Setup for NeqSim, JDK & Jupyter notebook on windows 11

[ngom52]

Hi everyone,

I've been using NeqSim for about 2 years on a Windows 10 laptop with JDK 20; recently I've switched to using Windows 11 with JDK 21, and I'm having some trouble to get NeqSim working again.

I had set up the JDK following the guide here https://azimuahamed.medium.com/java-environment-variables-setup-windows-11-58fe71e43b5e and verified that the JAVA_HOME environment was setup correctly based on the guide.

I have tried to run my Python program with NeqSim libraries using Anaconda Navigator 2.6.4 > Jupyter Notebook 7.2.2, and so far whenever the program reaches the block with NeqSim code I will receive the error:

The kernel for XXXXXX appears to have died. It will restart automatically.

I am hoping that some can suggest what I can do to get it running again, thanks in advance for your help!

[EvenSol]

I know that others also had problems using neqsim via Anaconda installation. A solution has been to run it via python directly (not anaconda). Anyone else have experience on this? Would be good to have somebody confirming that it can or can not run via Anaconda, and maybe propose a solution . @asmfstatoil ?

[ngom52]

Hi,

I'm currently attempting to reinstall everything to run neqsim via python directly (not using anaconda), but I have encountered the following error when trying to install neqsim:

C:\Users\10091992>pip install neqsim
Collecting neqsim
Using cached neqsim-3.0.13-py3-none-any.whl.metadata (4.3 kB)
Collecting JPype1<2.0.0,>=1.5.0 (from neqsim)
Downloading jpype1-1.5.2-cp313-cp313-win_amd64.whl.metadata (5.0 kB)
Collecting numpy<2.0.0,>=1.25.2 (from neqsim)
Downloading numpy-1.26.4.tar.gz (15.8 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.8/15.8 MB 12.4 MB/s eta 0:00:00
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [21 lines of output]
+ C:\Users\10091992\AppData\Local\Programs\Python\Python313\python.exe C:\Users\10091992\AppData\Local\Temp\pip-install-7ceisrj0\numpy_acac2f3ffb26452cb9dd7d9b434e3b71\vendored-meson\meson\meson.py setup C:\Users\10091992\AppData\Local\Temp\pip-install-7ceisrj0\numpy_acac2f3ffb26452cb9dd7d9b434e3b71 C:\Users\10091992\AppData\Local\Temp\pip-install-7ceisrj0\numpy_acac2f3ffb26452cb9dd7d9b434e3b71.mesonpy-y5z07jif -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=C:\Users\10091992\AppData\Local\Temp\pip-install-7ceisrj0\numpy_acac2f3ffb26452cb9dd7d9b434e3b71.mesonpy-y5z07jif\meson-python-native-file.ini
The Meson build system
Version: 1.2.99
Source dir: C:\Users\10091992\AppData\Local\Temp\pip-install-7ceisrj0\numpy_acac2f3ffb26452cb9dd7d9b434e3b71
Build dir: C:\Users\10091992\AppData\Local\Temp\pip-install-7ceisrj0\numpy_acac2f3ffb26452cb9dd7d9b434e3b71.mesonpy-y5z07jif
Build type: native build
Project name: NumPy
Project version: 1.26.4
WARNING: Failed to activate VS environment: Could not find C:\Program Files (x86)\Microsoft Visual Studio\Installer\vswhere.exe

  ..\meson.build:1:0: ERROR: Unknown compiler(s): [['icl'], ['cl'], ['cc'], ['gcc'], ['clang'], ['clang-cl'], ['pgcc']]
  The following exception(s) were encountered:
  Running `icl ""` gave "[WinError 2] The system cannot find the file specified"
  Running `cl /?` gave "[WinError 2] The system cannot find the file specified"
  Running `cc --version` gave "[WinError 2] The system cannot find the file specified"
  Running `gcc --version` gave "[WinError 2] The system cannot find the file specified"
  Running `clang --version` gave "[WinError 2] The system cannot find the file specified"
  Running `clang-cl /?` gave "[WinError 2] The system cannot find the file specified"
  Running `pgcc --version` gave "[WinError 2] The system cannot find the file specified"

  A full log can be found at C:\Users\10091992\AppData\Local\Temp\pip-install-7ceisrj0\numpy_acac2f3ffb26452cb9dd7d9b434e3b71\.mesonpy-y5z07jif\meson-logs\meson-log.txt
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

I hope to get a suggestion on how to remedy this error

[EvenSol]

Could you try to Install a Python version (3.10 or 3.11) that already has prebuilt wheels for Numpy, JPype, and so forth. Then pip install neqsim should work without a compiler.

[asmfstatoil]

I think we can loosen the requirement for numpy version in neqsimpython for the next release. That will help. Existing version requires 1.26.4 for python 3.9 and up which is an old version.

[ngom52]

Hi, I have downgraded my Python version to 3.10, and by doing this I was able to install NeqSim without any errors

Then I proceeded to run jupyter notebook directly from python (not anaconda), when I try to run the code, the program encounters the following error as it tries to run the neqsim code block (the same error that I had when using anaconda):

The kernel for XXXXXX appears to have died. It will restart automatically.

[EvenSol]

I dont have Win 11, so Im not able to test. THis is what ChatGPT gives as suggestions:

This typically indicates a low-level crash in the JVM or the Python-Java bridge (e.g., JPype).

Possible Causes

1. Incompatible or misconfigured Java installation
2. Missing/incorrect JAVA_HOME or PATH environment variables
3. JPype or py4j bridging issues
4. Insufficient JVM memory or improper JVM arguments
5. Package conflicts in the Python environment

Troubleshooting Steps

1. Check Java Installation

   • Run java -version in a terminal to confirm you have a compatible Java version (e.g., 8, 11, or 17).
   • If multiple Java versions are installed, ensure your JAVA_HOME and PATH point to the correct JDK/JRE:
     • Set JAVA_HOME in Windows:

       Control Panel > System > Advanced system settings > Environment Variables
       

       Add C:\Program Files\Java\jdk-XX to JAVA_HOME, and append %JAVA_HOME%\bin to PATH.

2. Verify JPype and NeqSim Installations

   • Check if JPype is installed:

     pip show jpype1
     

     If missing, install it:

     pip install jpype1
     

   • Verify NeqSim is installed:

     pip show neqsim
     

     If missing:

     pip install neqsim
     

   • Test imports in Python:

     import jpype
     import neqsim

3. Adjust JVM Memory

   • Sometimes the JVM needs a lower (or higher) memory limit. For example:

     import jpype
     if not jpype.isJVMStarted():
         jpype.startJVM(jpype.getDefaultJVMPath(), "-Xmx2G")

4. Run a Minimal Test Script Outside Jupyter

   • Create test_neqsim.py:

     import jpype
     import neqsim
     
     if not jpype.isJVMStarted():
         jpype.startJVM(jpype.getDefaultJVMPath(), "-Xmx2G")
     
     system = neqsim.thermo.thermoTools.create("test")
     print("NeqSim system created:", system)
     
     jpype.shutdownJVM()

   • Run from the command line:

     python test_neqsim.py
     

   • If this works fine, the crash may be specific to Jupyter or environment conflicts.

5. Use a Clean Virtual Environment

   • Create a new environment (using Conda or venv), then install packages:

     conda create -n neqsim_env python=3.9
     conda activate neqsim_env
     pip install jpype1 neqsim notebook
     jupyter notebook
     

   • Test NeqSim in a notebook launched from this fresh environment.

6. Gather More Logs

   • Launch Jupyter from a terminal and watch for error traces when the kernel dies.
   • Check Windows Event Viewer for Java-related crash logs.

---

If the problem persists, please provide:

• The Java version used (java -version)
• The Python version and list of installed packages (pip freeze)
• Any error messages or stack traces from the terminal or Event Viewer.

[ngom52]

Hi everyone,

I've been searching high and low for the solution to this issue. At this moment, I think I've narrowed it down to failure for the JVM to start.

import jpype
print(jpype.getDefaultJVMPath())
>>> C:\Program Files\Java\jdk-23\bin\server\jvm.dll
print(jpype.isJVMStarted())
>>> False
jpype.startJVM(jpype.getDefaultJVMPath())

Basically the above states that the JVM is not running, and when I try to start the JVM (the last line of code), the python kernel dies. In the standard windows command prompt and Jupyter it dies without giving out any error messages. As I run the code again using Spyder, I received the following error message in the IPython Console when trying to start the JVM:

`
Windows fatal exception: access violation

Main thread:
Current thread 0x0000787c (most recent call first):
File "C:\Users\10091992\AppData\Local\anaconda3\Lib\site-packages\jpype_core.py", line 357 in startJVM
File "c:\users\10091992\test_neqsim.py", line 5 in
File "C:\Users\10091992\AppData\Local\anaconda3\Lib\site-packages\spyder_kernels\py3compat.py", line 356 in compat_exec
File "C:\Users\10091992\AppData\Local\anaconda3\Lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 473 in exec_code
File "C:\Users\10091992\AppData\Local\anaconda3\Lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 615 in _exec_file
File "C:\Users\10091992\AppData\Local\anaconda3\Lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 528 in runfile
File "C:\Users\10091992\AppData\Local\Temp\ipykernel_31564\1754979725.py", line 1 in

Main thread:
Current thread 0x0000787c (most recent call first):
File "C:\Users\10091992\AppData\Local\anaconda3\Lib\site-packages\jpype_core.py", line 357 in startJVM
File "c:\users\10091992\test_neqsim.py", line 5 in
File "C:\Users\10091992\AppData\Local\anaconda3\Lib\site-packages\spyder_kernels\py3compat.py", line 356 in compat_exec
File "C:\Users\10091992\AppData\Local\anaconda3\Lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 473 in exec_code
File "C:\Users\10091992\AppData\Local\anaconda3\Lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 615 in _exec_file
File "C:\Users\10091992\AppData\Local\anaconda3\Lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 528 in runfile
File "C:\Users\10091992\AppData\Local\Temp\ipykernel_31564\1754979725.py", line 1 in

Restarting kernel...
`

I hope that someone can advise me if this finding is on the right path towards solving this issue, and any possible solutions