Ormorod cmake

.github/workflows/CI.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [ master ]
   pull_request:
-    branches: [ master ]
+    branches: [ master, cmake-dev ]
 # don't run the CRON part in my fork
 #  schedule:
 #    - cron: "0 0 * * *"
@@ -42,3 +42,44 @@ jobs:
 
     - name: Test pypolychord (MPI)
       run: mpirun -np 2 python run_pypolychord.py
+
+  pip_macos:
+    runs-on: macos-12
+    # env:
+    #   FC: gfortran-11
+    #   # CXX: gcc-11
+    #   CXX: gfortran-11
+    strategy:
+      matrix:
+        # cc: [gcc]
+        cc: [clang]
+        python-version: [3.9.13]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        brew install cmake openmpi gcc gfortran 
+        python -m pip install --upgrade pip
+
+    - name: Install pypolychord
+      run: |
+        python -m pip install -v .
+
+    - name: Import pypolychord
+      run: python -c "import pypolychord"
+
+    - name: Hello world
+      run: python hello_world.py
+
+    - name: Test pypolychord
+      run: |
+        python run_pypolychord.py
+
+    # - name: Test pypolychord (MPI)
+    #   run: mpirun -np 2 python run_pypolychord.py

CMakeLists.txt

@@ -82,9 +82,10 @@ if (python)
     # The Compiled .so file
     #################################################################
 
+
     # PyPolyChord stuff
     message(STATUS "Enabling Python package build")
-    find_package(Python3 COMPONENTS Interpreter Development NumPy REQUIRED)
+    find_package(Python3 COMPONENTS Interpreter Development NumPy REQUIRED) 
 
     # find out the suffix for the current python version
     EXECUTE_PROCESS(
@@ -112,31 +113,5 @@ if (python)
     # place all outputs in one place
     install(TARGETS _pypolychord
             LIBRARY DESTINATION ${target_lib_dir})
-
-    #################################################################
-    # The simple python module
-    #################################################################
-
-    set(SETUP_PY_IN "${CMAKE_CURRENT_SOURCE_DIR}/setup_cmake_template.py")
-    set(SETUP_PY "${CMAKE_CURRENT_BINARY_DIR}/setup.py")
-    set(DEPS "${CMAKE_CURRENT_SOURCE_DIR}/pypolychord/__init__.py")
-    set(OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/build/timestamp") # dummy target for dependence
-
-    # fill in the variables of the setup.py file
-    configure_file(${SETUP_PY_IN} ${SETUP_PY})
-
-    # custom target
-    add_custom_command(OUTPUT ${OUTPUT}
-            COMMAND ${Python3_EXECUTABLE} ${SETUP_PY} build
-            COMMAND ${CMAKE_COMMAND} -E touch ${OUTPUT}
-            DEPENDS ${DEPS} _pypolychord)
-    add_custom_target(target ALL DEPENDS ${OUTPUT})
-
-    # installation with setup.py
-    if (python_user_install)
-        install(CODE "execute_process(COMMAND ${Python3_EXECUTABLE} ${SETUP_PY} install)")
-    else (python_user_install)
-        install(CODE "execute_process(COMMAND ${Python3_EXECUTABLE} ${SETUP_PY} install --user)")
-    endif (python_user_install)
-
+
 endif (python)

Makefile_cray

@@ -10,13 +10,13 @@ LDSHARED = $(LD) -shared
 # Archive tool
 AR = ar rv
 
-FFLAGS += -fpp -fpic -qopenmp -dynamic
-CXXFLAGS += -fpic -qopenmp -dynamic
+FFLAGS += -cpp -fpic -fopenmp -dynamic
+CXXFLAGS += -fpic -fopenmp -dynamic
 CFLAGS += -fpic
 #setting for Edison/Cori on NERSC
 ifneq ($(NERSC_HOST),)
-FFLAGS += -axMIC-AVX512,CORE-AVX2
-CXXFLAGS += -axMIC-AVX512,CORE-AVX2
+FFLAGS += -ffree-line-length-none -fallow-argument-mismatch 
+CXXFLAGS += -ffree-line-length-none -fallow-argument-mismatch 
 endif
 
 ifdef IPO

hello_world.py

@@ -0,0 +1,57 @@
+print("hello world")
+from scipy.special import erfinv
+print("from numpy import pi, log, sqrt")
+from numpy import pi, log, sqrt
+print("import pypolychord")
+import pypolychord
+print("from pypolychord.settings import PolyChordSettings")
+from pypolychord.settings import PolyChordSettings
+print("from pypolychord.priors import UniformPrior")
+from pypolychord.priors import UniformPrior
+try:
+    from mpi4py import MPI
+except ImportError:
+    pass
+
+
+#| Define a four-dimensional spherical gaussian likelihood,
+#| width sigma=0.1, centered on the 0 with one derived parameter.
+#| The derived parameter is the squared radius
+
+nDims = 4
+nDerived = 1
+sigma = 0.1
+
+def likelihood(theta):
+    """ Simple Gaussian Likelihood"""
+
+    nDims = len(theta)
+    r2 = sum(theta**2)
+    logL = -log(2*pi*sigma*sigma)*nDims/2.0
+    logL += -r2/2/sigma/sigma
+
+    return logL, [r2]
+
+#| Define a box uniform prior from -1 to 1
+
+def prior(hypercube):
+    """ Uniform prior from [-1,1]^D. """
+    return UniformPrior(-1, 1)(hypercube)
+
+#| Optional dumper function giving run-time read access to
+#| the live points, dead points, weights and evidences
+
+def dumper(live, dead, logweights, logZ, logZerr):
+    print("Last dead point:", dead[-1])
+
+#| Initialise the settings
+print("about to create settings")
+settings = PolyChordSettings(nDims, nDerived)
+settings.file_root = 'gaussian'
+settings.nlive = 200
+settings.do_clustering = True
+settings.read_resume = False
+
+#| Run PolyChord
+print("about to run_pypolychord", flush=True)
+output = pypolychord.run_polychord(likelihood, nDims, nDerived, settings, prior, dumper)

pypolychord/polychord.py

@@ -176,6 +176,9 @@ def wrap_loglikelihood(theta, phi):
     def wrap_prior(cube, theta):
         theta[:] = prior(cube)
 
+    settings.grade_dims = [int(d) for d in settings.grade_dims]
+    settings.nlives = {float(logL):int(nlive) for logL, nlive in settings.nlives.items()}
+
     # Run polychord from module library
     _pypolychord.run(wrap_loglikelihood,
                      wrap_prior,

run_pypolychord.py

@@ -1,6 +1,10 @@
+print("from numpy import pi, log, sqrt")
 from numpy import pi, log, sqrt
+print("import pypolychord")
 import pypolychord
+print("from pypolychord.settings import PolyChordSettings")
 from pypolychord.settings import PolyChordSettings
+print("from pypolychord.priors import UniformPrior")
 from pypolychord.priors import UniformPrior
 try:
     from mpi4py import MPI
@@ -39,15 +43,15 @@ def dumper(live, dead, logweights, logZ, logZerr):
     print("Last dead point:", dead[-1])
 
 #| Initialise the settings
-
+print("about to create settings")
 settings = PolyChordSettings(nDims, nDerived)
 settings.file_root = 'gaussian'
 settings.nlive = 200
 settings.do_clustering = True
 settings.read_resume = False
 
 #| Run PolyChord
-
+print("about to run_pypolychord")
 output = pypolychord.run_polychord(likelihood, nDims, nDerived, settings, prior, dumper)
 
 #| Create a paramnames file

setup.py

@@ -92,13 +92,38 @@ def build_extension(self, ext) -> None:
 
     def build_cmake(self, ext):
         print(self.build_temp)
-        cwd = pathlib.Path().absolute()
+        cwd = pathlib.Path().cwd()
         build_temp = pathlib.Path(self.build_temp)
         build_temp.mkdir(parents=True, exist_ok=True)
 
+        # os.chdir(str(build_temp))
+        # self.spawn(["cmake", str(cwd), f"-DPython3_EXECUTABLE={sys.executable}"])
+        # self.spawn(["make"])
+        env = {}
+        env["PATH"] = os.environ["PATH"]
+        if self.distribution.no_mpi is None:
+            env["MPI"] = "1"
+            # These need to be set so that build_ext uses the right compilers
+            cc_compiler = subprocess.check_output(["make", "print_CC"]).decode('utf-8').strip()
+            os.environ["CC"] = cc_compiler
+
+            cxx_compiler = subprocess.check_output(["make", "print_CXX"]).decode('utf-8').strip()
+            os.environ["CXX"] = cxx_compiler
+        else:
+            env["MPI"] = "0"
+
+        if self.distribution.debug_flags is not None:
+            self.distribution.ext_modules[0].extra_compile_args += ["-g", "-O0"]
+            env["DEBUG"] = "1"
+
+        # BASE_PATH = os.path.dirname(os.path.abspath(__file__))
         os.chdir(str(build_temp))
-        self.spawn(["cmake", str(cwd)])
-        self.spawn(["make"])
+        print("managed to change directory")
+        env["PWD"] = str(build_temp)
+        env.update({k : os.environ[k] for k in ["CC", "CXX", "FC"] if k in os.environ})
+        subprocess.check_call(["cmake", str(cwd), f"-DPython3_EXECUTABLE={sys.executable}"], env=env) #, cwd=str(build_temp))
+        print("cmade")
+        subprocess.check_call(["make", "-e"], env=env) #, cwd=str(build_temp))
         os.chdir(cwd)
 
 class DistributionWithOption(Distribution, object):