pip install & ImportError

[Borda]

Describe the bug
I am facing some difficulty with compiling the

To Reproduce
Steps to reproduce the behavior:

1. pip install cmake
2. pip install git+https://github.com/ANTsX/ANTsPy.git
3. run https://github.com/Borda/BIRL/blob/master/scripts/Python/run_ANTsPy.py
   python3 BIRL/results/BmANTsPy/run_ANTsPy.py BIRL/data_images/rat-kidney_/scale-5pc/Rat_Kidney_HE.jpg BIRL/data_images/rat-kidney_/scale-5pc/Rat_Kidney_PanCytokeratin.jpg BIRL/data_images/rat-kidney_/scale-5pc/Rat_Kidney_PanCytokeratin.csv BIRL/results/BmANTsPy/0
4. See error

Traceback (most recent call last):
  File "/home.dokt/borovji3/Medical-temp/experiments_anhir/BmANTsPy_20190325-153014/run_ANTsPy.py", line 18, in <module>
    import ants
  File "~/vEnv3/lib/python3.5/site-packages/ants/__init__.py", line 7, in <module>
    from .core import *
  File "~/vEnv3/lib/python3.5/site-packages/ants/core/__init__.py", line 2, in <module>
    from .ants_image import *
  File "~/vEnv3/lib/python3.5/site-packages/ants/core/ants_image.py", line 27, in <module>
    from .. import utils, registration, segmentation, viz
  File "~/vEnv3/lib/python3.5/site-packages/ants/utils/__init__.py", line 2, in <module>
    from .bias_correction import *
  File "~/vEnv3/lib/python3.5/site-packages/ants/utils/bias_correction.py", line 9, in <module>
    from . import process_args as pargs
  File "~/vEnv3/lib/python3.5/site-packages/ants/utils/process_args.py", line 13, in <module>
    from .. import lib
  File "~/vEnv3/lib/python3.5/site-packages/ants/lib/__init__.py", line 35, in <module>
    from .antsRegistration import *
ImportError: ~/vEnv3/lib/python3.5/site-packages/ants/lib/antsRegistration.cpython-35m-x86_64-linux-gnu.so: undefined symbol: _Z14ANTSFileExistsRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE

Desktop (please complete the following information):

• (sysname='Linux', nodename='cmpgrid-73', release='4.9.0-6-amd64', version='#1 SMP Debian 4.9.82-1+deb9u3 (2018-03-02)', machine='x86_64')
• Python 3.5.3 (default, Jan 19 2017, 14:11:04) ; [GCC 6.3.0 20170118] on linux

[stnava]

did you try the more standard approach of

• git clone https://github.com/ANTsX/ANTsPy.git
• cd ANTsPy
• python3 setup.py install

[Borda]

It does not help for installing on that particular server machine... I was instaling it on ma personal machine, and it works there... so it probably linked to the specific configuration, could it be?

[stnava]

Unclear if this can/will be addressed. Please reopen if needed.

[muschellij2]

Got the same issue/error. https://travis-ci.com/muschellij2/deepbleed/jobs/281243452#L7693. I think this may be due to the fact I forgot the ITKR (which builds a lib for ITK) was built on trusty. Trying on trusty now. Edit - that was not true - they were built on xenial and so was the build I refernced above.

[wmdatah]

The following attempts were made on a POWER 9, with nvidia tesla, running Ubuntu 22.04:

straight to bare metal

• conda env (py3.9) + pip install antspyx (0.3.7 and 0.3.8)
• git clone (a few different tags were tried) + python setup.py install

docker containers

• nvidia/cuda:12.1.1-cudnn8-devel-ubi8
• quay.io/rocketce/tensorflow:py39-rce180 (ubi8)
  on both: conda... + pip install... or git clone/setup.py

This is just a summary, I've been trying for a few days now, but today I gave up after trying with docker build and getting the exact same error as every other attempt:

ImportError: /opt/conda/lib/python3.10/site-packages/ants/lib/antsRegistration.cpython-310-powerpc64le-linux-gnu.so: undefined symbol: _Z14ANTSFileExistsRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE

In one of the attempts, in a container, I launched a
scanelf -s _Z14ANTSFileExistsRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE -R / 2>/dev/null | grep _Z14ANT...
and I noticed that only other files in the same directory as antsRegistration.cpython-310-powerpc64le-linux-gnu.so have such a symbol. I haven't looked for such a symbol using other tools for other file types.

Could someone give me a hug to lessen my frustration? 😅 Or else shed some light on my ignorance? Any tip is worth. Thanks in advance.

Here is part of the docker build output:

Welcome to Ubuntu 22.04.2 LTS (GNU/Linux 5.15.0-73-generic ppc64le)
...
  System information as of Tue Jun  6 04:06:40 PM -03 2023
...
git clone https://github.com/ANTsX/ANTsPy.git
cd ANTsPy
docker build -t antspy:master .
...
 => [internal] load build definition from Dockerfile
...
 => [stage-1 1/2] FROM docker.io/library/debian:bullseye-20230109-slim@sha256:98d3b4b0cee264301eb1354e0b549323af2d0633e1c43375d0b25c01826b6790
...
 => [builder 1/9] FROM docker.io/continuumio/miniconda3:22.11.1@sha256:10b38c9a8a51692838ce4517e8c74515499b68d58c8a2000d8a9df7f0f08fc5e
...
 => [internal] load build context
 => => transferring context: 105.30MB
 => [builder 2/9] RUN apt-get update && apt-get install -y --no-install-recommends apt-transport-https bash build-essential git libpng-dev
 => [builder 3/9] RUN conda install -c anaconda cmake
 => [builder 4/9] WORKDIR /usr/local/src
 => [builder 5/9] COPY environment.yml .
 => [builder 6/9] RUN conda env update -n base
 => [builder 7/9] COPY . .
 => [builder 8/9] RUN pip --no-cache-dir -v install .
 => ERROR [builder 9/9] RUN bash tests/run_tests.sh
------
 > [builder 9/9] RUN bash tests/run_tests.sh:
#0 0.415 /usr/local/src/tests /usr/local/src
#0 0.415 Running core tests
#0 1.720 Traceback (most recent call last):
#0 1.720   File "/usr/local/src/tests/test_core_ants_image.py", line 19, in <module>
#0 1.720     import ants
#0 1.720   File "/opt/conda/lib/python3.10/site-packages/ants/__init__.py", line 7, in <module>
#0 1.720     from .core import *
#0 1.720   File "/opt/conda/lib/python3.10/site-packages/ants/core/__init__.py", line 2, in <module>
#0 1.720     from .ants_image import *
#0 1.720   File "/opt/conda/lib/python3.10/site-packages/ants/core/ants_image.py", line 29, in <module>
#0 1.720     from .. import registration, segmentation, utils, viz
#0 1.720   File "/opt/conda/lib/python3.10/site-packages/ants/registration/__init__.py", line 3, in <module>
#0 1.720     from .affine_initializer import *
#0 1.720   File "/opt/conda/lib/python3.10/site-packages/ants/registration/affine_initializer.py", line 7, in <module>
#0 1.721     from .. import utils
#0 1.721   File "/opt/conda/lib/python3.10/site-packages/ants/utils/__init__.py", line 2, in <module>
#0 1.721     from .bias_correction import *
#0 1.721   File "/opt/conda/lib/python3.10/site-packages/ants/utils/bias_correction.py", line 4, in <module>
#0 1.721     from . import process_args as pargs
#0 1.721   File "/opt/conda/lib/python3.10/site-packages/ants/utils/process_args.py", line 14, in <module>
#0 1.721     from .. import lib
#0 1.721   File "/opt/conda/lib/python3.10/site-packages/ants/lib/__init__.py", line 44, in <module>
#0 1.721     from .antsRegistration import *
#0 1.721 ImportError: /opt/conda/lib/python3.10/site-packages/ants/lib/antsRegistration.cpython-310-powerpc64le-linux-gnu.so: undefined symbol: _Z14ANTSFileExistsRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE
------
Dockerfile:31
--------------------
  29 |     
  30 |     # run tests
  31 | >>> RUN bash tests/run_tests.sh
  32 |     
  33 |     # optimize layers
--------------------
ERROR: failed to solve: process "/bin/sh -c bash tests/run_tests.sh" did not complete successfully: exit code: 1