Issues with first use of tensorboard

[irc47]

Hi,
I installed songbird standalone using conda and the test-data set ran with no issues, but I'm not able to open tensor board:

---

(songbird_env) irc2@MuthlabIRC:~/Song_bird_practice$ tensorboard --logdir .

Traceback (most recent call last):
File "/home/irc2/mambaforge/envs/songbird_env/bin/tensorboard", line 7, in
from tensorboard.main import run_main
File "/home/irc2/mambaforge/envs/songbird_env/lib/python3.7/site-packages/tensorboard/main.py", line 40, in
from tensorboard import default
File "/home/irc2/mambaforge/envs/songbird_env/lib/python3.7/site-packages/tensorboard/default.py", line 38, in
from tensorboard.plugins.audio import audio_plugin
File "/home/irc2/mambaforge/envs/songbird_env/lib/python3.7/site-packages/tensorboard/plugins/audio/audio_plugin.py", line 25, in
from tensorboard import plugin_util
File "/home/irc2/mambaforge/envs/songbird_env/lib/python3.7/site-packages/tensorboard/plugin_util.py", line 24, in
import markdown
File "/home/irc2/mambaforge/envs/songbird_env/lib/python3.7/site-packages/markdown/init.py", line 42, in
from .core import Markdown, markdown, markdownFromFile
File "/home/irc2/mambaforge/envs/songbird_env/lib/python3.7/site-packages/markdown/core.py", line 27, in
from . import util
File "/home/irc2/mambaforge/envs/songbird_env/lib/python3.7/site-packages/markdown/util.py", line 32, in
from typing import TYPE_CHECKING, Generic, Iterator, NamedTuple, TypeVar, TypedDict, overload
ImportError: cannot import name 'TypedDict' from 'typing' (/home/irc2/mambaforge/envs/songbird_env/lib/python3.7/typing.py)

---

I get the same error with two different machines/2 different installs. Is there something else I need to do to get tensorboard set up?
-Ilana

[irc47]

As a small update, I also tried installing through qiime2 and also get a tensorflow related error:

(qiime2-amplicon-2024.5) irc2@MuthlabIRC:~$
qiime tools import
--input-path Song_bird_practice/redseadata/redsea.biom
--output-path Song_bird_practice/redsea.biom.qza
--type FeatureTable[Frequency]
2024-10-21 13:45:13.302644: I tensorflow/core/util/port.cc:153] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable TF_ENABLE_ONEDNN_OPTS=0.
2024-10-21 13:45:13.303865: I external/local_xla/xla/tsl/cuda/cudart_stub.cc:32] Could not find cuda drivers on your machine, GPU will not be used.
2024-10-21 13:45:13.311053: I external/local_xla/xla/tsl/cuda/cudart_stub.cc:32] Could not find cuda drivers on your machine, GPU will not be used.
2024-10-21 13:45:13.324574: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:485] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
2024-10-21 13:45:13.344165: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:8454] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
2024-10-21 13:45:13.349693: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1452] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2024-10-21 13:45:13.365618: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-21 13:45:14.289653: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
Traceback (most recent call last):
File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/builtin/tools.py", line 852, in _import
artifact = qiime2.sdk.Artifact.import_data(
File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/result.py", line 304, in import_data
pm = qiime2.sdk.PluginManager()
File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/plugin_manager.py", line 67, in new
self._init(add_plugins=add_plugins)
File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init
plugin = entry_point.load()
File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/pkg_resources/init.py", line 2765, in load
return self.resolve()
File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/pkg_resources/init.py", line 2771, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/songbird/q2/init.py", line 2, in
from ._method import multinomial
File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/songbird/q2/_method.py", line 8, in
from songbird.multinomial import MultRegression
File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/songbird/multinomial.py", line 3, in
from tensorflow.contrib.distributions import Multinomial, Normal
ModuleNotFoundError: No module named 'tensorflow.contrib'

An unexpected error has occurred:

No module named 'tensorflow.contrib'

See above for debug info.

[mortonjt]

You need to downgrade q2 to work. This software is not being maintained, so hard to say how to install. Theres ancom-bc, aldex2 plugins that provide similar output. We also have aldex-like functions in skbio that will be maintained long term

…

On Mon, Oct 21, 2024 at 1:48 PM irc47 ***@***.***> wrote: As a small update, I also tried installing through qiime2 and also get a tensorflow related error: (qiime2-amplicon-2024.5) ***@***.***:~$ qiime tools import --input-path Song_bird_practice/redseadata/redsea.biom --output-path Song_bird_practice/redsea.biom.qza --type FeatureTable[Frequency] 2024-10-21 13:45:13.302644: I tensorflow/core/util/port.cc:153] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable TF_ENABLE_ONEDNN_OPTS=0. 2024-10-21 13:45:13.303865: I external/local_xla/xla/tsl/cuda/cudart_stub.cc:32] Could not find cuda drivers on your machine, GPU will not be used. 2024-10-21 13:45:13.311053: I external/local_xla/xla/tsl/cuda/cudart_stub.cc:32] Could not find cuda drivers on your machine, GPU will not be used. 2024-10-21 13:45:13.324574: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:485] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered 2024-10-21 13:45:13.344165: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:8454] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered 2024-10-21 13:45:13.349693: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1452] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered 2024-10-21 13:45:13.365618: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: AVX2 AVX_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. 2024-10-21 13:45:14.289653: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT Traceback (most recent call last): File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/builtin/tools.py", line 852, in _import artifact = qiime2.sdk.Artifact.import_data( File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/result.py", line 304, in import_data pm = qiime2.sdk.PluginManager() File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/plugin_manager.py", line 67, in *new* self._init(add_plugins=add_plugins) File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init plugin = entry_point.load() File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/pkg_resources/ *init*.py", line 2765, in load return self.resolve() File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/pkg_resources/ *init*.py", line 2771, in resolve module = *import*(self.module_name, fromlist=['*name*'], level=0) File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/songbird/q2/ *init*.py", line 2, in from ._method import multinomial File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/songbird/q2/_method.py", line 8, in from songbird.multinomial import MultRegression File "/home/irc2/mambaforge/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/songbird/multinomial.py", line 3, in from tensorflow.contrib.distributions import Multinomial, Normal ModuleNotFoundError: No module named 'tensorflow.contrib' An unexpected error has occurred: No module named 'tensorflow.contrib' See above for debug info. — Reply to this email directly, view it on GitHub <#171 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA75VXKU73FDBYJOTF6R3XLZ4U45FAVCNFSM6AAAAABQKVILBWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRXGM2TENJQGY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>