[workspace] Upgrade petsc to latest release v3.17.1 (RobotLocomotion#…

…17273)

Co-authored-by: Betsy McPhail <betsy.mcphail@kitware.com>
Co-authored-by: Xuchen Han <xuchen.han@tri.global>

tools/workspace/petsc/package.BUILD.bazel

@@ -70,6 +70,7 @@ _SRCS = glob([
     "src/dm/impls/da/hypre/**",
     "src/dm/impls/da/usfft/**",
     "src/dm/impls/forest/p4est/**",
+    "src/dm/impls/plex/adaptors/**",
     "src/dm/impls/plex/generators/**",
     "src/ksp/ksp/impls/gmres/agmres/**",
     "src/ksp/ksp/interface/saws/**",
@@ -100,6 +101,7 @@ _SRCS = glob([
     "src/mat/impls/sbaij/seq/cholmod/**",
     "src/mat/impls/scalapack/**",
     "src/mat/order/amd/**",
+    "src/mat/order/metisnd/**",
     "src/mat/partition/impls/chaco/**",
     "src/mat/partition/impls/party/**",
     "src/mat/partition/impls/pmetis/**",
@@ -119,6 +121,7 @@ _SRCS = glob([
     "src/sys/classes/viewer/impls/socket/**",
     "src/sys/logging/utils/**",
     "src/ts/**",
+    "src/vec/is/sf/impls/basic/neighbor/**",
     "src/vec/is/sf/impls/window/**",
     "src/vec/vec/impls/seq/seqcuda/**",
 ])

tools/workspace/petsc/patches/baij.patch

@@ -4,8 +4,8 @@ index 7cf0f8e22a..c83e639fd7 100644
 +++ src/mat/impls/baij/seq/baij.c
 @@ -1797,7 +1797,8 @@ PetscErrorCode MatGetValues_SeqBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscIn
      row = im[k]; brow = row/bs;
-     if (row < 0) {v += n; continue;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row"); */
-     if (row >= A->rmap->N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D too large", row);
+     if (row < 0) {v += n; continue;} /* negative row */
+     PetscCheck(row < A->rmap->N,PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %" PetscInt_FMT " too large", row);
 -    rp   = aj + ai[brow]; ap = aa + bs2*ai[brow];
 +    rp   = aj ? aj + ai[brow] : NULL;
 +    ap   = aa ? aa + bs2*ai[brow] : NULL;

tools/workspace/petsc/patches/destroy.patch

@@ -1,7 +1,7 @@
 --- src/sys/objects/destroy.c
 +++ src/sys/objects/destroy.c
-@@ -110,7 +111,8 @@ PetscErrorCode PetscObjectViewFromOptions(PetscObject obj,PetscObject bobj,const
-   PetscErrorCode    ierr;
+@@ -94,7 +94,8 @@ PetscErrorCode PetscObjectViewFromOptions(PetscObject obj,PetscObject bobj,const
+ {
    PetscViewer       viewer;
    PetscBool         flg;
 -  static PetscBool  incall = PETSC_FALSE;

tools/workspace/petsc/patches/dlregispetsc.patch

@@ -9,10 +9,10 @@
 
  /*
 @@ -108,7 +107,6 @@ PETSC_EXTERN PetscErrorCode PetscDLLibraryRegister_petscsys(void)
-   ierr = PetscDLLibraryRegister_petscdm();CHKERRQ(ierr);
-   ierr = PetscDLLibraryRegister_petscksp();CHKERRQ(ierr);
-   ierr = PetscDLLibraryRegister_petscsnes();CHKERRQ(ierr);
--  ierr = PetscDLLibraryRegister_petscts();CHKERRQ(ierr);
+   PetscCall(PetscDLLibraryRegister_petscdm());
+   PetscCall(PetscDLLibraryRegister_petscksp());
+   PetscCall(PetscDLLibraryRegister_petscsnes());
+-  PetscCall(PetscDLLibraryRegister_petscts());
  #endif
    PetscFunctionReturn(0);
  }

tools/workspace/petsc/patches/inherit.patch

@@ -14,10 +14,10 @@
  {
 -  static PetscInt idcnt = 1;
 +  static atomic_int atomic_idcnt = 1;
-   PetscErrorCode  ierr;
  #if defined(PETSC_USE_LOG)
    PetscObject     *newPetscObjects;
-@@ -48,7 +49,7 @@ PetscErrorCode  PetscHeaderCreate_Private(PetscObject h,PetscClassId classid,con
+   PetscInt         newPetscObjectsMaxCounts,i;
+@@ -47,7 +48,7 @@ PetscErrorCode  PetscHeaderCreate_Private(PetscObject h,PetscClassId classid,con
  #if defined(PETSC_HAVE_SAWS)
    h->amsmem                = PETSC_FALSE;
  #endif

tools/workspace/petsc/patches/mal.patch

@@ -1,11 +1,9 @@
-diff --git a/src/sys/memory/mal.c b/src/sys/memory/mal.c
-index 87678c5f2f..eabd9b2b97 100644
 --- src/sys/memory/mal.c
 +++ src/sys/memory/mal.c
-@@ -414,9 +414,15 @@ PetscErrorCode PetscMallocA(int n,PetscBool clear,int lineno,const char *functio
+@@ -399,9 +399,15 @@ PetscErrorCode PetscMallocA(int n,PetscBool clear,int lineno,const char *functio
    if (petscmalloccoalesce) {
      char *p;
-     ierr = (*PetscTrMalloc)(sumbytes,clear,lineno,function,filename,(void**)&p);CHKERRQ(ierr);
+     PetscCall((*PetscTrMalloc)(sumbytes,clear,lineno,function,filename,(void**)&p));
 -    for (i=0; i<n; i++) {
 -      *ptr[i] = bytes[i] ? p : NULL;
 -      p = (char*)PetscAddrAlign(p + bytes[i]);

tools/workspace/petsc/patches/matrix.patch

@@ -1,6 +1,6 @@
 --- src/mat/interface/matrix.c
 +++ src/mat/interface/matrix.c
-@@ -5536,7 +5536,7 @@ PetscErrorCode MatNorm(Mat mat,NormType type,PetscReal *nrm)
+@@ -5316,7 +5316,7 @@ PetscErrorCode MatNorm(Mat mat,NormType type,PetscReal *nrm)
       This variable is used to prevent counting of MatAssemblyBegin() that
     are called from within a MatAssemblyEnd().
  */
@@ -9,10 +9,10 @@
  /*@
     MatAssemblyBegin - Begins assembling the matrix.  This routine should
     be called after completing all calls to MatSetValues().
-@@ -5656,7 +5656,7 @@ PetscErrorCode MatAssembled(Mat mat,PetscBool  *assembled)
+@@ -5433,7 +5433,7 @@ PetscErrorCode MatAssembled(Mat mat,PetscBool *assembled)
+ @*/
  PetscErrorCode MatAssemblyEnd(Mat mat,MatAssemblyType type)
  {
-   PetscErrorCode  ierr;
 -  static PetscInt inassm = 0;
 +  static _Thread_local PetscInt inassm = 0;
    PetscBool       flg    = PETSC_FALSE;

tools/workspace/petsc/patches/petscimpl.patch

@@ -8,20 +8,20 @@
 
  #if defined(PETSC_CLANG_STATIC_ANALYZER)
  #define PetscDisableStaticAnalyzerForExpressionUnderstandingThatThisIsDangerousAndBugprone(expr)
-@@ -886,9 +887,9 @@ PETSC_EXTERN PetscMPIInt Petsc_ShmComm_keyval;
+@@ -852,9 +853,9 @@ struct PetscCommStash {
    PetscCommDuplicate(), PetscCommDestroy(), PetscCommGetNewTag(), PetscObjectGetName()
  */
  typedef struct {
--  PetscMPIInt tag;              /* next free tag value */
--  PetscInt    refcount;         /* number of references, communicator can be freed when this reaches 0 */
--  PetscInt    namecount;        /* used to generate the next name, as in Vec_0, Mat_1, ... */
-+  atomic_int atomic_tag;        /* next free tag value */
-+  atomic_int atomic_refcount;   /* number of references, communicator can be freed when this reaches 0 */
-+  atomic_int atomic_namecount;  /* used to generate the next name, as in Vec_0, Mat_1, ... */
-   PetscMPIInt *iflags;          /* length of comm size, shared by all calls to PetscCommBuildTwoSided_Allreduce/RedScatter on this comm */
+-  PetscMPIInt           tag;              /* next free tag value */
+-  PetscInt              refcount;         /* number of references, communicator can be freed when this reaches 0 */
+-  PetscInt              namecount;        /* used to generate the next name, as in Vec_0, Mat_1, ... */
++  atomic_int            atomic_tag;       /* next free tag value */
++  atomic_int            atomic_refcount;  /* number of references, communicator can be freed when this reaches 0 */
++  atomic_int            atomic_namecount; /* used to generate the next name, as in Vec_0, Mat_1, ... */
+   PetscMPIInt           *iflags;          /* length of comm size, shared by all calls to PetscCommBuildTwoSided_Allreduce/RedScatter on this comm */
+   struct PetscCommStash *comms;           /* communicators available for PETSc to pass off to other packages */
  } PetscCommCounter;
-
-@@ -972,7 +973,7 @@ PETSC_STATIC_INLINE PetscErrorCode PetscSpinlockDestroy(PetscSpinlock *omp_lock)
+@@ -939,7 +940,7 @@ static inline PetscErrorCode PetscSpinlockDestroy(PetscSpinlock *omp_lock)
    return 0;
  }
  #else

tools/workspace/petsc/patches/pname.patch

@@ -1,11 +1,11 @@
 --- src/sys/objects/pname.c
 +++ src/sys/objects/pname.c
-@@ -131,7 +131,7 @@ PetscErrorCode  PetscObjectName(PetscObject obj)
+@@ -127,7 +127,7 @@ PetscErrorCode  PetscObjectName(PetscObject obj)
      /* If the union has extra bytes, their value is implementation-dependent, but they will normally be what we set last
       * in 'ucomm.ptr = NULL'.  This output is always implementation-defined (and varies from run to run) so the union
       * abuse acceptable. */
--    ierr = PetscSNPrintf(name,64,"%s_%p_%D",obj->class_name,ucomm.ptr,counter->namecount++);CHKERRQ(ierr);
-+    ierr = PetscSNPrintf(name,64,"%s_%p_%D",obj->class_name,ucomm.ptr,atomic_fetch_add(&counter->atomic_namecount,1));CHKERRQ(ierr);
-     ierr = PetscStrallocpy(name,&obj->name);CHKERRQ(ierr);
+-    PetscCall(PetscSNPrintf(name,64,"%s_%p_%" PetscInt_FMT,obj->class_name,ucomm.ptr,counter->namecount++));
++    PetscCall(PetscSNPrintf(name,64,"%s_%p_%" PetscInt_FMT,obj->class_name,ucomm.ptr,atomic_fetch_add(&counter->atomic_namecount,1)));
+     PetscCall(PetscStrallocpy(name,&obj->name));
    }
    PetscFunctionReturn(0);

tools/workspace/petsc/patches/remove_packages.patch

@@ -1,22 +1,21 @@
 Do not load unused packages to reduce build footprint
 --- src/sys/dll/reg.c
 +++ src/sys/dll/reg.c
-@@ -114,9 +114,6 @@ PETSC_INTERN PetscErrorCode PetscInitialize_DynamicLibraries(void)
+@@ -112,9 +112,6 @@ PETSC_INTERN PetscErrorCode PetscInitialize_DynamicLibraries(void)
  #if defined(PETSC_USE_SINGLE_LIBRARY)
-   ierr = AOInitializePackage();CHKERRQ(ierr);
-   ierr = PetscSFInitializePackage();CHKERRQ(ierr);
+   PetscCall(AOInitializePackage());
+   PetscCall(PetscSFInitializePackage());
 -#if !defined(PETSC_USE_COMPLEX)
--  ierr = CharacteristicInitializePackage();CHKERRQ(ierr);
+-  PetscCall(CharacteristicInitializePackage());
 -#endif
-   ierr = ISInitializePackage();CHKERRQ(ierr);
-   ierr = VecInitializePackage();CHKERRQ(ierr);
-   ierr = MatInitializePackage();CHKERRQ(ierr);
-@@ -124,8 +121,6 @@ PETSC_INTERN PetscErrorCode PetscInitialize_DynamicLibraries(void)
-   ierr = PCInitializePackage();CHKERRQ(ierr);
-   ierr = KSPInitializePackage();CHKERRQ(ierr);
-   ierr = SNESInitializePackage();CHKERRQ(ierr);
--  ierr = TSInitializePackage();CHKERRQ(ierr);
--  ierr = TaoInitializePackage();CHKERRQ(ierr);
+   PetscCall(ISInitializePackage());
+   PetscCall(VecInitializePackage());
+   PetscCall(MatInitializePackage());
+@@ -123,7 +120,5 @@ PETSC_INTERN PetscErrorCode PetscInitialize_DynamicLibraries(void)
+   PetscCall(KSPInitializePackage());
+   PetscCall(SNESInitializePackage());
+-  PetscCall(TSInitializePackage());
+-  PetscCall(TaoInitializePackage());
  #else
    SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Cannot use -library_preload with multiple static PETSc libraries");
  #endif

tools/workspace/petsc/patches/tagm.patch

@@ -1,15 +1,16 @@
 --- src/sys/objects/tagm.c
 +++ src/sys/objects/tagm.c
-@@ -66,14 +66,14 @@ PetscErrorCode  PetscCommGetNewTag(MPI_Comm comm,PetscMPIInt *tag)
-   ierr = MPI_Comm_get_attr(comm,Petsc_Counter_keyval,&counter,&flg);CHKERRMPI(ierr);
-   if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_CORRUPT,"Bad MPI communicator supplied; must be a PETSc communicator");
+@@ -63,15 +63,15 @@ PetscErrorCode  PetscCommGetNewTag(MPI_Comm comm,PetscMPIInt *tag)
+   PetscCallMPI(MPI_Comm_get_attr(comm,Petsc_Counter_keyval,&counter,&flg));
+   PetscCheck(flg,PETSC_COMM_SELF,PETSC_ERR_ARG_CORRUPT,"Bad MPI communicator supplied; must be a PETSc communicator");
 
 -  if (counter->tag < 1) {
--    ierr = PetscInfo1(NULL,"Out of tags for object, starting to recycle. Comm reference count %d\n",counter->refcount);CHKERRQ(ierr);
 +  if (atomic_load(&counter->atomic_tag) < 1) {
-+    ierr = PetscInfo1(NULL,"Out of tags for object, starting to recycle. Comm reference count %d\n",atomic_load(&counter->atomic_refcount));CHKERRQ(ierr);
-     ierr = MPI_Comm_get_attr(MPI_COMM_WORLD,MPI_TAG_UB,&maxval,&flg);CHKERRMPI(ierr);
-     if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"MPI error: MPI_Comm_get_attr() is not returning a MPI_TAG_UB");
+
+-    PetscCall(PetscInfo(NULL,"Out of tags for object, starting to recycle. Comm reference count %" PetscInt_FMT "\n",counter->refcount));
++    PetscCall(PetscInfo(NULL,"Out of tags for object, starting to recycle. Comm reference count %" PetscInt_FMT "\n",atomic_load(&counter->atomic_refcount)));
+     PetscCallMPI(MPI_Comm_get_attr(MPI_COMM_WORLD,MPI_TAG_UB,&maxval,&flg));
+     PetscCheck(flg,PETSC_COMM_SELF,PETSC_ERR_LIB,"MPI error: MPI_Comm_get_attr() is not returning a MPI_TAG_UB");
 -    counter->tag = *maxval - 128; /* hope that any still active tags were issued right at the beginning of the run */
 +    atomic_store(&counter->atomic_tag, *maxval - 128); /* hope that any still active tags were issued right at the beginning of the run */
    }
@@ -19,25 +20,25 @@
    if (PetscDefined(USE_DEBUG)) {
      /*
       Hanging here means that some processes have called PetscCommGetNewTag() and others have not.
-@@ -126,7 +126,7 @@ PetscErrorCode  PetscCommDuplicate(MPI_Comm comm_in,MPI_Comm *comm_out,PetscMPII
-       ierr = MPI_Comm_get_attr(MPI_COMM_WORLD,MPI_TAG_UB,&maxval,&flg);CHKERRMPI(ierr);
-       if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"MPI error: MPI_Comm_get_attr() is not returning a MPI_TAG_UB");
-       ierr = PetscNew(&counter);CHKERRQ(ierr); /* all fields of counter are zero'ed */
+@@ -208,7 +208,7 @@ PetscErrorCode  PetscCommDuplicate(MPI_Comm comm_in,MPI_Comm *comm_out,PetscMPII
+       PetscCallMPI(MPI_Comm_get_attr(MPI_COMM_WORLD,MPI_TAG_UB,&maxval,&flg));
+       PetscCheck(flg,PETSC_COMM_SELF,PETSC_ERR_LIB,"MPI error: MPI_Comm_get_attr() is not returning a MPI_TAG_UB");
+       PetscCall(PetscNew(&counter)); /* all fields of counter are zero'ed */
 -      counter->tag = *maxval;
 +      atomic_store(&counter->atomic_tag, *maxval);
-       ierr = MPI_Comm_set_attr(*comm_out,Petsc_Counter_keyval,counter);CHKERRMPI(ierr);
-       ierr = PetscInfo3(NULL,"Duplicating a communicator %ld %ld max tags = %d\n",(long)comm_in,(long)*comm_out,*maxval);CHKERRQ(ierr);
+       PetscCallMPI(MPI_Comm_set_attr(*comm_out,Petsc_Counter_keyval,counter));
+       PetscCall(PetscInfo(NULL,"Duplicating a communicator %ld %ld max tags = %d\n",(long)comm_in,(long)*comm_out,*maxval));
 
-@@ -153,16 +153,16 @@ PetscErrorCode  PetscCommDuplicate(MPI_Comm comm_in,MPI_Comm *comm_out,PetscMPII
-     ierr = MPI_Barrier(comm_in);CHKERRMPI(ierr);
+@@ -235,16 +235,16 @@ PetscErrorCode  PetscCommDuplicate(MPI_Comm comm_in,MPI_Comm *comm_out,PetscMPII
+     PetscCallMPI(MPI_Barrier(comm_in));
    }
 
 -  if (counter->tag < 1) {
--    ierr = PetscInfo1(NULL,"Out of tags for object, starting to recycle. Comm reference count %d\n",counter->refcount);CHKERRQ(ierr);
+-    PetscCall(PetscInfo(NULL,"Out of tags for object, starting to recycle. Comm reference count %" PetscInt_FMT "\n",counter->refcount));
 +  if (atomic_load(&counter->atomic_tag) < 1) {
-+    ierr = PetscInfo1(NULL,"Out of tags for object, starting to recycle. Comm reference count %d\n",atomic_load(&counter->atomic_refcount));CHKERRQ(ierr);
-     ierr = MPI_Comm_get_attr(MPI_COMM_WORLD,MPI_TAG_UB,&maxval,&flg);CHKERRMPI(ierr);
-     if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"MPI error: MPI_Comm_get_attr() is not returning a MPI_TAG_UB");
++    PetscCall(PetscInfo(NULL,"Out of tags for object, starting to recycle. Comm reference count %" PetscInt_FMT "\n",atomic_load(&counter->atomic_refcount)));
+     PetscCallMPI(MPI_Comm_get_attr(MPI_COMM_WORLD,MPI_TAG_UB,&maxval,&flg));
+     PetscCheck(flg,PETSC_COMM_SELF,PETSC_ERR_LIB,"MPI error: MPI_Comm_get_attr() is not returning a MPI_TAG_UB");
 -    counter->tag = *maxval - 128; /* hope that any still active tags were issued right at the beginning of the run */
 +    atomic_store(&counter->atomic_tag,  *maxval - 128); /* hope that any still active tags were issued right at the beginning of the run */
    }
@@ -47,17 +48,17 @@
 
 -  counter->refcount++; /* number of references to this comm */
 +  atomic_fetch_add(&counter->atomic_refcount,1); /* number of references to this comm */
-   ierr = PetscSpinlockUnlock(&PetscCommSpinLock);CHKERRQ(ierr);
+   PetscCall(PetscSpinlockUnlock(&PetscCommSpinLock));
    PetscFunctionReturn(0);
  }
-@@ -199,9 +199,7 @@ PetscErrorCode  PetscCommDestroy(MPI_Comm *comm)
-     if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_CORRUPT,"Inner MPI_Comm does not have expected tag/name counter, problem with corrupted memory");
+@@ -280,9 +280,7 @@ PetscErrorCode  PetscCommDestroy(MPI_Comm *comm)
+     PetscCheck(flg,PETSC_COMM_SELF,PETSC_ERR_ARG_CORRUPT,"Inner MPI_Comm does not have expected tag/name counter, problem with corrupted memory");
    }
 
 -  counter->refcount--;
 -
 -  if (!counter->refcount) {
 +  if (!atomic_fetch_sub(&counter->atomic_refcount,1)) {
      /* if MPI_Comm has outer comm then remove reference to inner MPI_Comm from outer MPI_Comm */
-     ierr = MPI_Comm_get_attr(icomm,Petsc_OuterComm_keyval,&ucomm,&flg);CHKERRMPI(ierr);
+     PetscCallMPI(MPI_Comm_get_attr(icomm,Petsc_OuterComm_keyval,&ucomm,&flg));
      if (flg) {

tools/workspace/petsc/repository.bzl

@@ -8,8 +8,8 @@ def petsc_repository(
     github_archive(
         name = name,
         repository = "petsc/petsc",
-        commit = "v3.16.5",
-        sha256 = "1adf81bfb42104af469443fbcdb4211a7cae674dcb46b6c312ff29a7ffb8ff45",  # noqa
+        commit = "v3.17.1",
+        sha256 = "6dfe03613ccf5cd2d19f6267057ebb734a49e81e300f11ba7fc1601bbe585796",  # noqa
         build_file = "@drake//tools/workspace/petsc:package.BUILD.bazel",
         mirrors = mirrors,
         patches = [

tools/workspace/petsc/stubs/petscconf.h

@@ -1,9 +1,9 @@
 #pragma once
 
 // TODO(jwnimmer-tri): This file is a lightly-edited version of what comes out
-// of upstream's configure script. Between some combination of hard-coded
-// settings and platform-specific word size sensing, we need to reconstruct
-// and/or generate this file on the fly.
+// of upstream's configure script that has been tweaked to work on all of our
+// supported platforms, and to remove some unwanted bits. We need to document
+// a more careful procedure for how to update and/or re-create this file.
 
 #define MPI_Comm_create_errhandler(p_err_fun, p_errhandler) \
   MPI_Errhandler_create((p_err_fun), (p_errhandler))
@@ -38,7 +38,6 @@
 #define PETSC_HAVE_CXX 1
 #define PETSC_HAVE_CXX_COMPLEX 1
 #define PETSC_HAVE_CXX_COMPLEX_FIX 1
-#define PETSC_HAVE_CXX_DIALECT_CXX03 1
 #define PETSC_HAVE_CXX_DIALECT_CXX11 1
 #define PETSC_HAVE_CXX_DIALECT_CXX14 1
 #define PETSC_HAVE_CXX_DIALECT_CXX17 1
@@ -73,9 +72,6 @@
 #define PETSC_HAVE_MEMMOVE 1
 #define PETSC_HAVE_MMAP 1
 #define PETSC_HAVE_MPIUNI 1
-#define PETSC_HAVE_MPI_IN_PLACE 1
-#define PETSC_HAVE_MPI_TYPE_DUP 1
-#define PETSC_HAVE_MPI_TYPE_GET_ENVELOPE 1
 #define PETSC_HAVE_NANOSLEEP 1
 #define PETSC_HAVE_NETDB_H 1
 #define PETSC_HAVE_NETINET_IN_H 1