Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Failed to find class org/cellprofiler/runnablequeue/RunnableQueue #195

Open
neilyio opened this issue Oct 11, 2021 · 8 comments
Open

Failed to find class org/cellprofiler/runnablequeue/RunnableQueue #195

neilyio opened this issue Oct 11, 2021 · 8 comments

Comments

@neilyio
Copy link

neilyio commented Oct 11, 2021 •
edited
Loading

I'm having trouble running javabridge on my MacOS Big Sur (M1) with Azul Zulu OpenJDK. pip install works correctly, though I have to set CFLAGS to make the numpy dependency compile in my virtualenv:

export CFLAGS="-I${VENV_PATH}/lib/python3.9/site-packages/numpy/core/include $CFLAGS"

I'm running:

javabridge.start_vm(
    run_headless=True, class_path=classpath_args
)

where classpath_args is:

['src',
 'resources',
 '/Users/neil/.m2/repository/cider/cider-nrepl/0.25.5/cider-nrepl-0.25.5.jar',
 '/Users/neil/.m2/repository/clj-python/libpython-clj/2.000/libpython-clj-2.000.jar',
 '/Users/neil/.m2/repository/funcool/cuerdas/2021.05.29-0/cuerdas-2021.05.29-0.jar',
 '/Users/neil/.m2/repository/http-kit/http-kit/2.5.3/http-kit-2.5.3.jar',
 '/Users/neil/.m2/repository/nrepl/nrepl/0.8.3/nrepl-0.8.3.jar',
 '/Users/neil/.m2/repository/org/clojure/clojure/1.10.1/clojure-1.10.1.jar',
 '/Users/neil/.m2/repository/org/clojure/clojurescript/1.10.879/clojurescript-1.10.879.jar',
 '/Users/neil/.m2/repository/org/clojure/core.async/1.3.618/core.async-1.3.618.jar',
 '/Users/neil/.m2/repository/org/clojure/data.json/2.4.0/data.json-2.4.0.jar',
 '/Users/neil/.m2/repository/refactor-nrepl/refactor-nrepl/2.5.1/refactor-nrepl-2.5.1.jar',
 '/Users/neil/.m2/repository/cnuernber/dtype-next/8.024/dtype-next-8.024.jar',
 '/Users/neil/.m2/repository/net/java/dev/jna/jna/5.7.0/jna-5.7.0.jar',
 '/Users/neil/.m2/repository/org/clojure/core.specs.alpha/0.2.44/core.specs.alpha-0.2.44.jar',
 '/Users/neil/.m2/repository/org/clojure/spec.alpha/0.2.176/spec.alpha-0.2.176.jar',
 '/Users/neil/.m2/repository/com/cognitect/transit-clj/0.8.309/transit-clj-0.8.309.jar',
 '/Users/neil/.m2/repository/com/google/javascript/closure-compiler-unshaded/v20210505/closure-compiler-unshaded-v20210505.jar',
 '/Users/neil/.m2/repository/org/clojure/google-closure-library/0.0-20201211-3e6c510d/google-closure-library-0.0-20201211-3e6c510d.jar',
 '/Users/neil/.m2/repository/org/clojure/tools.reader/1.3.3/tools.reader-1.3.3.jar',
 '/Users/neil/.m2/repository/org/clojure/tools.analyzer.jvm/1.1.0/tools.analyzer.jvm-1.1.0.jar',
 '/Users/neil/.m2/repository/camel-snake-kebab/camel-snake-kebab/0.4.2/camel-snake-kebab-0.4.2.jar',
 '/Users/neil/.m2/repository/com/github/wendykierp/JTransforms/3.1/JTransforms-3.1.jar',
 '/Users/neil/.m2/repository/insn/insn/0.5.2/insn-0.5.2.jar',
 '/Users/neil/.m2/repository/it/unimi/dsi/fastutil/8.2.1/fastutil-8.2.1.jar',
 '/Users/neil/.m2/repository/org/apache/commons/commons-math3/3.6.1/commons-math3-3.6.1.jar',
 '/Users/neil/.m2/repository/org/ow2/asm/asm/9.0/asm-9.0.jar',
 '/Users/neil/.m2/repository/org/roaringbitmap/RoaringBitmap/0.9.0/RoaringBitmap-0.9.0.jar',
 '/Users/neil/.m2/repository/org/xerial/larray/larray-mmap/0.4.1/larray-mmap-0.4.1.jar',
 '/Users/neil/.m2/repository/primitive-math/primitive-math/0.1.6/primitive-math-0.1.6.jar',
 '/Users/neil/.m2/repository/techascent/tech.resource/5.04/tech.resource-5.04.jar',
 '/Users/neil/.m2/repository/com/cognitect/transit-java/0.8.332/transit-java-0.8.332.jar',
 '/Users/neil/.m2/repository/org/clojure/google-closure-library-third-party/0.0-20201211-3e6c510d/google-closure-library-third-party-0.0-20201211-3e6c510d.jar',
 '/Users/neil/.m2/repository/org/clojure/core.memoize/1.0.236/core.memoize-1.0.236.jar',
 '/Users/neil/.m2/repository/org/clojure/tools.analyzer/1.0.0/tools.analyzer-1.0.0.jar',
 '/Users/neil/.m2/repository/pl/edu/icm/JLargeArrays/1.5/JLargeArrays-1.5.jar',
 '/Users/neil/.m2/repository/org/roaringbitmap/shims/0.9.0/shims-0.9.0.jar',
 '/Users/neil/.m2/repository/org/xerial/larray/larray-buffer/0.4.1/larray-buffer-0.4.1.jar',
 '/Users/neil/.m2/repository/org/clojure/tools.logging/1.1.0/tools.logging-1.1.0.jar',
 '/Users/neil/.m2/repository/com/fasterxml/jackson/core/jackson-core/2.8.7/jackson-core-2.8.7.jar',
 '/Users/neil/.m2/repository/commons-codec/commons-codec/1.10/commons-codec-1.10.jar',
 '/Users/neil/.m2/repository/org/msgpack/msgpack/0.6.12/msgpack-0.6.12.jar',
 '/Users/neil/.m2/repository/org/clojure/core.cache/1.0.207/core.cache-1.0.207.jar',
 '/Users/neil/.m2/repository/com/googlecode/json-simple/json-simple/1.1.1/json-simple-1.1.1.jar',
 '/Users/neil/.m2/repository/org/javassist/javassist/3.18.1-GA/javassist-3.18.1-GA.jar',
 '/Users/neil/.m2/repository/org/clojure/data.priority-map/1.0.0/data.priority-map-1.0.0.jar']

And I'm getting the following output.

Failed to find class org/cellprofiler/runnablequeue/RunnableQueue

Traceback (most recent call last):
  File "/Users/neil/Library/Caches/pypoetry/virtualenvs/blisp-97-MdyRi-py3.9/lib/python3.9/site-packages/javabridge/jutil.py", line 327, in start_thread
    vm.create_mac(args, RQCLS, library_path, libjli_path)
  File "_javabridge.pyx", line 709, in _javabridge.JB_VM.create_mac
RuntimeError: Failed to create Java VM. Return code = -1
Failed to create Java VM

A couple print() statements in javabridge/jutil.py showed me that the start_thread() function is finding library_path and libjli_path, each at:

/Library/Java/JavaVirtualMachines/zulu-11.jdk/Contents/Home/lib/server/libjvm.dylib
/Library/Java/JavaVirtualMachines/zulu-11.jdk/Contents/Home/lib/jli/libjli.dylib

start_thread() is failing at the next line after that, which is vm.create_mac(args, RQCLS, library_path, libjli_path).

Hoping it's something simple I'm doing wrong!
@LeeKamentsky
Copy link
Owner

LeeKamentsky commented Oct 12, 2021 via email

@neilyio
Copy link
Author

neilyio commented Oct 12, 2021 •
edited
Loading

Hi Lee, thanks for your reply.

I've done some logging inside javabridge/jutil.py inside the start_thread function (defined in start_vm). I placed the following print() calls:

321                library_path = _find_mac_lib("libjvm")
322                libjli_path = _find_mac_lib("libjli")
323                print("library_path =", library_path)
324                print("libjli_path =", libjli_path)

On Eclispe Temurin OpenJDK 8, I get:

library_path = /Library/Java/JavaVirtualMachines/temurin-8.jdk/Contents/Home/jre/lib/server/libjvm.dylib
libjli_path = /Library/Java/JavaVirtualMachines/temurin-8.jdk/Contents/Home/jre/lib/jli/libjli.dylib

On Zulu Azul 11 JDK, I get:

library_path = /Library/Java/JavaVirtualMachines/zulu-11.jdk/Contents/Home/lib/server/libjvm.dylib
libjli_path = /Library/Java/JavaVirtualMachines/zulu-11.jdk/Contents/Home/lib/jli/libjli.dylib

On Microsoft OpenJDK 17, I get:

library_path = /Library/Java/JavaVirtualMachines/microsoft-17.jdk/Contents/Home/lib/server/libjvm.dylib
libjli_path = /Library/Java/JavaVirtualMachines/microsoft-17.jdk/Contents/Home/lib/libjli.dylib

Same error for all three. I've verified in my file browser that all files exist.

@JKelle
Copy link

JKelle commented Oct 28, 2021 •
edited
Loading

I'm having the same problem. My computer is an M1 Mac with MacOS Big Sur 11.6.
Java-related details of my system:

$ /usr/libexec/java_home -V
Matching Java Virtual Machines (1):
    11.0.13 (arm64) "Azul Systems, Inc." - "Zulu 11.52.13" /Library/Java/JavaVirtualMachines/zulu-11.jdk/Contents/Home
/Library/Java/JavaVirtualMachines/zulu-11.jdk/Contents/Home

$ echo $JAVA_HOME
/Library/Java/JavaVirtualMachines/zulu-11.jdk/Contents/Home

$ ls -l /Library/Java/JavaVirtualMachines/zulu-11.jdk/Contents/Home/lib/jli/libjli.dylib
-rw-r--r--  1 root  wheel  115584 Oct 16 09:54 /Library/Java/JavaVirtualMachines/zulu-11.jdk/Contents/Home/lib/jli/libjli.dylib

When I run this code:

import javabridge
import bioformats
javabridge.start_vm(class_path=bioformats.JARS, run_headless=True)

I get this error:

Failed to open libjli.dylib.

Traceback (most recent call last):
  File "/Users/jkelle/opt/miniconda3/envs/worker/lib/python3.8/site-packages/javabridge/jutil.py", line 282, in start_thread
    vm.create_mac(args, RQCLS, library_path, libjli_path)
  File "_javabridge.pyx", line 709, in _javabridge.JB_VM.create_mac
RuntimeError: Failed to create Java VM. Return code = -1
Failed to create Java VM
Traceback (most recent call last):
  File "temp.py", line 4, in <module>
    javabridge.start_vm(class_path=bioformats.JARS, run_headless=True)
  File "/Users/jkelle/opt/miniconda3/envs/worker/lib/python3.8/site-packages/javabridge/jutil.py", line 319, in start_vm
    raise RuntimeError("Failed to start Java VM")
RuntimeError: Failed to start Java VM

I don't know why it failed to open libjli.dylib.

@JKelle
Copy link

JKelle commented Oct 28, 2021 •
edited
Loading

I was using a conda environment, and I installed javabridge and bioformats into that conda environment via pip.
I was able to resolve this issue by installing openjdk via conda (conda install openjdk) and unsetting my JAVA_HOME env variable.

@neilyio
Copy link
Author

neilyio commented Oct 28, 2021

@JKelle That's really helpful, thanks!

Could you provide some details about your new conda-based installation? Do you know where libjli.dylib and libjvm.dylib are located? Do you know if your conda environment is setting JAVA_HOME to a different value?

@JKelle
Copy link

JKelle commented Oct 28, 2021

@neilyio When I run os.getenv("JAVA_HOME") in my conda environment, I get '/Users/jkelle/opt/miniconda3/envs/worker' ('worker' is the name of my conda environment).

When I run the code in _find_mac_lib, javabridge finds libjli.dylib at /Users/jkelle/opt/miniconda3/envs/worker/lib/jli/libjli.dylib

@neilyio
Copy link
Author

neilyio commented Oct 28, 2021

Thanks for checking on that. I wonder what it is about conda's OpenJDK that makes it suddenly work.

@LeeKamentsky
Copy link
Owner

Thanks for looking into this guys.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@LeeKamentsky @JKelle @neilyio