Populate clijx-deconvolution Fiji update site

[bnorthan]

There is already a clijx-deconvoluiton update site. In the near future we could add all deconvolution and fft related artifacts to this site to make it easier to update the deconvolution independently of the larger clij2 update site.

We would need to remove the following from clij2 and add to clijx-deconvolution

plugins/clij2-ffft_.jar
lib/linux64/libclij2fft.so
lib/linux64/libjniclij2fftWrapper.so
lib/linux64/libclFFT.so
lib/macosx/libclij2fft.dylib
lib/macosx/libclij2fft.so
lib/macosx/libclFFT.2.12.2.dylib
lib/macosx/libclFFT.2.dylib
lib/win64/clFFT.dll
lib/win64/clij2fft.dll
lib/win64/jniclij2fftWrapper.dll

Then also add the clijx-faclon-heavy stuff too?

[NicoKiaru]

Then also add the clijx-faclon-heavy stuff too?

Yes, it depends a bit on Robert and clij/clijx-parallel#3.

[NicoKiaru]

@haesleinhuepf gave me control of the faclon repo which I renamed to https://github.com/clij/clijx-parallel, I will attempt to make a release from the current SNAPSHOT version, and I'll think we'll be able to move on pretty soon

[bnorthan]

Are you going to put clij2 parallel on the clij2 or clijx update site? I also have a clijx-deconvolution update site which I am not using yet, but thinking maybe I should move all deconvolution related artifacts to it (so I don't have to mess with the main clij update sites for deconvolution only changes). So we could put cljx-parallel on the clijx-deconvolution site or we could put it on the main clijx site... not sure which is best.

[bnorthan]

Also @NicoKiaru I don't have a Mac so I was wondering do you have access to a Mac for testing and building the .dylibs? If not I know a couple of people who may be able to build Mac native libaries for us if it is just running a script. I can build Windows and Linux myself.

[NicoKiaru]

So we could put cljx-parallel on the clijx-deconvolution site or we could put it on the main clijx site ?

Ideally putting clij-parallel on the clij2 update site makes more sense (I don't think a clijx update site exists, does it?).

but thinking maybe I should move all deconvolution related artifacts to it (so I don't have to mess with the main clij update sites for deconvolution only changes)

Sure!

do you have access to a Mac for testing and building the .dylibs

I have one, a mac mini M1 - that's actually the reason the facility bought one - to be able to test such things. We power it very rarely I guess it's still alive. I have no idea how to build dylibs but I can give it a shot, provided I have enough time.

[NicoKiaru]

Also, I wanted to ping @StRigaud and @JonathanCSmith - I don't know well enough the CLIJ ecosystem but I see that there's continuous work on clij3 and especially regarding CI. A nice goal would be to use what they've done to make a nice CI for clij2-fft and clijx-parallel.

[StRigaud]

Hi @NicoKiaru, @bnorthan,

I was also going to ping you on the faclon repo to see if we could make it compatible with the clesperanto ecosystem (which is the rework of the CLIJ).

I am happy to help where I can, and also available to discuss this in more details if needed.

Quickly for the CLIJ ecosystem:

I have been reworking clij which is pure Java into a C++ library with Java and Python bindings to be deploy everywhere. This is the clEsperanto project basically.

The Java API library is clesperantoJ and is available on the maven.scijava. It comes directly with connectors for ImagePlus and Imglib2 image format. And the current clij3 fiji plugin relies on it.

Currently the FFT of @bnorthan is not yet in clEsperanto but my goal is to integrate it directly into the C++ layer. But I would most likely need time (and help).

[bnorthan]

Hi

I've uploaded the clij2-fft jar and the Linux and Windows native libraries to the update site located at https://sites.imagej.net/clijx-deconvolution/. Hoping to get @NicoKiaru added to this site so he can update any changes he makes. I think we still need to add the clijx-parallel jar to the clij2 update site. We also need to build the Mac version. This shouldn't be too hard, just running a script. I have to compile some notes on the build process and pass on to @NicoKiaru who said he has access to a Mac.

To get integrated into clij3 I think we need to figure out the representation for complex numbers and (in addition to wrapping FFTs) need to implement some complex math functions (like multiplication for FFT convolution). First step is probably just to get the clij2 fft and deconvolution all set, then improve the documentation so it is clear what needs to implemented to move to clij3.

More to come...

Brian

[bnorthan]

Hi @NicoKiaru you can find WIP instruction to build the native code here.

Checkout the MacOSX and Mac Silicon Native M1 section. Hopefully those instructions work. If not just ping me. I'd build this myself except I do not have access to a Mac.

[NicoKiaru]

Ok, I'll take the M1 out of the cave

[NicoKiaru]

In the instructions, this link is broken: https://formulae.brew.sh/formula/clfft any idea where to find it ?

Edit: ah, maybe I get it wrong, I actually need to build them, not to get them from homebrew ?

[NicoKiaru]

I manage to install brew, cmake and gmake

I ran ./native/cppbuild.sh and got this:

~/Documents/biop-dev/clij2-fft/native/clij2fft/cppbuild ~/Documents/biop-dev/clij2-fft/native
-- The C compiler identification is AppleClang 14.0.3.14030022
-- The CXX compiler identification is AppleClang 14.0.3.14030022
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for CL_VERSION_3_0
-- Looking for CL_VERSION_3_0 - not found
-- Looking for CL_VERSION_2_2
-- Looking for CL_VERSION_2_2 - not found
-- Looking for CL_VERSION_2_1
-- Looking for CL_VERSION_2_1 - not found
-- Looking for CL_VERSION_2_0
-- Looking for CL_VERSION_2_0 - not found
-- Looking for CL_VERSION_1_2
-- Looking for CL_VERSION_1_2 - found
-- Found OpenCL: /Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/System/Library/Frameworks/OpenCL.framework (found version "1.2")
-- Found Python3: /Users/biopstaff/mambaforge/bin/python3.10 (found version "3.10.12") found components: Interpreter
-- Configuring done (5.6s)
-- Generating done (0.0s)
-- Build files have been written to: /Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/cppbuild
[ 33%] Converting totalvarationterm.cl to string.
calling python stringify
[ 33%] Built target generate_preamble
[ 66%] Building CXX object CMakeFiles/clij2fft.dir/clij2fft.cpp.o
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:966:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  delete platformIds;
  ^
        []
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:907:33: note: allocated with 'new[]' here
  cl_platform_id *platformIds = new cl_platform_id[MAXPLATFORMS];
                                ^
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:967:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  delete deviceIDs;
  ^
        []
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:920:29: note: allocated with 'new[]' here
  cl_device_id *deviceIDs = new cl_device_id[MAXDEVICESPERPLATFORM];
                            ^
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:1223:9: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete deviceName;
        ^
              []
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:1219:29: note: allocated with 'new[]' here
        char * deviceName = new char[1000];
                            ^
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:1227:7: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
      delete platformName;
      ^
            []
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:1210:29: note: allocated with 'new[]' here
      char * platformName = new char[1000];
                            ^
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:1228:7: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
      delete deviceIDs;
      ^
            []
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:1214:32: note: allocated with 'new[]' here
            cl_device_id *deviceIDs = new cl_device_id[MAXDEVICESPERPLATFORM];
                                      ^
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:1313:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  delete platformIds;
  ^
        []
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:1242:33: note: allocated with 'new[]' here
  cl_platform_id *platformIds = new cl_platform_id[MAXPLATFORMS];
                                ^
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:1314:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  delete deviceIDs;
  ^
        []
/Users/biopstaff/Documents/biop-dev/clij2-fft/native/clij2fft/clij2fft.cpp:1256:29: note: allocated with 'new[]' here
  cl_device_id *deviceIDs = new cl_device_id[MAXDEVICESPERPLATFORM];
                            ^
7 warnings generated.
[100%] Linking CXX shared library libclij2fft.dylib
ld: warning: directory not found for option '-L/Users/haase/code/ops-experiments/ops-experiments-opencl/native'
[100%] Built target clij2fft
[ 33%] Converting totalvarationterm.cl to string.
calling python stringify
[ 33%] Built target generate_preamble
[100%] Built target clij2fft
Install the project...
-- Install configuration: "Release"
-- Installing: /Users/biopstaff/Documents/biop-dev/clij2-fft/lib/macosx-arm64/./libclij2fft.dylib

When I exectute the demo with the option -Djava.library.path="/Users/biopstaff/Documents/biop-dev/clij2-fft/lib/macosx-arm64" I got this error:

So I copied the file libjniclij2fftWrapper from macosx folder to macosx-arm64 and re ran the test:

Exception in thread "main" java.lang.UnsatisfiedLinkError: /Users/biopstaff/Documents/biop-dev/clij2-fft/lib/macosx-arm64/libjniclij2fftWrapper.dylib: dlopen(/Users/biopstaff/Documents/biop-dev/clij2-fft/lib/macosx-arm64/libjniclij2fftWrapper.dylib, 0x0001): Library not loaded: @rpath/libclFFT.2.dylib
  Referenced from: <3E49929E-6AC8-3E60-B168-387671715378> /Users/biopstaff/Documents/biop-dev/clij2-fft/lib/macosx-arm64/libjniclij2fftWrapper.dylib
  Reason: tried: '/Users/biopstaff/Documents/biop-dev/clij2-fft/lib/macosx-arm64/./libclFFT.2.dylib' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')), '/Users/haase/code/clij2-fft/lib/win64/libclFFT.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/haase/code/clij2-fft/lib/win64/libclFFT.2.dylib' (no such file), '/Users/haase/code/clij2-fft/lib/linux64/libclFFT.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/haase/code/clij2-fft/lib/linux64/libclFFT.2.dylib' (no such file), '/Users/haase/code/clij2-fft/lib/macosx/libclFFT.2.dylib' (no such file), '/Sys

I ll keep trying a few times

[NicoKiaru]

I tried (base) biopstaff@SV-01M-033 clij2fft % ./cppbuild.sh

but got:

./cppbuild.sh: line 14: PLATFORM: unbound variable

Link to chatgpt initial attempt: https://chatgpt.com/share/679ca386-81fc-8013-a9dd-7cb368493e45

I'll stop here for today. If you want we can try to do a zoom session but my schedule and probably yours is tight

[StRigaud]

Hey @NicoKiaru

I managed to rebuild it for my M2 (but didn't test it):

1 - No need of rebuilding or downloading the clFFT bins, they are already in the repo in the ./lib folder. But:

• You need to replace the libs in the macosx folder which are for x86_64 by the libs in macosx-universal2 which contains both x86_64 and arm64 achitectures combined.
• Delete the linux folder which contains .so which seems to interfere in the build process. (I also deleted the windows folder for safefy).

2 - Run mvn clean install -U to build at the root folder

You may need to update some of the dependencies versions. I build the main branch and needed to update the clijx-parallel version and I used the latest javacpp version from the parent pom.xml.

To smooth a bit the build you may want to update the pom.xml to correctly target the correct lib folder based on the OS. I let you look at what we did on clesperantoJ which you the exact same approach as the clij2-fft (thanks to @bnorthan helping us starting it).

---

The native/cppbuild.sh script is execute from the pom.xml, if you run it yourself, you will miss variables passed by the pom, hence the ./cppbuild.sh: line 14: PLATFORM: unbound variable.

➡ The question I have me is where does the clFFT macosx libs come from. The main repo only provides binaries for Linux and Windows. I tried to build them from source on my M2 but failed unless I start medling with the code.

[bnorthan]

@psobolewskiPhD and I worked out and tested the build a couple of years ago when we sat down and worked it out on his Mac.

The macosx clFFT was installed from here using homebrew. I think we then copied the libraries into the clij2-fft repo.

@NicoKiaru try running this script when you have time.

It looks like you are using the x86_64 version of libjniclij2fftWrapper.dylib but need the arm64 (or universal) version. This line here should copy the newly build version which should be the arm64 version. I need to improve that script to copy the arm64 version of libjniclij2fftWrapper.dylib to the lib/macosx-arm64 directory, but for now it will overwrite the version in the lib/macosx directory and you can manually copy that to lib\macosx-arm64

Or alternatively after the build, look in target/classes/net/haesinhuepf/clijx/plugins/$PLATFORM/ to find the newly built libjniclij2fftWrapper.dylib and copy it to the right place.