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 159 |
+
2022-10-06 08:40:21.551892: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 160 |
+
2022-10-06 08:40:21.551909: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 161 |
+
2022-10-06 08:40:21.551924: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 162 |
+
2022-10-06 08:40:21.551938: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 163 |
+
2022-10-06 08:40:21.551952: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 164 |
+
2022-10-06 08:40:21.551966: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 165 |
+
2022-10-06 08:40:21.551980: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 166 |
+
2022-10-06 08:40:21.551994: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 167 |
+
2022-10-06 08:40:21.554055: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 168 |
+
2022-10-06 08:40:21.554089: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 169 |
+
2022-10-06 08:40:22.082613: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
|
| 170 |
+
2022-10-06 08:40:22.082751: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
|
| 171 |
+
2022-10-06 08:40:22.082764: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
|
| 172 |
+
2022-10-06 08:40:22.086270: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 37440 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-SXM4-40GB, pci bus id: 0000:47:00.0, compute capability: 8.0)
|
| 173 |
+
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
|
| 174 |
+
2022-10-06 08:41:26.685430: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
|
| 175 |
+
2022-10-06 08:41:26.687932: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2000015000 Hz
|
| 176 |
+
2022-10-06 08:41:26.746557: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 177 |
+
2022-10-06 08:41:27.233910: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 178 |
+
2022-10-06 08:41:27.235604: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 179 |
+
/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/metrics.py:69: RuntimeWarning: invalid value encountered in true_divide
|
| 180 |
+
cur_jsd=jensenshannon(true_counts[idx,:]/np.nansum(true_counts[idx,:]),pred_probs[idx,:])
|
| 181 |
+
/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/utils/metrics_utils.py:196: RuntimeWarning: invalid value encountered in true_divide
|
| 182 |
+
profile_prob = profile / np.sum(profile)
|
| 183 |
+
/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/metrics.py:78: RuntimeWarning: invalid value encountered in true_divide
|
| 184 |
+
shuffled_labels_prob=shuffled_labels/np.nansum(shuffled_labels)
|
| 185 |
+
/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/metrics.py:88: RuntimeWarning: invalid value encountered in true_divide
|
| 186 |
+
curr_jsd_rnd=jensenshannon(true_counts[idx,:]/np.nansum(true_counts[idx,:]),shuffled_labels_prob)
|
| 187 |
+
No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
|
| 188 |
+
findfont: Font family ['normal'] not found. Falling back to DejaVu Sans.
|
| 189 |
+
findfont: Font family ['normal'] not found. Falling back to DejaVu Sans.
|
| 190 |
+
findfont: Font family ['normal'] not found. Falling back to DejaVu Sans.
|
| 191 |
+
No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
|
| 192 |
+
No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
|
| 193 |
+
2022-10-06 08:43:22.247728: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 194 |
+
2022-10-06 08:43:24.962590: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 195 |
+
2022-10-06 08:43:24.963628: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
|
| 196 |
+
2022-10-06 08:43:25.381277: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 197 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 198 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 199 |
+
2022-10-06 08:43:25.381436: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 200 |
+
2022-10-06 08:43:25.383758: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 201 |
+
2022-10-06 08:43:25.383812: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 202 |
+
2022-10-06 08:43:25.384808: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 203 |
+
2022-10-06 08:43:25.385001: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 204 |
+
2022-10-06 08:43:25.387296: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 205 |
+
2022-10-06 08:43:25.387794: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 206 |
+
2022-10-06 08:43:25.387929: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 207 |
+
2022-10-06 08:43:25.390724: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 208 |
+
2022-10-06 08:43:25.391060: 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
|
| 209 |
+
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
|
| 210 |
+
2022-10-06 08:43:25.391154: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 211 |
+
2022-10-06 08:43:25.392571: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 212 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 213 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 214 |
+
2022-10-06 08:43:25.392597: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 215 |
+
2022-10-06 08:43:25.392617: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 216 |
+
2022-10-06 08:43:25.392634: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 217 |
+
2022-10-06 08:43:25.392676: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 218 |
+
2022-10-06 08:43:25.392694: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 219 |
+
2022-10-06 08:43:25.392710: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 220 |
+
2022-10-06 08:43:25.392725: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 221 |
+
2022-10-06 08:43:25.392740: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 222 |
+
2022-10-06 08:43:25.395394: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 223 |
+
2022-10-06 08:43:25.395426: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 224 |
+
2022-10-06 08:43:25.924393: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
|
| 225 |
+
2022-10-06 08:43:25.924538: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
|
| 226 |
+
2022-10-06 08:43:25.924552: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
|
| 227 |
+
2022-10-06 08:43:25.928099: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 37440 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-SXM4-40GB, pci bus id: 0000:47:00.0, compute capability: 8.0)
|
| 228 |
+
2022-10-06 08:44:31.304546: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
|
| 229 |
+
2022-10-06 08:44:31.306407: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2000015000 Hz
|
| 230 |
+
2022-10-06 08:44:31.344922: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 231 |
+
2022-10-06 08:44:31.841835: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 232 |
+
2022-10-06 08:44:31.843618: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 233 |
+
/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/metrics.py:69: RuntimeWarning: invalid value encountered in true_divide
|
| 234 |
+
cur_jsd=jensenshannon(true_counts[idx,:]/np.nansum(true_counts[idx,:]),pred_probs[idx,:])
|
| 235 |
+
/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/utils/metrics_utils.py:196: RuntimeWarning: invalid value encountered in true_divide
|
| 236 |
+
profile_prob = profile / np.sum(profile)
|
| 237 |
+
/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/metrics.py:78: RuntimeWarning: invalid value encountered in true_divide
|
| 238 |
+
shuffled_labels_prob=shuffled_labels/np.nansum(shuffled_labels)
|
| 239 |
+
/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/metrics.py:88: RuntimeWarning: invalid value encountered in true_divide
|
| 240 |
+
curr_jsd_rnd=jensenshannon(true_counts[idx,:]/np.nansum(true_counts[idx,:]),shuffled_labels_prob)
|
| 241 |
+
No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
|
| 242 |
+
findfont: Font family ['normal'] not found. Falling back to DejaVu Sans.
|
| 243 |
+
findfont: Font family ['normal'] not found. Falling back to DejaVu Sans.
|
| 244 |
+
findfont: Font family ['normal'] not found. Falling back to DejaVu Sans.
|
| 245 |
+
No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
|
| 246 |
+
No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
|
| 247 |
+
2022-10-06 08:45:33.461820: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 248 |
+
2022-10-06 08:45:34.653575: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 249 |
+
2022-10-06 08:45:34.654597: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
|
| 250 |
+
2022-10-06 08:45:34.960526: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 251 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 252 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 253 |
+
2022-10-06 08:45:34.960677: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 254 |
+
2022-10-06 08:45:34.963190: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 255 |
+
2022-10-06 08:45:34.963302: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 256 |
+
2022-10-06 08:45:34.964368: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 257 |
+
2022-10-06 08:45:34.964580: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 258 |
+
2022-10-06 08:45:34.967059: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 259 |
+
2022-10-06 08:45:34.967592: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 260 |
+
2022-10-06 08:45:34.967743: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 261 |
+
2022-10-06 08:45:34.969607: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 262 |
+
2022-10-06 08:45:34.969968: 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
|
| 263 |
+
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
|
| 264 |
+
2022-10-06 08:45:34.970051: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 265 |
+
2022-10-06 08:45:34.970940: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 266 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 267 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 268 |
+
2022-10-06 08:45:34.970970: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 269 |
+
2022-10-06 08:45:34.970988: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 270 |
+
2022-10-06 08:45:34.971003: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 271 |
+
2022-10-06 08:45:34.971017: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 272 |
+
2022-10-06 08:45:34.971031: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 273 |
+
2022-10-06 08:45:34.971045: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 274 |
+
2022-10-06 08:45:34.971059: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 275 |
+
2022-10-06 08:45:34.971074: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 276 |
+
2022-10-06 08:45:34.972707: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 277 |
+
2022-10-06 08:45:34.972744: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 278 |
+
2022-10-06 08:45:35.474310: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
|
| 279 |
+
2022-10-06 08:45:35.474505: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
|
| 280 |
+
2022-10-06 08:45:35.474519: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
|
| 281 |
+
2022-10-06 08:45:35.478043: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 37440 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-SXM4-40GB, pci bus id: 0000:47:00.0, compute capability: 8.0)
|
| 282 |
+
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
|
| 283 |
+
2022-10-06 08:45:52.912299: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
|
| 284 |
+
2022-10-06 08:45:52.912897: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2000015000 Hz
|
| 285 |
+
2022-10-06 08:45:53.117874: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 286 |
+
2022-10-06 08:45:53.657560: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 287 |
+
2022-10-06 08:45:53.659493: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 288 |
+
mkdir: cannot create directory ‘/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR038POV//chrombppnet_model_encsr283tme_bias_fold_2//footprints’: File exists
|
| 289 |
+
2022-10-06 08:47:43.333470: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 290 |
+
2022-10-06 08:47:44.506085: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 291 |
+
2022-10-06 08:47:44.507050: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
|
| 292 |
+
2022-10-06 08:47:44.810125: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 293 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 294 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 295 |
+
2022-10-06 08:47:44.810288: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 296 |
+
2022-10-06 08:47:44.812706: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 297 |
+
2022-10-06 08:47:44.812769: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 298 |
+
2022-10-06 08:47:44.813874: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 299 |
+
2022-10-06 08:47:44.814068: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 300 |
+
2022-10-06 08:47:44.816524: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 301 |
+
2022-10-06 08:47:44.817062: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 302 |
+
2022-10-06 08:47:44.817220: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 303 |
+
2022-10-06 08:47:44.819030: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
|
| 304 |
+
2022-10-06 08:47:44.819370: 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
|
| 305 |
+
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
|
| 306 |
+
2022-10-06 08:47:44.819456: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
|
| 307 |
+
2022-10-06 08:47:44.820330: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
|
| 308 |
+
pciBusID: 0000:47:00.0 name: NVIDIA A100-SXM4-40GB computeCapability: 8.0
|
| 309 |
+
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 39.45GiB deviceMemoryBandwidth: 1.41TiB/s
|
| 310 |
+
2022-10-06 08:47:44.820386: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
|
| 311 |
+
2022-10-06 08:47:44.820405: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
|
| 312 |
+
2022-10-06 08:47:44.820420: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
|
| 313 |
+
2022-10-06 08:47:44.820435: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
|
| 314 |
+
2022-10-06 08:47:44.820450: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
|
| 315 |
+
2022-10-06 08:47:44.820464: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
|
| 316 |
+
2022-10-06 08:47:44.820479: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
|
| 317 |
+
2022-10-06 08:47:44.820493: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
|
| 318 |
+
2022-10-06 08:47:44.822132: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
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2022-10-06 08:47:44.822217: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
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2022-10-06 08:47:45.328901: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
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| 321 |
+
2022-10-06 08:47:45.329057: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
|
| 322 |
+
2022-10-06 08:47:45.329070: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
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| 323 |
+
2022-10-06 08:47:45.332643: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 37440 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-SXM4-40GB, pci bus id: 0000:47:00.0, compute capability: 8.0)
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2022-10-06 08:48:02.541578: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
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2022-10-06 08:48:02.542209: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2000015000 Hz
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2022-10-06 08:48:02.684827: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
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2022-10-06 08:48:03.225780: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
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+
2022-10-06 08:48:03.227733: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
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fold_2/logs.models.fold_2.ENCSR038POV/logfile.modelling.fold_2.ENCSR038POV.stdout.txt
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