Error in installation
Closed this issue · 25 comments
aidinbii commented
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
dweindl commented
Hi, can you please share the output of python -m pip install -v amici?
aidinbii commented
@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 commented
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.
FFroehlich commented
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 commented
@FFroehlich , I've installed swig and openBLAS
and still there is an error
dweindl commented
Hi, you'll have to use a more recent compiler with better C++17 support. gcc>=9.1 or clang>=12 should do.
aidinbii commented
Hi @dweindl , I upgraded it to gcc=10.3.1
But still it's not working
amici_error.txt
dweindl commented
That's an issue with your Python library. Which Python distribution are you using? Is it self-compiled?
aidinbii commented
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 commented
With conda it works!
Thank you for your help!
aidinbii commented
@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 commented
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 commented
@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 commented
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 commented
So, I just need to set HDF5_ROOT and reinstall amici pip install --verbose amici --no-cache?
dweindl commented
So, I just need to set
HDF5_ROOTand reinstall amicipip install --verbose amici --no-cache?
Hope so.
aidinbii commented
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 commented
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 commented
Yep, I followed these instructions
dweindl commented
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 commented
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
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 commented
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 commented
Here is the config log
config.log
I guess I have --enable-languages=c,c++
but not --enable-hl
aidinbii commented
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!