| /petsc/lib/petsc/bin/maint/ |
| H A D | xclude | 1 petsc-dist/.readthedocs.yml
2 petsc-dist/.travis.yml
3 petsc-dist/.dir-locals.el
4 petsc-dist/.gitmessage
5 petsc-dist/.gitlab-ci.yml
6 petsc-dist/.gitlab-alcf-ci.yml
7 petsc-dist/.gitlab
8 petsc-dist/.git
9 petsc-dist/.mailmap
10 petsc-dist/.gitignore
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| H A D | builddist | 1 #!/bin/bash -ex
3 # This script builds the PETSc tar file distribution
5 # Usage: builddist petscrepo [branch/commit] [version-suffix]
9 # when version-suffix="SETVERSION", obtain it from include/petscversion.h
12 # builddist /sandbox/petsc/petsc.clone balay/foo [creates petsc-HASH.tar.gz]
13 # builddist /sandbox/petsc/petsc.clone main ver-suffix [creates petsc-ver-suffix.tar.gz]
14 # builddist /sandbox/petsc/petsc.clone release SETVERSION [creates petsc-3.24.5.tar.gz]
18 # ignore command line options in CI mode - and build tarball from current state setup by CI
19 if [ ! -z "${CI_PIPELINE_ID+x}" ]; then
20 petscrepo=`pwd -P`
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| H A D | createpatch | 6 # example usage: createpatch /sandbox/petsc/petsc-dist
16 if [ ! -d $petscrepo ]; then
22 if [ ! -f include/petscversion.h ]; then
27 if [ ! -f doc/install/download.md ]; then
33 a=`git status --untracked-files=no --short | wc -l`
36 git status --untracked-files=no --short
40 #git_branch=`git symbolic-ref HEAD 2>/dev/null | cut -d"/" -f 3`
46 …elease=`grep '^#define PETSC_VERSION_RELEASE ' include/petscversion.h |tr -s ' ' | cut -d ' ' -f 3`
47 …on_major=`grep '^#define PETSC_VERSION_MAJOR ' include/petscversion.h |tr -s ' ' | cut -d ' ' -f 3`
48 …on_minor=`grep '^#define PETSC_VERSION_MINOR ' include/petscversion.h |tr -s ' ' | cut -d ' ' -f 3`
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| H A D | runjobs.py | 6 # runjobs.py [-f] [job1 job2 ... jobN]
10 # -f: when commits in the local "branch" are not in sync with "origin/branch" - runjobs.py will no…
11 # for the specified "jobs list". Use '-f' to force the creation of this commit [and then use '…
12 # branch's contents at GitLab] - if the intention is to overwrite these differences with your …
16 # lib/petsc/bin/maint/runjobs.py -f linux-cuda-pkgs
17 # lib/petsc/bin/maint/runjobs.py -f freebsd-cxx-pkgs-opt linux-clang-avx linux-clang-ubsan
18 …ib/petsc/bin/maint/runjobs.py -f $(grep -lE "download-(mpich|openmpi)" config/examples/arch-ci-*.p…
20 # Note: If no jobs are listed, then all jobs in the pipeline are run but without a need to un-paus…
22 # lib/petsc/bin/maint/runjobs.py
27 if ('-f' in jobs):
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| /petsc/src/mat/graphops/color/interface/ |
| H A D | matcoloring.c | 1 #include <petsc/private/matimpl.h> /*I "petscmat.h" I*/
8 MatColoringRegister - Adds a new sparse matrix coloring to the matrix package.
13 + sname - name of Coloring (for example `MATCOLORINGSL`)
14 - function - function pointer that creates the coloring
24 `-mat_coloring_type my_color`
37 MatColoringCreate - Creates a matrix coloring context.
42 . m - a `Mat` from which a coloring is derived
45 . mcptr - the new `MatColoring` context
48 + -mat_coloring_type - the type of coloring algorithm used. See `MatColoringType`.
49 . -mat_coloring_maxcolors - the maximum number of relevant colors, all nodes not in a color are in …
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| /petsc/src/vec/is/utils/tests/ |
| H A D | ex1.c | 3 #include <petsc.h>
7 PetscReal dist = 0; in Distance() local
8 for (PetscInt j = 0; j < dim; j++) dist += PetscSqr(x[j] - y[j]); in Distance()
9 return PetscSqrtReal(dist); in Distance()
25 PetscCall(PetscLogDefaultBegin()); // So we can use PetscLogEventGetPerfInfo without -log_view in main()
29 …PetscCall(PetscOptionsInt("-num_coords", "Number of coordinates", "", PETSC_FALSE, &num_coords, NU… in main()
30 PetscCall(PetscOptionsInt("-dim", "Dimension of the coordinates", "", PETSC_FALSE, &dim, NULL)); in main()
31 …PetscCall(PetscOptionsInt("-bucket_size", "Size of the bucket at each leaf", "", bucket_size, &buc… in main()
32 …PetscCall(PetscOptionsBoundedInt("-loops", "Number of times to loop through KDTree creation and qu… in main()
33 …PetscCall(PetscOptionsEnum("-copy_mode", "Copy mode to use with KDTree", "PetscKDTreeCreate", Pets… in main()
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| /petsc/src/mat/graphops/color/utils/ |
| H A D | weights.c | 1 #include <petsc/private/matimpl.h> /*I "petscmat.h" I*/
7 Mat G = mc->mat; in MatColoringCreateLexicalWeights()
11 for (i = s; i < e; i++) weights[i - s] = i; in MatColoringCreateLexicalWeights()
20 Mat G = mc->mat; in MatColoringCreateRandomWeights()
29 weights[i - s] = PetscAbsReal(r); in MatColoringCreateRandomWeights()
37 PetscInt j, i, s, e, n, ln, lm, degree, bidx, idx, dist; in MatColoringGetDegrees() local
52 n = e - s; in MatColoringGetDegrees()
61 aij = (Mat_SeqAIJ *)lG->data; in MatColoringGetDegrees()
62 Gi = aij->i; in MatColoringGetDegrees()
63 Gj = aij->j; in MatColoringGetDegrees()
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| H A D | valid.c | 1 #include <petsc/private/matimpl.h> /*I "petscmat.h" I*/
8 Mat m = mc->mat; in MatColoringTest()
17 PetscInt dist = mc->dist; in MatColoringTest() local
37 for (k = 0; k < ncols; k++) statecol[k] = -1; in MatColoringTest()
40 for (k = 0; k < nindices; k++) statecol[indices[k] - s] = indices[k]; in MatColoringTest()
43 for (k = 0; k < dist; k++) { in MatColoringTest()
85 …- s] != indices[k]) PetscCall(PetscPrintf(PetscObjectComm((PetscObject)mc), "%" PetscInt_FMT " of … in MatColoringTest()
128 nnz = cia[col + 1] - cia[col]; in MatISColoringTest()
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| /petsc/src/mat/graphops/color/impls/power/ |
| H A D | power.c | 1 #include <petsc/private/matimpl.h> /*I "petscmat.h" I*/
5 Mat m = mc->mat, mp, ms; in MatColoringApply_Power()
12 if (mc->dist == 1) { in MatColoringApply_Power()
16 for (i = 2; i < mc->dist; i++) { in MatColoringApply_Power()
28 PetscCall(MatColoringSetWeightType(imc, mc->weight_type)); in MatColoringApply_Power()
37 MATCOLORINGPOWER - Take the matrix's nth power, then do one-coloring on it.
51 mc->ops->apply = MatColoringApply_Power; in MatColoringCreate_Power()
52 mc->ops->view = NULL; in MatColoringCreate_Power()
53 mc->ops->destroy = NULL; in MatColoringCreate_Power()
54 mc->ops->setfromoptions = NULL; in MatColoringCreate_Power()
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| /petsc/src/vec/is/utils/ |
| H A D | kdtree.c | 3 #include <petsc/private/petscimpl.h>
11 …eaves; // Bit-wise boolean for whether the greater_handle and less_equal_handle ind…
36 PetscKDTreeDestroy - destroy a `PetscKDTree`
41 . tree - tree to destroy
51 PetscCall(PetscFree((*tree)->stems)); in PetscKDTreeDestroy()
52 PetscCall(PetscFree((*tree)->leaves)); in PetscKDTreeDestroy()
53 PetscCall(PetscFree((*tree)->bucket_indices)); in PetscKDTreeDestroy()
54 PetscCall(PetscFree((*tree)->coords_owned)); in PetscKDTreeDestroy()
74 v--; in RoundToNextPowerOfTwo()
90 // See "Building a Balanced k-d Tree in O(kn log n) Time" https://jcgt.org/published/0004/01/03/
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| /petsc/src/mat/graphops/color/impls/minpack/ |
| H A D | color.c | 5 #include <petsc/private/matimpl.h>
6 #include <petsc/private/isimpl.h>
10 MatFDColoringDegreeSequence_Minpack - Calls the MINPACK routine seqr() that
33 Mat mat = mc->mat; in MatColoringApply_SL()
43 PetscCheck(mc->dist == 2, PETSC_COMM_SELF, PETSC_ERR_SUP, "SL may only do distance 2 coloring"); in MatColoringApply_SL()
75 …PetscCheck(ncolors <= IS_COLORING_MAX - 1, PETSC_COMM_SELF, PETSC_ERR_SUP, "Maximum color size exc… in MatColoringApply_SL()
78 for (i = 0; i < n; i++) s[i] = (ISColoringValue)(coloring[i] - 1); in MatColoringApply_SL()
87 rstart = mat->rmap->rstart / bs; in MatColoringApply_SL()
88 rend = mat->rmap->rend / bs; in MatColoringApply_SL()
89 N_loc = rend - rstart; /* number of local nodes */ in MatColoringApply_SL()
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| /petsc/src/binding/petsc4py/ |
| H A D | .gitignore | 2 dist
15 src/petsc4py/PETSc.c
16 src/petsc4py/PETSc.h
18 src/petsc4py/PETSc.pyi
19 src/petsc4py/lib/*/PETSc.*.so
20 src/petsc4py.egg-info/
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| H A D | makefile | 1 -include ../../../petscdir.mk
4 default: opt=--inplace
7 MODULE = PETSc
12 # ----
21 test-%:
22 ${MPIEXEC} -n $* ${VALGRIND} ${PYTHON} ${PWD}/test/runtests.py ${opt}
28 -${RM} src/${package}/${MODULE}.c
29 -${RM} src/${package}/${MODULE}.h
30 -${RM} src/${package}/${MODULE}_api.h
34 ${PYTHON} setup.py clean --all
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| /petsc/doc/install/ |
| H A D | index.md | 6 PETSc is available from multiple package managers.
8 you to install PETSc.
9 Always verify that the package manager is providing a recent enough release of PETSc with support f…
10 Some package managers provide separate packages for the complex number installation of PETSc.
12 - Archlinux <https://aur.archlinux.org/packages/petsc>
13 - Conda: <https://anaconda.org/conda-forge/petsc>
14 : `conda install -c conda-forge petsc`
15 - Debian: <https://packages.debian.org/petsc-dev>
16 : `sudo apt install petsc-dev`
17 - E4S: <https://e4s.io/download.html>
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| /petsc/src/binding/petsc4py/test/ |
| H A D | runtests.py | 11 'PETSc',
19 '-q',
20 '--quiet',
28 '-v',
29 '--verbose',
37 '-i',
38 '--include',
47 '-e',
48 '--exclude',
57 '-k',
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| /petsc/src/ksp/pc/impls/bddc/ |
| H A D | bddcgraph.c | 1 #include <petsc/private/petscimpl.h>
2 #include <petsc/private/pcbddcprivateimpl.h>
3 #include <petsc/private/pcbddcstructsimpl.h>
4 #include <petsc/private/hashmapi.h>
5 #include <petsc/private/pcbddcgraphhashmap.h>
13 for (PetscInt i = 0; i < cand->nfc; i++) PetscCall(ISDestroy(&cand->Faces[i])); in PCBDDCDestroyGraphCandidatesIS()
14 for (PetscInt i = 0; i < cand->nec; i++) PetscCall(ISDestroy(&cand->Edges[i])); in PCBDDCDestroyGraphCandidatesIS()
15 PetscCall(PetscFree(cand->Faces)); in PCBDDCDestroyGraphCandidatesIS()
16 PetscCall(PetscFree(cand->Edges)); in PCBDDCDestroyGraphCandidatesIS()
17 PetscCall(ISDestroy(&cand->Vertices)); in PCBDDCDestroyGraphCandidatesIS()
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| /petsc/src/ksp/pc/impls/amgx/ |
| H A D | amgx.cxx | 2 This file implements an AmgX preconditioner in PETSc as part of PC.
7 pcimpl.h - private include file intended for use by all preconditioners
10 #include <petsc/private/pcimpl.h> /*I "petscpc.h" I*/
132 // Cached state for re-setup
177 if (amgx->verbose && !amgx_output.empty()) { in amgx_output_messages()
179 PetscCall(PetscPrintf(amgx->comm, "AMGX: %s", amgx_output.c_str())); in amgx_output_messages()
198 SETERRQ(amgx->comm, PETSC_ERR_LIB, "%s", msg); \
203 PCSetUp_AMGX - Prepares for the use of the AmgX preconditioner
207 . pc - the preconditioner context
217 PC_AMGX *amgx = (PC_AMGX *)pc->data; in PCSetUp_AMGX()
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| /petsc/src/dm/impls/plex/kokkos/ |
| H A D | plexlocalizationletkf.kokkos.cxx | 1 #include <petsc/private/dmpleximpl.h>
30 return -0.25 * r5 + 0.5 * r4 + 0.625 * r3 - (5.0 / 3.0) * r2 + 1.0; in GaspariCohn()
33 …return (1.0 / 12.0) * r5 - 0.5 * r4 + 0.625 * r3 + (5.0 / 3.0) * r2 - 5.0 * r + 4.0 - (2.0 / 3.0) … in GaspariCohn()
38 …DMPlexGetLETKFLocalizationMatrix - Compute localization weight matrix for LETKF [move to ml/da/int…
43 + n_obs_vertex - Number of nearest observations to use per vertex (eg, MAX_Q_NUM_LOCAL_OBSERVATIONS…
44 . n_obs_local - Number of local observations
45 . n_dof - Number of degrees of freedom
46 . Vecxyz - Array of vectors containing the coordinates
47 - H - Observation operator matrix
50 . Q - Localization weight matrix (sparse, AIJ format)
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| /petsc/src/dm/impls/plex/ |
| H A D | plexdistribute.c | 1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/
2 #include <petsc/private/dmlabelimpl.h> /*I "petscdmlabel.h" I*/
3 #include <petsc/private/partitionerimpl.h>
6 DMPlexSetAdjacencyUser - Define adjacency in the mesh using a user-provided callback
9 + dm - The DM object
10 . user - The user callback, may be `NULL` (to clear the callback)
11 - ctx - context for callback evaluation, may be `NULL`
24 DM_Plex *mesh = (DM_Plex *)dm->data; in DMPlexSetAdjacencyUser()
28 mesh->useradjacency = user; in DMPlexSetAdjacencyUser()
29 mesh->useradjacencyctx = ctx; in DMPlexSetAdjacencyUser()
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| /petsc/src/sys/tests/ |
| H A D | ex64.cxx | 3 #include <petsc/private/cpp/unordered_map.hpp>
15 // see https://stackoverflow.com/questions/2590677/how-do-i-combine-hash-values-in-c0x
43 using namespace Petsc::util;
132 PetscCallAbort(PETSC_COMM_SELF, this->printer(value, this->buffer)); in operator ()()
133 PetscFunctionReturn(this->buffer.c_str()); in operator ()()
164 using map_type = Petsc::UnorderedMap<T...>;
181 PetscCallCXX(oss << "map: '" << this->map_name << "'\n"); in view_map()
189 …entry : map) PetscCallCXX(oss << " key: [" << this->key_printer(entry.first) << "] -> [" << thi… in view_map()
198 PetscCall(this->view_map(map__)); \
199 SETERRQ(comm__, ierr__, "%s: " base_mess__, this->map_name.c_str(), __VA_ARGS__); \
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| /petsc/src/mat/graphops/color/impls/greedy/ |
| H A D | greedy.c | 1 #include <petsc/private/matimpl.h> /*I "petscmat.h" I*/
13 PetscCall(PetscFree(mc->data)); in MatColoringDestroy_Greedy()
20 Mat m = mc->mat; in GreedyColoringLocalDistanceOne_Private()
21 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)m->data; in GreedyColoringLocalDistanceOne_Private()
35 n = e - s; in GreedyColoringLocalDistanceOne_Private()
43 /* get the CSR data for on and off-diagonal portions of m */ in GreedyColoringLocalDistanceOne_Private()
46 md = aij->A; in GreedyColoringLocalDistanceOne_Private()
47 dseq = (Mat_SeqAIJ *)md->data; in GreedyColoringLocalDistanceOne_Private()
48 mo = aij->B; in GreedyColoringLocalDistanceOne_Private()
49 oseq = (Mat_SeqAIJ *)mo->data; in GreedyColoringLocalDistanceOne_Private()
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| /petsc/src/binding/petsc4py/src/petsc4py/PETSc/ |
| H A D | DMPlex.pyx | 1 # --------------------------------------------------------------------
14 def create(self, comm: Comm | None = None) -> Self:
20 ----------
25 --------
26 DM, DMPlex, DM.create, DM.setType, petsc.DMPlexCreate
35 …[int], coords: Sequence[float], interpolate: bool | None = True, comm: Comm | None = None) -> Self:
41 ----------
54 --------
56 petsc.DMPlexCreateFromCellListPetsc
91 …ationHeight: int | None = 0, sparseLocalize: bool | None = True, comm: Comm | None = None) -> Self:
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| H A D | Mat.pyx | 1 # --------------------------------------------------------------------
7 --------
8 petsc.MatType
107 --------
108 petsc.MatOption
144 --------
145 petsc.MatAssemblyType
167 --------
168 petsc.MatStructure
187 --------
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| /petsc/src/mat/impls/aij/mpi/strumpack/ |
| H A D | strumpack.c | 14 STRUMPACK_SparseSolver *S = (STRUMPACK_SparseSolver *)A->data; in MatDestroy_STRUMPACK()
19 PetscCall(PetscFree(A->data)); in MatDestroy_STRUMPACK()
53 STRUMPACK_SparseSolver *S = (STRUMPACK_SparseSolver *)F->data; in MatSTRUMPACKSetReordering_STRUMPACK()
61 STRUMPACK_SparseSolver *S = (STRUMPACK_SparseSolver *)F->data; in MatSTRUMPACKGetReordering_STRUMPACK()
69 …MatSTRUMPACKSetReordering - Set STRUMPACK <https://portal.nersc.gov/project/sparse/strumpack/maste…
74 + F - the factored matrix obtained by calling `MatGetFactor()` from PETSc-STRUMPACK interf…
75 - reordering - the code to be used to find the fill-reducing reordering
78 . -mat_strumpack_reordering <METIS> - Sparsity reducing matrix reordering, see `MatSTRUMPACKReorder…
93 …MatSTRUMPACKGetReordering - Get STRUMPACK <https://portal.nersc.gov/project/sparse/strumpack/maste…
98 . F - the factored matrix obtained by calling `MatGetFactor()` from PETSc-STRUMPACK interface
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| /petsc/ |
| H A D | makefile | 2 # See https://petsc.org/release/install/ for instructions on installing PETSc
4 # This is the top level makefile for compiling PETSc.
5 # * make help - useful messages on functionality
6 # * make all - compile the PETSc libraries and utilities, run after ./configure
7 # * make check - runs a quick test that the libraries are built correctly and PETSc applications …
9 # * make install - for use with ./configure is run with the --prefix=directory option
10 # * make test - runs a comprehensive test suite (requires gnumake)
11 # * make docs - build the entire PETSc website of documentation (locally)
13 # * a variety of rules for PETSc developers
15 # gmakefile - manages the compiling PETSc in parallel
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