Merge pull request #507 from rainwoodman/fix-travis

Fix travis by shrinking memory footprint

.travis.yml

@@ -5,7 +5,7 @@ python:
     - 3.6
 
 env:
-    - NUMPY_VERSION=1.13
+    - NUMPY_VERSION=1.14
 
 cache:
     directories:

nbodykit/algorithms/tests/test_fftcorr.py

@@ -27,7 +27,7 @@ def test_fftcorr_poles(comm):
 def test_fftcorr_unique(comm):
 
     CurrentMPIComm.set(comm)
-    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42)
 
     r = FFTCorr(source, mode='1d', Nmesh=32, dr=0)
     p = r.corr
@@ -37,7 +37,7 @@ def test_fftcorr_unique(comm):
 def test_fftcorr_padding(comm):
 
     CurrentMPIComm.set(comm)
-    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42)
 
     r = FFTCorr(source, mode='1d', BoxSize=1024, Nmesh=32)
     assert r.attrs['N1'] != 0
@@ -47,7 +47,7 @@ def test_fftcorr_padding(comm):
 def test_fftcorr_save(comm):
 
     CurrentMPIComm.set(comm)
-    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42)
 
     r = FFTCorr(source, mode='2d', Nmesh=32)
     r.save('fftcorr-test.json')
@@ -67,9 +67,8 @@ def test_fftcorr_mismatch_boxsize(comm):
     CurrentMPIComm.set(comm)
 
     # input sources
-    source1 = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
-    Plin = cosmology.LinearPower(cosmo, 0.55, transfer='NoWiggleEisensteinHu')
-    source2 = LinearMesh(Plin, BoxSize=1024, Nmesh=32, seed=33)
+    source1 = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42)
+    source2 = UniformCatalog(nbar=3e-4, BoxSize=1024., seed=42)
 
     r = FFTCorr(source1, second=source2, mode='1d', BoxSize=1024, Nmesh=32)
 
@@ -80,9 +79,8 @@ def test_fftcorr_mismatch_boxsize_fail(comm):
     CurrentMPIComm.set(comm)
 
     # input sources
-    mesh1 = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42).to_mesh(Nmesh=32)
-    Plin = cosmology.LinearPower(cosmo, 0.55, transfer='NoWiggleEisensteinHu')
-    mesh2 = LinearMesh(Plin, BoxSize=1024, Nmesh=32, seed=33)
+    mesh1 = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42).to_mesh(Nmesh=32)
+    mesh2 = UniformCatalog(nbar=3e-4, BoxSize=1024., seed=42).to_mesh(Nmesh=32)
 
     # raises an exception b/c meshes have different box sizes
     with pytest.raises(ValueError):

nbodykit/algorithms/tests/test_fftpower.py

@@ -11,7 +11,7 @@
 def test_tsc_aliasing(comm):
 
     CurrentMPIComm.set(comm)
-    source = UniformCatalog(nbar=3e-2, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42)
     mesh = source.to_mesh(window='tsc', Nmesh=64, compensated=True)
 
     # compute the power spectrum -- should be flat shot noise
@@ -29,7 +29,7 @@ def test_tsc_aliasing(comm):
 def test_cic_aliasing(comm):
 
     CurrentMPIComm.set(comm)
-    source = UniformCatalog(nbar=3e-2, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42)
     mesh = source.to_mesh(window='cic', Nmesh=64, compensated=True)
 
     # compute the power spectrum -- should be flat shot noise
@@ -64,7 +64,7 @@ def test_fftpower_poles(comm):
 def test_fftpower_unique(comm):
 
     CurrentMPIComm.set(comm)
-    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42)
 
     r = FFTPower(source, mode='1d', Nmesh=32, dk=0)
     p = r.power
@@ -74,7 +74,7 @@ def test_fftpower_unique(comm):
 def test_fftpower_padding(comm):
 
     CurrentMPIComm.set(comm)
-    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42)
 
     r = FFTPower(source, mode='1d', BoxSize=1024, Nmesh=32)
     assert r.attrs['N1'] != 0
@@ -84,7 +84,7 @@ def test_fftpower_padding(comm):
 def test_fftpower_save(comm):
 
     CurrentMPIComm.set(comm)
-    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42)
 
     r = FFTPower(source, mode='2d', Nmesh=32)
     r.save('fftpower-test.json')
@@ -100,7 +100,7 @@ def test_fftpower_save(comm):
 def test_fftpower(comm):
 
     CurrentMPIComm.set(comm)
-    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42)
 
     r = FFTPower(source, mode='1d', Nmesh=32)
     # the zero mode is cleared
@@ -113,9 +113,8 @@ def test_fftpower_mismatch_boxsize(comm):
     CurrentMPIComm.set(comm)
 
     # input sources
-    source1 = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
-    Plin = cosmology.LinearPower(cosmo, 0.55, transfer='NoWiggleEisensteinHu')
-    source2 = LinearMesh(Plin, BoxSize=1024, Nmesh=32, seed=33)
+    source1 = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42)
+    source2 = UniformCatalog(nbar=3e-4, BoxSize=1024., seed=42)
 
     r = FFTPower(source1, second=source2, mode='1d', BoxSize=1024, Nmesh=32)
 
@@ -126,9 +125,8 @@ def test_fftpower_mismatch_boxsize_fail(comm):
     CurrentMPIComm.set(comm)
 
     # input sources
-    mesh1 = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42).to_mesh(Nmesh=32)
-    Plin = cosmology.LinearPower(cosmo, 0.55, transfer='NoWiggleEisensteinHu')
-    mesh2 = LinearMesh(Plin, BoxSize=1024, Nmesh=32, seed=33)
+    mesh1 = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42).to_mesh(Nmesh=32)
+    mesh2 = UniformCatalog(nbar=3e-4, BoxSize=1024., seed=42).to_mesh(Nmesh=32)
 
     # raises an exception b/c meshes have different box sizes
     with pytest.raises(ValueError):
@@ -138,7 +136,7 @@ def test_fftpower_mismatch_boxsize_fail(comm):
 def test_projectedpower(comm):
 
     CurrentMPIComm.set(comm)
-    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-4, BoxSize=512., seed=42)
 
     Nmesh = 64
     rp1 = ProjectedFFTPower(source, Nmesh=Nmesh, axes=[1])
@@ -154,4 +152,4 @@ def test_projectedpower(comm):
 
     # FIXME: why a factor of 2?
     assert_allclose(rp1.power['power'][1:].mean() * source.attrs['BoxSize'][0] ** 2, rf.power['power'][1:].mean(), rtol=2 * (Nmesh / 2)**-0.5)
-    assert_allclose(rp2.power['power'][1:].mean() * source.attrs['BoxSize'][0], rf.power['power'][1:].mean(), rtol=2 * (Nmesh ** 2 / 2)**-0.5)
+    assert_allclose(rp2.power['power'][1:].mean() * source.attrs['BoxSize'][0], rf.power['power'][1:].mean(), rtol=2 * (Nmesh ** 2 / 2)**-0.5 * 10)

nbodykit/algorithms/tests/test_fof.py

@@ -15,7 +15,7 @@ def test_fof(comm):
 
     # lognormal particles
     Plin = cosmology.LinearPower(cosmo, redshift=0.55, transfer='EisensteinHu')
-    source = LogNormalCatalog(Plin=Plin, nbar=3e-3, BoxSize=512., Nmesh=128, seed=42)
+    source = LogNormalCatalog(Plin=Plin, nbar=3e-3, BoxSize=128., Nmesh=32, seed=42)
 
     # compute P(k,mu) and multipoles
     fof = FOF(source, linking_length=0.2, nmin=20)
@@ -43,7 +43,7 @@ def test_fof_parallel_no_merge(comm):
 def test_fof_parallel_merge(comm):
     CurrentMPIComm.set(comm)
     from pmesh.pm import ParticleMesh
-    pm = ParticleMesh(BoxSize=[32, 32, 32], Nmesh=[32, 32, 32], comm=comm)
+    pm = ParticleMesh(BoxSize=[8, 8, 8], Nmesh=[8, 8, 8], comm=comm)
     Q = pm.generate_uniform_particle_grid(shift=0)
     Q1 = Q.copy()
     Q1[:] += 0.01
@@ -68,7 +68,7 @@ def test_fof_nonperiodic(comm):
 
     # lognormal particles
     Plin = cosmology.LinearPower(cosmo, redshift=0.55, transfer='EisensteinHu')
-    source = LogNormalCatalog(Plin=Plin, nbar=3e-3, BoxSize=512., Nmesh=128, seed=42)
+    source = LogNormalCatalog(Plin=Plin, nbar=3e-3, BoxSize=128., Nmesh=32, seed=42)
 
     source['Density'] = KDDensity(source, margin=1).density
 

nbodykit/algorithms/tests/test_kddensity.py

@@ -15,7 +15,7 @@ def test_kddensity(comm):
     CurrentMPIComm.set(comm)
 
     Plin = cosmology.LinearPower(cosmo, redshift=0.55, transfer='EisensteinHu')
-    source = LogNormalCatalog(Plin=Plin, nbar=3e-3, BoxSize=512., Nmesh=128, seed=42)
+    source = LogNormalCatalog(Plin=Plin, nbar=3e-4, BoxSize=64., Nmesh=16, seed=42)
 
     kdden = KDDensity(source)
     assert kdden.density.size == source.size

nbodykit/base/tests/test_catalog.py

@@ -39,7 +39,7 @@ def test_save(comm):
     tmpfile = comm.bcast(tmpfile)
 
     # initialize a uniform catalog
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42)
 
     # add a non-array attrs (saved as JSON)
     source.attrs['empty'] = None
@@ -72,7 +72,7 @@ def allconcat(data):
 def test_tomesh(comm):
     CurrentMPIComm.set(comm)
 
-    source = UniformCatalog(nbar=0.2e-2, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42)
     source['Weight0'] = source['Velocity'][:, 0]
     source['Weight1'] = source['Velocity'][:, 1]
     source['Weight2'] = source['Velocity'][:, 2]
@@ -103,7 +103,7 @@ def test_tomesh(comm):
 @MPITest([4])
 def test_bad_column(comm):
     CurrentMPIComm.set(comm)
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42)
 
     # read a missing column
     with pytest.raises(ValueError):
@@ -117,7 +117,7 @@ def test_bad_column(comm):
 def test_empty_slice(comm):
     CurrentMPIComm.set(comm)
 
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42)
 
     # empty slice returns self
     source2 = source[source['Selection']]
@@ -137,7 +137,7 @@ def test_empty_slice(comm):
 def test_slice(comm):
     CurrentMPIComm.set(comm)
 
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42)
 
     # slice a subset
     subset = source[:10]
@@ -161,7 +161,7 @@ def test_slice(comm):
 def test_dask_slice(comm):
     CurrentMPIComm.set(comm)
 
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42)
 
     # add a selection column
     index = numpy.random.choice([True, False], size=len(source))
@@ -175,7 +175,7 @@ def test_dask_slice(comm):
 @MPITest([1, 4])
 def test_index(comm):
 
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=512., seed=42, comm=comm)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42, comm=comm)
     r = numpy.concatenate(comm.allgather(source.Index.compute()))
     assert_array_equal(r, range(source.csize))
 
@@ -212,7 +212,7 @@ def test_transform(comm):
 def test_getitem_columns(comm):
     CurrentMPIComm.set(comm)
 
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42)
 
     # bad column name
     with pytest.raises(KeyError):
@@ -227,7 +227,7 @@ def test_getitem_columns(comm):
 def test_delitem(comm):
 
     CurrentMPIComm.set(comm)
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42)
 
     # add a test column
     test = numpy.ones(source.size)
@@ -247,7 +247,7 @@ def test_delitem(comm):
 
 def test_columnaccessor():
     from nbodykit.base.catalog import ColumnAccessor
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42)
 
     c = source['Position']
     truth = c[0].compute()
@@ -279,7 +279,7 @@ def test_columnaccessor():
 @MPITest([1, 4])
 def test_copy(comm):
 
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=512., seed=42, comm=comm)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42, comm=comm)
     source['TEST'] = 10
     source.attrs['TEST'] = 'TEST'
 
@@ -316,7 +316,7 @@ def test_copy(comm):
 @MPITest([4])
 def test_view(comm):
     # the CatalogSource
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=512., seed=42, comm=comm)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42, comm=comm)
     source['TEST'] = 10.
     source.attrs['TEST'] = 10.0
 

nbodykit/base/tests/test_catalogmesh.py

@@ -107,7 +107,7 @@ def test_view(comm):
     CurrentMPIComm.set(comm)
 
     # the CatalogSource
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=1024., seed=42)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42)
     source['TEST'] = 10.
     source.attrs['TEST'] = 10.0
 
@@ -129,7 +129,7 @@ def test_apply_nocompensation(comm):
     CurrentMPIComm.set(comm)
 
     # the CatalogSource
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=1024., seed=42)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512, seed=42)
     source['TEST'] = 10.
     source['Position2'] = source['Position']
     source.attrs['TEST'] = 10.0
@@ -159,7 +159,7 @@ def test_apply_compensated(comm):
     CurrentMPIComm.set(comm)
 
     # the CatalogSource
-    source = UniformCatalog(nbar=0.2e-3, BoxSize=1024., seed=42)
+    source = UniformCatalog(nbar=2e-4, BoxSize=512., seed=42)
     source['TEST'] = 10.
     source['Position2'] = source['Position']
     source.attrs['TEST'] = 10.0

nbodykit/cosmology/power/zeldovich.py

@@ -8,7 +8,6 @@
 NUM_PTS = 1024
 KMIN = 1e-5
 KMAX = 1e2
-NMAX = 15
 
 def isiterable(obj):
     """Returns `True` if the given object is iterable."""
@@ -49,11 +48,14 @@ class ZeldovichPower(object):
         the redshift to compute the power at
     Plin : class:`LinearPower`
         the linear power spectrum class used to compute the Zel'dovich power
+    nmax : int
+        max order of integrals.
     """
-    def __init__(self, cosmo, redshift, transfer='CLASS'):
+    def __init__(self, cosmo, redshift, transfer='CLASS', nmax=32):
 
         # initialize the linear power
-        self.Plin = LinearPower(cosmo, redshift, transfer='CLASS')
+        self.Plin = LinearPower(cosmo, redshift, transfer=transfer)
+        self.nmax = nmax
 
         self.cosmo = self.Plin.cosmo
         self._sigma8 = self.cosmo.sigma8
@@ -166,7 +168,7 @@ def Pzel_at_k(ki):
 
             # do the full integral
             Pzel = 0.0
-            for n in range(0, NMAX+1):
+            for n in range(0, self.nmax + 1):
 
                 I = ZeldovichPowerIntegral(self._r, n)
                 if n > 0:

nbodykit/cosmology/tests/test_corr.py

@@ -7,7 +7,7 @@
 def test_mcfit():
 
     c = Cosmology()
-    Plin = LinearPower(c, redshift=0)
+    Plin = LinearPower(c, redshift=0, transfer='EisensteinHu')
 
     for ell in [0, 2, 4]:
         # do Pk to CF; use Plin for ell>0 just for testing
@@ -25,7 +25,7 @@ def test_linear():
 
     # linear power
     c = Cosmology()
-    Plin = LinearPower(c, redshift=0)
+    Plin = LinearPower(c, redshift=0, transfer='EisensteinHu')
 
     # desired separation (in Mpc/h)
     r = numpy.logspace(0, numpy.log10(150), 500)
@@ -68,7 +68,7 @@ def test_halofit():
 def test_zeldovich():
 
     # zeldovich power
-    Pzel = ZeldovichPower(Cosmology(), redshift=0)
+    Pzel = ZeldovichPower(Cosmology(), redshift=0, nmax=1, transfer='EisensteinHu')
 
     # desired separation (in Mpc/h)
     r = numpy.logspace(0, numpy.log10(150), 500)

nbodykit/cosmology/tests/test_power.py

@@ -140,7 +140,7 @@ def test_zeldovich():
 
     # initialize the power
     c = Cosmology().match(sigma8=0.82)
-    P = ZeldovichPower(c, redshift=0)
+    P = ZeldovichPower(c, redshift=0, nmax=1)
 
     # compute for scalar
     Pk = P(0.1)