Merge pull request #110 from prj-/jolivet/pchpddm

PC-HPDDM interface

Author: JordiManyer

.github/workflows/ci.yml

@@ -25,7 +25,6 @@ jobs:
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v5
         with:
-          file: lcov.info
           verbose: true
           token: ${{ secrets.CODECOV_TOKEN }}
   docs:

.github/workflows/ci_extra.yml

@@ -17,7 +17,7 @@ jobs:
         arch:
           - x64
         petsc_version:
-          - '3.23.0'
+          - '3.23.4'
     steps:
       - uses: actions/checkout@v4
       - name: Cache petsc
@@ -29,13 +29,12 @@ jobs:
          restore-keys: |
           ${{ runner.os }}-build-${{ env.JULIA_PETSC_LIBRARY }}-
           ${{ runner.os }}-build-
-          ${{ runner.os }}-  
+          ${{ runner.os }}-
       - name: Install petsc dependencies
         run: |
-           sudo apt-get update 
-           sudo apt-get install -y wget gfortran g++ openmpi-bin libopenmpi-dev  
+           sudo apt-get update
+           sudo apt-get install -y wget gfortran g++ openmpi-bin libopenmpi-dev
       - name: Install petsc
-        ##if: steps.cache-petsc.outputs.cache-hit != 'true'
         run: |
           CURR_DIR=$(pwd)
           PACKAGE=petsc

.gitignore

@@ -7,6 +7,6 @@ LocalPreferences.toml
 /dev/
 /docs/build/
 /docs/site/
-deps/build.log 
+deps/build.log
 deps/deps.jl
 deps/PetscDataTypes.jl

README.md

@@ -9,13 +9,13 @@
 
 ## Documentation
 
-Take a look at this [tutorial](https://gridap.github.io/Tutorials/dev/pages/t016_poisson_distributed/#Tutorial-16:-Poisson-equation-on-parallel-distributed-memory-computers-1) for learning how to use `GridapPETSc` in distributed-memory simulations of PDEs. 
+Take a look at this [tutorial](https://gridap.github.io/Tutorials/dev/pages/t016_poisson_distributed/#Tutorial-16:-Poisson-equation-on-parallel-distributed-memory-computers-1) for learning how to use `GridapPETSc` in distributed-memory simulations of PDEs.
 
 It can also be used in the serial case, as shown in this [test](https://github.com/gridap/GridapPETSc.jl/blob/master/test/sequential/PoissonDriver.jl).
 
 ## Installation
 
-`GridapPETSc` julia package requires the `PETSC` library ([Portable, Extensible Toolkit for Scientific Computation](https://www.mcs.anl.gov/petsc/)) and `MPI` to work correctly. You have two main options to install these dependencies. 
+`GridapPETSc` julia package requires the `PETSC` library ([Portable, Extensible Toolkit for Scientific Computation](https://www.mcs.anl.gov/petsc/)) and `MPI` to work correctly. You have two main options to install these dependencies.
 
 - **Do nothing [recommended in most cases].** Use the default precompiled `MPI` installation provided by [`MPI.jl`](https://github.com/JuliaParallel/MPI.jl) and the pre-compiled `PETSc` library provided by [`PETSc_jll`](https://github.com/JuliaBinaryWrappers/PETSc_jll.jl). This will happen under the hood when you install `GridapPETSc`. In the case of `GridapPETSc`, you can also force the installation of these default dependencies by setting the environment variable `JULIA_PETSC_LIBRARY` to an empty value.
 
@@ -27,5 +27,5 @@ It can also be used in the serial case, as shown in this [test](https://github.c
 ## Notes
 
 * `GridapPETSc` default sparse matrix format is 0-based compressed sparse row. This type of sparse matrix storage format can be described by the `SparseMatrixCSR{0,PetscReal,PetscInt}` and `SymSparseMatrixCSR{0,PetscReal,PetscInt}` Julia types as implemented in the [SparseMatricesCSR](https://gridap.github.io/SparseMatricesCSR.jl/stable/) Julia package.
-* **When running in MPI parallel mode** (i.e., with a MPI communicator different from `MPI.COMM_SELF`), `GridapPETSc` implements a sort of limited garbage collector in order to automatically deallocate PETSc objects. This garbage collector can be manually triggered by a call to the function `GridapPETSc.gridap_petsc_gc()`. `GridapPETSc` automatically calls this function inside at different strategic points, and **this will be sufficient for most applications**. However, for some applications, with a very frequent allocation of PETSc objects, it might be needed to call this function from application code. This need will be signaled by PETSc via the following internal message error `PETSC ERROR: No more room in array, limit 256 
+* **When running in MPI parallel mode** (i.e., with a MPI communicator different from `MPI.COMM_SELF`), `GridapPETSc` implements a sort of limited garbage collector in order to automatically deallocate PETSc objects. This garbage collector can be manually triggered by a call to the function `GridapPETSc.gridap_petsc_gc()`. `GridapPETSc` automatically calls this function inside at different strategic points, and **this will be sufficient for most applications**. However, for some applications, with a very frequent allocation of PETSc objects, it might be needed to call this function from application code. This need will be signaled by PETSc via the following internal message error `PETSC ERROR: No more room in array, limit 256
 recompile src/sys/objects/destroy.c with larger value for MAXREGDESOBJS`

deps/build.jl

@@ -105,19 +105,19 @@ open(joinpath(@__DIR__,"PetscDataTypes.jl"),"w") do f
   println(f)
   println(f,:("\"\"\""))
   println(f, "Julia alias for `PetscReal` C type.\n")
-  println(f, "See [PETSc manual](https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscReal.html).")
+  println(f, "See [PETSc manual](https://petsc.org/release/manualpages/Sys/PetscReal/).")
   println(f,:("\"\"\""))
   println(f,:(const PetscReal = $(PetscReal)))
   println(f)
   println(f,:("\"\"\""))
   println(f, "Julia alias for `PetscScalar` C type.\n")
-  println(f, "See [PETSc manual](https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscScalar.html).")
+  println(f, "See [PETSc manual](https://petsc.org/release/manualpages/Sys/PetscScalar/).")
   println(f,:("\"\"\""))
   println(f,:(const PetscScalar = $(PetscScalar)))
   println(f)
   println(f,:("\"\"\""))
   println(f, "Julia alias for `PetscInt` C type.\n")
-  println(f, "See [PETSc manual](https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscInt.html).")
+  println(f, "See [PETSc manual](https://petsc.org/release/manualpages/Sys/PetscInt/).")
   println(f,:("\"\"\""))
   println(f,:(const PetscInt = $(PetscInt)))
 end

src/Config.jl

@@ -2,21 +2,21 @@
 """
 Julia alias to `PetscErrorCode` C type.
 
-See [PETSc manual](https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscErrorCode.html).
+See [PETSc manual](https://petsc.org/release/manualpages/Sys/PetscErrorCode/).
 """
 const PetscErrorCode = Cint
 
 """
 Julia alias to `PetscBool` C enum.
 
-See [PETSc manual](https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscBool.html).
+See [PETSc manual](https://petsc.org/release/manualpages/Sys/PetscBool/).
 """
 @enum PetscBool PETSC_FALSE PETSC_TRUE
 
 """
 Julia alias to `PetscDataType` C enum.
 
-See [PETSc manual](https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscDataType.html).
+See [PETSc manual](https://petsc.org/release/manualpages/Sys/PetscDataType/).
 """
 @enum PetscDataType begin
   PETSC_DATATYPE_UNKNOWN = 0
@@ -42,7 +42,7 @@ end
 """
     PetscDataTypeFromString(name,ptype,found)
 
-See [PETSc manual](https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscDataTypeFromString.html).
+See [PETSc manual](https://petsc.org/release/manualpages/Sys/PetscDataTypeFromString/).
 """
 function PetscDataTypeFromString(name,ptype,found)
   ccall(
@@ -54,7 +54,7 @@ end
 """
     PetscDataTypeGetSize(ptype,size)
 
-See [PETSc manual](https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscDataTypeGetSize.html).
+See [PETSc manual](https://petsc.org/release/manualpages/Sys/PetscDataTypeGetSize/).
 """
 function PetscDataTypeGetSize(ptype,size)
   ccall(

src/GridapPETSc.jl

@@ -69,17 +69,19 @@ end
 include("PETSC.jl")
 
 using GridapPETSc.PETSC: @check_error_code
-using GridapPETSc.PETSC: PetscBool, PetscInt, PetscReal, PetscScalar, Vec, Mat, KSP, PC, SNES
-#export PETSC
+using GridapPETSc.PETSC: PetscBool, PetscInt, PetscReal, PetscScalar, Vec, Mat, KSP, PC, SNES, IS
+
 export @check_error_code
 export PetscBool, PetscInt, PetscReal, PetscScalar, Vec, Mat, KSP, PC, SNES
 
 include("Environment.jl")
 
 export PETScVector
 export PETScMatrix
+export PETScIndexSet
 export petsc_sparse
 include("PETScArrays.jl")
+include("PETScIndexSets.jl")
 include("PartitionedArrays.jl")
 
 export PETScLinearSolver