Comments (21)
beckermr
commented on September 11, 2024
1
Rebuild is merged. This issue can be closed. Should be ready in a few hours.
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beckermr
commented on September 11, 2024
1
Sure sure understood. We are trying to tag v2 so I wanted to make sure nothjng was actually broken.
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beckermr
commented on September 11, 2024
I am rebuilding the conda package. It was simply out of date. Try again in a bit!
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nikfilippas
commented on September 11, 2024
I attempted another install of NaMaster through conda and apparently it still tries to install gsl=2.5, instead of gsl=2.6+.
I did this twice, one time trying with just conda install -c conda-forge namaster, and another one (after I had looked up conda search namaster to see which is the latest version) with conda install -c conda-forge namaster=1.0. It is still conflicting with gsl, and here are the packages it is trying to install:
chealpix conda-forge/linux-64::chealpix-3.30.0-h14c3975_1000
fftw conda-forge/linux-64::fftw-3.3.8-nompi_h7f3a6c3_1109
gsl conda-forge/linux-64::gsl-2.5-h294904e_1
libsharp conda-forge/linux-64::libsharp-1.0.0-h14c3975_1000
namaster conda-forge/linux-64::namaster-1.0-py37heade8f8_1
Am I doing something wrong? Where is the fixed version located?
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nikfilippas
commented on September 11, 2024
At the moment, I have found a workaround by building CCL and creating a symbolic link in my conda environment pointing to the pyccl directory in the CCL build, so it is not very urgent.
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beckermr
commented on September 11, 2024
Conda forge globally uses a single version of gsl. It is currently 2.5. This ensures that all codes can use the same env. If the install works with 2.5, then there is no bug. It sounds like it does, right?
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beckermr
commented on September 11, 2024
Ahhh wait. I see the issue. It is pyccl. Let me fix it
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beckermr
commented on September 11, 2024
Alright. It turns out pyccl was using the wrong version of gsl for technical reasons related to conda. I think this is fixed now. Try again in a bit and sorry for the trouble!
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nikfilippas
commented on September 11, 2024
Alright, thanks a lot, it w̶o̶r̶k̶s̶ (doesn't work) now. No package conflicts but CCL rc3, which is the most recent version of CCL on conda, is broken. This is not an issue with NaMaster though, so I am closing this and opening a new issue on CCL's page.
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beckermr
commented on September 11, 2024
What is broken with it?
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beckermr
commented on September 11, 2024
Everything works great for me
(anl) localhost:~ Matt$ conda install pyccl
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Users/Matt/miniconda3/envs/anl
added / updated specs:
- pyccl
The following packages will be downloaded:
package | build
---------------------------|-----------------
camb-1.0.6 | py37hb7221d7_3 878 KB conda-forge
gfortran_impl_osx-64-7.3.0 | hf4212f2_2 9.3 MB conda-forge
gfortran_osx-64-7.3.0 | h22b1bf0_6 21 KB conda-forge
gsl-2.5 | ha2d443c_1 2.7 MB conda-forge
isl-0.19 | 0 1.3 MB conda-forge
pycamb-1.0.6 | py37_3 33 KB conda-forge
pyccl-2.0.0rc3 | py37h96385ee_2 642 KB conda-forge
------------------------------------------------------------
Total: 14.8 MB
The following NEW packages will be INSTALLED:
camb conda-forge/osx-64::camb-1.0.6-py37hb7221d7_3
cctools conda-forge/osx-64::cctools-921-h5ba7a2e_4
clang conda-forge/osx-64::clang-9.0.0-h28b9765_1
fastcache conda-forge/osx-64::fastcache-1.1.0-py37h01d97ff_0
gfortran_impl_osx~ conda-forge/osx-64::gfortran_impl_osx-64-7.3.0-hf4212f2_2
gfortran_osx-64 conda-forge/osx-64::gfortran_osx-64-7.3.0-h22b1bf0_6
gmp conda-forge/osx-64::gmp-6.1.2-h0a44026_1000
gmpy2 conda-forge/osx-64::gmpy2-2.1.0b1-py37h1744cca_0
gsl conda-forge/osx-64::gsl-2.5-ha2d443c_1
isl conda-forge/osx-64::isl-0.19-0
ld64 conda-forge/osx-64::ld64-409.12-h3c32e8a_4
libllvm9 conda-forge/osx-64::libllvm9-9.0.0-h770b8ee_2
mpc conda-forge/osx-64::mpc-1.1.0-h3aece09_1006
mpfr conda-forge/osx-64::mpfr-4.0.2-h44b798e_0
mpmath conda-forge/noarch::mpmath-1.1.0-py_0
pycamb conda-forge/osx-64::pycamb-1.0.6-py37_3
pyccl conda-forge/osx-64::pyccl-2.0.0rc3-py37h96385ee_2
sympy conda-forge/osx-64::sympy-1.4-py37_0
tapi conda-forge/osx-64::tapi-1000.10.8-h770b8ee_3
Proceed ([y]/n)? y
Downloading and Extracting Packages
pycamb-1.0.6 | 33 KB | ############################################################################################################################################################# | 100%
gfortran_impl_osx-64 | 9.3 MB | ############################################################################################################################################################# | 100%
gsl-2.5 | 2.7 MB | ############################################################################################################################################################# | 100%
isl-0.19 | 1.3 MB | ############################################################################################################################################################# | 100%
pyccl-2.0.0rc3 | 642 KB | ############################################################################################################################################################# | 100%
gfortran_osx-64-7.3. | 21 KB | ############################################################################################################################################################# | 100%
camb-1.0.6 | 878 KB | ############################################################################################################################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
INFO: deactivate-gfortran_osx-64.sh made the following environmental changes:
+LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/Matt/miniconda3/lib -L/Users/Matt/miniconda3/lib
(anl) localhost:~ Matt$ ipy
Python 3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.8.0 -- An enhanced Interactive Python. Type '?' for help.
In [1]: import pyccl as ccl
...: import numpy as np
...:
...: # Create new Cosmology object with a given set of parameters. This keeps track
...: # of previously-computed cosmological functions
...: cosmo = ccl.Cosmology(
...: Omega_c=0.27, Omega_b=0.045, h=0.67, sigma8=0.8, n_s=0.96,
...: transfer_function='bbks')
...:
...: # Define a simple binned galaxy number density curve as a function of redshift
...: z_n = np.linspace(0., 1., 200)
...: n = np.ones(z_n.shape)
...:
...: # Create objects to represent tracers of the weak lensing signal with this
...: # number density (with has_intrinsic_alignment=False)
...: lens1 = ccl.WeakLensingTracer(cosmo, dndz=(z_n, n))
...: lens2 = ccl.WeakLensingTracer(cosmo, dndz=(z_n, n))
...:
...: # Calculate the angular cross-spectrum of the two tracers as a function of ell
...: ell = np.arange(2, 10)
...: cls = ccl.angular_cl(cosmo, lens1, lens2, ell)
...: print(cls)
[8.66780883e-09 1.17822402e-08 1.30401125e-08 1.35000276e-08
1.35645508e-08 1.34173983e-08 1.31528650e-08 1.28233003e-08]
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beckermr
commented on September 11, 2024
CAMB works too
In [2]: import pyccl as ccl
...: import numpy as np
...:
...: # Create new Cosmology object with a given set of parameters. This keeps track
...: # of previously-computed cosmological functions
...: cosmo = ccl.Cosmology(
...: Omega_c=0.27, Omega_b=0.045, h=0.67, sigma8=0.8, n_s=0.96)
...:
...: # Define a simple binned galaxy number density curve as a function of redshift
...: z_n = np.linspace(0., 1., 200)
...: n = np.ones(z_n.shape)
...:
...: # Create objects to represent tracers of the weak lensing signal with this
...: # number density (with has_intrinsic_alignment=False)
...: lens1 = ccl.WeakLensingTracer(cosmo, dndz=(z_n, n))
...: lens2 = ccl.WeakLensingTracer(cosmo, dndz=(z_n, n))
...:
...: # Calculate the angular cross-spectrum of the two tracers as a function of ell
...: ell = np.arange(2, 10)
...: cls = ccl.angular_cl(cosmo, lens1, lens2, ell)
...: print(cls)
[9.31280743e-09 1.26656483e-08 1.40114330e-08 1.44869501e-08
1.45274865e-08 1.43334458e-08 1.40087568e-08 1.36118779e-08]
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nikfilippas
commented on September 11, 2024
I was about to open an issue on CCL's page, but since you're asking:
Try running ccl.halo_bias(cosmo, 1e14, 1), for example, and you get the following error:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/koukoufilippasn/anaconda3/envs/spyder4b/lib/python3.7/site-packages/pyccl/massfunction.py", line 70, in halo_bias
lib.halo_bias_vec, cosmo, halo_mass, a, overdensity)
File "/home/koukoufilippasn/anaconda3/envs/spyder4b/lib/python3.7/site-packages/pyccl/pyutils.py", line 281, in _vectorize_fn4
check(status, cosmo_in)
File "/home/koukoufilippasn/anaconda3/envs/spyder4b/lib/python3.7/site-packages/pyccl/pyutils.py", line 29, in check
raise CCLError("Error %s: %s" % (error_types[status], msg))
pyccl.errors.CCLError: Error CCL_ERROR_MF: ccl_massfunc.c: ccl_halo_b1(): No b(M) fitting function implemented for mass_function_method: 1
PS: Only CCL rc3 can be installed alongside NaMaster with conda, if someone tries to install an older version (currently the only other available is rc2), they still get package conflicts with gsl.
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nikfilippas
commented on September 11, 2024
WeakLensingTracer works fine for me too.
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beckermr
commented on September 11, 2024
Your mass function may not have a bias function. Which one are you using?
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beckermr
commented on September 11, 2024
In [1]: import pyccl as ccl
...: import numpy as np
...:
...: # Create new Cosmology object with a given set of parameters. This keeps track
...: # of previously-computed cosmological functions
...: cosmo = ccl.Cosmology(
...: Omega_c=0.27, Omega_b=0.045, h=0.67, sigma8=0.8, n_s=0.96)
...:
...: # Define a simple binned galaxy number density curve as a function of redshift
...: z_n = np.linspace(0., 1., 200)
...: n = np.ones(z_n.shape)
...:
...: # Create objects to represent tracers of the weak lensing signal with this
...: # number density (with has_intrinsic_alignment=False)
...: lens1 = ccl.WeakLensingTracer(cosmo, dndz=(z_n, n))
...: lens2 = ccl.WeakLensingTracer(cosmo, dndz=(z_n, n))
...:
...: # Calculate the angular cross-spectrum of the two tracers as a function of ell
...: ell = np.arange(2, 10)
...: cls = ccl.angular_cl(cosmo, lens1, lens2, ell)
...: print(cls)
[9.31280743e-09 1.26656483e-08 1.40114330e-08 1.44869501e-08
1.45274865e-08 1.43334458e-08 1.40087568e-08 1.36118779e-08]
In [2]: ccl.halo_bias(cosmo, 1e14, 1)
Out[2]: 1.8196490114414752
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beckermr
commented on September 11, 2024
Only tinker10 and shethtormen have bias functions.
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nikfilippas
commented on September 11, 2024
Yes, if I remember correctly @damonge helped me to hard code the bias function before building CCL, and this is still work in progress. I use the 'tinker' mass function.
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nikfilippas
commented on September 11, 2024
And I've seen that on CCL's page it has been suggested that mixed models should be allowed in case anyone wants to try new stuff. So don't worry about it for now. Thanks a lot for your help!
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beckermr
commented on September 11, 2024
So the tinker mass function does not have a bias function
Use tinker10 and it will work.
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nikfilippas
commented on September 11, 2024
Yes, yes, but mixed models is another issue which is currently on the table for CCL. (For example, one might want to define a 'tinker' cosmology object, but use the 'tinker10' bias function.)
Thanks again Matt!
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