Error in installation #2187

aidinbii · 2023-11-05T07:21:50Z

Hi, when installing AMICI with
python -m pip install amici
I get this error:

==> Configuring:
      $ cmake -S /tmp/pip-install-5koy7_c9/amici_5071826e906b4bdeb91d95b5c1e68f90/amici -B /tmp/pip-install-5koy7_c9/amici_5071826e906b4bdeb91d95b5c1e68f90/build/temp.linux-x86_64-cpython-310_amici -GNinja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX:PATH=/tmp/pip-install-5koy7_c9/amici_5071826e906b4bdeb91d95b5c1e68f90/build/lib.linux-x86_64-cpython-310/amici -DCMAKE_MAKE_PROGRAM=/tmp/pip-build-env-utfljnew/overlay/bin/ninja -DCMAKE_VERBOSE_MAKEFILE=ON -Wno-error=dev -DAMICI_PYTHON_BUILD_EXT_ONLY=ON -DPython3_EXECUTABLE=/home/aidinbiib/bin/Python-3.10.13/Python/bin/python3
      
      ==> Building:
      $ cmake --build /tmp/pip-install-5koy7_c9/amici_5071826e906b4bdeb91d95b5c1e68f90/build/temp.linux-x86_64-cpython-310_amici --config Release
      
      ==> Installing:
      $ cmake --install /tmp/pip-install-5koy7_c9/amici_5071826e906b4bdeb91d95b5c1e68f90/build/temp.linux-x86_64-cpython-310_amici
      
      Traceback (most recent call last):
        File "/home/aidinbiib/bin/Python-3.10.13/Python/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/home/aidinbiib/bin/Python-3.10.13/Python/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/home/aidinbiib/bin/Python-3.10.13/Python/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
          return _build_backend().build_wheel(wheel_directory, config_settings,
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 434, in build_wheel
          return self._build_with_temp_dir(
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 419, in _build_with_temp_dir
          self.run_setup()
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 341, in run_setup
          exec(code, locals())
        File "<string>", line 180, in <module>
        File "<string>", line 164, in main
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 103, in setup
          return distutils.core.setup(**attrs)
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
          self.run_command(cmd)
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 989, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/wheel/bdist_wheel.py", line 369, in run
          self.run_command("build")
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
          self.distribution.run_command(command)
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 989, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 131, in run
          self.run_command(cmd_name)
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
          self.distribution.run_command(command)
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 989, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-5koy7_c9/amici_5071826e906b4bdeb91d95b5c1e68f90/amici/custom_commands.py", line 124, in run
          self.run_command("build_ext")
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
          self.distribution.run_command(command)
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 989, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-5koy7_c9/amici_5071826e906b4bdeb91d95b5c1e68f90/amici/custom_commands.py", line 150, in run
          result = super().run()
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/cmake_build_extension/build_extension.py", line 113, in run
          self.build_extension(ext)
        File "/tmp/pip-install-5koy7_c9/amici_5071826e906b4bdeb91d95b5c1e68f90/amici/custom_commands.py", line 177, in build_extension
          super().build_extension(ext)
        File "/tmp/pip-build-env-utfljnew/overlay/lib/python3.10/site-packages/cmake_build_extension/build_extension.py", line 229, in build_extension
          subprocess.check_call(configure_command)
        File "/home/aidinbiib/bin/Python-3.10.13/Python/lib/python3.10/subprocess.py", line 369, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['cmake', '-S', '/tmp/pip-install-5koy7_c9/amici_5071826e906b4bdeb91d95b5c1e68f90/amici', '-B', '/tmp/pip-install-5koy7_c9/amici_5071826e906b4bdeb91d95b5c1e68f90/build/temp.linux-x86_64-cpython-310_amici', '-GNinja', '-DCMAKE_BUILD_TYPE=Release', '-DCMAKE_INSTALL_PREFIX:PATH=/tmp/pip-install-5koy7_c9/amici_5071826e906b4bdeb91d95b5c1e68f90/build/lib.linux-x86_64-cpython-310/amici', '-DCMAKE_MAKE_PROGRAM=/tmp/pip-build-env-utfljnew/overlay/bin/ninja', '-DCMAKE_VERBOSE_MAKEFILE=ON', '-Wno-error=dev', '-DAMICI_PYTHON_BUILD_EXT_ONLY=ON', '-DPython3_EXECUTABLE=/home/aidinbiib/bin/Python-3.10.13/Python/bin/python3']' returned non-zero exit status 1.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for amici
Failed to build amici
ERROR: Could not build wheels for amici, which is required to install pyproject.toml-based projects

I'm installing it on an AWS EC2 machine

The text was updated successfully, but these errors were encountered:

dweindl · 2023-11-06T09:25:09Z

Hi, can you please share the output of python -m pip install -v amici?

aidinbii · 2023-11-06T09:38:07Z

@dweindl, sure
It's a long output, so here are the last lines

 ==> Configuring:
  $ cmake -S /tmp/pip-install-8a1h22tb/amici_e784897b2334483c8425e8e9e77e2964/amici -B /tmp/pip-install-8a1h22tb/amici_e784897b2334483c8425e8e9e77e2964/build/temp.linux-x86_64-cpython-310_amici -GNinja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX:PATH=/tmp/pip-install-8a1h22tb/amici_e784897b2334483c8425e8e9e77e2964/build/lib.linux-x86_64-cpython-310/amici -DCMAKE_MAKE_PROGRAM=/tmp/pip-build-env-i_yzyu8k/overlay/bin/ninja -DCMAKE_VERBOSE_MAKEFILE=ON -Wno-error=dev -DAMICI_PYTHON_BUILD_EXT_ONLY=ON -DPython3_EXECUTABLE=/home/aidinbiib/bin/Python-3.10.13/Python/bin/python3

  ==> Building:
  $ cmake --build /tmp/pip-install-8a1h22tb/amici_e784897b2334483c8425e8e9e77e2964/build/temp.linux-x86_64-cpython-310_amici --config Release

  ==> Installing:
  $ cmake --install /tmp/pip-install-8a1h22tb/amici_e784897b2334483c8425e8e9e77e2964/build/temp.linux-x86_64-cpython-310_amici

  Traceback (most recent call last):
    File "/home/aidinbiib/bin/Python-3.10.13/Python/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
      main()
    File "/home/aidinbiib/bin/Python-3.10.13/Python/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/home/aidinbiib/bin/Python-3.10.13/Python/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
      return _build_backend().build_wheel(wheel_directory, config_settings,
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 434, in build_wheel
      return self._build_with_temp_dir(
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 419, in _build_with_temp_dir
      self.run_setup()
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 341, in run_setup
      exec(code, locals())
    File "<string>", line 180, in <module>
    File "<string>", line 164, in main
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 103, in setup
      return distutils.core.setup(**attrs)
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
      return run_commands(dist)
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
      dist.run_commands()
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
      self.run_command(cmd)
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 989, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/wheel/bdist_wheel.py", line 369, in run
      self.run_command("build")
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
      self.distribution.run_command(command)
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 989, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 131, in run
      self.run_command(cmd_name)
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
      self.distribution.run_command(command)
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 989, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/tmp/pip-install-8a1h22tb/amici_e784897b2334483c8425e8e9e77e2964/amici/custom_commands.py", line 124, in run
      self.run_command("build_ext")
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
      self.distribution.run_command(command)
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 989, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/tmp/pip-install-8a1h22tb/amici_e784897b2334483c8425e8e9e77e2964/amici/custom_commands.py", line 150, in run
      result = super().run()
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/cmake_build_extension/build_extension.py", line 113, in run
      self.build_extension(ext)
    File "/tmp/pip-install-8a1h22tb/amici_e784897b2334483c8425e8e9e77e2964/amici/custom_commands.py", line 177, in build_extension
      super().build_extension(ext)
    File "/tmp/pip-build-env-i_yzyu8k/overlay/lib/python3.10/site-packages/cmake_build_extension/build_extension.py", line 229, in build_extension
      subprocess.check_call(configure_command)
    File "/home/aidinbiib/bin/Python-3.10.13/Python/lib/python3.10/subprocess.py", line 369, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['cmake', '-S', '/tmp/pip-install-8a1h22tb/amici_e784897b2334483c8425e8e9e77e2964/amici', '-B', '/tmp/pip-install-8a1h22tb/amici_e784897b2334483c8425e8e9e77e2964/build/temp.linux-x86_64-cpython-310_amici', '-GNinja', '-DCMAKE_BUILD_TYPE=Release', '-DCMAKE_INSTALL_PREFIX:PATH=/tmp/pip-install-8a1h22tb/amici_e784897b2334483c8425e8e9e77e2964/build/lib.linux-x86_64-cpython-310/amici', '-DCMAKE_MAKE_PROGRAM=/tmp/pip-build-env-i_yzyu8k/overlay/bin/ninja', '-DCMAKE_VERBOSE_MAKEFILE=ON', '-Wno-error=dev', '-DAMICI_PYTHON_BUILD_EXT_ONLY=ON', '-DPython3_EXECUTABLE=/home/aidinbiib/bin/Python-3.10.13/Python/bin/python3']' returned non-zero exit status 1.
  error: subprocess-exited-with-error
  
  × Building wheel for amici (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /home/aidinbiib/bin/Python-3.10.13/Python/bin/python3 /home/aidinbiib/bin/Python-3.10.13/Python/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmph6kigjba
  cwd: /tmp/pip-install-8a1h22tb/amici_e784897b2334483c8425e8e9e77e2964
  Building wheel for amici (pyproject.toml) ... error
  ERROR: Failed building wheel for amici
Failed to build amici
ERROR: Could not build wheels for amici, which is required to install pyproject.toml-based projects

dweindl · 2023-11-09T12:51:10Z

It's a long output, so here are the last lines

That's pretty much the same output as before. The omitted part is the interesting part.

aidinbii · 2023-11-09T14:06:03Z

@dweindl , here is the full output

amici_error.txt

FFroehlich · 2023-11-09T20:36:51Z

Hi @aidinbii, looks like neither swig nor BLAS are installed on the system. Please see https://amici.readthedocs.io/en/latest/python_installation.html on how to get those libraries installed.

aidinbii · 2023-11-13T14:03:07Z

@FFroehlich , I've installed swig and openBLAS
and still there is an error

amici_error.txt

dweindl · 2023-11-14T07:25:41Z

Hi, you'll have to use a more recent compiler with better C++17 support. gcc>=9.1 or clang>=12 should do.

aidinbii · 2023-11-14T12:21:41Z

Hi @dweindl , I upgraded it to gcc=10.3.1
But still it's not working
amici_error.txt

dweindl · 2023-11-16T08:56:30Z

That's an issue with your Python library. Which Python distribution are you using? Is it self-compiled?

aidinbii · 2023-11-16T11:49:14Z

Yes, it is self-compiled in my home directory (AWS EC2 machine)
Python-3.10.13

I guess it is better to use conda?

aidinbii · 2023-11-16T13:13:10Z

With conda it works!

Thank you for your help!

aidinbii · 2023-11-16T16:22:51Z

@dweindl , I got another error during parameter estimation

%%capture
result = optimize.minimize(
    problem=problem,
    optimizer=optimizer,
    n_starts=n_starts,
    startpoint_method=startpoint_method,
    engine=engine,
    options=opt_options,
    history_options=history_options,
    progress_bar=True
);

AttributeError                            Traceback (most recent call last)
Cell In[132], line 6
      1 # do the optimization
      2 # https://pypesto.readthedocs.io/en/latest/api/pypesto.optimize.html#pypesto.optimize.minimize
      4 from IPython.utils import io
----> 6 result = optimize.minimize(
      7     problem=problem,
      8     optimizer=optimizer,
      9     n_starts=n_starts,
     10     startpoint_method=startpoint_method,
     11     engine=engine,
     12     options=opt_options,
     13     history_options=history_options,
     14     progress_bar=True
     15 );

File ~/miniconda3/envs/modeling_env/lib/python3.10/site-packages/pypesto/optimize/optimize.py:156, in minimize(problem, optimizer, n_starts, ids, startpoint_method, result, engine, progress_bar, options, history_options, filename, overwrite)
    153     tasks.append(task)
    155 # perform multistart optimization
--> 156 ret = engine.execute(tasks, progress_bar=progress_bar)
    158 # merge hdf5 history files
    159 if history_requires_postprocessing:

File ~/miniconda3/envs/modeling_env/lib/python3.10/site-packages/pypesto/engine/multi_process.py:64, in MultiProcessEngine.execute(self, tasks, progress_bar)
     53 """Pickle tasks and distribute work over parallel processes.
     54 
     55 Parameters
   (...)
     60     Whether to display a progress bar.
     61 """
     62 n_tasks = len(tasks)
---> 64 pickled_tasks = [pickle.dumps(task) for task in tasks]
     66 n_procs = min(self.n_procs, n_tasks)
     67 logger.debug(f"Parallelizing on {n_procs} processes.")

File ~/miniconda3/envs/modeling_env/lib/python3.10/site-packages/pypesto/engine/multi_process.py:64, in <listcomp>(.0)
     53 """Pickle tasks and distribute work over parallel processes.
     54 
     55 Parameters
   (...)
     60     Whether to display a progress bar.
     61 """
     62 n_tasks = len(tasks)
---> 64 pickled_tasks = [pickle.dumps(task) for task in tasks]
     66 n_procs = min(self.n_procs, n_tasks)
     67 logger.debug(f"Parallelizing on {n_procs} processes.")

File ~/miniconda3/envs/modeling_env/lib/python3.10/site-packages/cloudpickle/cloudpickle.py:1479, in dumps(obj, protocol, buffer_callback)
   1477 with io.BytesIO() as file:
   1478     cp = Pickler(file, protocol=protocol, buffer_callback=buffer_callback)
-> 1479     cp.dump(obj)
   1480     return file.getvalue()

File ~/miniconda3/envs/modeling_env/lib/python3.10/site-packages/cloudpickle/cloudpickle.py:1245, in Pickler.dump(self, obj)
   1243 def dump(self, obj):
   1244     try:
-> 1245         return super().dump(obj)
   1246     except RuntimeError as e:
   1247         if len(e.args) > 0 and "recursion" in e.args[0]:

File ~/miniconda3/envs/modeling_env/lib/python3.10/site-packages/pypesto/objective/amici/amici.py:276, in AmiciObjective.__getstate__(self)
    273 try:
    274     # write amici solver settings to file
    275     try:
--> 276         amici.writeSolverSettingsToHDF5(self.amici_solver, _file)
    277     except AttributeError as e:
    278         e.args += (
    279             "Pickling the AmiciObjective requires an AMICI "
    280             "installation with HDF5 support.",
    281         )

File ~/miniconda3/envs/modeling_env/lib/python3.10/site-packages/amici/swig_wrappers.py:221, in writeSolverSettingsToHDF5(solver, file, location)
    208 def writeSolverSettingsToHDF5(
    209     solver: AmiciSolver,
    210     file: Union[str, object],
    211     location: Optional[str] = "solverSettings",
    212 ) -> None:
    213     """
    214     Convenience wrapper for :py:func:`amici.amici.writeSolverSettingsToHDF5`
    215 
   (...)
    219     :param location: location of solver settings in hdf5 file
    220     """
--> 221     amici_swig.writeSolverSettingsToHDF5(_get_ptr(solver), file, location)

AttributeError: ("module 'amici.amici' has no attribute 'writeSolverSettingsToHDF5'", 'Pickling the AmiciObjective requires an AMICI installation with HDF5 support.')

I've installed the hdf5 Python package before installing Amici

dweindl · 2023-11-18T08:21:46Z

I've installed the hdf5 Python package before installing Amici

You'll have to install the hdf5 c/c++ libraries https://amici.readthedocs.io/en/latest/python_installation.html

aidinbii · 2023-11-21T06:32:21Z

@dweindl , I've installed hdf5 c/c++ with parallel support
It works if I use a single core engine = pypesto.engine.SingleCoreEngine()

But with multi-core engine = pypesto.engine.MultiProcessEngine()
I get the same error

AttributeError: ("module 'amici.amici' has no attribute 'writeSolverSettingsToHDF5'", 'Pickling the AmiciObjective requires an AMICI installation with HDF5 support.')

The way I installed hdf5
INSTALL="home/aidinbiib/hdf5-1.14.3/bin/install-sh -c" CC=/home/aidinbiib/openmpi_lib/bin/mpicc ../hdf5-1.14.3/configure --prefix=/home/aidinbiib/hdf5_lib --enable-parallel

And amici
AMICI_TRY_ENABLE_HDF5=ON pip install --verbose amici --no-cache

dweindl · 2023-11-27T08:52:48Z

If you install to a non-default location, you will have to set the environment variable HDF5_ROOT to point to your installation directory.

--enable-parallel is not necessary.

aidinbii · 2023-11-27T09:11:42Z

So, I just need to set HDF5_ROOT and reinstall amici pip install --verbose amici --no-cache?

dweindl · 2023-11-27T09:46:59Z

So, I just need to set HDF5_ROOT and reinstall amici pip install --verbose amici --no-cache?

Hope so.

aidinbii · 2023-11-27T10:20:31Z

Same error ...
export HDF5_ROOT=/home/aidinbiib/hdf5_lib

Should I also reinstall hdf5? But without --enable-parallel

INSTALL="home/aidinbiib/hdf5-1.14.3/bin/install-sh -c" CC=/home/aidinbiib/openmpi_lib/bin/mpicc ../hdf5-1.14.3/configure --prefix=/home/aidinbiib/hdf5_lib

dweindl · 2023-11-28T12:19:19Z

The way I installed hdf5
INSTALL="home/aidinbiib/hdf5-1.14.3/bin/install-sh -c" CC=/home/aidinbiib/openmpi_lib/bin/mpicc ../hdf5-1.14.3/configure --prefix=/home/aidinbiib/hdf5_lib --enable-parallel

Just to make sure - you did build/install HDF5, not just configure it, right?

aidinbii · 2023-11-28T12:28:38Z

Yep, I followed these instructions

dweindl · 2023-11-29T10:04:21Z

Yep, I followed these instructions

Good. Note that that's a 10 year old version of HDF5, but it might still work.

You used HDF5_ROOT=/home/aidinbiib/hdf5_lib ?

What's the current output of python -m pip install --no-cache-dir -v amici?

aidinbii · 2023-11-29T10:56:38Z

Haha, I didn't notice.
The version I've installed is hdf5=1.14.3 and the up-to-date install instructions are pretty much the same

amici_error.txt

Ok, it can't find hdf5

-- Could NOT find HDF5 (missing: HDF5_INCLUDE_DIRS) (found version "1.14.3")

You used HDF5_ROOT=/home/aidinbiib/hdf5_lib ?

Yes. Should have I used HDF5_ROOT=/home/aidinbiib/hdf5_lib/bin?

dweindl · 2023-11-29T11:03:12Z

Ok, it can't find hdf5

-- Could NOT find HDF5 (missing: HDF5_INCLUDE_DIRS) (found version "1.14.3")

It found some of it, but not all required header files.

You used HDF5_ROOT=/home/aidinbiib/hdf5_lib ?

Yes. Should have I used HDF5_ROOT=/home/aidinbiib/hdf5_lib/bin?

No, should be fine.

You might have to configure/build HDF5 with --enable-hl --enable-cxx, not sure what's included by default.

aidinbii · 2023-11-29T11:25:15Z

Here is the config log
config.log

I guess I have --enable-languages=c,c++
but not --enable-hl

aidinbii · 2023-11-30T08:36:39Z

Reinstalling hdf5 with config:
INSTALL="home/aidinbiib/hdf5-1.14.3/bin/install-sh -c" ../hdf5-1.14.3/configure --prefix=/home/aidinbiib/hdf5_lib --enable-hl --enable-cxx
Made it work!

Thank you very much for your help!

aidinbii added the new Newly created label Nov 5, 2023

aidinbii closed this as completed Nov 16, 2023

aidinbii reopened this Nov 16, 2023

dweindl removed the new Newly created label Nov 27, 2023

aidinbii closed this as completed Nov 30, 2023

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Error in installation #2187

Error in installation #2187

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