Comments (21)
Rebuild is merged. This issue can be closed. Should be ready in a few hours.
from namaster.
Sure sure understood. We are trying to tag v2 so I wanted to make sure nothjng was actually broken.
from namaster.
I am rebuilding the conda package. It was simply out of date. Try again in a bit!
from namaster.
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?
from namaster.
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.
from namaster.
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?
from namaster.
Ahhh wait. I see the issue. It is pyccl. Let me fix it
from namaster.
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!
from namaster.
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.
from namaster.
What is broken with it?
from namaster.
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]
from namaster.
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]
from namaster.
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
.
from namaster.
WeakLensingTracer
works fine for me too.
from namaster.
Your mass function may not have a bias function. Which one are you using?
from namaster.
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
from namaster.
Only tinker10 and shethtormen have bias functions.
from namaster.
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.
from namaster.
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!
from namaster.
So the tinker mass function does not have a bias function
Use tinker10 and it will work.
from namaster.
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!
from namaster.
Related Issues (20)
- nan's with map read from fits file HOT 2
- random seed in synfast_flat
- I am not seeing a real improvement in performance, but it might be my own compiler being a bit outdated. Still worth merging, since libsharp2 is the one being maintained, but will open an issue to investigate further.
- configure fails to find cfitsio HOT 7
- Missing version number in pymaster
- Help installing NaMaster on M2 macOS HOT 17
- cannot find _nmtbin module HOT 4
- Error when setting lmax < 3 * nside - 1 in compute_full_master HOT 2
- Missing different lmax for mask and coupling coefficients for covariances HOT 1
- f_ell does not seem to do anything in NmtBin HOT 1
- Conda installation fails if conda installs gsl=2.7.1 instead of gsl=2.7
- Inconsistency in results between MacOS and Ubuntu HOT 13
- Make exception message more informative
- Weird power in compute_coupled_cell HOT 3
- pymaster installation problem HOT 3
- Pseudo-cl's in the covariance computation - pixel window function HOT 3
- Floating point errors with full sky CAR pixellization HOT 1
- NaMaster installation CFITSIO issue
- Apodisation window functions HOT 3
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from namaster.