issues runninng arcsi on Mac M1

[raco...@gmail.com]

Hi Pete, and all

I have changed to a Mac M1 last year and tryong to run ARCSI now to perform the corrections as I have done previously, I now get a bunch of errors. I supposed the Arm64 compiler was the issue so I changed the architecture to intel but the error persists. I have also updated arcsi package but that dit not solve it.

I am running python 3.11.4 with arcsi v 4.0.4 and rsglislib 5.0.14

Here is what I am getting when I run the shell script S2ARCSICmds_Alps.sh containing the arcsi commands. Thanks for any ideas, been stuck at this for weeks-

--------------------------

Intel MKL WARNING: Support of Intel(R) Streaming SIMD Extensions 4.2 (Intel(R) SSE4.2) enabled only processors has been deprecated. Intel oneAPI Math Kernel Library 2025.0 will require Intel(R) Advanced Vector Extensions (Intel(R) AVX) instructions.

Intel MKL WARNING: Support of Intel(R) Streaming SIMD Extensions 4.2 (Intel(R) SSE4.2) enabled only processors has been deprecated. Intel oneAPI Math Kernel Library 2025.0 will require Intel(R) Advanced Vector Extensions (Intel(R) AVX) instructions.

Traceback (most recent call last):

  File "/Users/adina/opt/miniconda3/envs/arcsi/bin/arcsi.py", line 48, in <module>

    import arcsilib.arcsirun

  File "/Users/adina/opt/miniconda3/envs/arcsi/lib/python3.11/site-packages/arcsilib/arcsirun.py", line 49, in <module>

    import rsgislib.imagecalc

  File "/Users/adina/opt/miniconda3/envs/arcsi/lib/python3.11/site-packages/rsgislib/imagecalc/__init__.py", line 17, in <module>

    from ._imagecalc import *

ImportError: dlopen(/Users/adina/opt/miniconda3/envs/arcsi/lib/python3.11/site-packages/rsgislib/imagecalc/_imagecalc.so, 0x0002): Library not loaded: '@rpath/libgsl.25.dylib'

  Referenced from: '/Users/adina/opt/miniconda3/envs/arcsi/lib/librsgis_cmds.1.1.0.dylib'

  Reason: tried: '/Users/adina/opt/miniconda3/envs/arcsi/lib/libgsl.25.dylib' (no such file), '/Users/adina/opt/miniconda3/envs/arcsi/lib/python3.11/site-packages/rsgislib/imagecalc/../../../../libgsl.25.dylib' (no such file), '/Users/adina/opt/miniconda3/envs/arcsi/lib/python3.11/site-packages/rsgislib/imagecalc/../../../../libgsl.25.dylib' (no such file), '/Users/adina/opt/miniconda3/envs/arcsi/bin/../lib/libgsl.25.dylib' (no such file), '/Users/adina/opt/miniconda3/envs/arcsi/bin/../lib/libgsl.25.dylib' (no such file), '/usr/local/lib/libgsl.25.dylib' (no such file), '/usr/lib/libgsl.25.dylib' (no such file)

[Peter Bunting]

Hi, 

I have it all working on MacOS on MX processors. ARCSI is not yet available natively for ARM yet, I have not checked recently but some of the dependencies were not available so I setup an x86 environment and install into that using the following commands:

CONDA_SUBDIR=osx-64 conda create -n your_environment_name python=3.11   # Create a new environment called your_environment_name with intel packages.

conda activate your_environment_name

conda env config vars set CONDA_SUBDIR=osx-64  # Make sure that conda commands in this environment use intel packages.

conda deactivate

conda activate your_environment_name

python -c "import platform;print(platform.machine())"  # Should print "x86_64"

echo "CONDA_SUBDIR: $CONDA_SUBDIR"  # Should print "CONDA_SUBDIR: osx-64"

conda install -c conda-forge arcsi

Let me know if that works OK for you. 

Cheers, Pete

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[Adina Racoviteanu]

thanks Pete, will try that on the M1 machine.

In the meantime,  I tried running it all on my previous machine (Mac intel) and I now get a similar error with some packages not found etc..

is this a compatibility issue?

ImportError: dlopen(/Users/adina/opt/miniconda3/envs/arcsi/lib/python3.11/site-packages/rsgislib/imagecalc/_imagecalc.so, 0x0002): Library not loaded: '@rpath/libgdal.33.dylib'

  Referenced from: '/Users/adina/opt/miniconda3/envs/arcsi/lib/librsgis_cmds.1.1.0.dylib'

  Reason: tried: '/Users/adina/opt/miniconda3/envs/arcsi/lib/libgdal.33.dylib' (no such file), '/Users/adina/opt/miniconda3/envs/arcsi/lib/python3.11/site-packages/rsgislib/imagecalc/../../../../libgdal.33.dylib' (no such file), '/Users/adina/opt/miniconda3/envs/arcsi/lib/python3.11/site-packages/rsgislib/imagecalc/../../../../libgdal.33.dylib' (no such file), '/Users/adina/opt/miniconda3/envs/arcsi/bin/../lib/libgdal.33.dylib' (no such file), '/Users/adina/opt/miniconda3/envs/arcsi/bin/../lib/libgdal.33.dylib' (no such file), '/usr/local/lib/libgdal.33.dylib' (no such file), '/usr/lib/libgdal.33.dylib' (no such file)

I had tried with an environment created with python 3.10, same thing..

A

[raco...@gmail.com]

An update regarding this,, I managed to create the platform and install arcsi, but when running I still get the error with imagecalc , and the arcsy.py command won't run..there seems to be an issue with the libraries, tried a few things but no success..

Traceback (most recent call last):

  File "/Users/adina/miniconda3/envs/arcsi/bin/arcsi.py", line 48, in <module>

    import arcsilib.arcsirun

  File "/Users/adina/miniconda3/envs/arcsi/lib/python3.11/site-packages/arcsilib/arcsirun.py", line 49, in <module>

    import rsgislib.imagecalc

  File "/Users/adina/miniconda3/envs/arcsi/lib/python3.11/site-packages/rsgislib/imagecalc/__init__.py", line 17, in <module>

    from ._imagecalc import *

ImportError: dlopen(/Users/adina/miniconda3/envs/arcsi/lib/python3.11/site-packages/rsgislib/imagecalc/_imagecalc.so, 0x0002): Library not loaded: '@rpath/libgsl.25.dylib'

  Referenced from: '/Users/adina/miniconda3/envs/arcsi/lib/librsgis_cmds.1.1.0.dylib'

  Reason: tried: '/Users/adina/miniconda3/envs/arcsi/lib/libgsl.25.dylib' (no such file), '/Users/adina/miniconda3/envs/arcsi/lib/python3.11/site-packages/rsgislib/imagecalc/../../../../libgsl.25.dylib' (no such file), '/Users/adina/miniconda3/envs/arcsi/lib/python3.11/site-packages/rsgislib/imagecalc/../../../../libgsl.25.dylib' (no such file), '/Users/adina/miniconda3/envs/arcsi/bin/../lib/libgsl.25.dylib' (no such file), '/Users/adina/miniconda3/envs/arcsi/bin/../lib/libgsl.25.dylib' (no such file), '/usr/local/lib/libgsl.25.dylib' (no such file), '/usr/lib/libgsl.25.dylib' (no such file)

[Peter Bunting]

Hi, 

I just tried it and it worked for me. I setup the environment as I said earlier with python 3.11 and then installed arcsi with the following command:

mamba install -c conda-forge rsgislib arcsi

Check what versions it is trying to install, it should be:

GDAL 3.8.0

RSGISLib 5.0.17

ARCSI 4.0.4

Cheers, Pete

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[Adina Racoviteanu]

Hi Pete

those exact packages are well installed in the arcsi environment, so I am not sure what else to try...

-Adina

[Peter Bunting]

Can you run "conda list" and send the output?

[Peter Bunting]

Hi Adina, 

I don’t generally find uninstalling things from conda environments works very well so I would recommend creating a new environment and trying to install things again but with mamba. 

Cheers, Pete

On 21 Nov 2023, at 16:27, Adina Racoviteanu <raco...@gmail.com> wrote:

Hi again Pete

some progress, I uninstalled and them installed with mamba, it arcsy.py now gets stuck at gdal

ModuleNotFoundError: No module named '_gdal'

but gdal version 3.8.0 is installed..

A

[Adina Racoviteanu]

That finally worked!

Thank you so much Pete!!

-Adina