pax_global_header00006660000000000000000000000064130175203450014512gustar00rootroot0000000000000052 comment=4fa8b97c8cb8a923e9aebd23bcf06e0ade3c109b dijitso-2016.2.0/000077500000000000000000000000001301752034500134075ustar00rootroot00000000000000dijitso-2016.2.0/COPYING000066400000000000000000001045131301752034500144460ustar00rootroot00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU General Public License is a free, copyleft license for software and other kinds of works. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. 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If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. 13. Use with the GNU Affero General Public License. Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. 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If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation. If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program. Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version. 15. Disclaimer of Warranty. THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. 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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . dijitso-2016.2.0/COPYING.LESSER000066400000000000000000000167271301752034500154530ustar00rootroot00000000000000 GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below. 0. Additional Definitions. As used herein, "this License" refers to version 3 of the GNU Lesser General Public License, and the "GNU GPL" refers to version 3 of the GNU General Public License. "The Library" refers to a covered work governed by this License, other than an Application or a Combined Work as defined below. An "Application" is any work that makes use of an interface provided by the Library, but which is not otherwise based on the Library. Defining a subclass of a class defined by the Library is deemed a mode of using an interface provided by the Library. A "Combined Work" is a work produced by combining or linking an Application with the Library. The particular version of the Library with which the Combined Work was made is also called the "Linked Version". The "Minimal Corresponding Source" for a Combined Work means the Corresponding Source for the Combined Work, excluding any source code for portions of the Combined Work that, considered in isolation, are based on the Application, and not on the Linked Version. 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If you modify a copy of the Library, and, in your modifications, a facility refers to a function or data to be supplied by an Application that uses the facility (other than as an argument passed when the facility is invoked), then you may convey a copy of the modified version: a) under this License, provided that you make a good faith effort to ensure that, in the event an Application does not supply the function or data, the facility still operates, and performs whatever part of its purpose remains meaningful, or b) under the GNU GPL, with none of the additional permissions of this License applicable to that copy. 3. Object Code Incorporating Material from Library Header Files. The object code form of an Application may incorporate material from a header file that is part of the Library. You may convey such object code under terms of your choice, provided that, if the incorporated material is not limited to numerical parameters, data structure layouts and accessors, or small macros, inline functions and templates (ten or fewer lines in length), you do both of the following: a) Give prominent notice with each copy of the object code that the Library is used in it and that the Library and its use are covered by this License. b) Accompany the object code with a copy of the GNU GPL and this license document. 4. Combined Works. 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Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation. If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library. dijitso-2016.2.0/ChangeLog000066400000000000000000000006401301752034500151610ustar00rootroot000000000000002016.2.0 [2016-11-30] - Introduce commandline script 'dijitso' with various subcommands to interact with the cache - Improve extraction of source files to reproduce compilation failure during jit - Implement support for linking between jit modules - Add optional dependency on subprocess32 to handle fork safety on infiniband clusters - Remove instant dependency 2016.1.0 [2016-06-23] - Initial implementation dijitso-2016.2.0/README.rst000066400000000000000000000071111301752034500150760ustar00rootroot00000000000000dijitso ======= *A Python module for distributed just-in-time shared library building* Authors: - Martin Sandve Alnæs (martinal@simula.no) - Garth N. Wells (gnw20@cam.ac.uk) - Johannes Ring (johannr@simula.no) Contributors: - Jan Blechta (blechta@karlin.mff.cuni.cz) Documentation ------------- Documentation can be viewed at http://fenics-dijitso.readthedocs.org/. .. image:: https://readthedocs.org/projects/fenics-dijitso/badge/?version=latest :target: http://fenics.readthedocs.io/projects/dijitso/en/latest/?badge=latest :alt: Documentation Status Automated Testing ----------------- We use Bitbucket Pipelines and Atlassian Bamboo to perform automated testing. .. image:: https://bitbucket-badges.useast.atlassian.io/badge/fenics-project/dijitso.svg :target: https://bitbucket.org/fenics-project/dijitso/addon/pipelines/home :alt: Pipelines Build Status .. image:: http://fenics-bamboo.simula.no:8085/plugins/servlet/wittified/build-status/DIJ-DIDO :target: http://fenics-bamboo.simula.no:8085/browse/DIJ-DIDO/latest :alt: Bamboo Build Status Code Coverage ------------- Code coverage reports can be viewed at https://coveralls.io/repos/bitbucket/fenics-project/dijitso. .. image:: https://coveralls.io/repos/bitbucket/fenics-project/dijitso/badge.svg?branch=master :target: https://coveralls.io/bitbucket/fenics-project/dijitso?branch=master :alt: Coverage Status Motivation ---------- This module was written to improve a core component of the FEniCS framework, namely the just in time compilation of C++ code that is generated from Python modules, but is only called from within a C++ library, and thus do not need wrapping in a nice Python interface. The main approach of dijitso is to use ctypes to import the dynamic shared library directly with no attempt at wrapping it in a Python interface. As long as the compiled code can provide a simple factory function to a class implementing a predefined C++ interface, there is no limit to the complexity of that interface as long as it is only called from C++ code, If you want a Python interface to your generated code, dijitso is probably not the answer. Although dijitso serves a very specific role within the FEniCS project, it does not depend on other FEniCS components. The parallel support depends on the mpi4py interface, although mpi4py is not actually imported within the dijitso module so it would be possible to mock the communicator object with a similar interface. Feature list ------------ - Disk cache system based on user provided signature string (user is responsible of the quality of the signature) - Lazy evaluation of possibly costly code generation through user-provided callback, called only if signature is not found in disk cache - Low overhead invocation of C++ compiler to produce a shared library with no Python wrapping - Portable shared library import using ctypes - Automatic compression of source code in the cache directory saves space - Autodetect which MPI processes share the same physical cache directory (doesn't matter if this is all cores on a node or shared across nodes with network mapped storage) - Automatic avoidance of race conditions in disk cache by only compiling on one process per physical cache directory - Optional MPI based distribution of shared library binary file - Configurable parallel behaviour: - "root": build only on single root node and distribute binary to each physical cache directory with MPI - "node": build on one process per physical cache directory - "process": build on each process, automatic separation of cache directories dijitso-2016.2.0/dijitso/000077500000000000000000000000001301752034500150545ustar00rootroot00000000000000dijitso-2016.2.0/dijitso/__init__.py000066400000000000000000000023671301752034500171750ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . from __future__ import unicode_literals """This is dijitso -- a lightweight distributed just-in-time shared library builder.""" __author__ = "Martin Sandve Alnæs" __version__ = "2016.2.0" __all__ = ["validate_params", "jit", "extract_factory_function", "set_log_level"] from dijitso.params import validate_params from dijitso.jit import jit from dijitso.jit import extract_factory_function from dijitso.log import set_log_level # Import main function, entry point to script from dijitso.__main__ import main dijitso-2016.2.0/dijitso/__main__.py000066400000000000000000000073621301752034500171560ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . """This is the commandline interface to dijitso. For usage help, run 'dijitso --help'.""" from __future__ import print_function import sys import argparse from dijitso.params import validate_params import dijitso.cmdline as cmd_namespace def build_commands(cmd_namespace): """Collects functions called cmd_ from given namespace. Returns dict {basename: function}. """ commands = {} cmd_args = {} for name in list(cmd_namespace.keys()): if name.startswith("cmd_"): cmd_name = name.replace("cmd_", "") cmd = cmd_namespace[name] commands[cmd_name] = cmd args_name = "args_" + cmd_name if args_name in cmd_namespace: cmd_args[cmd_name] = cmd_namespace.get(args_name) return commands, cmd_args def add_top_arguments(parser): "Add arguments to top level parser." parser.add_argument("--verbose", "-v", default=False, help="set logging level") parser.add_argument("--cache-dir", "-r", default=None, help="use non-default cache root path") parser.add_argument("--dry-run", "-n", default=False, help="only show what would be done, don't modify filesystem") def extract_params_from_args(args): p = {} p["cache"] = {} if args.cache_dir is not None: p["cache"]["cache_dir"] = args.cache_dir return p def add_common_arguments(parser): "Add arguments to each subparser." pass def add_cmd_arguments(cmd, parser, args): "Add arguments specific to a command." if hasattr(cmd, "add_arguments"): cmd.add_arguments(parser) def build_parsers(commands, args): """Builds a top parser with subparsers for each command.""" top_parser = argparse.ArgumentParser() add_top_arguments(top_parser) subparsers = top_parser.add_subparsers(help="command description", dest="cmd_name") cmd_parsers = {} for cmd_name, cmd in commands.items(): parser = subparsers.add_parser(cmd_name, help=cmd.__doc__) add_common_arguments(parser) if cmd_name in args: args[cmd_name](parser) cmd_parsers[cmd_name] = parser return top_parser, subparsers, cmd_parsers def main(args=None): """This is the commandline tool for the python module dijitso.""" if args is None: args = sys.argv[1:] # Build subparsers for each command commands, cmd_args = build_commands(vars(cmd_namespace)) top_parser, subparsers, cmd_parsers = build_parsers(commands, cmd_args) # Populate args namespace args_ns = argparse.Namespace() top_parser.parse_args(args, namespace=args_ns) # Extract generic params params = extract_params_from_args(args_ns) params = validate_params(params) # Run the chosen command (argparse doesn't allow # getting to this point with an invalid cmd_name) assert args_ns.cmd_name in commands cmd = commands[args_ns.cmd_name] return cmd(args_ns, params) if __name__ == "__main__": sys.exit(main()) dijitso-2016.2.0/dijitso/build.py000066400000000000000000000216331301752034500165320ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . """Utilities for building libraries with dijitso.""" from __future__ import unicode_literals import tempfile import os import sys from dijitso.system import get_status_output, lockfree_move_file from dijitso.system import make_dirs, make_executable, store_textfile from dijitso.log import info, debug from dijitso.cache import ensure_dirs, make_lib_dir, make_inc_dir from dijitso.cache import create_fail_dir_path from dijitso.cache import create_lib_filename, create_lib_basename, create_libname from dijitso.cache import create_src_filename, create_src_basename from dijitso.cache import create_inc_filename, create_inc_basename from dijitso.cache import create_log_filename from dijitso.cache import compress_source_code def make_unique(dirs): """Take a sequence of hashable items and return a tuple including each only once. Preserves original ordering. """ udirs = [] found = set() for d in dirs: if d not in found: udirs.append(d) found.add(d) return tuple(udirs) def make_compile_command(src_filename, lib_filename, dependencies, build_params, cache_params): """Piece together the compile command from build params. Returns the command as a list with the command and its arguments. """ # Get dijitso dirs based on cache_params inc_dir = make_inc_dir(cache_params) lib_dir = make_lib_dir(cache_params) # Add dijitso directories to includes, libs, and rpaths include_dirs = make_unique(build_params["include_dirs"] + (inc_dir,)) lib_dirs = make_unique(build_params["lib_dirs"] + (lib_dir,)) rpath_dirs = make_unique(build_params["rpath_dirs"] + (lib_dir,)) # Make all paths absolute include_dirs = [os.path.abspath(d) for d in include_dirs] lib_dirs = [os.path.abspath(d) for d in lib_dirs] rpath_dirs = [os.path.abspath(d) for d in rpath_dirs] # Build options (defaults assume gcc compatibility) cxxflags = list(build_params["cxxflags"]) if build_params["debug"]: cxxflags.extend(build_params["cxxflags_debug"]) else: cxxflags.extend(build_params["cxxflags_opt"]) # Create library names for all dependencies and additional given libs deplibs = tuple(create_libname(depsig, cache_params) for depsig in dependencies) # Get compiler name args = [build_params["cxx"]] # Compiler args args.extend(cxxflags) args.extend("-I" + path for path in include_dirs) # The input source args.append(src_filename) # Linker args args.extend("-L" + path for path in lib_dirs) args.extend("-Wl,-rpath," + path for path in rpath_dirs) args.extend("-l" + lib for lib in deplibs) # OSX specific: if sys.platform == "darwin": full_lib_filename = os.path.join(cache_params["cache_dir"], cache_params["lib_dir"], os.path.basename(lib_filename)) args.append("-Wl,-install_name,%s" % full_lib_filename) # The output library args.append("-o" + lib_filename) return args def temp_dir(cache_params): """Return a uniquely named temp directory. Optionally residing under temp_dir_root from cache_params. """ return tempfile.mkdtemp(dir=cache_params["temp_dir_root"]) def build_shared_library(signature, header, source, dependencies, params): """Build shared library from a source file and store library in cache.""" cache_params = params["cache"] build_params = params["build"] # Create basenames inc_basename = create_inc_basename(signature, cache_params) src_basename = create_src_basename(signature, cache_params) lib_basename = create_lib_basename(signature, cache_params) # Create a temp directory and filenames within it tmpdir = temp_dir(cache_params) temp_inc_filename = os.path.join(tmpdir, inc_basename) temp_src_filename = os.path.join(tmpdir, src_basename) temp_lib_filename = os.path.join(tmpdir, lib_basename) # Store source and header in temp dir if header: store_textfile(temp_inc_filename, header) store_textfile(temp_src_filename, source) # Build final command as list of arguments cmd = make_compile_command(temp_src_filename, temp_lib_filename, dependencies, build_params, cache_params) # Execute command to compile generated source code to dynamic library status, output = get_status_output(cmd) # Move files to cache on success or a local dir on failure, # using safe lockfree move if status == 0: # Ensure dirnames exist in cache dirs ensure_dirs(cache_params) # Move library first lib_filename = create_lib_filename(signature, cache_params) assert os.path.exists(os.path.dirname(lib_filename)) lockfree_move_file(temp_lib_filename, lib_filename) # Write header only if there is one if header: inc_filename = create_inc_filename(signature, cache_params) assert os.path.exists(os.path.dirname(inc_filename)) lockfree_move_file(temp_inc_filename, inc_filename) else: inc_filename = None # Compress or delete source code based on params temp_src_filename = compress_source_code(temp_src_filename, cache_params) if temp_src_filename: src_filename = create_src_filename(signature, cache_params) if temp_src_filename.endswith(".gz"): src_filename = src_filename + ".gz" assert os.path.exists(os.path.dirname(src_filename)) lockfree_move_file(temp_src_filename, src_filename) else: src_filename = None # Write compiler command and output to log file if cache_params["enable_build_log"]: # Recreate compiler command without the tempdir cmd = make_compile_command(src_basename, lib_basename, dependencies, build_params, cache_params) log_contents = "%s\n\n%s" % (" ".join(cmd), output) log_filename = create_log_filename(signature, cache_params) assert os.path.exists(os.path.dirname(log_filename)) store_textfile(log_filename, log_contents) else: log_filename = None files = set((inc_filename, src_filename, lib_filename, log_filename)) files = files - set((None,)) files = sorted(files) debug("Compilation succeeded. Files written to cache:\n" + "\n".join(files)) else: # Create filenames in a local directory to store files for reproducing failure fail_dir = create_fail_dir_path(signature, cache_params) make_dirs(fail_dir) # Library name is returned below lib_filename = None # Write header only if there is one if header: inc_filename = os.path.join(fail_dir, inc_basename) lockfree_move_file(temp_inc_filename, inc_filename) # Always write source for inspection after compilation failure src_filename = os.path.join(fail_dir, src_basename) lockfree_move_file(temp_src_filename, src_filename) # Write compile command to failure dir, adjusted to use local # source file name so it can be rerun cmd = make_compile_command(src_basename, lib_basename, dependencies, build_params, cache_params) cmds = " ".join(cmd) script = "#!/bin/bash\n# Execute this file to recompile locally\n" + cmds cmd_filename = os.path.join(fail_dir, "recompile.sh") store_textfile(cmd_filename, script) make_executable(cmd_filename) # Write readme file with instructions readme = "Run or source recompile.sh to compile locally and reproduce the build failure.\n" readme_filename = os.path.join(fail_dir, "README") store_textfile(readme_filename, readme) # Write compiler output to failure dir (will refer to temp paths) log_filename = os.path.join(fail_dir, "error.log") store_textfile(log_filename, output) info("Compilation failed! Sources, command, and " "errors have been written to: %s" % (fail_dir,)) return status, output, lib_filename dijitso-2016.2.0/dijitso/cache.py000066400000000000000000000400101301752034500164640ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . """Utilities for disk cache features of dijitso.""" from __future__ import unicode_literals from glob import glob import os import re import ctypes from dijitso.system import ldd from dijitso.system import make_dirs from dijitso.system import try_delete_file, try_copy_file from dijitso.system import gzip_file, gunzip_file from dijitso.system import read_textfile, store_textfile from dijitso.log import debug, error, warning def extract_files(signature, cache_params, prefix="", path=os.curdir, categories=("inc", "src", "lib", "log")): """Make a copy of files stored under this signature. Target filenames are '/-.*' """ path = os.path.join(path, prefix + signature) make_dirs(path) if "inc" in categories: inc_filename = create_inc_filename(signature, cache_params) try_copy_file(inc_filename, path) if "src" in categories: src_filename = create_src_filename(signature, cache_params) if not os.path.exists(src_filename): src_filename = src_filename + ".gz" if os.path.exists(src_filename): try_copy_file(src_filename, path) if src_filename.endswith(".gz"): gunzip_file(os.path.join(path, os.path.basename(src_filename))) if "lib" in categories: lib_filename = create_lib_filename(signature, cache_params) try_copy_file(lib_filename, path) if "log" in categories: log_filename = create_log_filename(signature, cache_params) try_copy_file(log_filename, path) return path def extract_lib_signatures(cache_params): "Extract signatures from library files in cache." p = os.path.join(cache_params["cache_dir"], cache_params["lib_dir"]) filenames = glob(os.path.join(p, "*")) r = re.compile(create_lib_filename("(.*)", cache_params)) sigs = [] for f in filenames: m = r.match(f) if m: sigs.append(m.group(1)) return sigs def clean_cache(cache_params, dryrun=True, categories=("inc", "src", "lib", "log")): "Delete files from cache." gc = glob_cache(cache_params, categories=categories) for category in gc: for fn in gc[category]: if dryrun: print("rm %s" % (fn,)) else: try_delete_file(fn) def glob_cache(cache_params, categories=("inc", "src", "lib", "log")): """Return dict with contents of cache subdirectories.""" g = {} for foo in categories: p = os.path.join(cache_params["cache_dir"], cache_params[foo + "_dir"]) g[foo] = glob(os.path.join(p, "*")) return g def grep_cache(regex, cache_params, linenumbers=False, countonly=False, signature=None, categories=("inc", "src", "log")): "Search through files in cache for a pattern." allmatches = {} gc = glob_cache(cache_params, categories=categories) for category in categories: for fn in gc.get(category, ()): # Skip non-matches if specific signature is specified if signature is not None and signature not in fn: continue if countonly: matches = 0 else: matches = [] if category == "lib": # If category is "lib", use ldd # TODO: on mac need to use otool libs = ldd(fn) for k, libpath in sorted(libs.items()): if not libpath: continue m = regex.match(libpath) if m: if countonly: matches += 1 else: line = "%s => %s" % (k, libpath) matches.append(line) else: content = read_textfile(fn) lines = content.splitlines() if content else () for i, line in enumerate(lines): m = regex.match(line) if m: if countonly: matches += 1 else: line = line.rstrip("\n\r") if linenumbers: line = (i, line) matches.append(line) if matches: allmatches[fn] = matches return allmatches def extract_function(lines): "Extract function code starting at first line of lines." n = len(lines) # Function starts at line 0 by assumption begin = 0 # Worst case body range body_begin = begin body_end = n # Body starts at first { for i in range(begin, n): if "{" in lines[i]: body_begin = i break # Body ends when {} are balanced back to 0 braces = 0 for i in range(body_begin, n): if "{" in lines[i]: braces += 1 if "}" in lines[i]: braces -= 1 if braces == 0: body_end = i break # Include the last line in range end = body_end + 1 sublines = lines[begin:end] return "".join(sublines) def _create_basename(foo, signature, cache_params): return "".join((cache_params.get(foo + "_prefix", ""), cache_params.get(foo + "_basename", ""), signature, cache_params.get(foo + "_postfix", ""))) def _create_filename(foo, signature, cache_params): basename = _create_basename(foo, signature, cache_params) return os.path.join(cache_params["cache_dir"], cache_params[foo + "_dir"], basename) def create_log_filename(signature, cache_params): "Create log filename based on signature and params." return _create_filename("log", signature, cache_params) def create_inc_basename(signature, cache_params): "Create header filename based on signature and params." return _create_basename("inc", signature, cache_params) def create_inc_filename(signature, cache_params): "Create header filename based on signature and params." return _create_filename("inc", signature, cache_params) def create_src_filename(signature, cache_params): "Create source code filename based on signature and params." return _create_filename("src", signature, cache_params) def create_src_basename(signature, cache_params): "Create source code filename based on signature and params." return _create_basename("src", signature, cache_params) def create_lib_basename(signature, cache_params): "Create library filename based on signature and params." return _create_basename("lib", signature, cache_params) def create_lib_filename(signature, cache_params): "Create library filename based on signature and params." return _create_filename("lib", signature, cache_params) def create_libname(signature, cache_params): """Create library name based on signature and params, without path, prefix 'lib', or extension '.so'.""" return cache_params["lib_basename"] + signature def create_fail_dir_path(signature, cache_params): "Create path name to place files after a module build failure." fail_root = cache_params["fail_dir_root"] or os.curdir fail_dir = os.path.join(fail_root, "jitfailure-" + signature) return os.path.abspath(fail_dir) def make_inc_dir(cache_params): d = os.path.join(cache_params["cache_dir"], cache_params["inc_dir"]) make_dirs(d) return d def make_src_dir(cache_params): d = os.path.join(cache_params["cache_dir"], cache_params["src_dir"]) make_dirs(d) return d def make_lib_dir(cache_params): d = os.path.join(cache_params["cache_dir"], cache_params["lib_dir"]) make_dirs(d) return d def make_log_dir(cache_params): d = os.path.join(cache_params["cache_dir"], cache_params["log_dir"]) make_dirs(d) return d _ensure_dirs_called = {} def ensure_dirs(cache_params): global _ensure_dirs_called # This ensures directories are created only once during a process # for each value that cache_dir takes, in case it changes during # the process lifetime. c = cache_params["cache_dir"] if c not in _ensure_dirs_called: make_inc_dir(cache_params) make_src_dir(cache_params) make_lib_dir(cache_params) make_log_dir(cache_params) _ensure_dirs_called[c] = True def read_library_binary(lib_filename): "Read compiled shared library as binary blob into a numpy byte array." import numpy return numpy.fromfile(lib_filename, dtype=numpy.uint8) def write_library_binary(lib_data, signature, cache_params): "Store compiled shared library from binary blob in numpy byte array to cache." make_lib_dir(cache_params) lib_filename = create_lib_filename(signature, cache_params) lib_data.tofile(lib_filename) # TODO: Set permissions? def analyse_load_error(e, lib_filename, cache_params): # Try to analyse error further for better error message: msg = str(e) r = re.compile("(" + create_lib_basename(".*", cache_params) + ")") m = r.match(msg) if m: # Found libname mentioned in message mlibname = m.group(1) mlibname = os.path.join(cache_params["cache_dir"], cache_params["lib_dir"], mlibname) else: mlibname = lib_filename if lib_filename != mlibname: # Message mentions some other dijitso library, # double check if this other file exists # (if it does, could be paths or rpath issue) if os.path.exists(mlibname): emsg = ("dijitso failed to load library:\n\t%s\n" "but dependency file exists:\n\t%s\nerror is:\n\t%s" % ( lib_filename, mlibname, str(e))) else: emsg = ("dijitso failed to load library:\n\t%s\n" "dependency file missing:\n\t%s\nerror is:\n\t%s" % ( lib_filename, mlibname, str(e))) else: # Message doesn't mention another dijitso library, # double check if library file we tried to load exists # (if it does, could be paths issue) if os.path.exists(lib_filename): emsg = ("dijitso failed to load existing file:\n" "\t%s\nerror is:\n\t%s" % (lib_filename, str(e))) else: emsg = ("dijitso failed to load missing file:\n" "\t%s\nerror is:\n\t%s" % (lib_filename, str(e))) return emsg def load_library(signature, cache_params): """Load existing dynamic library from disk. Returns library module if found, otherwise None. If found, the module is placed in memory cache for later lookup_lib calls. """ lib_filename = create_lib_filename(signature, cache_params) if not os.path.exists(lib_filename): debug("File %s does not exist" % (lib_filename,)) return None debug("AAA") debug("Loading %s from %s" % (signature, lib_filename)) try: lib = ctypes.cdll.LoadLibrary(lib_filename) except os.error as e: lib = None emsg = analyse_load_error(e, lib_filename, cache_params) warning(emsg) else: debug("Loaded %s from %s" % (signature, lib_filename)) if lib is not None: # Disk loading succeeded, register loaded library in memory # cache for next time _lib_cache[signature] = lib return lib # A cache is always something to be careful about. This one stores # references to loaded jit-compiled libraries, which will stay in # memory unless manually unloaded anyway and should not cause any # trouble. _lib_cache = {} def lookup_lib(lib_signature, cache_params): """Lookup library in memory cache then in disk cache. Returns library module if found, otherwise None. """ # Look for already loaded library in memory cache lib = _lib_cache.get(lib_signature) if lib is None: # Cache miss in memory, try looking on disk lib = load_library(lib_signature, cache_params) else: debug("Fetched %s from memory cache" % (lib_signature,)) # Return library or None return lib def read_src(signature, cache_params): """Lookup source code in disk cache and return file contents or None.""" filename = create_src_filename(signature, cache_params) return read_textfile(filename) def read_inc(signature, cache_params): """Lookup header file in disk cache and return file contents or None.""" filename = create_inc_filename(signature, cache_params) return read_textfile(filename) def read_log(signature, cache_params): """Lookup log file in disk cache and return file contents or None.""" filename = create_log_filename(signature, cache_params) return read_textfile(filename) def store_src(signature, content, cache_params): "Store source code in file within dijitso directories." make_src_dir(cache_params) filename = create_src_filename(signature, cache_params) store_textfile(filename, content) return filename def store_inc(signature, content, cache_params): "Store header file within dijitso directories." make_inc_dir(cache_params) filename = create_inc_filename(signature, cache_params) store_textfile(filename, content) return filename def store_log(signature, content, cache_params): "Store log file within dijitso directories." make_log_dir(cache_params) filename = create_log_filename(signature, cache_params) store_textfile(filename, content) return filename def compress_source_code(src_filename, cache_params): """Keep, delete or compress source code based on value of cache parameter 'src_storage'. Can be "keep", "delete", or "compress". """ src_storage = cache_params["src_storage"] if src_storage == "keep": filename = src_filename elif src_storage == "delete": try_delete_file(src_filename) filename = None elif src_storage == "compress": filename = gzip_file(src_filename) try_delete_file(src_filename) else: error("Invalid src_storage parameter. Expecting 'keep', 'delete', or 'compress'.") return filename def get_dijitso_dependencies(libname, cache_params): "Run ldd and filter output to only include dijitso cache entries." libs = ldd(libname) dlibs = {} for k in libs: if k.startswith(cache_params["lib_prefix"]): dlibs[k] = libs[k] return dlibs # TODO: Use this in command-line tools? def check_cache_integrity(cache_params): "Check dijitso cache integrity." libnames = set(glob(cache_params["lib_prefix"] + "*" + cache_params["lib_postfix"])) dmissing = {} for libname in libnames: dlibs = get_dijitso_dependencies(libname, cache_params) # Missing on file system: missing = [k for k in dlibs if k not in libnames] for k in dlibs: if k not in missing: # ldd thinks file is missing but it's there, linker issue? pass if missing: dmissing[libname] = sorted(missing) return dmissing def report_cache_integrity(dmissing, out=warning): "Print cache integrity report." if dmissing: out("%d libraries are missing one or more dependencies:" % len(dmissing)) for k in sorted(dmissing): out("\t%s depends on missing libraries:" % k) for m in dmissing[k]: out("\t\t%s" % m) dijitso-2016.2.0/dijitso/cmdline.py000066400000000000000000000215141301752034500170440ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . """This file contains the commands available through command-line dijitso-cache. Each function cmd_ becomes a subcommand invoked by:: dijitso-cache cmdname ...args The docstrings in the cmd_ are shown when running:: dijitso-cache cmdname --help The 'args' argument to cmd_* is a Namespace object with the commandline arguments. """ from __future__ import unicode_literals from __future__ import print_function import os import re from dijitso import __version__ from dijitso.cache import glob_cache, grep_cache, clean_cache from dijitso.cache import extract_lib_signatures from dijitso.cache import extract_files, extract_function from dijitso.system import read_textfile def parse_categories(categories): if categories == "all": return ("inc", "src", "lib", "log") return categories.split(",") def args_version(parser): pass def cmd_version(args, params): "print dijitso version" print(__version__) def args_config(parser): parser.add_argument("--key", default="", help="specific key to show (e.g. build.cxxflags)") def cmd_config(args, params): "show configuration" # Show single value if asked for key = args.key if key: name = key value = params for k in key.split("."): value = value[k] # Compiler flags etc are more useful in space separated form: if isinstance(value, tuple): value = " ".join(value) print(" %s: %s" % (name, value)) return 0 # Pick non-empty categories categories = sorted(c for c in params if params[c]) print("Showing default flags for dijitso:") for category in categories: print("%s:" % (category,)) for name in sorted(params[category]): value = params[category][name] # Compiler flags etc are more useful in space separated form: if isinstance(value, tuple): value = " ".join(value) print(" %s: %s" % (name, value)) return 0 def args_show(parser): parser.add_argument("--categories", default="all", help="comma separated list to enable file types (inc,src,lib,log)") parser.add_argument("--no-summary", action="store_true", help="don't show summary") parser.add_argument("--files", action="store_true", help="show file lists") parser.add_argument("--signatures", action="store_true", help="show library signatures") def cmd_show(args, params): "show lists of files in cache" cache_params = params["cache"] summary = not args.no_summary files = args.files signatures = args.signatures categories = parse_categories(args.categories) gc = glob_cache(cache_params, categories=categories) if signatures: sigs = extract_lib_signatures(cache_params) print("\n".join("\t" + s for s in sorted(sigs))) if files: for cat in categories: print("\n".join("\t" + f for f in sorted(gc.get(cat, ())))) if summary: print("dijitso cache summary (number of cached files):") for cat in categories: print("%s: %d" % (cat, len(gc.get(cat, ())))) # TODO: Add summary of file sizes return 0 def args_clean(parser): parser.add_argument("--categories", default="inc,src,lib,log", help="comma separated list to enable file types (inc,src,lib,log)") def cmd_clean(args, params): "remove files from cache" cache_params = params["cache"] dryrun = args.dry_run categories = parse_categories(args.categories) clean_cache(cache_params, dryrun=dryrun, categories=categories) return 0 def args_grep(parser): parser.add_argument("--categories", default="inc,src", help="comma separated list to enable file types (inc,src,lib,log)") parser.add_argument("--pattern", default="", help="line search pattern") parser.add_argument("--regexmode", action="store_true", help="pattern is a regular expression (python style)") parser.add_argument("--linenumbers", action="store_true", help="show linenumbers on matches") parser.add_argument("--countonly", action="store_true", help="show only match line count for each file") parser.add_argument("--filesonly", action="store_true", help="show only filenames with matches") parser.add_argument("--signature", default="", help="look for module with this signature (default all)") def cmd_grep(args, params): "grep content of header and source file(s) in cache" cache_params = params["cache"] # Get command-line arguments pattern = args.pattern signature = args.signature regexmode = args.regexmode linenumbers = args.linenumbers countonly = args.countonly filesonly = args.filesonly categories = parse_categories(args.categories) if not regexmode: pattern = ".*(" + pattern + ").*" regex = re.compile(pattern) allmatches = grep_cache(regex, cache_params, linenumbers=linenumbers, countonly=countonly, signature=signature, categories=categories) if filesonly: print("\n".join(sorted(allmatches))) elif countonly: print("\n".join("%s: %d" % (k, v) for k, v in sorted(allmatches.items()))) else: for fn in sorted(allmatches): print("\nFile '%s' matches:" % (fn,)) if linenumbers: print("\n".join("%5d:\t%s" % line for line in allmatches[fn])) else: print("\n".join("\t" + line for line in allmatches[fn])) return 0 def args_grepfunction(parser): parser.add_argument("--categories", default="src", help="comma separated list to enable file types (inc,src,lib,log)") parser.add_argument("--name", default="", help="function name to search for") parser.add_argument("--signature", default="", help="look for module with this signature (default all)") parser.add_argument("--no-body", action="store_true", help="don't show function bodies") def cmd_grepfunction(args, params): "search for function name in source files in cache" cache_params = params["cache"] name = args.name signature = args.signature categories = parse_categories(args.categories) no_body = args.no_body pattern = ".*(" + name + ")[ ]*\((.*)" regex = re.compile(pattern) allmatches = grep_cache(regex, cache_params, linenumbers=True, countonly=False, signature=signature, categories=categories) for fn in sorted(allmatches): if no_body: # Just print signature lines print("\nFile '%s' matches:" % (fn,)) for i, line in allmatches[fn]: print("%5d: %s" % (i, line)) else: # Print function bodies content = read_textfile(fn) lines = content.splitlines() if content else () for i, line in allmatches[fn]: print("%s:%d" % (fn, i)) assert name in lines[i] print(extract_function(lines[i:])) print() return 0 def args_checkout(parser): parser.add_argument("--categories", default="inc,src,lib,log", help="comma separated list to enable file types (inc,src,lib,log)") parser.add_argument("--signature", help="module signature (required)") def cmd_checkout(args, params): "copy files from cache to a directory" cache_params = params["cache"] signature = args.signature categories = parse_categories(args.categories) prefix = "jitcheckout-" path = os.curdir path = extract_files(signature, cache_params, prefix=prefix, path=path, categories=categories) print("Extracted files to '%s'." % (path,)) return 0 dijitso-2016.2.0/dijitso/jit.py000066400000000000000000000205061301752034500162170ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . """This module contains the main jit() function and related utilities.""" from __future__ import unicode_literals import ctypes import numpy from dijitso.log import error from dijitso.params import validate_params from dijitso.py23 import as_unicode from dijitso.cache import lookup_lib, load_library from dijitso.cache import write_library_binary, read_library_binary from dijitso.build import build_shared_library from dijitso.signatures import hash_params def extract_factory_function(lib, name): """Extract function from loaded library. Assuming signature ``(void *)()``, for anything else use look at ctypes documentation. Returns the factory function or raises error. """ function = getattr(lib, name) function.restype = ctypes.c_void_p return function def jit_signature(name, params): # TODO: Unused? """Compute the signature that jit will use for given name and params.""" # Validation and completion with defaults for missing parameters params = validate_params(params) # Extend provided name of jitable with hash of relevant parameters signature_params = { "generator": params["generator"], "build": params["build"] } signature = "%s_%s" % (name, hash_params(signature_params)) return signature # TODO: send, receive, wait functionality is not currently in use, # decide to use it from dolfin or clean up the code and comments here. def jit(jitable, name, params, generate=None, send=None, receive=None, wait=None): """Just-in-time compile and import of a shared library with a cache mechanism. A signature is computed from the name, params["generator"], and params["build"]. The name should be a unique identifier for the jitable, preferrably produced by a good hash function. The signature is used to identity if the library has already been compiled and cached. A two-level memory and disk cache ensures good performance for repeated lookups within a single program as well as persistence across program runs. If no library has been cached, the passed 'generate' function is called to generate the source code: header, source, dependencies = \ generate(jitable, name, signature, params["generator"]) It is expected to translate the 'jitable' object into C or C++ (default) source code which will subsequently be compiled as a shared library and stored in the disk cache. The returned 'dependencies' should be a tuple of signatures returned from other completed dijitso.jit calls, and are linked to when building. The compiled shared library is then loaded with ctypes and returned. For use in a parallel (MPI) context, three functions send, receive, and wait can be provided. Each process can take on a different role depending on whether generate, or receive, or neither is provided. * Every process that gets a generate function is called a 'builder', and will generate and compile code as described above on a cache miss. If the function send is provided, it will then send the shared library binary file as a binary blob by calling send(numpy_array). * Every process that gets a receive function is called a 'receiver', and will call 'numpy_array = receive()' expecting the binary blob with a compiled binary shared library which will subsequently be written to file in the local disk cache. * The rest of the processes are called 'waiters' and will do nothing. * If provided, all processes will call wait() before attempting to load the freshly compiled library from disk cache. The intention of the above pattern is to be flexible, allowing several different strategies for sharing build results. The user of dijitso can determine groups of processes that share a disk cache, and assign one process per physical disk cache directory to write to that directory, avoiding multiple processes writing to the same files. This forms the basis for three main strategies: * Build on every process. * Build on one process per physical cache directory. * Build on a single global root node and send a copy of the binary to one process per physical cache directory. It is highly recommended to avoid have multiple builder processes sharing a physical cache directory. """ # TODO: Could simplify interface here and roll # (jitable, name, params["generator"]) into a single jitobject? # TODO: send/receive doesn't combine well with generate # triggering additional jit calls for dependencies. # It's possible that dependencies are hard to determine without # generate doing some analysis that we want to avoid. # Drop send/receive? Probably not that useful anyway. # Complete params with hardcoded defaults and config file defaults params = validate_params(params) # 0) Look for library in memory or disk cache # FIXME: use only name as signature for now # TODO: just remove one of signature or name from API? # signature = jit_signature(name, params) name = as_unicode(name) signature = name cache_params = params["cache"] lib = lookup_lib(signature, cache_params) if lib is None: # Since we didn't find the library in cache, we must build it. if receive and generate: # We're not supposed to generate if we're receiving error("Please provide only one of generate or receive.") elif generate: # 1) Generate source code header, source, dependencies = generate(jitable, name, signature, params["generator"]) # Ensure we got unicode from generate header = as_unicode(header) source = as_unicode(source) dependencies = [as_unicode(dep) for dep in dependencies] # 2) Compile shared library and 3) store in dijitso # inc/src/lib dir on success # NB! It's important to not raise exception on compilation # failure, such that we can reach wait() together with # other processes if any. status, output, lib_filename = \ build_shared_library(signature, header, source, dependencies, params) # 4a) Send library over network if we have a send function if send: if status == 0: lib_data = read_library_binary(lib_filename) else: lib_data = numpy.zeros((1,)) send(lib_data) elif receive: # 4b) Get library as binary blob from given receive # function and store in cache lib_data = receive() # Empty if compilation failed status = -1 if lib_data.shape == (1,) else 0 if status == 0: write_library_binary(lib_data, signature, cache_params) else: # Do nothing (we'll be waiting below for other process to # build) if not wait: error("Please provide wait if not providing one of generate or receive.") # 5) Notify waiters that we're done / wait for builder to # notify us if wait: wait() # Finally load library from disk cache (places in memory # cache) # NB! This returns None if the file does not exist, # i.e. if compilation failed on builder process lib = load_library(signature, cache_params) # TODO: Parse output to find error(s) for better error messages # Return built library and its signature return lib, signature dijitso-2016.2.0/dijitso/log.py000066400000000000000000000041421301752034500162100ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs, Jan Blechta # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . from __future__ import unicode_literals from six import string_types import logging __all__ = ['set_log_level', 'get_logger', 'get_log_handler', 'set_log_handler'] _log = logging.getLogger("dijitso") _loghandler = logging.StreamHandler() _log.addHandler(_loghandler) _log.setLevel(logging.INFO) def get_log_handler(): return _loghandler def get_logger(): return _log def set_log_handler(handler): global _loghandler _log.removeHandler(_loghandler) _loghandler = handler _log.addHandler(_loghandler) def set_log_level(level): """Set verbosity of logging. Argument is int or one of "INFO", "WARNING", "ERROR", or "DEBUG". """ if isinstance(level, string_types): level = level.upper() assert level in ("INFO", "WARNING", "ERROR", "DEBUG") level = getattr(logging, level) else: assert isinstance(level, int) _log.setLevel(level) # Logging interface for dijitso library def debug(*message): _log.debug(*message) def info(*message): _log.info(*message) def warning(*message): _log.warning(*message) def error(*message): _log.error(*message) text = message[0] % message[1:] raise RuntimeError(text) def dijitso_assert(condition, *message): if not condition: _log.error(*message) text = message[0] % message[1:] raise AssertionError(text) dijitso-2016.2.0/dijitso/mpi.py000066400000000000000000000224761301752034500162260ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . """Utilities for mpi features of dijitso.""" from __future__ import unicode_literals import io import os import uuid from glob import glob import numpy from dijitso.log import info, error from dijitso.system import try_delete_file def bcast_uuid(comm): "Create a unique id shared across all processes in comm." guid = numpy.ndarray((1,), dtype=numpy.uint64) if comm.rank == 0: # uuid creates a unique 128 bit id, we just pick the low 64 bits guid[0] = numpy.uint64(uuid.uuid4().int & ((1 << 64) - 1)) comm.Bcast(guid, root=0) return int(guid[0]) def discover_path_access_ranks(comm, path): """Discover which ranks share access to the same directory. This cannot be done by comparing paths, because a path string can represent a local work directory or a network mapped directory, depending on cluster configuration. Current approach is that each process touches a filename with its own rank in their given path. By reading in the filelist from the same path, we'll find which ranks have access to the same directory. To avoid problems with leftover files from previous program crashes, or collisions between simultaneously running programs, we use a random uuid in the filenames written. """ # Create a unique basename for rank files of this program guid = bcast_uuid(comm) # TODO: Run this in an init function and store for program duration? basename = os.path.join(path, "rank.%d." % guid) # Write the rank of this process to a filename filename = basename + str(comm.rank) with io.open(filename, "wb"): pass # Wait for all writes to take place. Don't know how robust this is # with nfs!!! comm.Barrier() # Read filelist noderanks = sorted([int(fn.replace(basename, "")) for fn in glob(basename + "*")]) # Wait for everyone to finish reading filelist comm.Barrier() # Clean up our own rank file. If the process is aborted, # this may fail to happen and leave a dangling file! # However the file takes no space, and the guid ensures # it won't be colliding with other filenames. # TODO: Include a gc command in dijitso to clean up this and other stuff. try_delete_file(filename) return noderanks def gather_global_partitions(comm, partition): """Gather an ordered list of unique partition values within comm.""" global_partitions = numpy.ndarray((comm.size,), dtype=numpy.uint64) local_partition = numpy.ndarray((1,), dtype=numpy.uint64) local_partition[0] = partition comm.Allgather(local_partition, global_partitions) return sorted(set(global_partitions)) def create_subcomm(comm, ranks): "Create a communicator for a set of ranks." group = comm.Get_group() subgroup = group.Incl(ranks) subcomm = comm.Create(subgroup) subgroup.Free() group.Free() return subcomm def create_node_comm(comm, comm_dir): """Create comms for communicating within a node.""" # Find ranks that share this physical comm_dir (physical dir, not same path string) node_ranks = discover_path_access_ranks(comm, comm_dir) # Partition comm into one communicator for each physical comm_dir assert len(node_ranks) >= 1 node_root = min(node_ranks) node_comm = comm.Split(node_root, node_ranks.index(comm.rank)) return node_comm, node_root def create_node_roots_comm(comm, node_root): """Build comm for communicating among the node roots.""" unique_global_node_roots = gather_global_partitions(comm, node_root) roots_comm = create_subcomm(comm, unique_global_node_roots) return roots_comm def create_comms_and_role_root(comm, node_comm, node_root): """Approach: global root builds and sends binary to node roots, everyone waits on their node group.""" copy_comm = create_node_roots_comm(comm, node_root) wait_comm = node_comm if comm.rank == 0: role = "builder" elif node_comm.rank == 0: assert comm.rank == node_root role = "receiver" else: assert comm.rank != node_root role = "waiter" return copy_comm, wait_comm, role def create_comms_and_role_node(comm, node_comm, node_root): """Approach: each node root builds, everyone waits on their node group.""" copy_comm = None wait_comm = node_comm if node_comm.rank == 0: assert comm.rank == node_root role = "builder" else: assert comm.rank != node_root role = "waiter" return copy_comm, wait_comm, role def create_comms_and_role_process(comm, node_comm, node_root): """Approach: each process builds its own module, no communication. To ensure no race conditions in this case independently of cache dir setup, we include an error check on the size of the autodetected node_comm. This should always be 1, or we provide the user with an informative message. TODO: Append program uid and process rank to basedir instead? """ if node_comm.size > 1: error("Asking for per-process building but processes share cache dir." " Please configure dijitso dirs to be distinct per process.") copy_comm = None wait_comm = None assert node_comm.rank == 0 assert comm.rank == node_root role = "builder" return copy_comm, wait_comm, role def create_comms_and_role(comm, comm_dir, buildon): """Determine which role each process should take, and create the right copy_comm and wait_comm for the build strategy. buildon must be one of "root", "node", or "process". Returns (copy_comm, wait_comm, role). """ # Now assign values to the copy_comm, wait_comm, and role, # depending on buildon strategy chosen. If we have no comm, # always return the builder role if comm is None: copy_comm, wait_comm, role = None, None, "builder" else: node_comm, node_root = create_node_comm(comm, comm_dir) if buildon == "root": copy_comm, wait_comm, role = create_comms_and_role_root(comm, node_comm, node_root) elif buildon == "node": copy_comm, wait_comm, role = create_comms_and_role_node(comm, node_comm, node_root) elif buildon == "process": copy_comm, wait_comm, role = create_comms_and_role_process(comm, node_comm, node_root) else: error("Invalid parameter buildon=%s" % (buildon,)) return copy_comm, wait_comm, role def send_binary(comm, lib_data): "Send compiled library as binary blob over MPI." # TODO: Test this in parallel locally. # TODO: Test this in parallel on clusters. # http://mpi4py.scipy.org/docs/usrman/tutorial.html # Check that we are the root root = 0 assert comm.rank == root # Send file size lib_size = numpy.ndarray((1,), dtype=numpy.uint32) lib_size[0] = lib_data.shape[0] info("rank %d: send size with root=%d." % (comm.rank, root)) comm.Bcast(lib_size, root=root) # Send file contents info("rank %d: send data with root=%d." % (comm.rank, root)) comm.Bcast(lib_data, root=root) def receive_binary(comm): "Store shared library received as a binary blob to cache." # Check that we are not the root root = 0 assert comm.rank != root # Receive file size lib_size = numpy.ndarray((1,), dtype=numpy.uint32) info("rank %d: receive size with root=%d." % (comm.rank, root)) comm.Bcast(lib_size, root=root) # Receive file contents lib_data = numpy.ndarray(lib_size[0], dtype=numpy.uint8) info("rank %d: receive data with root=%d." % (comm.rank, root)) comm.Bcast(lib_data, root=root) return lib_data """ def foo(): # TODO: Should call these once (for each comm at least) globally # in dolfin, not on each jit call def get_comm_dir(cache_params): return os.path.join(cache_params["cache_dir"], cache_params["comm_dir"]) comm_dir = get_comm_dir() copy_comm, wait_comm, role = create_comms_and_role(comm, comm_dir, buildon) if wait_comm is not None: def wait(): wait_comm.Barrier() else: wait = None if copy_comm is not None and copy_comm.size > 1: def send(lib_data): send_binary(copy_comm, lib_data) else: send = None def receive(): return receive_binary(copy_comm) """ dijitso-2016.2.0/dijitso/params.py000066400000000000000000000207041301752034500167140ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . """Utilities for dijitso parameters.""" from __future__ import unicode_literals from six import string_types from six.moves import configparser from glob import glob import os import sys import copy import numbers from dijitso.log import info, error, warning from dijitso.py23 import as_unicode # Warning for fenics backwards compatibility: if (os.environ.get("INSTANT_CACHE_DIR") and not os.environ.get("DIJITSO_CACHE_DIR")): warning("INSTANT_CACHE_DIR is no longer used by dijitso." " To set the cache directory for dijitso," " set DIJITSO_CACHE_DIR.") def discover_config_filename(): basename = ".dijitso.conf" search_paths = [ os.curdir, os.environ.get("DIJITSO_CONF"), os.path.expanduser("~"), "/etc/dijitso", ] for path in search_paths: if path is None: continue names = glob(os.path.join(path, basename)) if names: assert len(names) == 1 return names[0] return None _config_file_contents = None def read_config_file(): "Read config file and cache the contents for the duration of the process." global _config_file_contents if _config_file_contents is None: filename = discover_config_filename() _config_file_contents = {} if filename is not None: info("Using config file '%s'." % (filename,)) parser = configparser.SafeConfigParser() parser.read(filename) for category in parser.sections(): category = as_unicode(category) _config_file_contents[category] = {} for name, value in parser.items(category): name = as_unicode(name) value = as_unicode(value) _config_file_contents[category][name] = value return _config_file_contents def default_cache_params(): if sys.platform in ("win32", "cygwin"): default_lib_postfix = ".dll" else: default_lib_postfix = ".so" p = dict( cache_dir=None, # See validate_params inc_dir="include", src_dir="src", lib_dir="lib", fail_dir_root=None, temp_dir_root=None, comm_dir="comm", log_dir="log", enable_build_log=True, src_storage="compress", src_postfix=".cpp", log_postfix=".txt", inc_postfix=".h", lib_postfix=default_lib_postfix, lib_prefix="lib", lib_basename="dijitso-", ) return p def default_cxx_flags(): "Default C++ flags for all build modes." # Dropped because of some symbol sharing across dependent modules from ffc: # "-fvisibility=hidden", return ("-Wall", "-shared", "-fPIC", "-std=c++11") def default_cxx_debug_flags(): "Default C++ flags for debug=True. Note: FFC always overrides these." return ("-g", "-O0") def default_cxx_release_flags(): "Default C++ flags for debug=False. Note: FFC always overrides these." # These flags deal with handling of nan, inf, underflow, division # by zero, etc. which should be ok for most of our purposes. It # might be better to place them in ffc or make them dependent on # compiler or optional or whatever, just throwing them in here now # to see how it works out. safe_fastmath_parts = ("-fno-math-errno", "-fno-trapping-math", "-ffinite-math-only") return ("-O3",) + safe_fastmath_parts def default_build_params(): p = dict( cxx="c++", cxxflags=default_cxx_flags(), cxxflags_debug=default_cxx_debug_flags(), cxxflags_opt=default_cxx_release_flags(), include_dirs=(), lib_dirs=(), rpath_dirs=(), libs=(), debug=False, ) return p def default_generator_params(): return {} def default_params(): p = dict( cache=default_cache_params(), build=default_build_params(), generator=default_generator_params(),) return p _session_defaults = None def session_default_params(): global _session_defaults if _session_defaults is None: _session_defaults = validate_params() return copy.deepcopy(_session_defaults) def as_bool(value): if isinstance(value, bool): return value elif value in ("True", "true", "1"): return True elif value in ("False", "false", "0"): return False else: error("Invalid boolean value %s" % (value,)) def as_str_tuple(p): """Convert p to a tuple of strings, allowing a list or tuple of strings or a single string as input.""" if isinstance(p, string_types): return (as_unicode(p),) elif isinstance(p, (tuple, list)): if all(isinstance(item, string_types) for item in p): return tuple(as_unicode(item) for item in p) raise RuntimeError("Expecting a string or list of strings, not %s." % (p,)) def copy_params(params): "Copy two-level dict of params." return {k: v.copy() for k, v in params.items()} def check_params_keys(default, params): "Check that keys in params exist in defaults." for category in params: if category == "generator": continue if category not in default: error("Invalid parameter category '%s'." % category) if params[category] is not None: invalid = set(params[category]) - set(default[category]) if invalid: error("Invalid parameter names %s in category '%s'." % (sorted(invalid), category)) def merge_params(default, params): "Merge two-level param dicts." p = {} for category in default: d = default[category].copy() p[category] = d v = params.get(category) if v is not None: p[category].update(v) return p def validate_params(params): """Validate parameters to dijitso and fill in with defaults where missing.""" # Start with defaults p0 = default_params() p = p0 # Override with config file if any c = read_config_file() if c: check_params_keys(p, c) p = merge_params(p, c) # Override with runtime params if any if params: check_params_keys(p, params) p = merge_params(p, params) # Convert parameter types for category in p: category = as_unicode(category) if category == "generator": continue for name, value in p[category].items(): name = as_unicode(name) v0 = p0[category][name] if isinstance(v0, string_types): value = as_unicode(value) # Expand paths including "~" to include # full user home directory path if name.endswith("_dir") and "~" in value: value = os.path.expanduser(value) elif isinstance(v0, bool): value = as_bool(value) elif isinstance(v0, numbers.Number): value = type(v0)(value) elif isinstance(v0, tuple): value = as_str_tuple(value) p[category][name] = value # Allow environment variables to override default cache dir # Let dijitso specific dir win the contest cache_dir = os.environ.get("DIJITSO_CACHE_DIR") if not cache_dir: # Place default cache dir in virtualenv or conda prefix # if one of them are active, or under user's home directory home = os.path.expanduser("~") venv = os.environ.get("VIRTUAL_ENV") cenv = os.environ.get("CONDA_PREFIX") if venv == sys.prefix: env = venv elif cenv == sys.prefix: env = cenv else: env = home cache_dir = os.path.join(env, ".cache", "dijitso") p["cache"]["cache_dir"] = as_unicode(cache_dir) return p dijitso-2016.2.0/dijitso/py23.py000066400000000000000000000032361301752034500162270ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2016-2016 Martin Sandve Alnæs # # This file is part of UFL. # # UFL is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # UFL is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with UFL. If not, see . """Python 2/3 compatibility utilities.""" import six if not six.PY2: unicode = str def as_native_str(s): "Return s as unicode string, decoded using utf-8 if necessary." if isinstance(s, bytes): return s.decode("utf-8") else: return s else: def as_native_str(s): "Return s as bytes string, encoded using utf-8 if necessary." if isinstance(s, unicode): return s.encode("utf-8") else: return s def as_native_strings(stringlist): return [as_native_str(s) for s in stringlist] def as_bytes(s): "Return s if bytes, or encode unicode string to bytes using utf-8." if isinstance(s, unicode): return s.encode("utf-8") else: return s def as_unicode(s): "Return s if unicode string, or decode bytes to unicode string using utf-8." if isinstance(s, bytes): return s.decode("utf-8") else: return s dijitso-2016.2.0/dijitso/signatures.py000066400000000000000000000034041301752034500176130ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . from __future__ import unicode_literals from six import string_types import hashlib # Arbitrarily chosen hash digest cutoff to keep filename lengths # reasonably small. If this is too short hashes will collide! HASHLENGTH = 12 def hashit(data): "Return hash of anything with a repr implementation." h = hashlib.sha1() h.update(repr(data).encode('utf-8')) return h.hexdigest()[:HASHLENGTH] def canonicalize_params_for_hashing(params): if params: data = () else: assert isinstance(params, dict) keys = sorted(params) assert all(isinstance(key, string_types) for key in keys) items = [] for k in keys: k = k.encode('utf-8') v = params[k] if isinstance(v, dict): items.append((k, canonicalize_params_for_hashing(v))) else: items.append((k, repr(v).encode('utf-8'))) data = tuple(items) return data def hash_params(params): return hashit(canonicalize_params_for_hashing(params)) dijitso-2016.2.0/dijitso/system.py000066400000000000000000000262031301752034500167550ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . """Utilities for interfacing with the system.""" from __future__ import unicode_literals from six import string_types import os import sys import errno import io import gzip import shutil import stat import uuid import re from glob import glob import tempfile from dijitso.log import warning # NOTE: subprocess in Python 2 is not OFED-fork-safe! Check subprocess.py, # http://bugs.python.org/issue1336#msg146685 # OFED-fork-safety means that parent should not # touch anything between fork() and exec(), # which is not met in subprocess module. See # https://www.open-mpi.org/faq/?category=openfabrics#ofa-fork # http://www.openfabrics.org/downloads/OFED/release_notes/OFED_3.12_rc1_release_notes#3.03 # However, subprocess32 backports the fix from Python 3 to 2.7. if os.name == "posix" and sys.version_info[0] < 3: try: import subprocess32 as subprocess except: warning("subprocess32 module not found! Using unsafe built-in" "subprocess module instead. Install subprocess32 for " "thread-safety and safe usage on OFED/Infiniband networks.") import subprocess else: import subprocess def _get_status_output_subprocess(cmd, input=None, cwd=None, env=None): """Replacement for commands.getstatusoutput which does not work on Windows (or Python 3).""" if isinstance(cmd, string_types): cmd = cmd.strip().split() pipe = subprocess.Popen(cmd, shell=False, cwd=cwd, env=env, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) (output, errout) = pipe.communicate(input=input) assert not errout status = pipe.returncode if isinstance(output, bytes): output = output.decode('utf-8') return (status, output) def _get_status_output_system(cmd): """Replacement for commands.getstatusoutput which does not work on Windows (or Python 3).""" if not isinstance(cmd, string_types): cmd = " ".join(cmd) # Default return values status = 1 output = "not run" # Execute cmd with redirection to temporary file with tempfile.NamedTemporaryFile(delete=True) as f: cmd += ' > ' + f.name + ' 2>&1' # NOTE: Possibly OFED-fork-safe, tests needed! status = os.system(cmd) output = f.read() if isinstance(output, bytes): output = output.decode('utf-8') return (status, output) # Choose method for calling external programs. Use subprocess by default. _call_method = "SUBPROCESS" _call_method = os.environ.get("DIJITSO_SYSTEM_CALL_METHOD", _call_method) if _call_method == "OS_SYSTEM": get_status_output = _get_status_output_system else: get_status_output = _get_status_output_subprocess def make_executable(filename): "Make script executable by setting user eXecutable bit." permissions = stat.S_IMODE(os.lstat(filename).st_mode) os.chmod(filename, permissions | stat.S_IXUSR) def make_dirs(path): """Creates a directory (tree). Ignores error if the directory already exists. """ try: os.makedirs(path) except os.error as e: if e.errno != errno.EEXIST: raise def rename_file(src, dst): """Rename a file. Ignores error if the destination file exists. """ try: os.rename(src, dst) except os.error as e: # Windows may trigger on existing destination if e.errno not in errno.EEXIST: raise def try_rename_file(src, dst): """Try to rename a file. NB! Ignores error if the SOURCE doesn't exist or the destination already exists. """ try: os.rename(src, dst) except os.error as e: # Windows may trigger on existing destination, # everyone triggers on missing source if e.errno not in (errno.ENOENT, errno.EEXIST): raise def try_copy_file(src, dst): """Try to copy a file. NB! Ignores any error. """ try: shutil.copy(src, dst) except: pass def try_delete_file(filename): """Try to remove a file. Ignores error if filename doesn't exist. """ try: os.remove(filename) except os.error as e: if e.errno != errno.ENOENT: raise def gzip_file(filename): """Gzip a file. New file gets .gz extension added. Does nothing if the .gz file already exists. Original file is never touched. """ # Expecting source file to be there if not os.path.exists(filename): return None # Avoid doing work if file is already there gz_filename = filename + ".gz" if not os.path.exists(gz_filename): # Write gzipped contents to a temp file tmp_filename = filename + "-tmp-" + uuid.uuid4().hex + ".gz" with io.open(filename, "rb") as f_in, gzip.open(tmp_filename, "wb") as f_out: shutil.copyfileobj(f_in, f_out) # Safe move to target filename, other processes may compete here lockfree_move_file(tmp_filename, gz_filename) return gz_filename def gunzip_file(gz_filename): """Gunzip a file.""" assert gz_filename[-3:] == ".gz" filename = gz_filename[:-3] # Write gzipped contents to a temp file tmp_filename = filename + "-tmp-" + uuid.uuid4().hex with gzip.open(gz_filename, "rb") as f_in, io.open(tmp_filename, "wb") as f_out: shutil.copyfileobj(f_in, f_out) # Safe move to target filename, other processes may compete here lockfree_move_file(tmp_filename, filename) try_delete_file(gz_filename) return filename def read_textfile(filename): """Try to read file content, if necessary unzipped from filename.gz, return None if not found.""" if not os.path.exists(filename): filename = filename + ".gz" if not os.path.exists(filename): content = None else: if filename.endswith(".gz"): content = b"" with gzip.open(filename, "rb") as f: content = f.read() content = content.decode("utf-8") else: with io.open(filename, "r", encoding="utf-8") as f: content = f.read() return content def store_textfile(filename, content): """Store content to filename without race conditions. Works by first writing to a unique temp file and then moving to final destination. Handles both bytes and unicode. """ # Generate a unique temporary filename in same directory as the target file ui = uuid.uuid4().hex tmp_filename = "%s.%s" % (filename, ui) # Write the text to a temporary file if isinstance(content, bytes): # content is already bytes, write raw f = io.open(tmp_filename, "wb") else: f = io.open(tmp_filename, "w", encoding="utf8") with f: f.write(content) # Safely move file to target filename lockfree_move_file(tmp_filename, filename) return filename def move_file(srcfilename, dstfilename): """Move or copy a file.""" assert os.path.exists(srcfilename) shutil.move(srcfilename, dstfilename) assert not os.path.exists(srcfilename) assert os.path.exists(dstfilename) def lockfree_move_file(src, dst): """Lockfree and portable nfs safe file move operation. If target filename exists with different content, will move it to filename.old and emit a warning. Taken from textual description at http://stackoverflow.com/questions/11614815/a-safe-atomic-file-copy-operation """ return _lockfree_move_file(src, dst, False) def _lockfree_move_file(src, dst, recurse): if not os.path.exists(src): if recurse: return else: raise RuntimeError("Source file does not exist.") dst_exists = os.path.exists(dst) if dst_exists and recurse: warning("Backup file exists, overwriting.") elif dst_exists: # Destination file exists with io.open(src, "rb") as f: s = f.read() with io.open(dst, "rb") as f: d = f.read() if s == d: # Files are the same, just delete src instead of moving try_delete_file(src) return # Files differ, backup old file before moving file over it backup = dst + ".old" warning("Moving new file over differing existing file:\n" "src: %s\ndst: %s\nbackup: %s" % (src, dst, backup)) _lockfree_move_file(dst, backup, True) def priv(j): return dst + ".priv." + str(j) def pub(j): return dst + ".pub." + str(j) # Create a universally unique 128 bit integer id ui = uuid.uuid4().int # Move or copy file onto the target filesystem move_file(src, priv(ui)) # Atomic rename to make file visible to competing processes rename_file(priv(ui), pub(ui)) # Find uuids of competing files n = len(pub("*")) - 1 uuids = sorted(int(fn[n:]) for fn in glob(pub("*"))) # Try to delete all files with larger uuids for i in uuids: if i > ui: try_delete_file(pub(i)) for i in uuids: if i < ui: # Our file is the one with a larger uuid try_delete_file(pub(ui)) # Cooperate on handling uuid i ui = i if os.path.exists(dst): # If somebody else beat us to it, delete our file try_delete_file(pub(ui)) else: # Otherwise do an atomic rename to make our file final try_rename_file(pub(ui), dst) if os.path.exists(src): raise RuntimeError("Source file should not exist at this point!") if not os.path.exists(dst): raise RuntimeError("Destination file should exist at this point!") def ldd(libname): """Run the ldd system tool on libname. Returns output as a dict {basename: fullpath} with all dynamic library dependencies and their resolution path. This is a debugging tool and may fail if ldd is not available or behaves differently on this system. """ status, output = get_status_output(["ldd", libname]) libraries = {} for line in output.splitlines(): match = re.match(r'(.*)=>([^(]*)(.*)', line) if match: dlib = match.group(1).strip() dlibpath = match.group(2).strip() address = match.group(3).strip() if address: # Path can be empty for system libs assert dlibpath == "" or os.path.exists(dlibpath) libraries[dlib] = dlibpath else: assert not os.path.exists(dlibpath) libraries[dlib] = None return libraries dijitso-2016.2.0/doc/000077500000000000000000000000001301752034500141545ustar00rootroot00000000000000dijitso-2016.2.0/doc/man/000077500000000000000000000000001301752034500147275ustar00rootroot00000000000000dijitso-2016.2.0/doc/man/man1/000077500000000000000000000000001301752034500155635ustar00rootroot00000000000000dijitso-2016.2.0/doc/man/man1/dijitso.1.gz000066400000000000000000000011451301752034500177320ustar00rootroot00000000000000Wdijitso.1SAn0ZQAԎ8!|ŀ"UriAGi MjggfQwߒ7Q4~\J=+>2NAJY6xf'n/svwϗVuj>Ѩw>cIuǹ]g͡FYh*(mۢ!?zR]' where is one of" @echo " html to make standalone HTML files" @echo " dirhtml to make HTML files named index.html in directories" @echo " singlehtml to make a single large HTML file" @echo " pickle to make pickle files" @echo " json to make JSON files" @echo " htmlhelp to make HTML files and a HTML help project" @echo " qthelp to make HTML files and a qthelp project" @echo " applehelp to make an Apple Help Book" @echo " devhelp to make HTML files and a Devhelp project" @echo " epub to make an epub" @echo " epub3 to make an epub3" @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" @echo " latexpdf to make LaTeX files and run them through pdflatex" @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" @echo " text to make text files" @echo " man to make manual pages" @echo " texinfo to make Texinfo files" @echo " info to make Texinfo files and run them through makeinfo" @echo " gettext to make PO message catalogs" @echo " changes to make an overview of all changed/added/deprecated items" @echo " xml to make Docutils-native XML files" @echo " pseudoxml to make pseudoxml-XML files for display purposes" @echo " linkcheck to check all external links for integrity" @echo " doctest to run all doctests embedded in the documentation (if enabled)" @echo " coverage to run coverage check of the documentation (if enabled)" @echo " dummy to check syntax errors of document sources" .PHONY: clean clean: rm -rf $(BUILDDIR)/* .PHONY: html html: $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." .PHONY: dirhtml dirhtml: $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml @echo @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." .PHONY: singlehtml singlehtml: $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml @echo @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." .PHONY: pickle pickle: $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle @echo @echo "Build finished; now you can process the pickle files." .PHONY: json json: $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json @echo @echo "Build finished; now you can process the JSON files." .PHONY: htmlhelp htmlhelp: $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp @echo @echo "Build finished; now you can run HTML Help Workshop with the" \ ".hhp project file in $(BUILDDIR)/htmlhelp." .PHONY: qthelp qthelp: $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp @echo @echo "Build finished; now you can run "qcollectiongenerator" with the" \ ".qhcp project file in $(BUILDDIR)/qthelp, like this:" @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/dijitso.qhcp" @echo "To view the help file:" @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/dijitso.qhc" .PHONY: applehelp applehelp: $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp @echo @echo "Build finished. The help book is in $(BUILDDIR)/applehelp." @echo "N.B. You won't be able to view it unless you put it in" \ "~/Library/Documentation/Help or install it in your application" \ "bundle." .PHONY: devhelp devhelp: $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp @echo @echo "Build finished." @echo "To view the help file:" @echo "# mkdir -p $$HOME/.local/share/devhelp/dijitso" @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/dijitso" @echo "# devhelp" .PHONY: epub epub: $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub @echo @echo "Build finished. The epub file is in $(BUILDDIR)/epub." .PHONY: epub3 epub3: $(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3 @echo @echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3." .PHONY: latex latex: $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex @echo @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." @echo "Run \`make' in that directory to run these through (pdf)latex" \ "(use \`make latexpdf' here to do that automatically)." .PHONY: latexpdf latexpdf: $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex @echo "Running LaTeX files through pdflatex..." $(MAKE) -C $(BUILDDIR)/latex all-pdf @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." .PHONY: latexpdfja latexpdfja: $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex @echo "Running LaTeX files through platex and dvipdfmx..." $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." .PHONY: text text: $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text @echo @echo "Build finished. The text files are in $(BUILDDIR)/text." .PHONY: man man: $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man @echo @echo "Build finished. The manual pages are in $(BUILDDIR)/man." .PHONY: texinfo texinfo: $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo @echo @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." @echo "Run \`make' in that directory to run these through makeinfo" \ "(use \`make info' here to do that automatically)." .PHONY: info info: $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo @echo "Running Texinfo files through makeinfo..." make -C $(BUILDDIR)/texinfo info @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." .PHONY: gettext gettext: $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale @echo @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." .PHONY: changes changes: $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes @echo @echo "The overview file is in $(BUILDDIR)/changes." .PHONY: linkcheck linkcheck: $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck @echo @echo "Link check complete; look for any errors in the above output " \ "or in $(BUILDDIR)/linkcheck/output.txt." .PHONY: doctest doctest: $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest @echo "Testing of doctests in the sources finished, look at the " \ "results in $(BUILDDIR)/doctest/output.txt." .PHONY: coverage coverage: $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage @echo "Testing of coverage in the sources finished, look at the " \ "results in $(BUILDDIR)/coverage/python.txt." .PHONY: xml xml: $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml @echo @echo "Build finished. The XML files are in $(BUILDDIR)/xml." .PHONY: pseudoxml pseudoxml: $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml @echo @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." .PHONY: dummy dummy: $(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy @echo @echo "Build finished. Dummy builder generates no files." dijitso-2016.2.0/doc/sphinx/README000066400000000000000000000011571301752034500163510ustar00rootroot00000000000000==================== Sphinx documentation ==================== DIJITSO is documented using Sphinx and reStructured text. The documentation is hosted at http://fenics-dijitso.readthedocs.org/. The online documentation is automatically updated upon pushes to the UFL master branch. Building the documentation locally ================================== The HTML documentation can be built locally using:: make html In order for changes in the docstring to be propagated to the html pages, the package must be installed anew. In other words, sphinx reads the docstrings from the installed code, not the source code. dijitso-2016.2.0/doc/sphinx/source/000077500000000000000000000000001301752034500167655ustar00rootroot00000000000000dijitso-2016.2.0/doc/sphinx/source/conf.py000066400000000000000000000305411301752034500202670ustar00rootroot00000000000000# -*- coding: utf-8 -*- # # dijitso documentation build configuration file, created by # sphinx-quickstart on Mon Jul 25 11:18:03 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. import os # import sys # sys.path.insert(0, os.path.abspath('.')) # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', ] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'dijitso' copyright = u'2016, FEniCS Project' author = u'FEniCS Project' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # import dijitso dijitso_version = dijitso.__version__ # The short X.Y version. version = dijitso_version # The full version, including alpha/beta/rc tags. release = dijitso_version # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = [] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # # html_theme = 'default' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom themes here, relative to this directory. # html_theme_path = [] # The name for this set of Sphinx documents. # " v documentation" by default. # # html_title = u'dijitso v2016.02.1' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # # html_logo = None # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # # html_favicon = None # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # # html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # # html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. # # html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh' # # html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. # # html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. # # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'dijitsodoc' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'dijitso.tex', u'dijitso Documentation', u'FEniCS Project', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # # latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # # latex_use_parts = False # If true, show page references after internal links. # # latex_show_pagerefs = False # If true, show URL addresses after external links. # # latex_show_urls = False # Documents to append as an appendix to all manuals. # # latex_appendices = [] # It false, will not define \strong, \code, itleref, \crossref ... but only # \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added # packages. # # latex_keep_old_macro_names = True # If false, no module index is generated. # # latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'dijitso', u'dijitso Documentation', [author], 1) ] # If true, show URL addresses after external links. # # man_show_urls = False # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'dijitso', u'dijitso Documentation', author, 'dijitso', 'One line description of project.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # -- Options for Epub output ---------------------------------------------- # Bibliographic Dublin Core info. epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright # The basename for the epub file. It defaults to the project name. # epub_basename = project # The HTML theme for the epub output. Since the default themes are not # optimized for small screen space, using the same theme for HTML and epub # output is usually not wise. This defaults to 'epub', a theme designed to save # visual space. # # epub_theme = 'epub' # The language of the text. It defaults to the language option # or 'en' if the language is not set. # # epub_language = '' # The scheme of the identifier. Typical schemes are ISBN or URL. # epub_scheme = '' # The unique identifier of the text. This can be a ISBN number # or the project homepage. # # epub_identifier = '' # A unique identification for the text. # # epub_uid = '' # A tuple containing the cover image and cover page html template filenames. # # epub_cover = () # A sequence of (type, uri, title) tuples for the guide element of content.opf. # # epub_guide = () # HTML files that should be inserted before the pages created by sphinx. # The format is a list of tuples containing the path and title. # # epub_pre_files = [] # HTML files that should be inserted after the pages created by sphinx. # The format is a list of tuples containing the path and title. # # epub_post_files = [] # A list of files that should not be packed into the epub file. epub_exclude_files = ['search.html'] # The depth of the table of contents in toc.ncx. # # epub_tocdepth = 3 # Allow duplicate toc entries. # # epub_tocdup = True # Choose between 'default' and 'includehidden'. # # epub_tocscope = 'default' # Fix unsupported image types using the Pillow. # # epub_fix_images = False # Scale large images. # # epub_max_image_width = 0 # How to display URL addresses: 'footnote', 'no', or 'inline'. # # epub_show_urls = 'inline' # If false, no index is generated. # # epub_use_index = True def run_apidoc(_): modules = ['dijitso'] # Get location of Sphinx files sphinx_source_dir = os.path.abspath(os.path.dirname(__file__)) repo_dir = os.path.abspath(os.path.join(sphinx_source_dir, os.path.pardir, os.path.pardir, os.path.pardir)) apidoc_dir = os.path.join(sphinx_source_dir, "api-doc") from sphinx.apidoc import main for module in modules: # Generate .rst files ready for autodoc module_dir = os.path.join(repo_dir, module) main(["-f", "-d", "1", "-o", apidoc_dir, module_dir]) def setup(app): app.connect('builder-inited', run_apidoc) dijitso-2016.2.0/doc/sphinx/source/index.rst000066400000000000000000000007571301752034500206370ustar00rootroot00000000000000.. title:: dijitso documentation ======= dijitso ======= A Python module for distributed just-in-time shared library building. DIJITSO is part of the FEniCS Project. For more information, visit http://www.fenicsproject.org Documentation ============= .. toctree:: :titlesonly: :maxdepth: 1 installation manual API reference releases [FIXME: These links don't belong here, should go under API reference somehow.] * :ref:`genindex` * :ref:`modindex` dijitso-2016.2.0/doc/sphinx/source/installation.rst000066400000000000000000000044501301752034500222230ustar00rootroot00000000000000.. title:: Installation ============ Installation ============ DIJITSO is normally installed as part of an installation of FEniCS. If you are using DIJITSO as part of the FEniCS software suite, it is recommended that you follow the `installation instructions for FEniCS `__. To install DIJITSO itself, read on below for a list of requirements and installation instructions. Requirements and dependencies ============================= DIJITSO requires Python version 2.7 or later and depends on the following Python packages: * six * NumPy These packages will be automatically installed as part of the installation of DIJITSO, if not already present on your system. If running on a cluster with Infiniband with python 2, you also need to install a backport of the subprocess module from python 3 to get safe fork behaviour: * subprocess32 Additionally, to run tests the following packages are needed * pytest * mpi4py (for running tests with mpi) Installation instructions ========================= To install DIJITSO, download the source code from the `DIJITSO Bitbucket repository `__, and run the following command: .. code-block:: console pip install . To install to a specific location, add the ``--prefix`` flag to the installation command: .. code-block:: console pip install --prefix= . Environment =========== Instant's behaviour depened on following environment variables: - ``DIJITSO_CACHE_DIR`` This option overrides the placement of the cache directory. By default the cache directory is placed in ``.cache/dijitso`` either below the home directory or below the prefix of the currently active virtualenv or conda environment if any. - ``DIJITSO_SYSTEM_CALL_METHOD`` Choose method for calling external programs (c++ compiler). Available values: - ``SUBPROCESS`` Uses pipes. Not OFED-fork safe on Python 2 unless subprocess32 has been installed. Default. - ``OS_SYSTEM`` Uses temporary files. Probably OFED-fork safe. .. warning:: OFED-fork safe system call method might be required to avoid crashes on OFED-based (InfiniBand) clusters! If using python 2, installing subprocess32 is recommended. dijitso-2016.2.0/doc/sphinx/source/manual.rst000066400000000000000000000004771301752034500210040ustar00rootroot00000000000000.. title:: User manual =========== User manual =========== The commandline tool 'dijitso' is currently only documented on the commandline, run 'dijitso --help' for details and available subcommands. The python module dijitso is only used internally by ffc, and no manual has been written so far. See API reference. dijitso-2016.2.0/doc/sphinx/source/releases.rst000066400000000000000000000001601301752034500213170ustar00rootroot00000000000000============= Release notes ============= .. toctree:: :maxdepth: 2 releases/next releases/v2016.1.0 dijitso-2016.2.0/doc/sphinx/source/releases/000077500000000000000000000000001301752034500205705ustar00rootroot00000000000000dijitso-2016.2.0/doc/sphinx/source/releases/next.rst000066400000000000000000000010311301752034500222730ustar00rootroot00000000000000=========================== Changes in the next release =========================== Summary of changes ================== .. note:: Developers should use this page to track and list changes during development. At the time of release, this page should be published (and renamed) to list the most important changes in the new release. - Insert changes here Detailed changes ================ .. note:: At the time of release, make a verbatim copy of the ChangeLog here (and remove this note). dijitso-2016.2.0/doc/sphinx/source/releases/v2016.1.0.rst000066400000000000000000000005201301752034500223720ustar00rootroot00000000000000=========================== Changes in version 2016.1.0 =========================== UFL 2016.1.0 was released on 2016-06-23. - This is the first version that covers all the immediate needs of the FEniCS Form Compiler (FFC) for just in time compilation of generated code using ctypes to import a simple generated factory function. dijitso-2016.2.0/setup.cfg000066400000000000000000000001471301752034500152320ustar00rootroot00000000000000[flake8] max-line-length=100 exclude=.git,__pycache__,doc/sphinx/source/conf.py,build,dist,__init__.py dijitso-2016.2.0/setup.py000077500000000000000000000044731301752034500151340ustar00rootroot00000000000000# -*- coding: utf-8 -*- from __future__ import print_function from setuptools import setup from os.path import join import re import sys import codecs module_name = "dijitso" if sys.version_info < (2, 7): print("Python 2.7 or higher required, please upgrade.") sys.exit(1) # __init__.py has UTF-8 characters. Works in Python 2 and 3. version = re.findall('__version__ = "(.*)"', codecs.open(join(module_name, '__init__.py'), 'r', encoding='utf-8').read())[0] url = "https://bitbucket.org/fenics-project/%s/" % module_name tarball = None if 'dev' not in version: tarball = url + "downloads/%s-%s.tar.gz" % (module_name, version) script_names = ("dijitso",) entry_points = {'console_scripts': ['dijitso = dijitso.__main__:main']} scripts = [join("scripts", script) for script in script_names] man_files = [join("doc", "man", "man1", "%s.1.gz" % (script,)) for script in script_names] data_files = [(join("share", "man", "man1"), man_files)] CLASSIFIERS = """\ Development Status :: 5 - Production/Stable Intended Audience :: Developers Intended Audience :: Science/Research License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) Operating System :: POSIX Operating System :: POSIX :: Linux Operating System :: MacOS :: MacOS X Operating System :: Microsoft :: Windows Programming Language :: Python Programming Language :: Python :: 2 Programming Language :: Python :: 2.7 Programming Language :: Python :: 3 Programming Language :: Python :: 3.4 Programming Language :: Python :: 3.5 Programming Language :: Python :: 3.6 Topic :: Scientific/Engineering :: Mathematics Topic :: Software Development :: Libraries :: Python Modules """ requires = ["numpy", "six"] if sys.version_info[0] == 2: requires.append("subprocess32") setup(name="dijitso", version=version, description="Distributed just-in-time building of shared libraries", author="Martin Sandve Alnæs", author_email="martinal@simula.no", url=url, download_url=tarball, classifiers=[_f for _f in CLASSIFIERS.split('\n') if _f], # scripts=scripts, # Using entry_points instead entry_points=entry_points, packages=["dijitso"], package_dir={'dijitso': 'dijitso'}, install_requires=requires, data_files=data_files ) dijitso-2016.2.0/test/000077500000000000000000000000001301752034500143665ustar00rootroot00000000000000dijitso-2016.2.0/test/.coveragerc000066400000000000000000000000541301752034500165060ustar00rootroot00000000000000[html] directory=htmlcov${MPISIZE}${MYRANK} dijitso-2016.2.0/test/clean.sh000077500000000000000000000001421301752034500160040ustar00rootroot00000000000000#!/bin/bash rm -rf report*.xml htmlcov* output.* *.pyc *~ *.dst .test_* .coverage .dijitso .cache dijitso-2016.2.0/test/conftest.py000066400000000000000000000115231301752034500165670ustar00rootroot00000000000000#!/usr/bin/env py.test # -*- coding: utf-8 -*- from __future__ import print_function import pytest import os import dijitso import ctypes from six import string_types @pytest.fixture() def comm(): try: from mpi4py import MPI c = MPI.COMM_WORLD except ImportError: pytest.skip("Need mpi4py to test with comms.") c = None return c _code_template_params = """\ /** Arguments used to generate this code: %(generator_params)s */ """ _code_template_defines = """\ // Based on https://gcc.gnu.org/wiki/Visibility #if defined _WIN32 || defined __CYGWIN__ #ifdef __GNUC__ #define DLL_EXPORT extern "C" __attribute__ ((dllexport)) #else #define DLL_EXPORT extern "C" __declspec(dllexport) #endif #else #define DLL_EXPORT extern "C" __attribute__ ((visibility ("default"))) #endif """ _code_template_interface = """\ // This would be '#include ' class %(interfacename)s { public: virtual ~%(interfacename)s() {} virtual int get_test_value() const = 0; }; """ _code_template_class = """\ /// This would be the generated ufc::form code class %(classname)s: public %(interfacename)s { public: int get_test_value() const { return %(testvalue)s; } }; """ _code_template_factory = """\ /// Construct an object of class %(classname)s without any class interface wrapping DLL_EXPORT void * create_%(signature)s() { return new %(classname)s(); } """ _code_template_testhook = """\ #include "testinclude.h" DLL_EXPORT int get_test_value_%(testvalue)d(void * p) { %(interfacename)s * pp = static_cast<%(interfacename)s *>(p); int v = pp->get_test_value(); return v + TESTINCLUDE_MAGIC_VALUE; } """ def mygenerate(jitable, name, signature, generator_params): """.""" code_parts = dict( generator_params=str(generator_params), signature=signature, classname="class_%s" % (jitable,), interfacename="external_interface", testvalue=jitable, ) parts = [ _code_template_params % code_parts, _code_template_defines % code_parts, _code_template_interface % code_parts, _code_template_class % code_parts, _code_template_factory % code_parts, _code_template_testhook % code_parts, ] header = "// Dummy header" source = '\n'.join(parts) dependencies = () return header, source, dependencies _default_dijitso_cache_dir = os.path.join(os.path.dirname(__file__), ".dijitso") _testincludes = os.path.join(os.path.dirname(__file__), "testincludes") def _jit_integer(jitable, comm=None, buildon="node", dijitso_cache_dir=_default_dijitso_cache_dir): "A mock jit routine setup to exercise much of the library." # Setup params cache_params = dict( cache_dir=dijitso_cache_dir, src_storage="compress", ) build_params = dict( debug=True, include_dirs=(_testincludes,), ) generator_params = None params = dict( cache=cache_params, build=build_params, generator=generator_params, ) params = dijitso.validate_params(params) # Compute a name from dijitso.signatures import hashit name = "jit_integer_" + hashit(jitable) # Autodetect subcomms and role based on buildin option and # physical disk access of processes from dijitso.mpi import create_comms_and_role, send_binary, receive_binary from dijitso.system import make_dirs sync_dir = os.path.join(cache_params["cache_dir"], "sync") make_dirs(sync_dir) copy_comm, wait_comm, role = create_comms_and_role(comm, sync_dir, buildon) # Somewhat messy definitions of send/receive/wait... send = None receive = None wait = None if role == "builder": generate = mygenerate if copy_comm is not None: def send(lib_data): assert role == "builder" send_binary(copy_comm, lib_data) elif role == "receiver": generate = None assert copy_comm is not None def receive(): return receive_binary(copy_comm) elif role == "waiter": generate = None if wait_comm is not None: def wait(): wait_comm.barrier() # Jit it! lib, signature = dijitso.jit(jitable, name, params, generate, send, receive, wait) assert lib is not None assert isinstance(signature, string_types) # Extract the factory function we want from library factory = dijitso.extract_factory_function(lib, "create_" + signature) # ... and the test specific getter function get_test_value = getattr(lib, "get_test_value_%d" % jitable) get_test_value.argtypes = [ctypes.c_void_p] get_test_value.restype = ctypes.c_int # Return both library and factory return lib, factory, get_test_value @pytest.fixture() def jit_integer(): return _jit_integer dijitso-2016.2.0/test/debug_mpi_tests.sh000077500000000000000000000003201301752034500200750ustar00rootroot00000000000000#!/usr/bin/env bash set -e exit : ${PYTHON:=python} while [ $? -eq 0 ] do for p in 8; do echo RUNNING WITH p=$p mpirun -n $p xterm -e gdb -ex r -ex q -args ${PYTHON} -B -m pytest -svl done done dijitso-2016.2.0/test/mpipipe.sh000077500000000000000000000024211301752034500163670ustar00rootroot00000000000000#!/bin/sh # Copyright (C) 2015 Martin Alnæs # Copyright (C) 2015 Johannes Ring # # This file is part of DOLFIN. # # DOLFIN is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DOLFIN is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DOLFIN. If not, see . # This script redirects output from a command to output.MYRANK : ${PYTHON:=python} # See: http://docs.roguewave.com/threadspotter/2012.1/linux/manual_html/apas03.html if [ ! -z $OMPI_COMM_WORLD_RANK ]; then MYRANK=$OMPI_COMM_WORLD_RANK elif [ ! -z $PMI_RANK ]; then MYRANK=$PMI_RANK else MYRANK=`${PYTHON} -c "import dolfin;c=dolfin.mpi_comm_world();r=dolfin.MPI.rank(c);print(r);dolfin.MPI.barrier(c)"` fi OUT=output.$MYRANK echo My rank is $MYRANK, writing to $OUT if [ $MYRANK -eq 0 ]; then $@ | tee $OUT else $@ > $OUT fi dijitso-2016.2.0/test/mpipytest.sh000077500000000000000000000026251301752034500167700ustar00rootroot00000000000000#!/bin/sh # Copyright (C) 2015 Martin Alnæs # Copyright (C) 2015 Johannes Ring # # This file is part of DOLFIN. # # DOLFIN is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DOLFIN is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DOLFIN. If not, see . # This script redirects output from a command to output.MYRANK : ${PYTHON:=python} # See: http://docs.roguewave.com/threadspotter/2012.1/linux/manual_html/apas03.html if [ ! -z $OMPI_COMM_WORLD_RANK ]; then export MYRANK=$OMPI_COMM_WORLD_RANK elif [ ! -z $PMI_RANK ]; then export MYRANK=$PMI_RANK else export MYRANK=`${PYTHON} -c "import dolfin;c=dolfin.mpi_comm_world();r=dolfin.MPI.rank(c);print(r);dolfin.MPI.barrier(c)"` fi CMD=${PYTHON}' -B -m pytest -svl --cov-report html --cov=dijitso --junitxml report$MYRANK.xml' echo $CMD OUT=output.$MYRANK echo My rank is $MYRANK, writing to $OUT if [ $MYRANK -eq 0 ]; then $CMD | tee $OUT else $CMD > $OUT fi dijitso-2016.2.0/test/pytest.ini000066400000000000000000000000321301752034500164120ustar00rootroot00000000000000[pytest] minversion = 2.4 dijitso-2016.2.0/test/runtests.sh000077500000000000000000000004761301752034500166230ustar00rootroot00000000000000#!/usr/bin/env bash set -e exit : ${PYTHON:=python} echo Running tests in serial: export MYRANK= export MPISIZE= ${PYTHON} -B -m pytest -svl --cov-report html --cov=dijitso --junitxml report$MYRANK.xml for p in 1 4 8 16; do echo Running tests with mpi, n=$p export MPISIZE=$p mpirun -n $p ./mpipytest.sh done dijitso-2016.2.0/test/test_mpi_dijitso.py000066400000000000000000000063601301752034500203160ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . from __future__ import unicode_literals from __future__ import print_function import pytest import shutil import os @pytest.fixture(params=["root", "node", "process"]) def buildon(request): return request.param def test_mpi_jit_strategies(comm, jit_integer, buildon): """Jit a simple code generated by inserting a simple integer. Covers (if the cache is initially empty): - memory cache miss - memory cache hit - compiling - loading - factory function extraction """ # Note: this test was initially copied from # test_core_jit_framework in test_dijitso.py print(buildon, comm.rank) if buildon == "process": # One dir per process dijitso_cache_dir = ".test_dijitso_%d" % (comm.rank,) elif buildon == "node": # Less dirs than processes (gives some waiting for size > 2) dijitso_cache_dir = ".test_dijitso_%d" % (comm.rank % 2,) elif buildon == "root": # Less dirs than processes (gives a combination of copying # (size>1) and waiting (size>2)) dijitso_cache_dir = ".test_dijitso_%d" % (comm.rank % 2,) dijitso_cache_dir = os.path.join(os.path.dirname(__file__), dijitso_cache_dir) shutil.rmtree(dijitso_cache_dir, ignore_errors=True) comm.barrier() # This magic value is defined in testincludes/testinclude.h, # so this is used to confirm that includes work correctly. # Also the fact that the #include "testinclude.h" above compiles. magic_value = 42 stored = {} for repeat in range(2): for jitable in (234, 567): # Note different values than serial test # Each integer produces different code lib, factory, gettr = jit_integer(jitable, comm=comm, buildon=buildon, dijitso_cache_dir=dijitso_cache_dir) # Inspect values for testing assert jitable + magic_value == gettr(factory()) # Memory cache test if repeat == 0: # Make a record of this lib stored[jitable] = lib else: # Check that we fetched the lib from the memory cache assert lib is stored[jitable] # If all went well we clean up, if assertions triggered # above we allow this cleanup to not happen shutil.rmtree(dijitso_cache_dir, ignore_errors=True) comm.barrier() # TODO: Cover various failure situations with tests dijitso-2016.2.0/test/test_mpi_dummy.py000066400000000000000000000015651301752034500200060ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . from __future__ import print_function from __future__ import unicode_literals def test_mpi_dummy(comm): assert comm.rank < comm.size dijitso-2016.2.0/test/test_role_assignment.py000066400000000000000000000047051301752034500211760ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . from __future__ import unicode_literals from __future__ import print_function import pytest from dijitso.system import make_dirs from dijitso.mpi import create_comms_and_role @pytest.fixture() def lib_dir0(comm): # Fake some common and some shared libdirs path = ".test_roles_%d" % (comm.rank,) make_dirs(path) return path @pytest.fixture() def lib_dir2(comm): # Fake some common and some shared libdirs path = ".test_roles_%d_of_2" % (comm.rank % 2,) make_dirs(path) return path def test_role_root(comm, lib_dir2): buildon = "root" copy_comm, wait_comm, role = create_comms_and_role(comm, lib_dir2, buildon) if comm.rank == 0: expected_role = "builder" elif wait_comm.rank == 0: expected_role = "receiver" else: expected_role = "waiter" assert role == expected_role assert copy_comm is not None assert wait_comm is not None if role != "waiter": assert copy_comm.size == min(comm.size, 2) assert (comm.size // 2) <= wait_comm.size <= (comm.size // 2 + 1) def test_role_node(comm, lib_dir2): buildon = "node" copy_comm, wait_comm, role = create_comms_and_role(comm, lib_dir2, buildon) if comm.rank in (0, 1): expected_role = "builder" else: expected_role = "waiter" assert role == expected_role assert copy_comm is None assert wait_comm is not None assert (comm.size // 2) <= wait_comm.size <= (comm.size // 2 + 1) def test_role_process(comm, lib_dir0): buildon = "process" copy_comm, wait_comm, role = create_comms_and_role(comm, lib_dir0, buildon) expected_role = "builder" assert role == expected_role assert copy_comm is None assert wait_comm is None dijitso-2016.2.0/test/test_serial_dijitso.py000066400000000000000000000036751301752034500210160ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . from __future__ import unicode_literals from __future__ import print_function def test_core_jit_framework(jit_integer): """Jit a simple code generated by inserting a simple integer. Covers (if the cache is initially empty): - memory cache miss - memory cache hit - compiling - loading - factory function extraction """ # This magic value is defined in testincludes/testinclude.h, so # this is used to confirm that includes work correctly. Also the # fact that the #include "testinclude.h" above compiles. magic_value = 42 stored = {} for repeat in range(2): for jitable in (123, 456): # Each integer produces different code lib, factory, get_test_value = jit_integer(jitable) # Inspect values for testing assert jitable + magic_value == get_test_value(factory()) # Memory cache test if repeat == 0: # Make a record of this lib stored[jitable] = lib else: # Check that we fetched the lib from the memory cache assert lib is stored[jitable] # TODO: Cover various failure situations with tests dijitso-2016.2.0/test/test_system_utils.py000066400000000000000000000036561301752034500205550ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Copyright (C) 2015-2016 Martin Sandve Alnæs # # This file is part of DIJITSO. # # DIJITSO is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # DIJITSO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public License # along with DIJITSO. If not, see . from __future__ import unicode_literals from __future__ import print_function import io import os import uuid from dijitso.system import lockfree_move_file, make_dirs def test_get_status_output(): pass # FIXME def test_lockfree_move_file(): # Running this loop in multiple processes with mpi is perhaps a # decent test? # Fixed directory independent of mpi rank tmpdir = os.path.join(os.path.dirname(os.path.abspath(__file__)), ".test_lockfree_move_file") make_dirs(tmpdir) # source is different for each process and loop iteration n = 3 u = uuid.uuid4().int srcs = [os.path.join(tmpdir, "test_lockfree_move_file-%d.src-%d" % (u, i)) for i in range(n)] # fixed destination dst = os.path.join(tmpdir, "test_lockfree_move_file.dst") # try_delete_file(dst) # can't do this when testing with mpi! for src in srcs: with io.open(src, "w", encoding="utf-8") as f: f.write("dummy") assert os.path.exists(src) lockfree_move_file(src, dst) assert os.path.exists(dst) assert not os.path.exists(src) with io.open(dst, encoding="utf-8") as f: dummy = f.read() assert dummy == "dummy" dijitso-2016.2.0/test/testincludes/000077500000000000000000000000001301752034500170745ustar00rootroot00000000000000dijitso-2016.2.0/test/testincludes/testinclude.h000066400000000000000000000000431301752034500215650ustar00rootroot00000000000000#define TESTINCLUDE_MAGIC_VALUE 42