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/petsc/
H A D.gitlab-ci.yml2 # stage-1 take only a few minutes; they do not run the full test suite or external packages.
4 # stage-2 runs on MCS systems and may take 10 to 15 minutes. They run the full test suite but with …
6 # stage-3 runs on MCS systems and may take an hour or more. They run the full test suite and heavil…
8 # The stage-(n) tests are only started if all of the stage-(n-1) tests run without error
13 - stage-1
14 - stage-2
15 - stage-3
16 - stage-4
19 GIT_CLEAN_FLAGS: -ffdxq
21 BASE_EXTRA_OPTIONS: -nox -nox_warning -malloc_dump
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/petsc/config/examples/
H A Darch-ci-linux-cuda-single-cxx.py4 petsc_hash_pkgs=os.path.join(os.getenv('HOME'),'petsc-hash-pkgs')
12 '--package-prefix-hash='+petsc_hash_pkgs,
13 '--with-make-test-np=15',
14 'COPTFLAGS=-g -O',
15 'FOPTFLAGS=-g -O',
16 'CXXOPTFLAGS=-g -O',
17 '--with-fortran-bindings=0',
18 '--with-log=0',
19 '--with-info=0',
20 '--with-cuda=1',
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/petsc/config/BuildSystem/config/packages/
H A DSLEPc.py6 self.gitcommit = '2435073368006cab65837fb206144f409508c908' # main feb-20-2026
8 …itlab.com/slepc/slepc.git','https://gitlab.com/slepc/slepc/-/archive/'+self.gitcommit+'/slepc-'+se…
20 …help.addArgument('SLEPC', '-download-slepc-configure-arguments=string', nargs.Arg(None, None, 'Add…
31 self.cuda = framework.require('config.packages.CUDA',self)
35 self.odeps = [self.cuda,self.thrust,self.hypre,self.SuiteSparse]
40 if 'download-slepc' in self.argDB and self.argDB['download-slepc']:
41 …if 'download-slepc-configure-arguments' in self.argDB and '--with-slepc4py' in self.argDB['downloa…
42 …RuntimeError('You should set --with-slepc4py as a separate option of PETSc configure, not within -…
43 if self.argDB['with-petsc4py'] and not self.argDB['with-slepc4py']:
44 …raise RuntimeError('You should also set --with-slepc4py when using both --with-petsc4py and --down…
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H A Dhypre.py13 …e321e1d78882c62eade880dd6f3ae7' #v3.1.0 + fixes from https://github.com/hypre-space/hypre/pull/1463
14 …self.download = ['git://https://github.com/hypre-space/hypre','https://github.com/hypre-spa…
19 self.precisions = ['single', 'double', '__float128']
26 …help.addArgument('HYPRE', '-with-hypre-gpu-arch=<string>', nargs.ArgString(None, 0, 'Value passed…
27 …help.addArgument('HYPRE', '-download-hypre-openmp', nargs.ArgBool(None, 1, 'Let hypre use OpenMP i…
37 self.cuda = framework.require('config.packages.CUDA',self)
47 self.odeps = [self.cuda,self.hip,self.openmp,self.umpire,self.caliper]
55 args.append('--disable-fortran')
57 args.append('--without-MPI')
59 … # just use the first dir - and assume the subsequent one isn't necessary [relevant only on AIX?]
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H A DCUDA.py9 self.versioninclude = 'cuda.h'
15 # CUDA provides 2 variants of libcuda.so (for access to CUDA driver API):
16 # - fully functional compile, runtime libraries installed with the GPU driver
18 # - stub library - usable only for compiles
19 …# (for ex:) /usr/local/cuda/lib64/stubs/libcuda.so (without corresponding libcuda.so.1 for runt…
20 …# We are preferring this stub library - as it enables compiles on non-GPU nodes (for ex: login nod…
21 … # Using RPATH to this stub location is not appropriate - so skipping via libraries.rpathSkipDirs()
22 …# Note: PETSc does not use CUDA driver API (as of Sep 29, 2021), but external package for ex: Kokk…
25 self.stubliblist = [['libcuda.so','libnvidia-ml.so']]
26 …my' # existence of self.liblist is used by package.py to determine if --with-cuda-lib must be prov…
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/petsc/config/BuildSystem/config/
H A DcompilerOptions.py17 output = self.executeShellCommand(compiler + ' -show', log = self.log)[0]
28 flags.extend(['-Wall', '-Wwrite-strings', '-Wno-unknown-pragmas'])
30 # gcc does not support -Wno-implicit-float-conversion so -Wconversion is always noisy
31 …flags.extend(['-Wconversion', '-Wno-sign-conversion', '-Wno-float-conversion', '-Wno-implicit-floa…
33 flags.extend(['-fno-stack-check'])
35 flags.extend(['-Wno-lto-type-mismatch'])
37 flags.extend(['-Wno-stringop-overflow'])
39 … flags.extend(['-mfp16-format=ieee']) # ARM for utilizing 16 bit storage of floating point
40 # skip -fstack-protector for brew gcc - as this gives SEGV
42 flags.extend(['-fstack-protector'])
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H A DcompilerFlags.py20 …help.addArgument('Compiler Flags', '-optionsModule=<module name>', nargs.Arg(None, 'config.compile…
21 …help.addArgument('Compiler Flags', '-with-debugging=<bool>', nargs.ArgBool(None, 1, 'Specify debug…
22 …help.addArgument('Compiler Flags', '-C_VERSION=<string>', nargs.Arg(None, 'Unknown', 'The versio…
23 …help.addArgument('Compiler Flags', '-CXX_VERSION=<string>', nargs.Arg(None, 'Unknown', 'The versio…
24 …help.addArgument('Compiler Flags', '-FC_VERSION=<string>', nargs.Arg(None, 'Unknown', 'The versio…
25 …help.addArgument('Compiler Flags', '-CUDA_VERSION=<string>',nargs.Arg(None, 'Unknown', 'The versio…
26 …help.addArgument('Compiler Flags', '-HIP_VERSION=<string>',nargs.Arg(None, 'Unknown', 'The version…
27 …help.addArgument('Compiler Flags', '-SYCL_VERSION=<string>',nargs.Arg(None, 'Unknown', 'The versio…
28 …help.addArgument('Compiler Flags', '-COPTFLAGS=<string>', nargs.Arg(None, None, 'Override the de…
29 …help.addArgument('Compiler Flags', '-CXXOPTFLAGS=<string>', nargs.Arg(None, None, 'Override the de…
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H A Dcompilers.py10 if not line.startswith('ld: warning: text-based stub file'): retbuf.append(line)
41 self.skipdefaultpaths.append(os.path.join(loc,arch+'-linux-gnu'))
51 …help.addArgument('Compilers','-with-clib-autodetect=<bool>', nargs.ArgBool(None,1,'Autodetect…
52 …help.addArgument('Compilers','-with-fortranlib-autodetect=<bool>',nargs.ArgBool(None,1,'Autodetect…
53 …help.addArgument('Compilers','-with-cxxlib-autodetect=<bool>', nargs.ArgBool(None,1,'Autodetect…
54 …help.addArgument('Compilers','-with-dependencies=<bool>', nargs.ArgBool(None,1,'Compile wi…
62 names['CUDAC'] = 'No CUDA compiler found.'
63 names['CUDAPP'] = 'No CUDA preprocessor found.'
77 for language in ['C', 'CUDA', 'HIP', 'SYCL', 'Cxx', 'FC']:
88 names['CUDAPPFLAGS'] = 'No CUDA preprocessor flags found.'
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/petsc/doc/developers/
H A Dtesting.md7 - Formatted comments at the bottom of the tutorials and test source files that describes the tests …
8 - The *test generator* (`config/gmakegentest.py`) that parses the tutorial and test source files an…
10 - The *PETSc test harness* that consists of makefile and shell scripts that runs the executables wi…
35 args: -debug -fields v1,v2,v3
38 args: -foo bar
44 - A single shell script
46 - A single makefile
48 - An output file that represents the *expected results*. It is also possible -- though unusual -- t…
50 - Two or more command tests, usually:
52 - one or more `mpiexec` tests that run the executable
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H A Dstyle.md7 terminology *subclass*, *implementation*, or *type* [^footnote-1] to refer to a
27 - have an appended `_Private` (for example, `StashValues_Private`)
29 - have an appended `_Subtype` (for example, `MatMultSeq_AIJ`).
44 06. Each application-usable function begins with the name of the class
49 07. Functions that PETSc provides as defaults for user-providable
54 the word “set” or “get”, for example, `-ksp_gmres_restart`.
64 12. Use the abbreviation NaN for Not-a-Number.
71 is a signed 32-bit or 64-bit `int` depending on the `./configure` option
72 `--with-64-bit-indices`. There is the possibility of integer overflow with the
73 32-bit version.
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/petsc/doc/faq/
H A Dindex.md22 …e: A Guide to Good Style](https://www.cambridge.org/core/books/writing-scientific-software/2320670…
32 - Fast, **low-latency** interconnect; any ethernet (even 10 GigE) simply cannot provide
34 - High per-core **memory** performance. Each core needs to
61 collecting all of the output from the runs into the single file scaling.log. Copy
72 - [MPICH2 binding with the Hydra process manager](https://github.com/pmodels/mpich/blob/main/doc/wi…
75 $ mpiexec.hydra -n 4 --binding cpu:sockets
78 - [Open MPI binding](https://www.open-mpi.org/faq/?category=tuning#using-paffinity)
81 $ mpiexec -n 4 --map-by socket --bind-to socket --report-bindings
84 - `taskset`, part of the [util-linux](https://github.com/karelzak/util-linux) package
89 - `numactl`
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/petsc/doc/manual/
H A Dprofiling.md24 - `-log_view [:filename]` - Prints an ASCII version of performance data at the
26 and require little overhead; thus, `-log_view` is intended as the
28 - `-info [infofile]` - Prints verbose information about code to
33 - `-log_trace [logfile]` - Traces the beginning and ending of all
35 `-info`, is useful to see where a program is hanging without
43 ### Interpreting `-log_view` Output: The Basics
46 option `-log_view` `[:filename]` activates printing of profile data to standard
51 libraries, followed by any user-defined events (discussed in
74 lower-level operations in these packages. Note also that the nonlinear
90 - `KSPSetUp` - Set up linear solver
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/petsc/config/PETSc/
H A DConfigure.py27 banner_middle = '=' * (logger.get_global_divider_length() - 2 * len(banner_ends))
40 …help.addArgument('PETSc', '-prefix=<dir>', nargs.Arg(None, '', 'Spec…
41 …help.addArgument('PETSc', '-with-prefetch=<bool>', nargs.ArgBool(None, 1,'En…
42 …help.addArgument('Windows','-with-windows-graphics=<bool>', nargs.ArgBool(None, 1,'En…
43 …help.addArgument('PETSc', '-with-default-arch=<bool>', nargs.ArgBool(None, 1, 'A…
44 …p.addArgument('PETSc','-with-single-library=<bool>', nargs.ArgBool(None, 1,'Put a…
45 …help.addArgument('PETSc','-with-fortran-bindings=<bool>', nargs.ArgBool(None, 1,'Bu…
46 …help.addArgument('PETSc', '-with-library-name-suffix=<string>', nargs.Arg(None, '', 'Add …
47 …help.addArgument('PETSc', '-with-ios=<bool>', nargs.ArgBool(None, 0, 'B…
48 …help.addArgument('PETSc', '-with-display=<x11display>', nargs.Arg(None, '', 'Spec…
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/petsc/doc/
H A Dpetsc.bib3 % bibtool petsc.bib -- expand.macros=on -- print.line.length=100 -- pass.comments=on
17 % LiteralHTML: <a name="nano"><H3><center>Nano-simulations</center></H3>
19 @Misc{ semver-webpage,
25 title = {{D}-stability and {K}aps-{R}entrop-methods},
30 pages = {229--237},
41 pages = {93--113},
55 …title = {Generalized {R}unge--{K}utta methods of order four with stepsize control for sti…
59 pages = {55--68},
73 …gorithm for Structural Dynamics With Improved Numerical Dissipation: The Generalized-alpha Method},
77 pages = {371-375},
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