From jon.sauer at gmail.com  Sat Aug 26 17:10:03 2023
From: jon.sauer at gmail.com (Jon Sauer)
Date: Sat, 26 Aug 2023 17:10:03 -0400
Subject: openslide on m2 macs?
Message-ID: <885CE42C-5763-4071-BAEE-1A9AABF34E6B@gmail.com>

Hi, Is there a clean way to install openslide-python on m2 macs (like my new Mac Studio)?

Cheers,
  Jon


From jon.sauer at gmail.com  Wed Aug 30 15:43:21 2023
From: jon.sauer at gmail.com (Jon Sauer)
Date: Wed, 30 Aug 2023 15:43:21 -0400
Subject: openslide on Apple silicon?
Message-ID: <203284A6-C39C-4292-98EB-5F1701678AA6@gmail.com>

Hi,

I?m looking for a compatible python / Pytorch / openslide / numpy combination to run on my new m2 Mac Studio so I can continue to develop machine learning models for medical images. I would have thought that, by now, there would be a way to execute these four programs that underpin machine learning with medical images would have been made compatible by some group in the openslide community. If so, I hope they would be willing to share enough with me so I can continue my efforts.

Cheers,
  Jon

Jon.Sauer at gmail.com
cell: +1.303.579.3009
White River Junction, VT, USA
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From adam at spicenitz.org  Wed Aug 30 15:49:44 2023
From: adam at spicenitz.org (Adam Goode)
Date: Wed, 30 Aug 2023 15:49:44 -0400
Subject: openslide on Apple silicon?
In-Reply-To: <203284A6-C39C-4292-98EB-5F1701678AA6@gmail.com>
References: <203284A6-C39C-4292-98EB-5F1701678AA6@gmail.com>
Message-ID: <CACuduqp_1U0U51brXYAWz9OujcfT72Tyu8fKGSuVfnpCUZ3k2Q@mail.gmail.com>

Did you have a working setup on a previous Intel-based Mac?


Adam

On Wed, Aug 30, 2023 at 3:44?PM Jon Sauer <jon.sauer at gmail.com> wrote:

> Hi,
>
> I?m looking for a compatible python / Pytorch / openslide / numpy
> combination to run on my new m2 Mac Studio so I can continue to develop
> machine learning models for medical images. I would have thought that, by
> now, there would be a way to execute these four programs that underpin
> machine learning with medical images would have been made compatible by
> some group in the openslide community. If so, I hope they would be willing
> to share enough with me so I can continue my efforts.
>
> Cheers,
>   Jon
>
> Jon.Sauer at gmail.com
> cell: +1.303.579.3009
> White River Junction, VT, USA
> _______________________________________________
> openslide-users mailing list
> openslide-users at lists.andrew.cmu.edu
> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users
>
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From bgilbert at cs.cmu.edu  Thu Aug 31 00:58:24 2023
From: bgilbert at cs.cmu.edu (Benjamin Gilbert)
Date: Thu, 31 Aug 2023 00:58:24 -0400
Subject: openslide on Apple silicon?
In-Reply-To: <CACuduqp_1U0U51brXYAWz9OujcfT72Tyu8fKGSuVfnpCUZ3k2Q@mail.gmail.com>
References: <203284A6-C39C-4292-98EB-5F1701678AA6@gmail.com>
 <CACuduqp_1U0U51brXYAWz9OujcfT72Tyu8fKGSuVfnpCUZ3k2Q@mail.gmail.com>
Message-ID: <CANioFniSiVeyWDz1uXB==9Vs=F9M9XuWROn5x7xj3NurJTcVcQ@mail.gmail.com>

On Wed, Aug 30, 2023 at 3:50?PM Adam Goode <adam at spicenitz.org> wrote:
> Did you have a working setup on a previous Intel-based Mac?

I second that question.  From OpenSlide's perspective there isn't
anything special about ARM Macs.  Jon, is there a specific problem
you're encountering?

--Benjamin Gilbert

From jon.sauer at gmail.com  Thu Aug 31 11:27:11 2023
From: jon.sauer at gmail.com (Jon Sauer)
Date: Thu, 31 Aug 2023 11:27:11 -0400
Subject: openslide on Apple silicon?
In-Reply-To: <CANioFniSiVeyWDz1uXB==9Vs=F9M9XuWROn5x7xj3NurJTcVcQ@mail.gmail.com>
References: <203284A6-C39C-4292-98EB-5F1701678AA6@gmail.com>
 <CACuduqp_1U0U51brXYAWz9OujcfT72Tyu8fKGSuVfnpCUZ3k2Q@mail.gmail.com>
 <CANioFniSiVeyWDz1uXB==9Vs=F9M9XuWROn5x7xj3NurJTcVcQ@mail.gmail.com>
Message-ID: <0416A8DE-32D6-46B3-82C1-EFCA09997B74@gmail.com>

first, to guarantee a clean start, I execute the following in the shell:
# ----------------------
cd ~
date
python3 --version

python3 -u -m pip uninstall numpy
python3 -u -m pip uninstall openslide-python

python3 -u -m pip install numpy | tee install_numpy.log
python3 -u -m pip install openslide-python | tee install_openslide.log
# ???????????

the result was:

Successfully installed openslide-python-1.3.0

Then, trying to ?import openslide? from ?python? gives an immediate error:

(dl4cv) sauer : ~ $ python3 --version
Python 3.11.4
(dl4cv) sauer : ~ $ python3
Python 3.11.4 (v3.11.4:d2340ef257, Jun  6 2023, 19:15:51) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import openslide
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 74, in _load_library
    return try_load(['libopenslide.1.dylib', 'libopenslide.0.dylib'])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 58, in try_load
    return cdll.LoadLibrary(name)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 454, in LoadLibrary
    return self._dlltype(name)
           ^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 376, in __init__
    self._handle = _dlopen(self._name, mode)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: dlopen(libopenslide.0.dylib, 0x0006): tried: 'libopenslide.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibopenslide.0.dylib' (no such file), '/usr/lib/libopenslide.0.dylib' (no such file, not in dyld cache), 'libopenslide.0.dylib' (no such file), '/usr/lib/libopenslide.0.dylib' (no such file, not in dyld cache)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/__init__.py", line 31, in <module>
    from openslide import lowlevel
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 92, in <module>
    _lib = _load_library()
           ^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 87, in _load_library
    return cdll.LoadLibrary(lib)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 454, in LoadLibrary
    return self._dlltype(name)
           ^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 376, in __init__
    self._handle = _dlopen(self._name, mode)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: dlopen(/usr/local/lib/libopenslide.dylib, 0x0006): tried: '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libopenslide.dylib' (no such file), '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (no such file), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64?))u
(dl4cv) sauer : ~ $ python3 --version
Python 3.11.4
(dl4cv) sauer : ~ $ python3
Python 3.11.4 (v3.11.4:d2340ef257, Jun  6 2023, 19:15:51) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import openslide
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 74, in _load_library
    return try_load(['libopenslide.1.dylib', 'libopenslide.0.dylib'])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 58, in try_load
    return cdll.LoadLibrary(name)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 454, in LoadLibrary
    return self._dlltype(name)
           ^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 376, in __init__
    self._handle = _dlopen(self._name, mode)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: dlopen(libopenslide.0.dylib, 0x0006): tried: 'libopenslide.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibopenslide.0.dylib' (no such file), '/usr/lib/libopenslide.0.dylib' (no such file, not in dyld cache), 'libopenslide.0.dylib' (no such file), '/usr/lib/libopenslide.0.dylib' (no such file, not in dyld cache)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/__init__.py", line 31, in <module>
    from openslide import lowlevel
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 92, in <module>
    _lib = _load_library()
           ^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 87, in _load_library
    return cdll.LoadLibrary(lib)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 454, in LoadLibrary
    return self._dlltype(name)
           ^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 376, in __init__
    self._handle = _dlopen(self._name, mode)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: dlopen(/usr/local/lib/libopenslide.dylib, 0x0006): tried: '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libopenslide.dylib' (no such file), '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (no such file), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64?))
# ---------------------------------

> On Aug 31, 2023, at 12:58 AM, Benjamin Gilbert <bgilbert at cs.cmu.edu> wrote:
> 
> On Wed, Aug 30, 2023 at 3:50?PM Adam Goode <adam at spicenitz.org> wrote:
>> Did you have a working setup on a previous Intel-based Mac?
> 
> I second that question.  From OpenSlide's perspective there isn't
> anything special about ARM Macs.  Jon, is there a specific problem
> you're encountering?
> 
> --Benjamin Gilbert


From jon.sauer at gmail.com  Thu Aug 31 11:27:11 2023
From: jon.sauer at gmail.com (Jon Sauer)
Date: Thu, 31 Aug 2023 11:27:11 -0400
Subject: openslide on Apple silicon?
In-Reply-To: <CANioFniSiVeyWDz1uXB==9Vs=F9M9XuWROn5x7xj3NurJTcVcQ@mail.gmail.com>
References: <203284A6-C39C-4292-98EB-5F1701678AA6@gmail.com>
 <CACuduqp_1U0U51brXYAWz9OujcfT72Tyu8fKGSuVfnpCUZ3k2Q@mail.gmail.com>
 <CANioFniSiVeyWDz1uXB==9Vs=F9M9XuWROn5x7xj3NurJTcVcQ@mail.gmail.com>
Message-ID: <0416A8DE-32D6-46B3-82C1-EFCA09997B74@gmail.com>

first, to guarantee a clean start, I execute the following in the shell:
# ----------------------
cd ~
date
python3 --version

python3 -u -m pip uninstall numpy
python3 -u -m pip uninstall openslide-python

python3 -u -m pip install numpy | tee install_numpy.log
python3 -u -m pip install openslide-python | tee install_openslide.log
# ???????????

the result was:

Successfully installed openslide-python-1.3.0

Then, trying to ?import openslide? from ?python? gives an immediate error:

(dl4cv) sauer : ~ $ python3 --version
Python 3.11.4
(dl4cv) sauer : ~ $ python3
Python 3.11.4 (v3.11.4:d2340ef257, Jun  6 2023, 19:15:51) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import openslide
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 74, in _load_library
    return try_load(['libopenslide.1.dylib', 'libopenslide.0.dylib'])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 58, in try_load
    return cdll.LoadLibrary(name)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 454, in LoadLibrary
    return self._dlltype(name)
           ^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 376, in __init__
    self._handle = _dlopen(self._name, mode)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: dlopen(libopenslide.0.dylib, 0x0006): tried: 'libopenslide.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibopenslide.0.dylib' (no such file), '/usr/lib/libopenslide.0.dylib' (no such file, not in dyld cache), 'libopenslide.0.dylib' (no such file), '/usr/lib/libopenslide.0.dylib' (no such file, not in dyld cache)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/__init__.py", line 31, in <module>
    from openslide import lowlevel
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 92, in <module>
    _lib = _load_library()
           ^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 87, in _load_library
    return cdll.LoadLibrary(lib)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 454, in LoadLibrary
    return self._dlltype(name)
           ^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 376, in __init__
    self._handle = _dlopen(self._name, mode)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: dlopen(/usr/local/lib/libopenslide.dylib, 0x0006): tried: '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libopenslide.dylib' (no such file), '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (no such file), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64?))u
(dl4cv) sauer : ~ $ python3 --version
Python 3.11.4
(dl4cv) sauer : ~ $ python3
Python 3.11.4 (v3.11.4:d2340ef257, Jun  6 2023, 19:15:51) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import openslide
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 74, in _load_library
    return try_load(['libopenslide.1.dylib', 'libopenslide.0.dylib'])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 58, in try_load
    return cdll.LoadLibrary(name)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 454, in LoadLibrary
    return self._dlltype(name)
           ^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 376, in __init__
    self._handle = _dlopen(self._name, mode)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: dlopen(libopenslide.0.dylib, 0x0006): tried: 'libopenslide.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibopenslide.0.dylib' (no such file), '/usr/lib/libopenslide.0.dylib' (no such file, not in dyld cache), 'libopenslide.0.dylib' (no such file), '/usr/lib/libopenslide.0.dylib' (no such file, not in dyld cache)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/__init__.py", line 31, in <module>
    from openslide import lowlevel
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 92, in <module>
    _lib = _load_library()
           ^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/openslide/lowlevel.py", line 87, in _load_library
    return cdll.LoadLibrary(lib)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 454, in LoadLibrary
    return self._dlltype(name)
           ^^^^^^^^^^^^^^^^^^^
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 376, in __init__
    self._handle = _dlopen(self._name, mode)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: dlopen(/usr/local/lib/libopenslide.dylib, 0x0006): tried: '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libopenslide.dylib' (no such file), '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (no such file), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64?))
# ---------------------------------

> On Aug 31, 2023, at 12:58 AM, Benjamin Gilbert <bgilbert at cs.cmu.edu> wrote:
> 
> On Wed, Aug 30, 2023 at 3:50?PM Adam Goode <adam at spicenitz.org> wrote:
>> Did you have a working setup on a previous Intel-based Mac?
> 
> I second that question.  From OpenSlide's perspective there isn't
> anything special about ARM Macs.  Jon, is there a specific problem
> you're encountering?
> 
> --Benjamin Gilbert


From bgilbert at cs.cmu.edu  Thu Aug 31 12:34:39 2023
From: bgilbert at cs.cmu.edu (Benjamin Gilbert)
Date: Thu, 31 Aug 2023 12:34:39 -0400
Subject: openslide on Apple silicon?
In-Reply-To: <0416A8DE-32D6-46B3-82C1-EFCA09997B74@gmail.com>
References: <203284A6-C39C-4292-98EB-5F1701678AA6@gmail.com>
 <CACuduqp_1U0U51brXYAWz9OujcfT72Tyu8fKGSuVfnpCUZ3k2Q@mail.gmail.com>
 <CANioFniSiVeyWDz1uXB==9Vs=F9M9XuWROn5x7xj3NurJTcVcQ@mail.gmail.com>
 <0416A8DE-32D6-46B3-82C1-EFCA09997B74@gmail.com>
Message-ID: <CANioFng_RTbp_KpEikfZ-7KiHS44sPgH6+ptQde9SuXe2hBHOQ@mail.gmail.com>

On Thu, Aug 31, 2023 at 11:32?AM Jon Sauer <jon.sauer at gmail.com> wrote:
> OSError: dlopen(/usr/local/lib/libopenslide.dylib, 0x0006): tried: '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libopenslide.dylib' (no such file), '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (no such file), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64?))

OpenSlide Python found your Homebrew copy of OpenSlide in /usr/local,
but couldn't load it because it's an x86_64 binary instead of an arm64
binary.  On ARM, Homebrew installs into /opt/homebrew instead.  Is it
possible that your Homebrew installation was migrated from a previous
x86_64 machine?  You might consider removing and reinstalling Homebrew
so you have native ARM binaries.  That should also fix the error
you're seeing.

--Benjamin Gilbert

From jon.sauer at gmail.com  Thu Aug 31 14:53:48 2023
From: jon.sauer at gmail.com (Jon Sauer)
Date: Thu, 31 Aug 2023 14:53:48 -0400
Subject: openslide on Apple silicon?
In-Reply-To: <CANioFng_RTbp_KpEikfZ-7KiHS44sPgH6+ptQde9SuXe2hBHOQ@mail.gmail.com>
References: <203284A6-C39C-4292-98EB-5F1701678AA6@gmail.com>
 <CACuduqp_1U0U51brXYAWz9OujcfT72Tyu8fKGSuVfnpCUZ3k2Q@mail.gmail.com>
 <CANioFniSiVeyWDz1uXB==9Vs=F9M9XuWROn5x7xj3NurJTcVcQ@mail.gmail.com>
 <0416A8DE-32D6-46B3-82C1-EFCA09997B74@gmail.com>
 <CANioFng_RTbp_KpEikfZ-7KiHS44sPgH6+ptQde9SuXe2hBHOQ@mail.gmail.com>
Message-ID: <2153E73A-4EAA-43A9-8994-A2B65B738715@gmail.com>

Hi Benjamin,

Yes indeed, my whole environment on the new Mac Studio was migrated from my old 15? 2016 MacBook Pro, an x86_64 machine just as you surmised.

Many, many thanks. I?ll make the necessay changes, only mention something again if I can?t make it work.

Thanks again.

Cheers,
  Jon

Jon.Sauer at gmail.com
cell: +1.303.579.3009
White River Junction, VT, USA


> On Aug 31, 2023, at 12:34 PM, Benjamin Gilbert <bgilbert at cs.cmu.edu> wrote:
> 
> On Thu, Aug 31, 2023 at 11:32?AM Jon Sauer <jon.sauer at gmail.com> wrote:
>> OSError: dlopen(/usr/local/lib/libopenslide.dylib, 0x0006): tried: '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libopenslide.dylib' (no such file), '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (no such file), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64?))
> 
> OpenSlide Python found your Homebrew copy of OpenSlide in /usr/local,
> but couldn't load it because it's an x86_64 binary instead of an arm64
> binary.  On ARM, Homebrew installs into /opt/homebrew instead.  Is it
> possible that your Homebrew installation was migrated from a previous
> x86_64 machine?  You might consider removing and reinstalling Homebrew
> so you have native ARM binaries.  That should also fix the error
> you're seeing.
> 
> --Benjamin Gilbert

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From jon.sauer at gmail.com  Thu Aug 31 15:03:06 2023
From: jon.sauer at gmail.com (Jon Sauer)
Date: Thu, 31 Aug 2023 15:03:06 -0400
Subject: openslide on Apple silicon?
In-Reply-To: <CANioFng_RTbp_KpEikfZ-7KiHS44sPgH6+ptQde9SuXe2hBHOQ@mail.gmail.com>
References: <203284A6-C39C-4292-98EB-5F1701678AA6@gmail.com>
 <CACuduqp_1U0U51brXYAWz9OujcfT72Tyu8fKGSuVfnpCUZ3k2Q@mail.gmail.com>
 <CANioFniSiVeyWDz1uXB==9Vs=F9M9XuWROn5x7xj3NurJTcVcQ@mail.gmail.com>
 <0416A8DE-32D6-46B3-82C1-EFCA09997B74@gmail.com>
 <CANioFng_RTbp_KpEikfZ-7KiHS44sPgH6+ptQde9SuXe2hBHOQ@mail.gmail.com>
Message-ID: <B03F350D-A600-4108-98E7-C3A20C6AA4A4@gmail.com>

Hi again,

For your information, the machine learning I?m working on is in support of my daughter who just moved from Maine where she was the only pediatric neural oncologist (children?s brain tumors) in the state. She may well be the same, or at least one of very few,  in VT in her new position at Dartmouth-Hickock. I?ve followed her to VT to continue work on our grant which I can do as a semi-retired EE/physicist.

Cheers,
  Jon

Jon.Sauer at gmail.com
cell: +1.303.579.3009
White River Junction, VT, USA


> On Aug 31, 2023, at 12:34 PM, Benjamin Gilbert <bgilbert at cs.cmu.edu> wrote:
> 
> On Thu, Aug 31, 2023 at 11:32?AM Jon Sauer <jon.sauer at gmail.com> wrote:
>> OSError: dlopen(/usr/local/lib/libopenslide.dylib, 0x0006): tried: '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libopenslide.dylib' (no such file), '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (no such file), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64?))
> 
> OpenSlide Python found your Homebrew copy of OpenSlide in /usr/local,
> but couldn't load it because it's an x86_64 binary instead of an arm64
> binary.  On ARM, Homebrew installs into /opt/homebrew instead.  Is it
> possible that your Homebrew installation was migrated from a previous
> x86_64 machine?  You might consider removing and reinstalling Homebrew
> so you have native ARM binaries.  That should also fix the error
> you're seeing.
> 
> --Benjamin Gilbert

-------------- next part --------------
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From jon.sauer at gmail.com  Thu Aug 31 15:03:06 2023
From: jon.sauer at gmail.com (Jon Sauer)
Date: Thu, 31 Aug 2023 15:03:06 -0400
Subject: openslide on Apple silicon?
In-Reply-To: <CANioFng_RTbp_KpEikfZ-7KiHS44sPgH6+ptQde9SuXe2hBHOQ@mail.gmail.com>
References: <203284A6-C39C-4292-98EB-5F1701678AA6@gmail.com>
 <CACuduqp_1U0U51brXYAWz9OujcfT72Tyu8fKGSuVfnpCUZ3k2Q@mail.gmail.com>
 <CANioFniSiVeyWDz1uXB==9Vs=F9M9XuWROn5x7xj3NurJTcVcQ@mail.gmail.com>
 <0416A8DE-32D6-46B3-82C1-EFCA09997B74@gmail.com>
 <CANioFng_RTbp_KpEikfZ-7KiHS44sPgH6+ptQde9SuXe2hBHOQ@mail.gmail.com>
Message-ID: <B03F350D-A600-4108-98E7-C3A20C6AA4A4@gmail.com>

Hi again,

For your information, the machine learning I?m working on is in support of my daughter who just moved from Maine where she was the only pediatric neural oncologist (children?s brain tumors) in the state. She may well be the same, or at least one of very few,  in VT in her new position at Dartmouth-Hickock. I?ve followed her to VT to continue work on our grant which I can do as a semi-retired EE/physicist.

Cheers,
  Jon

Jon.Sauer at gmail.com
cell: +1.303.579.3009
White River Junction, VT, USA


> On Aug 31, 2023, at 12:34 PM, Benjamin Gilbert <bgilbert at cs.cmu.edu> wrote:
> 
> On Thu, Aug 31, 2023 at 11:32?AM Jon Sauer <jon.sauer at gmail.com> wrote:
>> OSError: dlopen(/usr/local/lib/libopenslide.dylib, 0x0006): tried: '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libopenslide.dylib' (no such file), '/usr/local/lib/libopenslide.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (no such file), '/usr/local/Cellar/openslide/3.4.1_7/lib/libopenslide.0.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64?))
> 
> OpenSlide Python found your Homebrew copy of OpenSlide in /usr/local,
> but couldn't load it because it's an x86_64 binary instead of an arm64
> binary.  On ARM, Homebrew installs into /opt/homebrew instead.  Is it
> possible that your Homebrew installation was migrated from a previous
> x86_64 machine?  You might consider removing and reinstalling Homebrew
> so you have native ARM binaries.  That should also fix the error
> you're seeing.
> 
> --Benjamin Gilbert

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