scziDesk
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Published
20 hours ago •
xuebaliang
xuebaliang
Problem in running few datasets
I tried few datasets provided in this repo. Only one "Romanov" is working at my system. Other incur some issues as shown in the log below. Any idea? One possible reason maybe, I am using the latest versions of Keras and TF with Python3.8 because of some reasons in installation for recommended versions.
$ python3 zidpkm.py --dataname Quake_Smart-seq2_Lung
2020-08-26 20:37:45.675009: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcudart.so.10.1: cannot open shared object file: No such file or directory
2020-08-26 20:37:45.675041: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
WARNING:tensorflow:From /home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
begin the pretraining
2020-08-26 20:37:50.473345: 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.
2020-08-26 20:37:50.498469: I tensorflow/core/platform/profile_utils/cpu_utils.cc:104] CPU Frequency: 2799925000 Hz
2020-08-26 20:37:50.498869: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55ab2c828240 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2020-08-26 20:37:50.498923: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version
2020-08-26 20:37:50.501941: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory
2020-08-26 20:37:50.502017: W tensorflow/stream_executor/cuda/cuda_driver.cc:312] failed call to cuInit: UNKNOWN ERROR (303)
2020-08-26 20:37:50.502080: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (TUD256255): /proc/driver/nvidia/version does not exist
Traceback (most recent call last):
File "zidpkm.py", line 67, in <module>
chencluster.pretrain(X, count_X, size_factor, args.batch_size, args.pretrain_epoch, args.gpu_option)
File "/home/tahmad/ogits/scziDesk/network.py", line 109, in pretrain
_, likelihood_loss, latent = self.sess.run(
File "/home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/client/session.py", line 957, in run
result = self._run(None, fetches, feed_dict, options_ptr,
File "/home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/client/session.py", line 1154, in _run
raise ValueError(
ValueError: Cannot feed value of shape (256, 499) for Tensor 'Placeholder_1:0', which has shape '(?, 500)'
$ python3 zidpkm.py --dataname Quake_10x_Bladder
2020-08-26 20:37:11.479722: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcudart.so.10.1: cannot open shared object file: No such file or directory
2020-08-26 20:37:11.479754: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
WARNING:tensorflow:From /home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
begin the pretraining
2020-08-26 20:37:16.896362: 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.
2020-08-26 20:37:16.918379: I tensorflow/core/platform/profile_utils/cpu_utils.cc:104] CPU Frequency: 2799925000 Hz
2020-08-26 20:37:16.918786: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55b73f466570 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2020-08-26 20:37:16.918837: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version
2020-08-26 20:37:16.921324: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory
2020-08-26 20:37:16.921384: W tensorflow/stream_executor/cuda/cuda_driver.cc:312] failed call to cuInit: UNKNOWN ERROR (303)
2020-08-26 20:37:16.921439: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (TUD256255): /proc/driver/nvidia/version does not exist
Traceback (most recent call last):
File "zidpkm.py", line 67, in <module>
chencluster.pretrain(X, count_X, size_factor, args.batch_size, args.pretrain_epoch, args.gpu_option)
File "/home/tahmad/ogits/scziDesk/network.py", line 109, in pretrain
_, likelihood_loss, latent = self.sess.run(
File "/home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/client/session.py", line 957, in run
result = self._run(None, fetches, feed_dict, options_ptr,
File "/home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/client/session.py", line 1154, in _run
raise ValueError(
ValueError: Cannot feed value of shape (256, 499) for Tensor 'Placeholder_1:0', which has shape '(?, 500)'
This is the log with Romanov dataset:
$ python3 zidpkm.py --dataname Romanov
2020-08-26 18:45:47.849892: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcudart.so.10.1: cannot open shared object file: No such file or directory
2020-08-26 18:45:47.849923: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
WARNING:tensorflow:From /home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
begin the pretraining
2020-08-26 18:45:53.861427: 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.
2020-08-26 18:45:53.885418: I tensorflow/core/platform/profile_utils/cpu_utils.cc:104] CPU Frequency: 2799925000 Hz
2020-08-26 18:45:53.885753: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x557076fa0140 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2020-08-26 18:45:53.885777: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version
2020-08-26 18:45:53.888498: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory
2020-08-26 18:45:53.888571: W tensorflow/stream_executor/cuda/cuda_driver.cc:312] failed call to cuInit: UNKNOWN ERROR (303)
2020-08-26 18:45:53.888619: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (TUD256255): /proc/driver/nvidia/version does not exist
begin the funetraining
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:18: FutureWarning: The linear_assignment_ module is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
begin the pretraining
begin the funetraining
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
begin the pretraining
begin the funetraining
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
begin the pretraining
begin the funetraining
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
begin the pretraining
begin the funetraining
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
begin the pretraining
begin the funetraining
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
begin the pretraining
begin the funetraining
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
begin the pretraining
begin the funetraining
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
begin the pretraining
begin the funetraining
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
begin the pretraining
begin the funetraining
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
/home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead.
warnings.warn(
dataset name kmeans accuracy kmeans ARI kmeans NMI accuracy ARI NMI
0 Romanov 0.87956 0.72475 0.71113 0.88199 0.72742 0.71808
1 Romanov 0.88407 0.74607 0.7135 0.89622 0.77092 0.73498
2 Romanov 0.87643 0.72001 0.70887 0.8799 0.72469 0.71408
3 Romanov 0.89448 0.75458 0.73029 0.90003 0.76492 0.74113
4 Romanov 0.87817 0.72162 0.71079 0.88997 0.75294 0.72513
5 Romanov 0.88199 0.73597 0.71028 0.90212 0.78338 0.74301
6 Romanov 0.89136 0.75587 0.73317 0.89969 0.77332 0.74383
7 Romanov 0.88476 0.72787 0.71705 0.89101 0.74291 0.72474
8 Romanov 0.88303 0.73709 0.71759 0.88858 0.74974 0.72634
9 Romanov 0.88199 0.73324 0.7164 0.89379 0.75698 0.73332
Thank you for your interest in our work. We are using tensorflow version 1.14 and we have not tested the version above 2.0. In addition, regarding the 499 and 500 that appear in the Tensor 'Placeholder_1:0', I suggest you can adjust the number of high-variable genes in "normalize" function in "preprocess.py" file, for example, set it to 499, and see if there is an error. If it still reports an error, it may be the version issue. Good luck.
Hi @xuebaliang, Thanks for the reply.
I am able to build a Singularity container for scziDesk with all its required dependencies. I have tested Romanov dataset is working with following command python3.6 zidpkm.py --dataname Romanov.
This container will be very useful for the people who want to use scziDesk and avoid searching/installing for required specific versions of its dependencies. Even you can add this file to your repo. But still some datasets are throwing Placeholder errors.
Can you please try using this container at your end? together we can make all the datasets running in this container.
Instructions for creating and using Singularity container
- Install Singularity software through stable release
- Place this scziDesk Singularity file in some dir
- Run the following command
sudo singularity build --sandbox scziDesk Singularity - scziDesk sandbox will be created, go inside it.
sudo singularity shell -B </your/home/> scziDesk/change your home dir path - Simply go inside scziDesk dir and run this.
python3.6 zidpkm.py --dataname Romanov
Please also try other datasets.
Let me know if you need any further help in setting up Singularity container on your system.
Hi @xuebaliang , A kind reminder!
Also can you please give the exact versions of these tools used in scziDesk?
tensorflow, keras, scikit-learn, jgraph, tqdm, scanpy
Hello, sorry for the late reply. Since I need to take an exam recently, I may be able to help you with this proposal (Singularity container) a while later. I just checked the version of each package, they are tensorflow 1.14.0 (GPU version); keras 2.2.4; scikit-learn 0.22.2.post1; jgraph 0.2.1; tqdm 4.32.2; scanpy 1.4.4. Good luck.
I tried few datasets provided in this repo. Only one "Romanov" is working at my system. Other incur some issues as shown in the log below. Any idea? One possible reason maybe, I am using the latest versions of Keras and TF with Python3.8 because of some reasons in installation for recommended versions.
$ python3 zidpkm.py --dataname Quake_Smart-seq2_Lung 2020-08-26 20:37:45.675009: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcudart.so.10.1: cannot open shared object file: No such file or directory 2020-08-26 20:37:45.675041: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. WARNING:tensorflow:From /home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term begin the pretraining 2020-08-26 20:37:50.473345: 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. 2020-08-26 20:37:50.498469: I tensorflow/core/platform/profile_utils/cpu_utils.cc:104] CPU Frequency: 2799925000 Hz 2020-08-26 20:37:50.498869: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55ab2c828240 initialized for platform Host (this does not guarantee that XLA will be used). Devices: 2020-08-26 20:37:50.498923: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version 2020-08-26 20:37:50.501941: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory 2020-08-26 20:37:50.502017: W tensorflow/stream_executor/cuda/cuda_driver.cc:312] failed call to cuInit: UNKNOWN ERROR (303) 2020-08-26 20:37:50.502080: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (TUD256255): /proc/driver/nvidia/version does not exist Traceback (most recent call last): File "zidpkm.py", line 67, in <module> chencluster.pretrain(X, count_X, size_factor, args.batch_size, args.pretrain_epoch, args.gpu_option) File "/home/tahmad/ogits/scziDesk/network.py", line 109, in pretrain _, likelihood_loss, latent = self.sess.run( File "/home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/client/session.py", line 957, in run result = self._run(None, fetches, feed_dict, options_ptr, File "/home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/client/session.py", line 1154, in _run raise ValueError( ValueError: Cannot feed value of shape (256, 499) for Tensor 'Placeholder_1:0', which has shape '(?, 500)'$ python3 zidpkm.py --dataname Quake_10x_Bladder 2020-08-26 20:37:11.479722: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcudart.so.10.1: cannot open shared object file: No such file or directory 2020-08-26 20:37:11.479754: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. WARNING:tensorflow:From /home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term begin the pretraining 2020-08-26 20:37:16.896362: 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. 2020-08-26 20:37:16.918379: I tensorflow/core/platform/profile_utils/cpu_utils.cc:104] CPU Frequency: 2799925000 Hz 2020-08-26 20:37:16.918786: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55b73f466570 initialized for platform Host (this does not guarantee that XLA will be used). Devices: 2020-08-26 20:37:16.918837: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version 2020-08-26 20:37:16.921324: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory 2020-08-26 20:37:16.921384: W tensorflow/stream_executor/cuda/cuda_driver.cc:312] failed call to cuInit: UNKNOWN ERROR (303) 2020-08-26 20:37:16.921439: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (TUD256255): /proc/driver/nvidia/version does not exist Traceback (most recent call last): File "zidpkm.py", line 67, in <module> chencluster.pretrain(X, count_X, size_factor, args.batch_size, args.pretrain_epoch, args.gpu_option) File "/home/tahmad/ogits/scziDesk/network.py", line 109, in pretrain _, likelihood_loss, latent = self.sess.run( File "/home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/client/session.py", line 957, in run result = self._run(None, fetches, feed_dict, options_ptr, File "/home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/client/session.py", line 1154, in _run raise ValueError( ValueError: Cannot feed value of shape (256, 499) for Tensor 'Placeholder_1:0', which has shape '(?, 500)'This is the log with Romanov dataset:
$ python3 zidpkm.py --dataname Romanov 2020-08-26 18:45:47.849892: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcudart.so.10.1: cannot open shared object file: No such file or directory 2020-08-26 18:45:47.849923: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. WARNING:tensorflow:From /home/tahmad/anaconda3/lib/python3.8/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term begin the pretraining 2020-08-26 18:45:53.861427: 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. 2020-08-26 18:45:53.885418: I tensorflow/core/platform/profile_utils/cpu_utils.cc:104] CPU Frequency: 2799925000 Hz 2020-08-26 18:45:53.885753: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x557076fa0140 initialized for platform Host (this does not guarantee that XLA will be used). Devices: 2020-08-26 18:45:53.885777: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version 2020-08-26 18:45:53.888498: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory 2020-08-26 18:45:53.888571: W tensorflow/stream_executor/cuda/cuda_driver.cc:312] failed call to cuInit: UNKNOWN ERROR (303) 2020-08-26 18:45:53.888619: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (TUD256255): /proc/driver/nvidia/version does not exist begin the funetraining /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:18: FutureWarning: The linear_assignment_ module is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( begin the pretraining begin the funetraining /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( begin the pretraining begin the funetraining /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( begin the pretraining begin the funetraining /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( begin the pretraining begin the funetraining /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( begin the pretraining begin the funetraining /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( begin the pretraining begin the funetraining /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( begin the pretraining begin the funetraining /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( begin the pretraining begin the funetraining /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( begin the pretraining begin the funetraining /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( /home/tahmad/anaconda3/lib/python3.8/site-packages/sklearn/utils/linear_assignment_.py:124: FutureWarning: The linear_assignment function is deprecated in 0.21 and will be removed from 0.23. Use scipy.optimize.linear_sum_assignment instead. warnings.warn( dataset name kmeans accuracy kmeans ARI kmeans NMI accuracy ARI NMI 0 Romanov 0.87956 0.72475 0.71113 0.88199 0.72742 0.71808 1 Romanov 0.88407 0.74607 0.7135 0.89622 0.77092 0.73498 2 Romanov 0.87643 0.72001 0.70887 0.8799 0.72469 0.71408 3 Romanov 0.89448 0.75458 0.73029 0.90003 0.76492 0.74113 4 Romanov 0.87817 0.72162 0.71079 0.88997 0.75294 0.72513 5 Romanov 0.88199 0.73597 0.71028 0.90212 0.78338 0.74301 6 Romanov 0.89136 0.75587 0.73317 0.89969 0.77332 0.74383 7 Romanov 0.88476 0.72787 0.71705 0.89101 0.74291 0.72474 8 Romanov 0.88303 0.73709 0.71759 0.88858 0.74974 0.72634 9 Romanov 0.88199 0.73324 0.7164 0.89379 0.75698 0.73332
Traceback (most recent call last): File "D:/Code/scziDesk/zidpkm.py", line 72, in chencluster.pretrain(X, count_X, size_factor, args.batch_size, args.pretrain_epoch, args.gpu_option) File "D:\Code\scziDesk\network.py", line 117, in pretrain (pre_index + 1) * batch_size)]}) File "C:\Users\ThinkPad.conda\envs\Tensor1\lib\site-packages\tensorflow\python\client\session.py", line 950, in run run_metadata_ptr) File "C:\Users\ThinkPad.conda\envs\Tensor1\lib\site-packages\tensorflow\python\client\session.py", line 1149, in _run str(subfeed_t.get_shape()))) ValueError: Cannot feed value of shape (256, 499) for Tensor 'Placeholder_1:0', which has shape '(?, 500)'
I met the same problem. How did you solve it. But my version of the tool all fit the bill
