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LiLabAtVT / DeepTE

Neural network classification of TE
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Check failed: ret == 0 (11 vs. 0)Thread tf_data_private_threadpool creation via pthread_create() failed #15

Open JiyangChang opened 2 years ago

JiyangChang commented 2 years ago

Hi,

Thanks for the great tools, I met some trouble when I was running DeepTE, how can I fix this?

2022-05-03 14:33:34.373174: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2022-05-03 14:33:35.005655: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1525] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 21318 MB memory:  -> device: 0, name: Quadro RTX 6000, pci bus id: 0000:3b:00.0, compute capability: 7.5
2022-05-03 14:33:51.610330: F tensorflow/core/platform/default/env.cc:73] Check failed: ret == 0 (11 vs. 0)Thread tf_data_private_threadpool creation via pthread_create() failed.
/var/spool/sge/firestorm/job_scripts/2012270: line 6: 196910 Aborted                 (core dumped) python3 /software/shared/apps/x86_64/DeepTE/26122020/DeepTE.py -i ../families.fa -d ./tmp -o ./result -sp P -m_dir ../Plants_model
songliVT commented 2 years ago

Looks like an error from a wrongly compiled tensorflow. Can you reinstall TensorFlow and see how it goes?

Song

On Tue, May 3, 2022 at 10:01 AM Elkan Chang @.***> wrote:

Hi,

Thanks for the great tools, I met some trouble when I was running DeepTE, how can I fix this?

2022-05-03 14:33:34.373174: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 2022-05-03 14:33:35.005655: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1525] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 21318 MB memory: -> device: 0, name: Quadro RTX 6000, pci bus id: 0000:3b:00.0, compute capability: 7.5 2022-05-03 14:33:51.610330: F tensorflow/core/platform/default/env.cc:73] Check failed: ret == 0 (11 vs. 0)Thread tf_data_private_threadpool creation via pthread_create() failed. /var/spool/sge/firestorm/job_scripts/2012270: line 6: 196910 Aborted (core dumped) python3 /software/shared/apps/x86_64/DeepTE/26122020/DeepTE.py -i ../families.fa -d ./tmp -o ./result -sp P -m_dir ../Plants_model

— Reply to this email directly, view it on GitHub https://github.com/LiLabAtVT/DeepTE/issues/15, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEEENRULGU23EFIUN4DCOTVIEWTNANCNFSM5U6732UQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Associate Professor in Plant Genomics and Bioinformatics School of Plant and Environmental Sciences Virginia Polytechnic Institute and State University

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JiyangChang commented 2 years ago

Looks like an error from a wrongly compiled tensorflow. Can you reinstall TensorFlow and see how it goes? Song … On Tue, May 3, 2022 at 10:01 AM Elkan Chang @.> wrote: Hi, Thanks for the great tools, I met some trouble when I was running DeepTE, how can I fix this? 2022-05-03 14:33:34.373174: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 2022-05-03 14:33:35.005655: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1525] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 21318 MB memory: -> device: 0, name: Quadro RTX 6000, pci bus id: 0000:3b:00.0, compute capability: 7.5 2022-05-03 14:33:51.610330: F tensorflow/core/platform/default/env.cc:73] Check failed: ret == 0 (11 vs. 0)Thread tf_data_private_threadpool creation via pthread_create() failed. /var/spool/sge/firestorm/job_scripts/2012270: line 6: 196910 Aborted (core dumped) python3 /software/shared/apps/x86_64/DeepTE/26122020/DeepTE.py -i ../families.fa -d ./tmp -o ./result -sp P -m_dir ../Plants_model — Reply to this email directly, view it on GitHub <#15>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEEENRULGU23EFIUN4DCOTVIEWTNANCNFSM5U6732UQ . You are receiving this because you are subscribed to this thread.Message ID: @.> -- Associate Professor in Plant Genomics and Bioinformatics School of Plant and Environmental Sciences Virginia Polytechnic Institute and State University zoom https://virginiatech.zoom.us/j/8790572835

Dear Song,

Many thanks for your quick reply.

I reinstall the tensorflow as you suggested and then rerun the job, this error still exists.

BRs Elkan

songliVT commented 2 years ago

This is still a TensorFlow error.

  1. Can you check whether you can load TensorFlow or not in a separate python environment? if not, you need to figure out how to install TensorFlow properly.

  2. Can you find a different computer to run DeepTE?

I am sorry I cannot provide more solid help because it is hard for us to troubleshoot problems that are related to third-party package installation.

Song

On Wed, May 4, 2022 at 2:28 AM Elkan Chang @.***> wrote:

Looks like an error from a wrongly compiled tensorflow. Can you reinstall TensorFlow and see how it goes? Song … <#m8786539577128634855> On Tue, May 3, 2022 at 10:01 AM Elkan Chang @.> wrote: Hi, Thanks for the great tools, I met some trouble when I was running DeepTE, how can I fix this? 2022-05-03 14:33:34.373174: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 2022-05-03 14:33:35.005655: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1525] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 21318 MB memory: -> device: 0, name: Quadro RTX 6000, pci bus id: 0000:3b:00.0, compute capability: 7.5 2022-05-03 14:33:51.610330: F tensorflow/core/platform/default/env.cc:73] Check failed: ret == 0 (11 vs. 0)Thread tf_data_private_threadpool creation via pthread_create() failed. /var/spool/sge/firestorm/job_scripts/2012270: line 6: 196910 Aborted (core dumped) python3 /software/shared/apps/x86_64/DeepTE/26122020/DeepTE.py -i ../families.fa -d ./tmp -o ./result -sp P -m_dir ../Plants_model — Reply to this email directly, view it on GitHub <#15 https://github.com/LiLabAtVT/DeepTE/issues/15>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEEENRULGU23EFIUN4DCOTVIEWTNANCNFSM5U6732UQ https://github.com/notifications/unsubscribe-auth/ACEEENRULGU23EFIUN4DCOTVIEWTNANCNFSM5U6732UQ . You are receiving this because you are subscribed to this thread.Message ID: @.> -- Associate Professor in Plant Genomics and Bioinformatics School of Plant and Environmental Sciences Virginia Polytechnic Institute and State University zoom https://virginiatech.zoom.us/j/8790572835

Dear Song,

Many thanks for your quick reply.

I reinstall the tensorflow as you suggested, this error still exists.

BRs Elkan

— Reply to this email directly, view it on GitHub https://github.com/LiLabAtVT/DeepTE/issues/15#issuecomment-1116970821, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEEENXZUG3CC274252INHTVIIKJ5ANCNFSM5U6732UQ . You are receiving this because you commented.Message ID: @.***>

-- Associate Professor in Plant Genomics and Bioinformatics School of Plant and Environmental Sciences Virginia Polytechnic Institute and State University

zoom https://virginiatech.zoom.us/j/8790572835

JiyangChang commented 2 years ago

This is still a TensorFlow error. 1. Can you check whether you can load TensorFlow or not in a separate python environment? if not, you need to figure out how to install TensorFlow properly. 2. Can you find a different computer to run DeepTE? I am sorry I cannot provide more solid help because it is hard for us to troubleshoot problems that are related to third-party package installation. Song

Many thanks for your reply, this might be caused by a different version of Tensorflow. The version installed on our cluster is 2.7.0 rather than 1.14.0.

Hope DeepTE would be compatible with Tensorflow2 soon.