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Fix TensorFlow installation on Debian #1601

Merged
merged 6 commits into from
Feb 15, 2018
Merged

Fix TensorFlow installation on Debian #1601

merged 6 commits into from
Feb 15, 2018

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perone
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@perone perone commented Feb 14, 2018

This PR is a fix for the Keras/TensorFlow installation on Debian, ref #1599.

@perone perone added the bug category: fixes an error in the code label Feb 14, 2018
@perone perone self-assigned this Feb 14, 2018
@jcohenadad
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@stephaniealley could you please test this branch on the station you had a problem and add your review this PR? Thanks

jcohenadad
jcohenadad reviewed Feb 14, 2018
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install_sct
@@ -416,6 +416,12 @@ else
and verify your internet connection before reinstalling"
exit $e_status
fi

# Install tensorflow for Debian
if python -c "import platform; print platform.dist()" | grep -qi 'debian'; then
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is this problem specific to debian or to debian-family, i.e., could some older versions of ubuntu experience the same problem?

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Really hard to tell without testing on older Ubuntu versions. But since Ubuntu is Debian-based, it can happen. However, it is rarer to see older Ubuntu versions, given that this would raise serious security concerns.

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Having some Ubuntu containers floating around, I tested this:

('Ubuntu', '16.04', 'xenial')
('Ubuntu', '18.04', 'bionic')

Now, as for debian, the test could probe for the older version, because eg. debian 8 (jessie) ships with glibc 2.19, and doesn't need to use the old tensorflow:

>>> import tensorflow as tf
>>> import platform; print platform.dist()
('debian', '8.10', '')
>>> import sys
>>> sys.executable
'/home/cJ/miniconda2/bin/python'
>>> tf.__version__
'1.5.0'

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It's ok if newer Debian versions use Tensorflow from conda, it will certainly be faster (tensorflow performance on CPU). We need to stick with the TensorFlow 1.3.0 because everyone in the lab is using this version and all our models were validated and developed in this version. There are also breaking API changes in newer TF versions.

@jcohenadad jcohenadad added this to the 3.1.1 milestone Feb 14, 2018
@jcohenadad jcohenadad added the installation category: install_sct or pip/setup.py label Feb 14, 2018
stephaniealley
stephaniealley reviewed Feb 14, 2018
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This fixes the problem. I tested sct_deepseg_sc and sct_deepseg_gm after installation, and they both ran successfully.

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@stephaniealley please run

sct_testing

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@jcohenadad I ran sct_testing, and everything passed.

@jcohenadad jcohenadad merged commit 8c232e3 into master Feb 15, 2018
@jcohenadad jcohenadad deleted the feature_tf_debian branch February 15, 2018 01:37
jcohenadad added a commit that referenced this pull request Feb 16, 2018
@jcohenadad
Merge branch 'jca-release' into release
f709a6f 
* jca-release: (88 commits)
  updated CHANGES.md
  Adding minimal Dockerfile for SCT. (#1600)
  Added a study in SCT applications section
  Fix TensorFlow installation on Debian (#1601)
  BUG: Fixed a small bug on None condition (#1594)
  Update deepseg_sc folder --> Add README.txt (#1598)
  Fixing links to the models. (#1596)
  DEV: Add Alternative mirror
  sct_deepseg_gm implementation (#1564)
  DEV: Modify install_sct to download the deepesg models
  DEV: rename API folder
  DEV: changes on the testing function
  DEV: update OSF link
  DEV: renaming functions
  DEV: Correction of the usage.set_description
  DEV: fill z_holes
  DEV: modify default features param
  DEV: NN architecture in spinalcordtoolbox folder
  DEV: New NN architecture
  DEV: No need for the prediction
  ...

# Conflicts:
#	dev/GM_atlas/concatenate_WM_and_GM_tracts.py
#	dev/GM_atlas/registration_gm_atlas.py
#	dev/atlas/create_atlas/create_masks_csf_and_gm.py
#	dev/atlas/validate_atlas/compute_dice.py
#	dev/atlas/validate_atlas/compute_fractional_volume_per_label.py
#	dev/atlas/validate_atlas/crop_image.py
#	dev/atlas/validate_atlas/generate_phantom.py
#	dev/atlas/validate_atlas/plot_abs_error_vs_csf_values.py
#	dev/atlas/validate_atlas/plot_abs_error_vs_fractional_volume.py
#	dev/atlas/validate_atlas/plot_auto_vs_manual.py
#	dev/atlas/validate_atlas/plot_map.py
#	dev/atlas/validate_atlas/plot_snr_and_tracts_std.py
#	dev/atlas/validate_atlas/validate_atlas.py
#	dev/control_points/make_centerline.py
#	dev/control_points/process.py
#	dev/control_points/processjeudi.py
#	dev/control_points/sct_utils.py
#	dev/control_points/segall.py
#	dev/control_points/smoothall.py
#	dev/control_points/splines_approximation_v2.py
#	dev/control_points/straighten.py
#	dev/control_points/test.py
#	dev/denoise/ornlm/setup.py
#	dev/generate_ml_data.py
#	dev/githook/pre_commit_hook.py
#	dev/itk_transfo/mat_to_displacement.py
#	dev/sct_detect_spinalcord/sct_detect_spinalcord.py
#	dev/sct_detect_spinalcord/sct_get_centerline_automatic.py
#	dev/sct_detect_spinalcord/sct_get_centerline_from_labels.py
#	dev/sct_dmri_moco__old.py
#	dev/sct_nin_convert_dcm2nii.py
#	dev/sct_register_graymatter/sct_register_graymatter.py
#	dev/sct_register_graymatter/sct_register_graymatter_old.py
#	dev/sct_register_graymatter/test_sct_register_graymatter.py
#	dev/sct_register_spine_straightened_to_template.py
#	dev/sct_register_straight_spinalcord_to_template.py
#	dev/sct_resample/sct_resample_new.py
#	dev/sct_resample/sct_resample_old.py
#	dev/sct_scad.py
#	dev/sct_segment_gray_matter_asman/2015-07-13_full_scripts_with_Old_unused_functions/sct_segment_graymatter.py
#	dev/sct_segment_gray_matter_asman/2015-08-17-full_scripts_before_cleaning/sct_segment_graymatter.py
#	dev/sct_segment_gray_matter_asman/2015-08-17-full_scripts_before_cleaning/sct_segment_graymatter_old.py
#	dev/sct_smooth_spinal_cord__ISABELLE.py
#	dev/spinal_level/sct_extract_spinal_levels.py
#	dev/straightening/optimize_straightening.py
#	dev/straightening/sct_straighten_spinalcord_LargeFOVOutput.py
#	dev/tamag/copydiffe.py
#	dev/tamag/create_generation_info_files.py
#	dev/tamag/make_warp_null.py
#	dev/tamag/old/add_noise.py
#	dev/tamag/old/create_line_on_slice.py
#	dev/tamag/old/curveSmoothing.py
#	dev/tamag/old/extract_sagitale.py
#	dev/tamag/old/get_warping_field.py
#	dev/tamag/old/msct_get_centerline_from_labels.py
#	dev/tamag/old/msct_register_reg.py
#	dev/tamag/old/pipeline_marseille.py
#	dev/tamag/old/pipeline_preprocessing.py
#	dev/tamag/old/pipeline_preprocessing_T1.py
#	dev/tamag/old/pipeline_preprocessing_after_segmentation.py
#	dev/tamag/old/pipeline_segmentation_T2.py
#	dev/tamag/old/pipeline_template.py
#	dev/tamag/old/pipeline_template_T1.py
#	dev/tamag/old/pipeline_template_T1_from_T2.py
#	dev/tamag/old/preprocess_data_T1.py
#	dev/tamag/old/preprocess_data_T2.py
#	dev/tamag/old/rename_all.py
#	dev/tamag/old/sct_addlabel.py
#	dev/tamag/old/sct_denoising_nlm.py
#	dev/tamag/old/sct_denoizing_nlm.py
#	dev/tamag/old/sct_function_preprocessing.py
#	dev/tamag/old/sct_get_centerline_from_labels2.py
#	dev/tamag/old/test_class_extract_cent.py
#	dev/tamag/old/test_denoizing_dipy.py
#	dev/tamag/old/test_filtering.py
#	dev/tamag/rename_all.py
#	dev/tamag/test_msct_image.py
#	dev/tamag/test_msct_register
#	dev/tamag/test_msct_register.py
#	dev/tamag/test_register_landmarks_for_images.py
#	dev/template/pipeline_template_2.py
#	dev/template_creation/sct_average_levels.py
#	dev/template_creation/sct_change_file_type.py
#	dev/template_creation/sct_generate_centerline.py
#	dev/template_creation/sct_normalize.py
#	dev/template_creation/sct_push_into_template_space.py
#	dev/template_creation/sct_symetrize.py
#	dev/template_creation/sct_template_crop_data.py
#	dev/template_preprocessing/README.md
#	dev/wt_scripts/sct_icv_RBM.py
#	dev/wt_scripts/sct_manage_dicom.py
@jcohenadad jcohenadad mentioned this pull request Mar 21, 2018
Closed
jcohenadad added a commit that referenced this pull request Dec 18, 2019
@jcohenadad
Merge branch 'jca-release' into release
260b315 
* jca-release: (88 commits)
  updated CHANGES.md
  Adding minimal Dockerfile for SCT. (#1600)
  Added a study in SCT applications section
  Fix TensorFlow installation on Debian (#1601)
  BUG: Fixed a small bug on None condition (#1594)
  Update deepseg_sc folder --> Add README.txt (#1598)
  Fixing links to the models. (#1596)
  DEV: Add Alternative mirror
  sct_deepseg_gm implementation (#1564)
  DEV: Modify install_sct to download the deepesg models
  DEV: rename API folder
  DEV: changes on the testing function
  DEV: update OSF link
  DEV: renaming functions
  DEV: Correction of the usage.set_description
  DEV: fill z_holes
  DEV: modify default features param
  DEV: NN architecture in spinalcordtoolbox folder
  DEV: New NN architecture
  DEV: No need for the prediction
  ...

# Conflicts:
#	dev/GM_atlas/concatenate_WM_and_GM_tracts.py
#	dev/GM_atlas/registration_gm_atlas.py
#	dev/atlas/create_atlas/create_masks_csf_and_gm.py
#	dev/atlas/validate_atlas/compute_dice.py
#	dev/atlas/validate_atlas/compute_fractional_volume_per_label.py
#	dev/atlas/validate_atlas/crop_image.py
#	dev/atlas/validate_atlas/generate_phantom.py
#	dev/atlas/validate_atlas/plot_abs_error_vs_csf_values.py
#	dev/atlas/validate_atlas/plot_abs_error_vs_fractional_volume.py
#	dev/atlas/validate_atlas/plot_auto_vs_manual.py
#	dev/atlas/validate_atlas/plot_map.py
#	dev/atlas/validate_atlas/plot_snr_and_tracts_std.py
#	dev/atlas/validate_atlas/validate_atlas.py
#	dev/control_points/make_centerline.py
#	dev/control_points/process.py
#	dev/control_points/processjeudi.py
#	dev/control_points/sct_utils.py
#	dev/control_points/segall.py
#	dev/control_points/smoothall.py
#	dev/control_points/splines_approximation_v2.py
#	dev/control_points/straighten.py
#	dev/control_points/test.py
#	dev/denoise/ornlm/setup.py
#	dev/generate_ml_data.py
#	dev/githook/pre_commit_hook.py
#	dev/itk_transfo/mat_to_displacement.py
#	dev/sct_detect_spinalcord/sct_detect_spinalcord.py
#	dev/sct_detect_spinalcord/sct_get_centerline_automatic.py
#	dev/sct_detect_spinalcord/sct_get_centerline_from_labels.py
#	dev/sct_dmri_moco__old.py
#	dev/sct_nin_convert_dcm2nii.py
#	dev/sct_register_graymatter/sct_register_graymatter.py
#	dev/sct_register_graymatter/sct_register_graymatter_old.py
#	dev/sct_register_graymatter/test_sct_register_graymatter.py
#	dev/sct_register_spine_straightened_to_template.py
#	dev/sct_register_straight_spinalcord_to_template.py
#	dev/sct_resample/sct_resample_new.py
#	dev/sct_resample/sct_resample_old.py
#	dev/sct_scad.py
#	dev/sct_segment_gray_matter_asman/2015-07-13_full_scripts_with_Old_unused_functions/sct_segment_graymatter.py
#	dev/sct_segment_gray_matter_asman/2015-08-17-full_scripts_before_cleaning/sct_segment_graymatter.py
#	dev/sct_segment_gray_matter_asman/2015-08-17-full_scripts_before_cleaning/sct_segment_graymatter_old.py
#	dev/sct_smooth_spinal_cord__ISABELLE.py
#	dev/spinal_level/sct_extract_spinal_levels.py
#	dev/straightening/optimize_straightening.py
#	dev/straightening/sct_straighten_spinalcord_LargeFOVOutput.py
#	dev/tamag/copydiffe.py
#	dev/tamag/create_generation_info_files.py
#	dev/tamag/make_warp_null.py
#	dev/tamag/old/add_noise.py
#	dev/tamag/old/create_line_on_slice.py
#	dev/tamag/old/curveSmoothing.py
#	dev/tamag/old/extract_sagitale.py
#	dev/tamag/old/get_warping_field.py
#	dev/tamag/old/msct_get_centerline_from_labels.py
#	dev/tamag/old/msct_register_reg.py
#	dev/tamag/old/pipeline_marseille.py
#	dev/tamag/old/pipeline_preprocessing.py
#	dev/tamag/old/pipeline_preprocessing_T1.py
#	dev/tamag/old/pipeline_preprocessing_after_segmentation.py
#	dev/tamag/old/pipeline_segmentation_T2.py
#	dev/tamag/old/pipeline_template.py
#	dev/tamag/old/pipeline_template_T1.py
#	dev/tamag/old/pipeline_template_T1_from_T2.py
#	dev/tamag/old/preprocess_data_T1.py
#	dev/tamag/old/preprocess_data_T2.py
#	dev/tamag/old/rename_all.py
#	dev/tamag/old/sct_addlabel.py
#	dev/tamag/old/sct_denoising_nlm.py
#	dev/tamag/old/sct_denoizing_nlm.py
#	dev/tamag/old/sct_function_preprocessing.py
#	dev/tamag/old/sct_get_centerline_from_labels2.py
#	dev/tamag/old/test_class_extract_cent.py
#	dev/tamag/old/test_denoizing_dipy.py
#	dev/tamag/old/test_filtering.py
#	dev/tamag/rename_all.py
#	dev/tamag/test_msct_image.py
#	dev/tamag/test_msct_register
#	dev/tamag/test_msct_register.py
#	dev/tamag/test_register_landmarks_for_images.py
#	dev/template/pipeline_template_2.py
#	dev/template_creation/sct_average_levels.py
#	dev/template_creation/sct_change_file_type.py
#	dev/template_creation/sct_generate_centerline.py
#	dev/template_creation/sct_normalize.py
#	dev/template_creation/sct_push_into_template_space.py
#	dev/template_creation/sct_symetrize.py
#	dev/template_creation/sct_template_crop_data.py
#	dev/template_preprocessing/README.md
#	dev/wt_scripts/sct_icv_RBM.py
#	dev/wt_scripts/sct_manage_dicom.py


Former-commit-id: f709a6f
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@stephaniealley stephaniealley stephaniealley left review comments

@jcohenadad jcohenadad jcohenadad approved these changes

@zougloub zougloub Awaiting requested review from zougloub

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@perone perone

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bug category: fixes an error in the code installation category: install_sct or pip/setup.py
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