Problem installing pylians on linux (Ubuntu 20.04)
cloud182 opened this issue · 18 comments
cloud182 commented
Hello,
I am trying to install Pylians on my machine, but I am getting an error. I have Ubuntu 20.04, and I am trying to install the package in a conda environment with Python 3.10 via python -m pip install Pylians, but I also tried older versions (python 3.8, python 3.9). I also tried to install the package on other machines with other Linux versions (CentOS 7) and I always got the same error:
Collecting Pylians
Using cached Pylians-0.5.tar.gz (2.0 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [21 lines of output]
Traceback (most recent call last):
File "/home/econgiu/miniconda3/envs/py31/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
main()
File "/home/econgiu/miniconda3/envs/py31/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/home/econgiu/miniconda3/envs/py31/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
File "/tmp/pip-build-env-o5mrd48o/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 338, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
File "/tmp/pip-build-env-o5mrd48o/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 320, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-o5mrd48o/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 335, in run_setup
exec(code, locals())
File "<string>", line 99, in <module>
File "/tmp/pip-build-env-o5mrd48o/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 970, in cythonize
module_list, module_metadata = create_extension_list(
File "/tmp/pip-build-env-o5mrd48o/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 816, in create_extension_list
for file in nonempty(sorted(extended_iglob(filepattern)), "'%s' doesn't match any files" % filepattern):
File "/tmp/pip-build-env-o5mrd48o/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 114, in nonempty
raise ValueError(error_msg)
ValueError: 'library/MAS_library/MAS_library.pyx' doesn't match any files
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel 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.
Can you help me find the origin of this issue?
Thanks!
franciscovillaescusa commented
Can you try to install it outside the conda environment. I know that sometimes combining conda and pip can led to conflicts.
YoRHazero commented
Can you try to install it outside the conda environment. I know that sometimes combining conda and pip can led to conflicts.
Hello,
I encontour the similar problem when I try to install.
And when I was trying to install the development version, the error message is more detailed, which reads
Error compiling Cython file:
------------------------------------------------------------
...
k_par, k_per = abs(ky), <int>sqrt(kx*kx + kz*kz)
else:
k_par, k_per = abs(kz), <int>sqrt(kx*kx + ky*ky)
# correct modes amplitude for MAS
MAS_factor = MAS_corr1[0]*MAS_corr1[1]*MAS_corr1[2]
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1689:42: local variable 'MAS_corr1' referenced before assignment
And there are a lot of other similar error messages about the variables MAS_corr MAS_corr2.
The whole message is:
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [284 lines of output]
Error compiling Cython file:
------------------------------------------------------------
...
# do a loop over all modes, computing their k,Pk. k's are in k_F units
start2 = time.time(); prefact = np.pi/dims
for kxx in range(dims):
kx = (kxx-dims if (kxx>middle) else kxx)
MAS_corr[0] = MAS_correction(prefact*kx,MAS_index)
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1387:8: local variable 'MAS_corr' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
kx = (kxx-dims if (kxx>middle) else kxx)
MAS_corr[0] = MAS_correction(prefact*kx,MAS_index)
for kyy in range(dims):
ky = (kyy-dims if (kyy>middle) else kyy)
MAS_corr[1] = MAS_correction(prefact*ky,MAS_index)
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1391:12: local variable 'MAS_corr' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
ky = (kyy-dims if (kyy>middle) else kyy)
MAS_corr[1] = MAS_correction(prefact*ky,MAS_index)
for kzz in range(middle+1): #kzz=[0,1,..,middle] --> kz>0
kz = (kzz-dims if (kzz>middle) else kzz)
MAS_corr[2] = MAS_correction(prefact*kz,MAS_index)
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1395:16: local variable 'MAS_corr' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
# compute |k| of the mode and its integer part
kmod = sqrt(kx*kx + ky*ky + kz*kz)
k_index = <int>kmod
# correct modes amplitude for MAS
MAS_factor = MAS_corr[0]*MAS_corr[1]*MAS_corr[2]
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1408:29: local variable 'MAS_corr' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
# compute |k| of the mode and its integer part
kmod = sqrt(kx*kx + ky*ky + kz*kz)
k_index = <int>kmod
# correct modes amplitude for MAS
MAS_factor = MAS_corr[0]*MAS_corr[1]*MAS_corr[2]
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1408:41: local variable 'MAS_corr' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
# compute |k| of the mode and its integer part
kmod = sqrt(kx*kx + ky*ky + kz*kz)
k_index = <int>kmod
# correct modes amplitude for MAS
MAS_factor = MAS_corr[0]*MAS_corr[1]*MAS_corr[2]
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1408:53: local variable 'MAS_corr' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
# do a loop over all modes, computing their k,Pk. k's are in k_F units
start2 = time.time(); prefact = np.pi/dims
for kxx in range(dims):
kx = (kxx-dims if (kxx>middle) else kxx)
MAS_corr1[0] = MAS_correction(prefact*kx,MAS_index1)
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1661:8: local variable 'MAS_corr1' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
# do a loop over all modes, computing their k,Pk. k's are in k_F units
start2 = time.time(); prefact = np.pi/dims
for kxx in range(dims):
kx = (kxx-dims if (kxx>middle) else kxx)
MAS_corr1[0] = MAS_correction(prefact*kx,MAS_index1)
MAS_corr2[0] = MAS_correction(prefact*kx,MAS_index2)
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1662:8: local variable 'MAS_corr2' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
MAS_corr1[0] = MAS_correction(prefact*kx,MAS_index1)
MAS_corr2[0] = MAS_correction(prefact*kx,MAS_index2)
for kyy in range(dims):
ky = (kyy-dims if (kyy>middle) else kyy)
MAS_corr1[1] = MAS_correction(prefact*ky,MAS_index1)
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1666:12: local variable 'MAS_corr1' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
MAS_corr2[0] = MAS_correction(prefact*kx,MAS_index2)
for kyy in range(dims):
ky = (kyy-dims if (kyy>middle) else kyy)
MAS_corr1[1] = MAS_correction(prefact*ky,MAS_index1)
MAS_corr2[1] = MAS_correction(prefact*ky,MAS_index2)
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1667:12: local variable 'MAS_corr2' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
MAS_corr1[1] = MAS_correction(prefact*ky,MAS_index1)
MAS_corr2[1] = MAS_correction(prefact*ky,MAS_index2)
for kzz in range(middle+1): #kzz=[0,1,..,middle] --> kz>0
kz = (kzz-dims if (kzz>middle) else kzz)
MAS_corr1[2] = MAS_correction(prefact*kz,MAS_index1)
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1671:16: local variable 'MAS_corr1' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
MAS_corr2[1] = MAS_correction(prefact*ky,MAS_index2)
for kzz in range(middle+1): #kzz=[0,1,..,middle] --> kz>0
kz = (kzz-dims if (kzz>middle) else kzz)
MAS_corr1[2] = MAS_correction(prefact*kz,MAS_index1)
MAS_corr2[2] = MAS_correction(prefact*kz,MAS_index2)
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1672:16: local variable 'MAS_corr2' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
k_par, k_per = abs(ky), <int>sqrt(kx*kx + kz*kz)
else:
k_par, k_per = abs(kz), <int>sqrt(kx*kx + ky*ky)
# correct modes amplitude for MAS
MAS_factor = MAS_corr1[0]*MAS_corr1[1]*MAS_corr1[2]
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1689:29: local variable 'MAS_corr1' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
k_par, k_per = abs(ky), <int>sqrt(kx*kx + kz*kz)
else:
k_par, k_per = abs(kz), <int>sqrt(kx*kx + ky*ky)
# correct modes amplitude for MAS
MAS_factor = MAS_corr1[0]*MAS_corr1[1]*MAS_corr1[2]
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1689:42: local variable 'MAS_corr1' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
k_par, k_per = abs(ky), <int>sqrt(kx*kx + kz*kz)
else:
k_par, k_per = abs(kz), <int>sqrt(kx*kx + ky*ky)
# correct modes amplitude for MAS
MAS_factor = MAS_corr1[0]*MAS_corr1[1]*MAS_corr1[2]
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1689:55: local variable 'MAS_corr1' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
k_par, k_per = abs(kz), <int>sqrt(kx*kx + ky*ky)
# correct modes amplitude for MAS
MAS_factor = MAS_corr1[0]*MAS_corr1[1]*MAS_corr1[2]
delta_k1[kxx,kyy,kzz] = delta_k1[kxx,kyy,kzz]*MAS_factor
MAS_factor = MAS_corr2[0]*MAS_corr2[1]*MAS_corr2[2]
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1691:29: local variable 'MAS_corr2' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
k_par, k_per = abs(kz), <int>sqrt(kx*kx + ky*ky)
# correct modes amplitude for MAS
MAS_factor = MAS_corr1[0]*MAS_corr1[1]*MAS_corr1[2]
delta_k1[kxx,kyy,kzz] = delta_k1[kxx,kyy,kzz]*MAS_factor
MAS_factor = MAS_corr2[0]*MAS_corr2[1]*MAS_corr2[2]
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1691:42: local variable 'MAS_corr2' referenced before assignment
Error compiling Cython file:
------------------------------------------------------------
...
k_par, k_per = abs(kz), <int>sqrt(kx*kx + ky*ky)
# correct modes amplitude for MAS
MAS_factor = MAS_corr1[0]*MAS_corr1[1]*MAS_corr1[2]
delta_k1[kxx,kyy,kzz] = delta_k1[kxx,kyy,kzz]*MAS_factor
MAS_factor = MAS_corr2[0]*MAS_corr2[1]*MAS_corr2[2]
^
------------------------------------------------------------
library/Pk_library/Pk_library.pyx:1691:55: local variable 'MAS_corr2' referenced before assignment
Compiling library/MAS_library/MAS_library.pyx because it depends on /tmp/pip-build-env-bfqccpns/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd.
Compiling library/Pk_library/Pk_library.pyx because it changed.
Compiling library/Pk_library/bispectrum_library.pyx because it changed.
Compiling library/MAS_library/field_properties.pyx because it depends on /tmp/pip-build-env-bfqccpns/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd.
Compiling library/redshift_space_library/redshift_space_library.pyx because it changed.
Compiling library/smoothing_library/smoothing_library.pyx because it changed.
Compiling library/void_library/void_library.pyx because it changed.
Compiling library/integration_library/integration_library.pyx because it changed.
Compiling library/density_field_library/density_field_library.pyx because it changed.
Compiling library/sorting_library/sorting_library.pyx because it changed.
Compiling library/HI_library/HI_library.pyx because it depends on /tmp/pip-build-env-bfqccpns/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd.
Compiling library/HI_clusters_library/HI_clusters_library.pyx because it depends on /tmp/pip-build-env-bfqccpns/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd.
[ 1/12] Cythonizing library/Pk_library/Pk_library.pyx
Traceback (most recent call last):
File "/home/zero/.conda/envs/myenv/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
main()
File "/home/zero/.conda/envs/myenv/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/home/zero/.conda/envs/myenv/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel
return hook(config_settings)
File "/tmp/pip-build-env-bfqccpns/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 338, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
File "/tmp/pip-build-env-bfqccpns/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 320, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-bfqccpns/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 335, in run_setup
exec(code, locals())
File "<string>", line 99, in <module>
File "/tmp/pip-build-env-bfqccpns/overlay/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1127, in cythonize
cythonize_one(*args)
File "/tmp/pip-build-env-bfqccpns/overlay/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1250, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: library/Pk_library/Pk_library.pyx
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel 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.
Note: you may need to restart the kernel to use updated packages.
Can you help to check what happens in the 'library.pyx'?
Thanks!
cloud182 commented
Hi @franciscovillaescusa, I tried to install it outside conda and I still get the same error message:
Collecting pylians
Using cached Pylians-0.5.tar.gz (2.0 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 /tmp/tmpetgn49fu get_requires_for_build_wheel /tmp/tmpgnm23i5b
cwd: /tmp/pip-install-aubhvbs6/pylians
Complete output (21 lines):
Traceback (most recent call last):
File "/tmp/tmpetgn49fu", line 280, in <module>
main()
File "/tmp/tmpetgn49fu", line 263, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/tmp/tmpetgn49fu", line 114, in get_requires_for_build_wheel
return hook(config_settings)
File "/tmp/pip-build-env-nxcwrgpc/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 338, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
File "/tmp/pip-build-env-nxcwrgpc/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 320, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-nxcwrgpc/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 335, in run_setup
exec(code, locals())
File "<string>", line 99, in <module>
File "/tmp/pip-build-env-nxcwrgpc/overlay/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 970, in cythonize
module_list, module_metadata = create_extension_list(
File "/tmp/pip-build-env-nxcwrgpc/overlay/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 816, in create_extension_list
for file in nonempty(sorted(extended_iglob(filepattern)), "'%s' doesn't match any files" % filepattern):
File "/tmp/pip-build-env-nxcwrgpc/overlay/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 114, in nonempty
raise ValueError(error_msg)
ValueError: 'library/MAS_library/MAS_library.pyx' doesn't match any files
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 /tmp/tmpetgn49fu get_requires_for_build_wheel /tmp/tmpgnm23i5b Check the logs for full command output.
adamrouhiainen commented
I have the same issue. Ubuntu 20.04.4, Python 3.8.10, tried installing outside of conda
ccoulombe commented
The releases (0.4 and 0.5) on PyPI are missing the file library/MAS_library/MAS_library.pyx
(12900) ~ $ tar --list -f Pylians-0.4.tar.gz | fgrep MAS_library.pyx
(12900) ~ $
(12900) ~ $ tar --list -f Pylians-0.5.tar.gz | fgrep MAS_library.pyx
(12900) ~ $
ccoulombe commented
The issue library/Pk_library/Pk_library.pyx:1689:42: local variable 'MAS_corr1' referenced before assignment was introduced in 05c1b98.
The variable MAS_corr1 assignation was removed, hence the variable being used before its assignation.
One can install from git checkout HEAD^1 or with pip install git+https://github.com/franciscovillaescusa/Pylians3.git@8f902be81cc1b0de13703dc011318daedc8eac27
Not sure what bug this fixes. @franciscovillaescusa
franciscovillaescusa commented
Hi guys, sorry about this. I recently fixed a bug for one routine but then there were some variables that were not defined anymore so cython complained. I believe I have fixed it and I have tested that I can compile the code properly on a fresh machine. Can you try and let me know if it works now? Sorry again about this and thanks for your patience.
cloud182 commented
I just tried to install the new version of the package and it was successful.
Thank you very much for your help!
franciscovillaescusa commented
Great thanks! and apologies once again for the misplace.
franciscovillaescusa commented
I believe this is now fixed so I'm closing this thread.
jwuphysics commented
Hi, sorry to bug you on a closed thread, but I'm getting a possibly related error to the one here. I've tried to install on a Debian Linux machine using pip, inside and outside a conda environment, but I get the same issue. Seems to be a Cython compilation error, which I've appended below. Any suggestions? Thanks for your help!
> pip install Pylians (base)
Collecting Pylians
Using cached Pylians-0.7.tar.gz (3.2 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [123 lines of output]
Error compiling Cython file:
------------------------------------------------------------
...
# RK4 example1 for debugging
cpdef RK4_example(double[::1] yinit, double x1, double x2, long nstep):
cdef double *result
result = CI.rkdumb(&yinit[0], yinit.shape[0], x1, x2, nstep,
NULL, NULL, 0, example)
^
------------------------------------------------------------
library/integration_library/integration_library.pyx:87:39: Cannot assign type 'void (double, double *, double *, double *, double *, long) except *' to 'void (*)(double, double *, double *, double *, double *, long) noexcept'
Error compiling Cython file:
------------------------------------------------------------
...
cpdef RK4_example2(double[::1] yinit, double x1, double x2, long nstep,
double[::1] a, double[::1] b):
cdef double *result
result = CI.rkdumb(&yinit[0], yinit.shape[0], x1, x2, nstep,
&a[0], &b[0], a.shape[0], example2)
^
------------------------------------------------------------
library/integration_library/integration_library.pyx:97:50: Cannot assign type 'void (double, double *, double *, double *, double *, long) except *' to 'void (*)(double, double *, double *, double *, double *, long) noexcept'
Error compiling Cython file:
------------------------------------------------------------
...
cdef long nok, nbad
nok = nbad = 0
CI.odeint(&yinit[0], yinit.shape[0], x1, x2, eps, h1, hmin, &nok, &nbad,
NULL, NULL, 0, example)
^
------------------------------------------------------------
library/integration_library/integration_library.pyx:110:29: Cannot assign type 'void (double, double *, double *, double *, double *, long) except *' to 'void (*)(double, double *, double *, double *, double *, long) noexcept'
Error compiling Cython file:
------------------------------------------------------------
...
cdef long nok, nbad
nok = nbad = 0
CI.odeint(&yinit[0], yinit.shape[0], x1, x2, eps, h1, hmin, &nok, &nbad,
&a[0], &b[0], a.shape[0], example2)
^
------------------------------------------------------------
library/integration_library/integration_library.pyx:128:40: Cannot assign type 'void (double, double *, double *, double *, double *, long) except *' to 'void (*)(double, double *, double *, double *, double *, long) noexcept'
Error compiling Cython file:
------------------------------------------------------------
...
cdef long nok, nbad
nok = nbad = 0
if function=='log' or function=='sigma':
CI.odeint(&yinit[0], yinit.shape[0], x1, x2, eps, h1, hmin, &nok, &nbad,
&a[0], &b[0], b.shape[0], sigma)
^
------------------------------------------------------------
library/integration_library/integration_library.pyx:147:44: Cannot assign type 'void (double, double *, double *, double *, double *, long) except *' to 'void (*)(double, double *, double *, double *, double *, long) noexcept'
Error compiling Cython file:
------------------------------------------------------------
...
CI.odeint(&yinit[0], yinit.shape[0], x1, x2, eps, h1, hmin, &nok, &nbad,
&a[0], &b[0], b.shape[0], sigma)
elif function=='linear':
CI.odeint(&yinit[0], yinit.shape[0], x1, x2, eps, h1, hmin, &nok, &nbad,
&a[0], &b[0], b.shape[0], linear)
^
------------------------------------------------------------
library/integration_library/integration_library.pyx:151:44: Cannot assign type 'void (double, double *, double *, double *, double *, long) except *' to 'void (*)(double, double *, double *, double *, double *, long) noexcept'
Compiling library/MAS_library/MAS_library.pyx because it changed.
Compiling library/Pk_library/Pk_library.pyx because it changed.
Compiling library/Pk_library/bispectrum_library.pyx because it changed.
Compiling library/MAS_library/field_properties.pyx because it changed.
Compiling library/redshift_space_library/redshift_space_library.pyx because it changed.
Compiling library/smoothing_library/smoothing_library.pyx because it changed.
Compiling library/void_library/void_library.pyx because it changed.
Compiling library/integration_library/integration_library.pyx because it changed.
Compiling library/density_field_library/density_field_library.pyx because it changed.
Compiling library/sorting_library/sorting_library.pyx because it changed.
Compiling library/HI_library/HI_library.pyx because it changed.
Compiling library/HI_clusters_library/HI_clusters_library.pyx because it changed.
[ 1/12] Cythonizing library/HI_clusters_library/HI_clusters_library.pyx
[ 2/12] Cythonizing library/HI_library/HI_library.pyx
[ 3/12] Cythonizing library/MAS_library/MAS_library.pyx
[ 4/12] Cythonizing library/MAS_library/field_properties.pyx
[ 5/12] Cythonizing library/Pk_library/Pk_library.pyx
[ 6/12] Cythonizing library/Pk_library/bispectrum_library.pyx
[ 7/12] Cythonizing library/density_field_library/density_field_library.pyx
[ 8/12] Cythonizing library/integration_library/integration_library.pyx
Traceback (most recent call last):
File "/home/john/miniconda3/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/home/john/miniconda3/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/john/miniconda3/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
File "/tmp/pip-build-env-apllxp7x/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
File "/tmp/pip-build-env-apllxp7x/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-apllxp7x/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 338, in run_setup
exec(code, locals())
File "<string>", line 99, in <module>
File "/tmp/pip-build-env-apllxp7x/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
cythonize_one(*args)
File "/tmp/pip-build-env-apllxp7x/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: library/integration_library/integration_library.pyx
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel 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.
Have you seen this before?
franciscovillaescusa commented
Hi John,
I haven't seen this error before but it seems it failed at getting the dependencies needed by Pylians to compile (perhaps cython). Can you perhaps install those separately, i.e.:
python -m pip install Cython
python -m pip install setuptools
python -m pip install numpy
python -m pip install h5py
python -m pip install hdf5plugin
and then try to install Pylians again with
python -m pip install Pylians
Let me know
jwuphysics commented
Hi Paco, thanks for the quick reply. I tried explicitly installing these (plus pyfftw and mpi4py) into a new environment, but I got the same error. I also tried installing on Google Colab, but I got the same error.
I've included the verbose error message here
python -m pip --verbose install Pylians (painting-galaxies)
Using pip 23.2 from /home/john/miniconda3/envs/painting-galaxies/lib/python3.10/site-packages/pip (python 3.10)
Collecting Pylians
Using cached Pylians-0.7.tar.gz (3.2 MB)
Running command pip subprocess to install build dependencies
Collecting setuptools
Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/c7/42/be1c7bbdd83e1bfb160c94b9cafd8e25efc7400346cf7ccdbdb452c467fa/setuptools-68.0.0-py3-none-any.whl.metadata
Using cached setuptools-68.0.0-py3-none-any.whl.metadata (6.4 kB)
Collecting Cython
Obtaining dependency information for Cython from https://files.pythonhosted.org/packages/6f/8c/68139f464aeee699b04ec401b9de0d7e05fdd3a123c4c13429b887e16c8f/Cython-3.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
Using cached Cython-3.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.1 kB)
Collecting numpy
Obtaining dependency information for numpy from https://files.pythonhosted.org/packages/d0/55/559e6f455a066e12058330377259a106b7fefa41c15dbdb1b71070cec429/numpy-1.25.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
Using cached numpy-1.25.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB)
Collecting h5py
Obtaining dependency information for h5py from https://files.pythonhosted.org/packages/0d/7a/e55589e4093cca1934db5e99644c1c2424a9b3aac104b7f6176605a5eeb7/h5py-3.9.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
Using cached h5py-3.9.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting hdf5plugin
Obtaining dependency information for hdf5plugin from https://files.pythonhosted.org/packages/eb/68/3b62574100cc20aeaf302cc6cef866f1675163a5bf1d787b759cb700616b/hdf5plugin-4.1.3-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
Using cached hdf5plugin-4.1.3-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.8 kB)
Using cached setuptools-68.0.0-py3-none-any.whl (804 kB)
Using cached Cython-3.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.6 MB)
Using cached numpy-1.25.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.6 MB)
Using cached h5py-3.9.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.8 MB)
Using cached hdf5plugin-4.1.3-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (40.9 MB)
Installing collected packages: setuptools, numpy, Cython, h5py, hdf5plugin
Successfully installed Cython-3.0.0 h5py-3.9.0 hdf5plugin-4.1.3 numpy-1.25.1 setuptools-68.0.0
Installing build dependencies ... done
Running command Getting requirements to build wheel
Error compiling Cython file:
------------------------------------------------------------
...
# RK4 example1 for debugging
cpdef RK4_example(double[::1] yinit, double x1, double x2, long nstep):
cdef double *result
result = CI.rkdumb(&yinit[0], yinit.shape[0], x1, x2, nstep,
NULL, NULL, 0, example)
^
------------------------------------------------------------
library/integration_library/integration_library.pyx:87:39: Cannot assign type 'void (double, double *, double *, double *, double *, long) except *' to 'void (*)(double, double *, double *, double *, double *, long) noexcept'
Error compiling Cython file:
------------------------------------------------------------
...
cpdef RK4_example2(double[::1] yinit, double x1, double x2, long nstep,
double[::1] a, double[::1] b):
cdef double *result
result = CI.rkdumb(&yinit[0], yinit.shape[0], x1, x2, nstep,
&a[0], &b[0], a.shape[0], example2)
^
------------------------------------------------------------
library/integration_library/integration_library.pyx:97:50: Cannot assign type 'void (double, double *, double *, double *, double *, long) except *' to 'void (*)(double, double *, double *, double *, double *, long) noexcept'
Error compiling Cython file:
------------------------------------------------------------
...
cdef long nok, nbad
nok = nbad = 0
CI.odeint(&yinit[0], yinit.shape[0], x1, x2, eps, h1, hmin, &nok, &nbad,
NULL, NULL, 0, example)
^
------------------------------------------------------------
library/integration_library/integration_library.pyx:110:29: Cannot assign type 'void (double, double *, double *, double *, double *, long) except *' to 'void (*)(double, double *, double *, double *, double *, long) noexcept'
Error compiling Cython file:
------------------------------------------------------------
...
cdef long nok, nbad
nok = nbad = 0
CI.odeint(&yinit[0], yinit.shape[0], x1, x2, eps, h1, hmin, &nok, &nbad,
&a[0], &b[0], a.shape[0], example2)
^
------------------------------------------------------------
library/integration_library/integration_library.pyx:128:40: Cannot assign type 'void (double, double *, double *, double *, double *, long) except *' to 'void (*)(double, double *, double *, double *, double *, long) noexcept'
Error compiling Cython file:
------------------------------------------------------------
...
cdef long nok, nbad
nok = nbad = 0
if function=='log' or function=='sigma':
CI.odeint(&yinit[0], yinit.shape[0], x1, x2, eps, h1, hmin, &nok, &nbad,
&a[0], &b[0], b.shape[0], sigma)
^
------------------------------------------------------------
library/integration_library/integration_library.pyx:147:44: Cannot assign type 'void (double, double *, double *, double *, double *, long) except *' to 'void (*)(double, double *, double *, double *, double *, long) noexcept'
Error compiling Cython file:
------------------------------------------------------------
...
CI.odeint(&yinit[0], yinit.shape[0], x1, x2, eps, h1, hmin, &nok, &nbad,
&a[0], &b[0], b.shape[0], sigma)
elif function=='linear':
CI.odeint(&yinit[0], yinit.shape[0], x1, x2, eps, h1, hmin, &nok, &nbad,
&a[0], &b[0], b.shape[0], linear)
^
------------------------------------------------------------
library/integration_library/integration_library.pyx:151:44: Cannot assign type 'void (double, double *, double *, double *, double *, long) except *' to 'void (*)(double, double *, double *, double *, double *, long) noexcept'
Compiling library/MAS_library/MAS_library.pyx because it changed.
Compiling library/Pk_library/Pk_library.pyx because it changed.
Compiling library/Pk_library/bispectrum_library.pyx because it changed.
Compiling library/MAS_library/field_properties.pyx because it changed.
Compiling library/redshift_space_library/redshift_space_library.pyx because it changed.
Compiling library/smoothing_library/smoothing_library.pyx because it changed.
Compiling library/void_library/void_library.pyx because it changed.
Compiling library/integration_library/integration_library.pyx because it changed.
Compiling library/density_field_library/density_field_library.pyx because it changed.
Compiling library/sorting_library/sorting_library.pyx because it changed.
Compiling library/HI_library/HI_library.pyx because it changed.
Compiling library/HI_clusters_library/HI_clusters_library.pyx because it changed.
[ 1/12] Cythonizing library/HI_clusters_library/HI_clusters_library.pyx
[ 2/12] Cythonizing library/HI_library/HI_library.pyx
[ 3/12] Cythonizing library/MAS_library/MAS_library.pyx
[ 4/12] Cythonizing library/MAS_library/field_properties.pyx
[ 5/12] Cythonizing library/Pk_library/Pk_library.pyx
[ 6/12] Cythonizing library/Pk_library/bispectrum_library.pyx
[ 7/12] Cythonizing library/density_field_library/density_field_library.pyx
[ 8/12] Cythonizing library/integration_library/integration_library.pyx
Traceback (most recent call last):
File "/home/john/miniconda3/envs/painting-galaxies/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/home/john/miniconda3/envs/painting-galaxies/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/john/miniconda3/envs/painting-galaxies/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
File "/tmp/pip-build-env-mezsjbx4/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
File "/tmp/pip-build-env-mezsjbx4/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-mezsjbx4/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 338, in run_setup
exec(code, locals())
File "<string>", line 99, in <module>
File "/tmp/pip-build-env-mezsjbx4/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
cythonize_one(*args)
File "/tmp/pip-build-env-mezsjbx4/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: library/integration_library/integration_library.pyx
error: subprocess-exited-with-error
× Getting requirements to build wheel 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/john/miniconda3/envs/painting-galaxies/bin/python /home/john/miniconda3/envs/painting-galaxies/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py get_requires_for_build_wheel /tmp/tmpwqakncp2
cwd: /tmp/pip-install-bhukjp6q/pylians_88bb8be887814b3d964e4db78390e9f0
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel 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.
ccoulombe commented
I can successfully build Pylians with Cython==0.29.33, the issue seems to be coming from Cython 3.0.0
Using cached Cython-3.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.6 MB)
@franciscovillaescusa Adding setup_requires = ['Cython<3.0.0'] would help to the setup.py.
franciscovillaescusa commented
Thanks @ccoulombe ! @jwuphysics can you try now? I have updated the configuration to use a cython version before 3.0. I'm still having problems installing it on google colab but it may be a different issue there. Let me know
jwuphysics commented
Thank you! I'm at work using my non-linux machine but I'll get back to you in a few hours.
jwuphysics commented
Splendid! Looks like it works 👍
franciscovillaescusa commented
Great! Thanks @jwuphysics for let us know about this issue with Cython that I was not aware of.