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austin-hooveraustin-hoover
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Merge branch 'PyORBIT-Collaboration:main' into mpi-bcast
2 parents 85e38f9 + 6cc7421 commit 36ce49b

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‎.github/workflows/compilation.yml‎

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- name: Print Versions
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run: |
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.github/workflows/conda-versions.sh
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mpich:
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runs-on: ubuntu-latest
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container:
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image: quay.io/centos/centos:stream9
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steps:
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- name: Install packages
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run: |
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dnf group install -y "Development Tools"
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dnf install -y python3-devel fftw3-devel mpich-devel hwloc-devel
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Build
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run: |
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.github/workflows/pip-build-mpich.sh
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- name: Test
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run: |
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.github/workflows/pip-tests-mpi.sh
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- name: Print Versions
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run: |
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.github/workflows/pip-versions.sh

‎.github/workflows/pip-build-mpich.sh‎

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python3 -m venv .po3
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sed -i 's|PATH="\$VIRTUAL_ENV\/"bin":\$PATH"|PATH="\$VIRTUAL_ENV\/"bin":\$PATH"\nsource /etc/profile.d/modules.sh\nmodule load mpi/mpich-x86_64|' .po3/bin/activate
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. .po3/bin/activate
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mpirun -V
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pip install -U pip
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pip install -r requirements.txt
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pip install -U setuptools
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pip install --verbose --config-settings=setup-args="-DUSE_MPI=mpich" .

‎.github/workflows/pip-tests-mpi.sh‎

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. .po3/bin/activate
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# Simple test to check if MPI was linked at all
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mpirun -np 2 python examples/MPI_Tests/mpi_initialization_test.py | tee test.txt
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calculated_sha1=$(sha1sum test.txt | awk '{ print $1 }')
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[ "$calculated_sha1" != "d94e03044bf06c7a42d07505b50fa58b4b30e49a" ] && exit 1
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# Uniformly charged sphere
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echo "Run with Ellipsoid space charge"
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mpirun -np 2 python examples/SpaceCharge/sc3D/sc_3d_drift_latt_uniform_sphere_bunch.py --SC ellipsoid| tee results.txt
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python examples/SpaceCharge/sc3D/read_sc_numbers.py
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[ $? != 0 ] && exit 1
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echo "Run with FFT3D space charge"
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mpirun -np 2 python examples/SpaceCharge/sc3D/sc_3d_drift_latt_uniform_sphere_bunch.py --SC fft3d| tee results.txt
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python examples/SpaceCharge/sc3D/read_sc_numbers.py
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[ $? != 0 ] && exit 1
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# this should fail as no space charge will give incorrect sphere size
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echo "Run with no space charge"
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mpirun -np 2 python examples/SpaceCharge/sc3D/sc_3d_drift_latt_uniform_sphere_bunch.py --SC none| tee results.txt
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python examples/SpaceCharge/sc3D/read_sc_numbers.py
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[ $? == 0 ] && exit 1
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# This tests that five nodes give the same result as one node
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echo "Run with 1 node."
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mpirun -np 1 python examples/SpaceCharge/sc3D/sc_3d_drift_latt_uniform_sphere_bunch.py | tee results1.txt
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calculated_sha1=$(sha1sum results1.txt | awk '{ print $1 }')
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echo "Run with 5 nodes."
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mpirun -np 5 python examples/SpaceCharge/sc3D/sc_3d_drift_latt_uniform_sphere_bunch.py | tee results5.txt
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calculated_sha5=$(sha1sum results5.txt | awk '{ print $1 }')
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echo "Diff between two runs."
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echo "$calculated_sha1" "$calculated_sha5"
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diff results1.txt results5.txt
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[ "$calculated_sha1" != "$calculated_sha5" ] && exit 1
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exit 0
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‎README.md‎

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# PyOrbit3 package installation
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# PyORBIT3 package installation
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## 1. Introduction
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This guide provides instructions how to install PyORBIT code. <br>
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cd examples/SNS_Linac/pyorbit3_linac_model/
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python pyorbit3_sns_linac_mebt_hebt2.py
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```
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## 5. MPI consideration
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By default, the build system will try to find MPI and compile against it. You can control which MPI to use with command line option when building.
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```bash
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pip install --config-settings=setup-args="-DUSE_MPI=none" .
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```
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Above will build PyORBIT without MPI even if MPI is present. You can change that option to `mpich`, `ompi`, `none` or `auto` (default).<br>
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| MPI flavor | Installation command |
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|---------------|--------------|
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| No MPI | `pip install --config-settings=setup-args="-DUSE_MPI=none" .` |
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| The first found MPI installation if any | `pip install --config-settings=setup-args="-DUSE_MPI=auto" .` |
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| OpenMPI | `pip install --config-settings=setup-args="-DUSE_MPI=ompi" .` |
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| MPICH | `pip install --config-settings=setup-args="-DUSE_MPI=mpich" .` |
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Meson uses PKG_CONFIG to discover packages. It could be useful to help it to find your MPI installation:
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```bash
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PKG_CONFIG_PATH=/opt/lib/pkgconfig pip install --verbose .
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```

‎examples/MPI_Tests/mpi_initialization_test.py‎

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mpi_init = orbit_mpi.MPI_Initialized()
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print ("debug mpi is initialized =",mpi_init," should be not zero.")
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rank = orbit_mpi.MPI_Comm_rank(mpi_comm.MPI_COMM_WORLD)
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size = orbit_mpi.MPI_Comm_size(mpi_comm.MPI_COMM_WORLD)
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if(rank == 0):
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print("debug mpi is initialized =", mpi_init, " should be not zero.")
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print ("debug there should only one line like this rank=",rank," N CPUs = ",size)
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n_particles = 10

‎examples/OrbitUtils_Tests/Polynomials/polynomial_fitting_test.py‎

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#----------------------------------------------
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# This is an example of a polymonial fitting
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#----------------------------------------------
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import sys
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import math
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import random
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from orbit.core.orbit_utils import Matrix
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from orbit.core.orbit_utils import Function
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from orbit.core.orbit_utils import SplineCH
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from orbit.utils.fitting import PolynomialFit
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random_err_range = 0.001
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f = Function()
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for i in range(15):
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x = 0.1*i
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y = -1+1.0*x**2+2.0*x**3 + 0.01*x**4
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y += random.uniform(-random_err_range,+random_err_range)
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f.add(x,y)
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print ("polynomial for fitting = y = -1+1.0*x**2+2.0*x**3 + 0.01*x**4")
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print ("================Function====================================")
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poly = PolynomialFit(4)
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poly.fitFunction(f)
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[coef_arr,err_arr] = poly.getCoefficientsAndErr()
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for i in range(len(coef_arr)):
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print ("i=",i," coef = %8.5f +- %8.5f"%(coef_arr[i],err_arr[i]))
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print ("================SplineCH====================================")
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spline = SplineCH()
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spline.compile(f)
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poly.fitSpline(f)
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[coef_arr,err_arr] = poly.getCoefficientsAndErr()
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for i in range(len(coef_arr)):
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print ("i=",i," coef = %8.5f +- %8.5f"%(coef_arr[i],err_arr[i]))
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print ("Stop.")
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sys.exit(0)

‎examples/OrbitUtils_Tests/Polynomials/polynomial_test.py‎

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#-------------------------------------------------------------
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# This is an example of Polynomial class
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# The methods "derivativeTo","derivative", "copyTo" and "value" are included.
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#-------------------------------------------------------------
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import sys
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import math
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from orbit.core.orbit_utils import Polynomial
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poly = Polynomial(4)
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print ("initial order = ",poly.order())
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poly.coefficient(2,2.0)
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print ("========Polynomial=======")
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order = poly.order()
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for i in range(order+1):
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print ("i=",i," coef=",poly.coefficient(i))
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x = 10.
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y = poly.value(x)
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print ("x=",x," y=",y)
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poly1 = Polynomial()
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poly.derivativeTo(poly1)
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print ("========Derivative polynomial=======")
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order = poly1.order()
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for i in range(order+1):
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print ("i=",i," coef=",poly1.coefficient(i))
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x = 10.
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y = poly1.value(x)
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yp = poly.derivative(x)
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print ("x=",x," y_prime=",y," yp =",yp)
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print ("========Copy of initial polynomial=======")
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poly2 = Polynomial()
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poly.copyTo(poly2)
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order = poly2.order()
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for i in range(order+1):
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print ("i=",i," coef=",poly2.coefficient(i))
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x = 10.
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y = poly2.value(x)
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yp = poly2.derivative(x)
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print ("x=",x," y=",y," y_prime=",yp)
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"""
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# Memory leak test
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count = 1
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while(1 < 2):
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poly1 = Polynomial()
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poly2 = Polynomial()
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poly.derivativeTo(poly1)
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poly.copyTo(poly2)
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count += 1
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if(count % 100000 == 0):
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print ("count=",count)
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"""
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print ("Stop.")
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sys.exit(0)
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