Merge branch 'main' into contact-dynamic-relaxation

Author: kaipartmann

.github/workflows/CI.yml

@@ -57,6 +57,11 @@ jobs:
           version: '1'
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
+      - run: |
+          julia --project=docs -e '
+            using Pkg;
+            Pkg.develop(PackageSpec(path=pwd()));
+            Pkg.instantiate()' 
       - uses: julia-actions/julia-docdeploy@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

Project.toml

@@ -1,7 +1,7 @@
 name = "Peridynamics"
 uuid = "4dc47793-80f3-4232-b30e-ca78ca9d621b"
 authors = ["Kai Partmann"]
-version = "0.4.1"
+version = "0.4.2-DEV"
 
 [deps]
 AbaqusReader = "bc6b9049-e460-56d6-94b4-a597b2c0390d"
@@ -30,7 +30,7 @@ LibGit2 = "1.8"
 LightXML = "0.9"
 LinearAlgebra = "1.8"
 MPI = "0.20.0"
-PointNeighbors = "0.4.5, 0.5"
+PointNeighbors = "0.5, 0.6"
 PrecompileTools = "1.0"
 Printf = "1.8"
 ProgressMeter = "1.0"

docs/servedocs.jl

@@ -6,8 +6,9 @@
 const REPO_ROOT = dirname(@__DIR__)
 
 # Make sure the docs environment is active and instantiated
-import Pkg
+using Pkg
 Pkg.activate(@__DIR__)
+Pkg.develop(PackageSpec(path=REPO_ROOT))
 Pkg.instantiate()
 
 # Communicate with make.jl that docs are build in live mode

test/auxiliary/test_mpi.jl

@@ -35,7 +35,10 @@ end
     job = Job(body, ts; path, freq=10)
     submit(job)
     """
-    cmd = `$(Peridynamics.MPI.mpiexec()) -n 2 $(Base.julia_cmd()) --project -e $(mpi_cmd)`
+    mpiexec = Peridynamics.MPI.mpiexec()
+    jlcmd = Base.julia_cmd()
+    pdir = pkgdir(Peridynamics)
+    cmd = `$(mpiexec) -n 2 $(jlcmd) --project=$(pdir) -e $(mpi_cmd)`
     @test success(cmd) # does not print anything
     # for debugging use the run command:
     # run(cmd)

test/auxiliary/test_process_each_export.jl

@@ -72,7 +72,10 @@
         return nothing
     end
     """
-    run(`$(Peridynamics.MPI.mpiexec()) -n 3 $(Base.julia_cmd()) --project -e $(mpi_cmd)`)
+    mpiexec = Peridynamics.MPI.mpiexec()
+    jlcmd = Base.julia_cmd()
+    pdir = pkgdir(Peridynamics)
+    run(`$(mpiexec) -n 2 $(jlcmd) --project=$(pdir) -e $(mpi_cmd)`)
     file_1_mpi = joinpath(root_post_mpi, "max_displacement_1.txt")
     @test isfile(file_1_mpi)
     @test contains(read(file_1_mpi, String), "maximum displacement x: 0.0")

test/core/test_halo_exchange.jl

@@ -316,7 +316,10 @@ end
         @test dh.chunk.storage.b_int[:,3:4] ≈ randbint[:,1:2]
     end
     """
-    cmd = `$(Peridynamics.MPI.mpiexec()) -n 2 $(Base.julia_cmd()) --project -e $(mpi_cmd)`
+    mpiexec = Peridynamics.MPI.mpiexec()
+    jlcmd = Base.julia_cmd()
+    pdir = pkgdir(Peridynamics)
+    cmd = `$(mpiexec) -n 2 $(jlcmd) --project=$(pdir) -e $(mpi_cmd)`
     @test success(cmd) # does not print anything
     # for debugging use the run command:
     # run(cmd)
@@ -363,7 +366,10 @@ end
         @test dh.chunk.storage.position[:,1:2] ≈ position[:,1:2] + randpos[:,3:4]
     end
     """
-    cmd = `$(Peridynamics.MPI.mpiexec()) -n 2 $(Base.julia_cmd()) --project -e $(mpi_cmd)`
+    mpiexec = Peridynamics.MPI.mpiexec()
+    jlcmd = Base.julia_cmd()
+    pdir = pkgdir(Peridynamics)
+    cmd = `$(mpiexec) -n 2 $(jlcmd) --project=$(pdir) -e $(mpi_cmd)`
     @test success(cmd) # does not print anything
     # for debugging use the run command:
     # run(cmd)

test/integration/mpi_threads_comparison.jl

@@ -47,7 +47,10 @@
     end
     sim_bb(30, "$path_mpi")
     """
-    run(`$(Peridynamics.MPI.mpiexec()) -n 2 $(Base.julia_cmd()) --project -e $(mpi_cmd)`)
+    mpiexec = Peridynamics.MPI.mpiexec()
+    jlcmd = Base.julia_cmd()
+    pdir = pkgdir(Peridynamics)
+    run(`$(mpiexec) -n 2 $(jlcmd) --project=$(pdir) -e $(mpi_cmd)`)
 
     @test isdir(path_threads_vtk)
     @test isdir(path_mpi_vtk)
@@ -112,7 +115,10 @@ end
     end
     sim_bb(30, "$path_mpi")
     """
-    run(`$(Peridynamics.MPI.mpiexec()) -n 2 $(Base.julia_cmd()) --project -e $(mpi_cmd)`)
+    mpiexec = Peridynamics.MPI.mpiexec()
+    jlcmd = Base.julia_cmd()
+    pdir = pkgdir(Peridynamics)
+    run(`$(mpiexec) -n 2 $(jlcmd) --project=$(pdir) -e $(mpi_cmd)`)
 
     @test isdir(path_threads_vtk)
     @test isdir(path_mpi_vtk)
@@ -182,7 +188,10 @@ end
     end
     sim_bb(30, "$path_mpi")
     """
-    run(`$(Peridynamics.MPI.mpiexec()) -n 2 $(Base.julia_cmd()) --project -e $(mpi_cmd)`)
+    mpiexec = Peridynamics.MPI.mpiexec()
+    jlcmd = Base.julia_cmd()
+    pdir = pkgdir(Peridynamics)
+    run(`$(mpiexec) -n 2 $(jlcmd) --project=$(pdir) -e $(mpi_cmd)`)
 
     @test isdir(path_threads_vtk)
     @test isdir(path_mpi_vtk)
@@ -247,7 +256,10 @@ end
     end
     sim_osb(30, "$path_mpi")
     """
-    run(`$(Peridynamics.MPI.mpiexec()) -n 2 $(Base.julia_cmd()) --project -e $(mpi_cmd)`)
+    mpiexec = Peridynamics.MPI.mpiexec()
+    jlcmd = Base.julia_cmd()
+    pdir = pkgdir(Peridynamics)
+    run(`$(mpiexec) -n 2 $(jlcmd) --project=$(pdir) -e $(mpi_cmd)`)
 
     @test isdir(path_threads_vtk)
     @test isdir(path_mpi_vtk)
@@ -312,7 +324,10 @@ end
     end
     sim_cc(30, "$path_mpi")
     """
-    run(`$(Peridynamics.MPI.mpiexec()) -n 2 $(Base.julia_cmd()) --project -e $(mpi_cmd)`)
+    mpiexec = Peridynamics.MPI.mpiexec()
+    jlcmd = Base.julia_cmd()
+    pdir = pkgdir(Peridynamics)
+    run(`$(mpiexec) -n 2 $(jlcmd) --project=$(pdir) -e $(mpi_cmd)`)
 
     @test isdir(path_threads_vtk)
     @test isdir(path_mpi_vtk)
@@ -378,7 +393,10 @@ end
     end
     sim_bac(30, "$path_mpi")
     """
-    run(`$(Peridynamics.MPI.mpiexec()) -n 2 $(Base.julia_cmd()) --project -e $(mpi_cmd)`)
+    mpiexec = Peridynamics.MPI.mpiexec()
+    jlcmd = Base.julia_cmd()
+    pdir = pkgdir(Peridynamics)
+    run(`$(mpiexec) -n 2 $(jlcmd) --project=$(pdir) -e $(mpi_cmd)`)
 
     @test isdir(path_threads_vtk)
     @test isdir(path_mpi_vtk)