Comments (5)
For posterity, here is what I did:
module load PrgEnv-gnu
module load gsl
conda create --name nbodykit_env python=3.7 pip
env MPICC=cc python -m pip install --no-cache-dir mpi4py
srun -n 5 python -m mpi4py.bench helloworld # test mpi4py
pip install numpy cython
pip install nbodykit[extras]
which seems to work on a perlmutter compute node
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Lagging behind Biwei I am just now running into this issue now that cori is gone forever (and have not yet found a way for this to work).
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Yu's suggestion works for me! I manually install the nbodykit dependencies and nbodykit with PrgEnv-gnu and pip install. Have you tried this?
By the way, if you are going to run nbodykit on jupyter lab, I think the conda install should work.
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@rainwoodman As you alluded to toward the top of this issue, recreating the bcast-pip scripts would be nice to have - I am running some <4 node jobs and am seeing 5-10 mins of startup time. IIRC bcast-pip improves this.
Biwei and I were discussing this today and may have some bandwidth to do this if you can get us started?
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Related Issues (20)
- support for indexing in newer `dask` release HOT 2
- Bug in nbodykit.transform.CartesianToSky
- nersc installation page doesn't exist HOT 1
- `CatalogMesh.to_real_field()` output attributes HOT 1
- Help with parallelising nbodykit code HOT 5
- TPCF calculation error: "Corrfunc.mocks.DDsmu_mocks.DDsmu_mock" fails.
- Problem with painting to mesh if value has zero mean HOT 5
- ```HDFCatalog.to_mesh``` generate negative values for the density field 'delta+1'. HOT 6
- FKPCatalog failing in absence of N(z)
- Trouble understanding the matter power spectrum of lognormal mocks
- Unequal shape partition during MPI parallel mesh.
- not read in correct file in FITs format HOT 4
- FFTPower in redshift-space produces nan in the output (related to #663)
- MPI Issue on Perlmutter HOT 1
- Is there any way to parallelize the computation of multiple convolutions? HOT 8
- Does this work on Python 3.7 and later? HOT 2
- Tutorial on readthedocs: FFTPower requires `mode` argument HOT 1
- Kdcount building fail during cython build on NERSC HOT 2
- Creating a linear mesh from a CLASS power spectrum.
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