Comments (5)
did you try the more standard approach of
git clone https://github.com/ANTsX/ANTsPy.git
cd ANTsPy
python3 setup.py install
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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?
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Unclear if this can/will be addressed. Please reopen if needed.
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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.
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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
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Related Issues (20)
- tidy "NO CLUE WHAT THIS DOES OR WHY IT'S NEEDED" HOT 2
- deblur in a single dimension? HOT 2
- B-spline SyN registration has too few control points HOT 7
- Unable to pip install antspyx on MacBook (M2) HOT 6
- Install antspynet in a requriements.txt but couod not find a version that satisfies tensorflow? HOT 3
- Check correct directory for existance of subdirectory pybind11
- `pip install antspyx` installs arm-compiled ANTsPy on intel-based mac (py=3.9) HOT 18
- Cannot re-create affine transform from parameters HOT 8
- What is the correct way to conduct PET-MR coregistration? HOT 9
- Wheel builds for arm64 on Github Actions HOT 1
- need help to install antspyx==0.2.4 HOT 1
- improve test coverage or start tracking again HOT 5
- Erroneous R_PACKAGE_LIBS reference in configure_ITK.sh
- cannot import name 'int64index' from python HOT 2
- ANTsImage operators don't work on Windows for right-sided operations HOT 3
- Descrepancy in performance of AntsPy Behaviour when running in a loop for a long time. HOT 7
- [question/feature quest] how to translate ANTs CLI call to Python call? HOT 1
- ants.atropos probimgs = [iio2.image_read(probsout[0])] HOT 8
- Error: no module named ants.lib.addNoiseToImage HOT 5
- mask default in n4_bias_field_correction
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