byuflowlab / mex.jl Goto Github PK

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Embedding Julia in the MATLAB process.

License: MIT License

MATLAB 37.95% Julia 61.81% M 0.24%

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mex.jl's Issues

Matlab closes quickly after executing mexjulia

Hi! I just tried this out and encountered the following issues (on Ubuntu 20.04)
*) I had to add the package to the MATLAB path manually
*) jlexec statements execute and return, but a few seconds later matlab just closes without without warning

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MEX.jl with Julia 1.10.1

Sadly, Mex.jl doesn't seem to work with Julia 1.10.1.

After some trial (by me) and error (by Matlab) yesterday I installed Julia's long term support version 1.6.7, installed MATLAB.jl and Mex.jl and it worked fine with my installation of Matlab R2021b. However, the actual Julia package I want to use installs an old version on Julia 1.6.7 which hasn't all the functionality that I will need, so it's not an option for me to use that old Julia version to get Mex.jl to work.

In theory I might be able to find some Julia version in between 1.6.7 and 1.10.1 where both packages work but that doesn't sound like a long term solution. Here's the output of a REPL session with a completely new Julia installation:

(@v1.10) pkg> add MATLAB
  Installing known registries into `C:\Users\Ronny\.julia`
    Updating registry at `C:\Users\Ronny\.julia\registries\General.toml`
   Resolving package versions...
   Installed MATLAB ─ v0.8.4
    Updating `C:\Users\Ronny\.julia\environments\v1.10\Project.toml`
  [10e44e05] + MATLAB v0.8.4
    Updating `C:\Users\Ronny\.julia\environments\v1.10\Manifest.toml`
  [10e44e05] + MATLAB v0.8.4
  [56f22d72] + Artifacts
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [2f01184e] + SparseArrays v1.10.0
  [e66e0078] + CompilerSupportLibraries_jll v1.1.0+0
  [4536629a] + OpenBLAS_jll v0.3.23+4
  [bea87d4a] + SuiteSparse_jll v7.2.1+1
  [8e850b90] + libblastrampoline_jll v5.8.0+1
    Building MATLAB → `C:\Users\Ronny\.julia\scratchspaces\44cfe95a-1eb2-52ea-b672-e2afdf69b78f\f640678d27790992e2a697f60e6afb1be3ebb7fc\build.log`
Precompiling project...
  2 dependencies successfully precompiled in 3 seconds. 2 already precompiled.

(@v1.10) pkg> test MATLAB
     Testing MATLAB
      Status `C:\Users\Ronny\AppData\Local\Temp\jl_0zgNbg\Project.toml`
  [2f01184e] SparseArrays v1.10.0
  [8dfed614] Test
      Status `C:\Users\Ronny\AppData\Local\Temp\jl_0zgNbg\Manifest.toml`
  [10e44e05] MATLAB v0.8.4
  [56f22d72] Artifacts
  [b77e0a4c] InteractiveUtils
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [2f01184e] SparseArrays v1.10.0
  [8dfed614] Test
  [e66e0078] CompilerSupportLibraries_jll v1.1.0+0
  [4536629a] OpenBLAS_jll v0.3.23+4
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [8e850b90] libblastrampoline_jll v5.8.0+1
Precompiling project...
  2 dependencies successfully precompiled in 3 seconds. 3 already precompiled.
     Testing Running tests...
     Testing MATLAB tests passed

(@v1.10) pkg> add Mex
   Resolving package versions...
   Installed Reexport ─ v1.2.2
   Installed Mex ────── v0.1.1
    Updating `C:\Users\Ronny\.julia\environments\v1.10\Project.toml`
  [5e29dd5e] + Mex v0.1.1
    Updating `C:\Users\Ronny\.julia\environments\v1.10\Manifest.toml`
  [5e29dd5e] + Mex v0.1.1
  [189a3867] + Reexport v1.2.2
    Building Mex → `C:\Users\Ronny\.julia\scratchspaces\44cfe95a-1eb2-52ea-b672-e2afdf69b78f\2e99a552c9b0f56718ed54e9427c4789f122f4af\build.log`
Precompiling project...
  2 dependencies successfully precompiled in 2 seconds. 4 already precompiled.

(@v1.10) pkg> test Mex
     Testing Mex
      Status `C:\Users\Ronny\AppData\Local\Temp\jl_nvUX8O\Project.toml`
  [10e44e05] MATLAB v0.8.4
  [5e29dd5e] Mex v0.1.1
  [8dfed614] Test
      Status `C:\Users\Ronny\AppData\Local\Temp\jl_nvUX8O\Manifest.toml`
  [10e44e05] MATLAB v0.8.4
  [5e29dd5e] Mex v0.1.1
  [189a3867] Reexport v1.2.2
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [b77e0a4c] InteractiveUtils
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [2f01184e] SparseArrays v1.10.0
  [8dfed614] Test
  [e66e0078] CompilerSupportLibraries_jll v1.1.0+0
  [4536629a] OpenBLAS_jll v0.3.23+4
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [8e850b90] libblastrampoline_jll v5.8.0+1
Precompiling project...
  2 dependencies successfully precompiled in 3 seconds. 5 already precompiled.
     Testing Running tests...
jl.eval: Error During Test at C:\Users\Ronny\.julia\packages\Mex\qcSLo\test\runtests.jl:7
  Got exception outside of a @test
  MATLAB.MEngineError("invalid engine session (err = 1)")
  Stacktrace:
    [1] eval_string(session::MSession, stmt::String)
      @ MATLAB C:\Users\Ronny\.julia\packages\MATLAB\xBhSu\src\engine.jl:135
    [2] eval_string(stmt::String)
      @ MATLAB C:\Users\Ronny\.julia\packages\MATLAB\xBhSu\src\engine.jl:147
    [3] macro expansion
      @ C:\Users\Ronny\.julia\packages\MATLAB\xBhSu\src\matstr.jl:161 [inlined]
    [4] macro expansion
      @ C:\Users\Ronny\.julia\packages\Mex\qcSLo\test\runtests.jl:9 [inlined]
    [5] macro expansion
      @ C:\Users\Ronny\AppData\Local\Programs\Julia-1.10.1\share\julia\stdlib\v1.10\Test\src\Test.jl:1577 [inlined]
    [6] top-level scope
      @ C:\Users\Ronny\.julia\packages\Mex\qcSLo\test\runtests.jl:9
    [7] include(fname::String)
      @ Base.MainInclude .\client.jl:489
    [8] top-level scope
      @ none:6
    [9] eval
      @ .\boot.jl:385 [inlined]
   [10] exec_options(opts::Base.JLOptions)
      @ Base .\client.jl:291
   [11] _start()
      @ Base .\client.jl:552
Test Summary: | Error  Total   Time
jl.eval       |     1      1  16.7s
ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken.
in expression starting at C:\Users\Ronny\.julia\packages\Mex\qcSLo\test\runtests.jl:5
ERROR: Package Mex errored during testing

If I hadn't done the test and instead tried to use Mex.jl from MATLAB, the result would be MATLAB crashing and closing without error whenever I use jl.eval().

I don't know what that "invalid engine session" error is trying to tell me, especially since it works with the same MATLAB installation and just an older Julia one. Did something vital change in MATLAB.jl or in Julia's C API? Maybe it's an easy fix for you?

Crashes in tight loops

First thank you very much for this awesome package.

I'm trying to run the stuff in performance.m and unfortunately, the first test fails. Could have to do with the JIT compiler of Matlab:

>> k=1;while(true), [q,r] = jl.call('divrem',7,3); k=k+1; end
Array indices must be positive integers or logical values.

Error in jl.mex (line 23)
            [err, varargout{1:nout}] = mexjulia('jl_mex', fn, varargin{:});

Error in jl.callkw (line 52)
            [varargout{1:nargout}] = jl.mex('Mex.jl_call_kw', fn, int32(npos), varargin{:});

Error in jl.call (line 59)
            [varargout{1:nargout}] = jl.callkw(fn, -1, varargin{:});

Using dbstop if error reveals, that the value of k differs a lot, sometimes it's in the range of 40, sometimes 10000. But it crashes. Is some kind of locking neeeded?

Thanks!

edit 1:
try, k=1;while(true), [q,r] = jl.call('divrem',7,3); pause(0.1), k=k+1; end, catch E, E, k, end always returns k=50 on my machine, regardless of the value in pause().

edit 2:
tic; for i=1:2000; [q,r] = divrem(7,3); end; elpsd = toc; always works. Is there something wrong with jl.call?

unexpected crashes

great that this project is still being updated! I just tried out with the newest release candidate for julia which again exports options, so the build script works.

I tried to use this package in the past to write bindings for matlab against a julia optimization library (I have attached a toy version
testmex.zip
). I want to call a julia function from matlab, and supply it with function handles. Then in turn, the julia function will call those matlab function handles with data.

This works, as you can see. However, if you run it often enough (matlab 2018a, ubuntu linux), I get an unexpected crash. The fact that this is sporadic makes me suspect the julia garbage collector, is there something to be mindful about when using mex?

I've tried debugging this but I'm hopelessly out of my depth, I never succesfully attached gdb to the matlab process.

Xcode build error when using mex

On macOS 10.15.4 with Julia 1.5:
Although mex -setup C++ goes through just fine, the mexjulia build process throws:

Error using mex
xcodebuild: error: SDK "macosx10.15.4" cannot be located.
xcrun: error: sh -c
'/Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild -sdk
macosx10.15.4 -find clang++ 2> /dev/null' failed with exit code 16384: (null)
(errno=No such file or directory)
xcrun: error: unable to find utility "clang++", not a developer tool or in PATH

This .m-snippet
This issue is more on the side of Matlabs Xcode integration, I however thought I post the solution here in case someone runs into the same issue as it did cost me half a day.

Issues on Windows 10 [SOLVED]

Hello,

I had some problems with the installation and the working of this package, and since I've already solved them I tought to share my findings in case someone incurred in the same issues.

I'm currently using Windows 10, Matlab R2019a and Julia 1.2.0-2.
MEX on matlab is configured to use 'MinGW64 Compiler (C++)' for C++ language compilation.

Problem 1 (installation): using "]add https://github.com/byuflowlab/Mex.jl" in Julia used to work for everything except for the compilation of mexjulia. However, this doesn't throw an error. Looking in "...\.juliapro\JuliaPro_v1.2.0-2\packages\Mex\ZlRZN\deps" and reading the textfile "build" at the very end it says

"Error using mex
g++: error: ...\AppData\Local\JuliaPro-1.1.1.1\Julia-1.1.1\bin\libjulia.dll.a: No such file or directory"

... and indeed the file "libjulia.dll.a" does not exist, whereas "libjulia.dll" does. To fix it, I naively copied "libjulia.dll" in the same folder and renamed it as "libjulia.dll.a". To my surprise, it worked and the compilation was successful.

Problem 2 (find libraries): I then tried to run jl.eval('1+1') in MATLAB, but it returned an error saying that some libraries could not be found. Long story short, I think there was a problem with the paths, and my fix was to change the jl.m (class definition) at lines 136-146 switching the order of the two operations, that is:
ORIGINAL:

                % tweak path to find shared libs
                if ispc
                    % This is a hack for windows which lets the mex function
                    % find the julia dlls during initialization without requiring that
                    % julia be on the path.
                    old_dir = pwd;
                    cd(jl.julia_home);
                end

                % basic runtime initialization
                jldict = load('jldict', 'julia_home', 'sys_image', 'lib_path');

MODIFIED:

                % basic runtime initialization
                jldict = load('jldict', 'julia_home', 'sys_image', 'lib_path');
                
                % tweak path to find shared libs
                if ispc
                    % This is a hack for windows which lets the mex function
                    % find the julia dlls during initialization without requiring that
                    % julia be on the path.
                    old_dir = pwd;
                    cd(jldict.julia_home);
                end

Possibly I'm the only one experiencing these issues, but I wanted to share : )

Pkg.test() fails

Hello,

I cannot get Mex to run.
In the beginning I had a problem that Mex could not build, but after adding the Mex path to

ENV["MATLABPATH"]="/home/user/.julia/packages/Mex/5WarT/mexjulia"

manually the Pkg.build() ran through.
Unfortunately, Pkg.test() throws the following error

pkg> test Mex
     Testing Mex
      Status `/tmp/jl_zvEiaW/Project.toml`
  [10e44e05] MATLAB v0.8.3
  [5e29dd5e] Mex v0.1.0
  [8dfed614] Test `@stdlib/Test`
      Status `/tmp/jl_zvEiaW/Manifest.toml`
  [10e44e05] MATLAB v0.8.3
  [5e29dd5e] Mex v0.1.0
  [189a3867] Reexport v1.2.2
  [56f22d72] Artifacts `@stdlib/Artifacts`
  [2a0f44e3] Base64 `@stdlib/Base64`
  [b77e0a4c] InteractiveUtils `@stdlib/InteractiveUtils`
  [8f399da3] Libdl `@stdlib/Libdl`
  [37e2e46d] LinearAlgebra `@stdlib/LinearAlgebra`
  [56ddb016] Logging `@stdlib/Logging`
  [d6f4376e] Markdown `@stdlib/Markdown`
  [9a3f8284] Random `@stdlib/Random`
  [ea8e919c] SHA v0.7.0 `@stdlib/SHA`
  [9e88b42a] Serialization `@stdlib/Serialization`
  [2f01184e] SparseArrays `@stdlib/SparseArrays`
  [8dfed614] Test `@stdlib/Test`
  [e66e0078] CompilerSupportLibraries_jll v0.5.2+0 `@stdlib/CompilerSupportLibraries_jll`
  [4536629a] OpenBLAS_jll v0.3.20+0 `@stdlib/OpenBLAS_jll`
  [8e850b90] libblastrampoline_jll v5.1.1+0 `@stdlib/libblastrampoline_jll`
Precompiling project...
  2 dependencies successfully precompiled in 2 seconds. 4 already precompiled.
  2 dependencies precompiled but different versions are currently loaded. Restart julia to access the new versions
     Testing Running tests...
Error using mexjulia
Unhandled Julia exception: ErrorException

Error in jl.init (line 145)
            mexjulia(true, 'using Mex')

Error in jl.check_init (line 112)
                jl.init()

Error in jl.mex (line 21)
            jl.check_init();

Error in jl.eval (line 30)
            [varargout{1:nargout}] = jl.mex('Mex.jl_eval', expr);
 
Error using save
Variable 'matlab_jl_2' not found.
 
jl.eval: Error During Test at /home/htc/bzfhelfm/.julia/packages/Mex/5WarT/test/runtests.jl:7
  Got exception outside of a @test
  MATLAB.MEngineError("failed to get variable matlab_jl_2 from MATLAB session")
  Stacktrace:
    [1] get_mvariable(session::MSession, name::Symbol)
      @ MATLAB ~/.julia/packages/MATLAB/SVjnA/src/engine.jl:164
    [2] get_mvariable
      @ ~/.julia/packages/MATLAB/SVjnA/src/engine.jl:168 [inlined]
    [3] get_variable(name::Symbol)
      @ MATLAB ~/.julia/packages/MATLAB/SVjnA/src/engine.jl:170
    [4] macro expansion
      @ ~/.julia/packages/MATLAB/SVjnA/src/matstr.jl:162 [inlined]
    [5] macro expansion
      @ ~/.julia/packages/Mex/5WarT/test/runtests.jl:9 [inlined]
    [6] macro expansion
      @ /data/numerik/people/bzfsikor/julia/julia-1.8.3/share/julia/stdlib/v1.8/Test/src/Test.jl:1360 [inlined]
    [7] top-level scope
      @ ~/.julia/packages/Mex/5WarT/test/runtests.jl:9
    [8] include(fname::String)
      @ Base.MainInclude ./client.jl:476
    [9] top-level scope
      @ none:6
   [10] eval
      @ ./boot.jl:368 [inlined]
   [11] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:276
   [12] _start()
      @ Base ./client.jl:522
Test Summary: | Error  Total  Time
jl.eval       |     1      1  7.4s
ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/htc/bzfhelfm/.julia/packages/Mex/5WarT/test/runtests.jl:5
ERROR: Package Mex errored during testing

Do you have any ideas on how to proceed?

Thanks,
Luzie

byuflowlab / mex.jl Goto Github PK

mex.jl's People

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mex.jl's Issues

Matlab closes quickly after executing mexjulia

TagBot trigger issue

MEX.jl with Julia 1.10.1

Crashes in tight loops

unexpected crashes

Xcode build error when using mex

Issues on Windows 10 [SOLVED]

Pkg.test() fails

Register v0.1.0

CI with Julia 1.8 fails

Release v0.1.1

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