update conda, hashdist, osx build, and chrono ANCF usage (#1261)

* update conda package versions

* update hashdist stack

* update chrono ANCF gravity usage

* relax tolerances on several tests

* change travis image to minimal (language: minimal)

* remove nose dependency

* remove hard-coded compilers and options on travis conda builds

* use conda-installed openblas in default darwin config (no Accelerate)

.travis.yml

@@ -1,7 +1,6 @@
 os: linux
 dist: focal
-language: python
-python: 3.9
+language: minimal
 
 notifications:
   email:
@@ -14,8 +13,6 @@ jobs:
     name: "conda linux"
     os: linux
     dist: focal
-    language: python
-    python: 3.9
     env: TEST_PROFILE="proteus-conda"
     install:
       - git lfs pull
@@ -29,13 +26,13 @@ jobs:
       - conda info -a
       - conda env create -f environment-dev.yml
       - conda activate proteus-dev
-      - PROTEUS_OPT="-g0 -O2 -DNDEBUG" FC=gfortran CC=mpicc CXX=mpicxx make develop-conda N=2
+      - make develop-conda N=2
     script:
       - export MPLBACKEND="AGG"
       - py.test -n 1 --forked -v proteus/tests --ignore proteus/tests/POD --ignore proteus/tests/solver_tests/test_nse_RANS2P_step.py
       - py.test -n 1 --forked -v air-water-vv/Tests/1st_set
       - py.test -n 1 --forked -v air-water-vv/Tests/2nd_set
-      - mpiexec -np 2 pytest -v proteus/tests/FSI
+      - py.test -n 1 --forked -v proteus/tests/FSI
     deploy:
       provider: script
       script: bash ./scripts/deploy.sh docs
@@ -45,9 +42,7 @@ jobs:
   - stage: test
     name: "conda osx"
     os: osx
-    osx_image: xcode12.2
-    language: ruby
-    python: 2.6.6
+    osx_image: xcode13.4
     env: TEST_PROFILE="proteus-conda-osx"
     install:
       - wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
@@ -60,11 +55,12 @@ jobs:
       - conda env create -f environment-dev.yml
       - conda activate proteus-dev
       - pip install gmsh
-      - PROTEUS_OPT="-g0 -O2 -DNDEBUG" FC=gfortran CC=mpicc CXX=mpicxx make develop-conda N=2
+      - make develop-conda N=2
     script:
       - export MPLBACKEND="AGG"
       - git lfs install
       - git lfs pull
       - py.test -n 1 --forked -v proteus/tests --ignore proteus/tests/solver_tests --ignore proteus/tests/POD --ignore=proteus/tests/MoveMeshMonitor --ignore proteus/tests/periodic
       - py.test -n 1 --forked -v air-water-vv/Tests/1st_set
       - py.test -n 1 --forked -v air-water-vv/Tests/2nd_set --ignore air-water-vv/Tests/2nd_set/test_randomWaves.py
+      - py.test -n 1 --forked -v proteus/tests/FSI

Makefile

@@ -197,7 +197,7 @@ develop: ${PROTEUS_PREFIX}/bin/proteus_env.sh stack/default.yaml ${PROTEUS_PREFI
 	@echo "Installing development version"
 	@echo "************************"
 	$(call show_info)
-	${PROTEUS_ENV} pip install py2gmsh pytest pytest-xdist pytest-cov nose tables future
+	${PROTEUS_ENV} pip install py2gmsh pytest pytest-xdist pytest-cov tables future
 	${PROTEUS_ENV} ${PROTEUS_DEVELOP_BUILD_CMD}
 	${PROTEUS_ENV} ${PROTEUS_DEVELOP_CMD}
 	@echo "************************"

environment-dev.yml

@@ -3,56 +3,55 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - pip =21.1.3
-  - compilers =1.2.0
+  - pip =22.1.2
+  - compilers =1.4.1
   - make
-  - setuptools =49.6.0
-  - cython =0.29.24
+  - setuptools =62.6.0
+  - cython =0.29.30
   - daetk =1.0.1
-  - hdf5 =1.10.6=*mpich*
-  - h5py =3.3.0=*mpich*
+  - hdf5 =1.12.1=*mpich*
+  - h5py =3.6.0=*mpich*
   - metis =5.1.0
-  - mpich =3.4.2
-  - mpich-mpicc =3.4.2
-  - mpich-mpicxx =3.4.2
-  - numpy =1.21.0
-  - openblas =0.3.17
+  - mpich =4.0.2
+  - mpich-mpicc =4.0.2
+  - mpich-mpicxx =4.0.2
+  - numpy =1.22.4
+  - openblas =0.3.20
   - parmetis =4.0.3
-  - petsc4py =3.14.1
-  - petsc =3.14.6
+  - petsc4py =3.17.2
+  - petsc =3.17.2
   - scorec =2.2.2
   - superlu =5.2.2
-  - superlu_dist =6.2.0
+  - superlu_dist =7.2.0
   - triangle =1.6
-  - pychrono =6.0.0
-  - gmsh =4.8.4
-  - matplotlib =3.4.2
-  - mpi4py =3.0.3
-  - nose
-  - pytables =3.6.1
+  - pychrono =7.0.0
+  - gmsh =4.10.4
+  - matplotlib =3.5.2
+  - mpi4py =3.1.3
+  - pytables =3.7.0
   - pytest
   - pytest-cov
   - pytest-xdist
-  - scipy =1.7.0
+  - scipy =1.8.1
   - tetgen =1.6.0
-  - ncurses =6.2
-  - python =3.9.6
+  - ncurses =6.3
+  - python =3.10.5
   - future =0.18.2
-  - ipyparallel =6.3.0
-  - pillow =8.3.1
-  - xtensor-python = 0.25.3
+  - ipyparallel =8.4.0
+  - pillow =9.1.1
+  - xtensor-python = 0.26.1
   - git-lfs
-  - eigen =3.3.9
-  - zoltan =3.83
-  - hypre =2.18.2
+  - eigen =3.4.0
+  - zoltan =3.901
+  - hypre =2.24.0
   - mumps-mpi =5.2.1
-  - numexpr =2.7.3
+  - numexpr =2.8.0
   - ptscotch =6.0.9
-  - scalapack =2.0.2
-  - tbb =2020.2
-  - zipp =3.5.0
-  - parso =0.8.2
-  - pycparser =2.20
-  - ipython =7.25.0
-  - decorator =5.0.9
-  - cffi =1.14.6
+  - scalapack =2.2.0
+  - tbb =2021.5.0
+  - zipp =3.8.0
+  - parso =0.8.3
+  - pycparser =2.21
+  - ipython =8.4.0
+  - decorator =5.1.1
+  - cffi =1.15.0

proteus/config/default.py

@@ -23,11 +23,10 @@
 platform_lapack_h = None
 platform_lapack_integer = None
 if sys.platform == 'darwin':
-    platform_extra_link_args = ['-framework', 'Accelerate']
-    platform_lapack_integer = '__CLPK_integer'
-    platform_blas_h = r'<Accelerate/Accelerate.h>'
-    platform_lapack_h = r'<Accelerate/Accelerate.h>'
-    platform_extra_compile_args = ['-flax-vector-conversions','-DPETSC_INCLUDE_AS_C','-DPETSC_SKIP_COMPLEX']
+    platform_extra_compile_args = ['-DPETSC_INCLUDE_AS_C', '-DPETSC_SKIP_COMPLEX']
+    platform_extra_link_args = ['-L'+PROTEUS_LIB_DIR,'-Wl,-rpath,' + PROTEUS_LIB_DIR]
+    platform_blas_h = r'"proteus_blas.h"'
+    platform_lapack_h = r'"proteus_lapack.h"'
     major,minor = platform.mac_ver()[0].split('.')[0:2]
     os.environ["MACOSX_DEPLOYMENT_TARGET"]= major+'.'+minor
 elif sys.platform.startswith('linux'):

proteus/mbd/CouplingFSI.pyx

@@ -2407,7 +2407,6 @@ cdef class ProtChMesh:
 
     def __cinit__(self, ProtChSystem system):
         self.ChMeshh = chrono_fea.ChMesh()
-        self.ChMeshh.SetAutomaticGravity(True)
         cdef SwigPyObject *swig_obj = <SwigPyObject*> self.ChMeshh.this
         cdef shared_ptr[ch.ChMesh]* pt_to_shp = <shared_ptr[ch.ChMesh]*> swig_obj.ptr;
         self.mesh = pt_to_shp[0]

proteus/mbd/ProtChMoorings.h

@@ -10,7 +10,7 @@
 #include "chrono/physics/ChLoadContainer.h"
 #include "chrono/physics/ChLinkMate.h"
 #include "chrono/physics/ChBodyEasy.h"
-#include "chrono/fea/ChElementBeamANCF.h"
+#include "chrono/fea/ChElementBeamANCF_3333.h"
 #include "chrono/fea/ChElementCableANCF.h"
 #include "chrono/fea/ChElementBeamEuler.h"
 #include "chrono/fea/ChBeamSection.h"
@@ -735,7 +735,7 @@ void cppCable::buildElementsCableANCF(bool set_lastnodes) {
     auto load = chrono_types::make_shared<ChLoadBeamWrench>(element);
     std::shared_ptr<ChLoad<MyLoaderTriangular>> loadtri(new ChLoad<MyLoaderTriangular>(element));
     auto load_volumetric = chrono_types::make_shared<ChLoad<ChLoaderGravity>>(element);
-    load_volumetric->loader.Set_G_acc(ChVector<>(0.,0.,0.));
+    load_volumetric->loader.Set_G_acc(system->Get_G_acc());
     /* loadcontainer->Add(load_distributed); */
     /* loadcontainer->Add(load); */
     loadcontainer->Add(loadtri);  // do not forget to add the load to the load container.
@@ -772,7 +772,7 @@ void cppCable::buildElementsBeamEuler(bool set_lastnodes) {
     auto load = chrono_types::make_shared<ChLoadBeamWrench>(element);
     std::shared_ptr<ChLoad<MyLoaderTriangular>> loadtri(new ChLoad<MyLoaderTriangular>(element));
     auto load_volumetric = chrono_types::make_shared<ChLoad<ChLoaderGravity>>(element);
-    load_volumetric->loader.Set_G_acc(ChVector<>(0.,0.,0.));
+    load_volumetric->loader.Set_G_acc(system->Get_G_acc());
     /* loadcontainer->Add(load_distributed); */
     /* loadcontainer->Add(load); */
     loadcontainer->Add(loadtri);  // do not forget to add the load to the load container.

proteus/tests/MeshAdaptPUMI/case_run/test_workflowPUMI.py

@@ -10,8 +10,5 @@ def test_workflowPUMI(verbose=0):
     currentPath = os.path.dirname(os.path.abspath(__file__))
     runCommand = "cd "+currentPath+"; parun -l5 couette_so.py;"
     subprocess.check_call(runCommand,shell=True )
-if __name__ == '__main__':
-    import nose
-    nose.main(defaultTest='test_workflowPUMI:test_workflowPUMI')
 
 

proteus/tests/MeshAdaptPUMI/gauge_compare/dambreak_Colagrossi_2D/test_MeshAdaptRestart.py

@@ -1,7 +1,5 @@
 #!/usr/bin/env python
 
-from nose.tools import eq_ as eq
-from nose.tools import ok_ as ok
 import subprocess
 import os
 import pytest
@@ -37,7 +35,3 @@ def test_MeshAdaptRestart(verbose=0):
             if(line1 != line2):
                 pytest.fail("pressure gauge values are not the same!\n")
 
-if __name__ == '__main__':
-    import nose
-    nose.main(defaultTest='test_MeshAdaptRestart:test_MeshAdaptRestart_generateMesh,test_MeshAdaptRestart:test_MeshAdaptRestart_adaptiveTime_BackwardEuler_baseline, test_MeshAdaptRestart:test_MeshAdaptRestart_adaptiveTime_BackwardEuler, test_MeshAdaptRestart:test_MeshAdaptRestart')
-

proteus/tests/MeshAdaptPUMI/gauge_compare/dambreak_Colagrossi_2D_rd/test_MeshAdaptRestart_withRedistancing.py

@@ -1,7 +1,5 @@
 #!/usr/bin/env python
 
-from nose.tools import eq_ as eq
-from nose.tools import ok_ as ok
 import subprocess
 import os
 import pytest
@@ -34,7 +32,3 @@ def test_MeshAdaptRestart_withRedistancing(verbose=0):
             if(line1 != line2):
                 pytest.fail("pressure gauge values are not the same!\n")
 
-if __name__ == '__main__':
-    import nose
-    nose.main(defaultTest='test_MeshAdaptRestart_withRedistancing:test_MeshAdaptRestart_generateMesh, test_MeshAdaptRestart_withRedistancing:test_MeshAdaptRestart_adaptiveTime_BackwardEuler_baseline_withRedistancing, test_MeshAdaptRestart_withRedistancing:test_MeshAdaptRestart_adaptiveTime_BackwardEuler_withRedistancing, test_MeshAdaptRestart_withRedistancing:test_MeshAdaptRestart_withRedistancing')
-

proteus/tests/MeshAdaptPUMI/gauge_compare/dambreak_Colagrossi_2D_rdmc/test_MeshAdaptRestart_withRDMC.py

@@ -1,7 +1,5 @@
 #!/usr/bin/env python
 
-from nose.tools import eq_ as eq
-from nose.tools import ok_ as ok
 import subprocess
 import os
 import pytest
@@ -34,8 +32,3 @@ def test_MeshAdaptRestart_withRDMC(verbose=0):
         for line1, line2 in zip(file1, file2):
             if(line1 != line2):
                 pytest.fail("pressure gauge values are not the same!\n")
-
-if __name__ == '__main__':
-    import nose
-    nose.main(defaultTest='test_MeshAdaptRestart_withRDMC:test_MeshAdaptRestart_generateMesh,test_MeshAdaptRestart_withRDMC:test_MeshAdaptRestart_adaptiveTime_BackwardEuler_baseline_withRDMC, test_MeshAdaptRestart_withRDMC:test_MeshAdaptRestart_adaptiveTime_BackwardEuler_withRDMC, test_MeshAdaptRestart_withRDMC:test_MeshAdaptRestart_withRDMC')
-

proteus/tests/MeshAdaptPUMI/test_gmshCheck.py

@@ -5,8 +5,6 @@
 from proteus import Domain
 from proteus import Comm
 from petsc4py import PETSc
-from nose.tools import eq_ as eq
-from nose.tools import ok_ as ok
 import os
 import pytest
 
@@ -76,9 +74,9 @@ def test_gmshLoadAndAdapt(verbose=0):
     domain.AdaptManager.PUMIAdapter.transferFieldToPUMI(b"vof", scalar)
 
     errorTotal=domain.AdaptManager.PUMIAdapter.get_local_error()
-    ok(errorTotal<1e-14)
+    assert (errorTotal<1e-14)
 
-    #ok(domain.AdaptManager.willAdapt(),1)
+    #assert (domain.AdaptManager.willAdapt(),1)
     domain.AdaptManager.PUMIAdapter.adaptPUMIMesh(b"")
 
     mesh = MeshTools.TetrahedralMesh()
@@ -88,7 +86,7 @@ def test_gmshLoadAndAdapt(verbose=0):
                      parallel = comm.size() > 1,
                      dim = domain.nd)
     nElements_final = mesh.nElements_global
-    ok(nElements_final>nElements_initial)
+    assert (nElements_final>nElements_initial)
 
 def test_2DgmshLoadAndAdapt(verbose=0):
     """Test for loading gmsh mesh through PUMI, estimating error and adapting for 
@@ -154,9 +152,9 @@ def test_2DgmshLoadAndAdapt(verbose=0):
     domain.AdaptManager.PUMIAdapter.transferFieldToPUMI(b"vof", scalar)
 
     errorTotal=domain.AdaptManager.PUMIAdapter.get_local_error()
-    ok(errorTotal<1e-14)
+    assert (errorTotal<1e-14)
 
-    #ok(domain.AdaptManager.willAdapt(),1)
+    #assert (domain.AdaptManager.willAdapt(),1)
 
     domain.AdaptManager.PUMIAdapter.adaptPUMIMesh(b"")
 
@@ -167,7 +165,7 @@ def test_2DgmshLoadAndAdapt(verbose=0):
                      parallel = comm.size() > 1,
                      dim = domain.nd)
     nElements_final = mesh.nElements_global
-    ok(nElements_final>nElements_initial)
+    assert (nElements_final>nElements_initial)
 
 def test_2DmultiRegion(verbose=0):
     """Test for loading gmsh mesh through PUMI with multiple-regions"""
@@ -186,10 +184,6 @@ def test_2DmultiRegion(verbose=0):
     mesh.cmesh = cmeshTools.CMesh()
     comm = Comm.init()
     mesh.convertFromPUMI(domain,domain.AdaptManager.PUMIAdapter, domain.faceList,domain.regList, parallel = comm.size() > 1, dim = domain.nd)
-    ok(mesh.elementMaterialTypes[0]==1)
-    ok(mesh.elementMaterialTypes[-1]==2)
-
-if __name__ == '__main__':
-    import nose
-    nose.main(defaultTest='test_gmshCheck:test_gmshLoadAndAdapt,test_gmshCheck:test_2DgmshLoadAndAdapt,test_gmshCheck:test_2DmultiRegion')
+    assert mesh.elementMaterialTypes[0]==1
+    assert mesh.elementMaterialTypes[-1]==2
 

proteus/tests/MeshAdaptPUMI/test_meshLoad.py

@@ -4,8 +4,6 @@
 from proteus import cmeshTools
 from proteus.MeshAdaptPUMI import MeshAdapt
 from proteus import Domain
-from nose.tools import eq_ as eq
-from nose.tools import ok_ as ok
 import os
 import pytest
 
@@ -25,12 +23,7 @@ def test_meshLoadPUMI(verbose=0):
     cmeshTools.allocateGeometricInfo_tetrahedron(mesh.cmesh)
     cmeshTools.computeGeometricInfo_tetrahedron(mesh.cmesh)
     mesh.buildFromC(mesh.cmesh)
-    eq(mesh.nElements_global,670)
-    eq(mesh.nNodes_global,190)
-    eq(mesh.nEdges_global,977)
-    eq(mesh.nElementBoundaries_global,1458)
-
-if __name__ == '__main__':
-    import nose
-    nose.main(defaultTest='test_meshLoad:test_meshLoadPUMI')
-
+    assert mesh.nElements_global == 670
+    assert mesh.nNodes_global == 190
+    assert mesh.nEdges_global == 977
+    assert mesh.nElementBoundaries_global == 1458

proteus/tests/MeshAdaptPUMI/test_parallelMeshLoad.py

@@ -4,8 +4,6 @@
 from proteus import Domain
 from proteus.MeshAdaptPUMI import MeshAdapt
 from proteus import Comm
-from nose.tools import eq_ as eq
-from nose.tools import ok_ as ok
 import os
 from petsc4py import PETSc
 import pytest
@@ -52,13 +50,8 @@ def test_2DparallelLoadPUMI(verbose=0):
     mesh = MeshTools.TriangularMesh()
     mesh.cmesh = cmeshTools.CMesh()
     mesh.convertFromPUMI(domain,domain.PUMIMesh, domain.faceList, domain.regList,parallel = comm.size() > 1, dim = domain.nd)
-    eq(mesh.nElements_global,8)
-    eq(mesh.nNodes_global,10)
-    eq(mesh.nEdges_global,17)
-    eq(mesh.nElementBoundaries_global,17)
-
-if __name__ == '__main__':
-    import nose
-    nose.main(defaultTest='test_parallelMeshLoad:test_3DparallelLoadPUMI,test_parallelMeshLoad:test_2DparallelLoadPUMI')
-
+    assert mesh.nElements_global == 8
+    assert mesh.nNodes_global == 10
+    assert mesh.nEdges_global == 17
+    assert mesh.nElementBoundaries_global == 17