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CRBS / cdeep3m

Please go to https://github.com/CRBS/cdeep3m2 for most recent version
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HDF5 error with Ubuntu 18.04 LTE #57

Closed haberlmatt closed 4 years ago

haberlmatt commented 5 years ago

When doing local installs on Ubuntu 18.04LTE an error shows up as: << error: h5write: support for HDF5 IO was unavailable or disabled when Octave was built >> everything works fine with Ubuntu 16

coleslaw481 commented 5 years ago

Ubuntu 18.04 uses a newer version of octave (4.2 I believe). You could try a newer version of the hdf5oct libraryfrom this repo:

https://github.com/stegro/hdf5oct

The commit being used is b047e6e611e874b02740e7465f5d139e74f9765f and there are a couple commits after this one. See the basic_cloudformation.json file on how the above commit is being downloaded.

TITC commented 4 years ago

Hi,

What's the number of b047e6e611e874b02740e7465f5d139e74f9765f,and how do you solve it?

Starting Training data Preprocessing
Training Image Path:

./most/soma/train/images
Reading file: ./most/soma/train/images/x.001.png
Reading file: ./most/soma/train/images/x.002.png
........................
Verifying images
Reading file: ./most/soma/train/labels/x.001.png
Reading file: ./most/soma/train/labels/x.002.png
...........................
Verifying labels
Checking image dimensions
Augmenting training data 1-8 and 9-16
Create variation 1 and 9
Saving: ./soma_augmented/training_full_stacks_v1.h5
error: h5write: support for HDF5 IO was unavailable or disabled when Octave was built
error: called from
    PreprocessTrainingData at line 96 column 5

machine

No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 18.04.3 LTS
Release:    18.04
Codename:   bionic

octave version

GNU Octave, version 4.2.2

hdf5 version

Package: libhdf5-dev
Status: install ok installed
Priority: optional
Section: libdevel
Installed-Size: 11294
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: amd64
Source: hdf5
Version: 1.10.0-patch1+docs-4
haberlmatt commented 4 years ago

This bug is only concerning local installs with CDeep3M Version 1, as you mentioned you are using the Colab installation of CDeep3M2 this issue is resolved

TITC commented 4 years ago

thanks, I will try it.