pax_global_header00006660000000000000000000000064131530057230014511gustar00rootroot0000000000000052 comment=1fdec9c5611661f1936df0411cbee33c04cedacf ParaFly-0.1.0/000077500000000000000000000000001315300572300130455ustar00rootroot00000000000000ParaFly-0.1.0/LICENSE000066400000000000000000000027241315300572300140570ustar00rootroot00000000000000Copyright (c) 2011, The Broad Institute, Inc. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: · Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. · Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. · Neither the name of the Broad Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.** THIS SOFTWARE IS PROVIDED BY THE BROAD INSTITUTE ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BROAD INSTITUTE BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ParaFly-0.1.0/Makefile000066400000000000000000000525421315300572300145150ustar00rootroot00000000000000# Makefile.in generated by automake 1.11.1 from Makefile.am. # Makefile. 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config.h. Generated from config.h.in by configure. */ /* config.h.in. Generated from configure.ac by autoheader. */ /* Name of package */ #define PACKAGE "parafly" /* Define to the address where bug reports for this package should be sent. */ #define PACKAGE_BUGREPORT "bug-report@address" /* Define to the full name of this package. */ #define PACKAGE_NAME "Parafly" /* Define to the full name and version of this package. */ #define PACKAGE_STRING "Parafly 0.1" /* Define to the one symbol short name of this package. */ #define PACKAGE_TARNAME "parafly" /* Define to the version of this package. */ #define PACKAGE_VERSION "0.1" /* Version number of package */ #define VERSION "0.1" ParaFly-0.1.0/config.h.in000066400000000000000000000010551315300572300150710ustar00rootroot00000000000000/* config.h.in. Generated from configure.ac by autoheader. */ /* Name of package */ #undef PACKAGE /* Define to the address where bug reports for this package should be sent. */ #undef PACKAGE_BUGREPORT /* Define to the full name of this package. */ #undef PACKAGE_NAME /* Define to the full name and version of this package. */ #undef PACKAGE_STRING /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME /* Define to the version of this package. */ #undef PACKAGE_VERSION /* Version number of package */ #undef VERSION ParaFly-0.1.0/config.log000066400000000000000000000246671315300572300150340ustar00rootroot00000000000000This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by Parafly configure 0.1, which was generated by GNU Autoconf 2.63. Invocation command line was $ ./configure --prefix=/home/unix/bhaas/GITHUB/ParaFly ## --------- ## ## Platform. ## ## --------- ## hostname = delanatii.broadinstitute.org uname -m = x86_64 uname -r = 2.6.32-696.3.2.el6.x86_64 uname -s = Linux uname -v = #1 SMP Wed Jun 7 11:51:39 EDT 2017 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = x86_64 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /seq/RNASEQ/FIRECLOUD/GCLOUD/google-cloud-sdk/bin PATH: /home/unix/bhaas/utilities/emboss PATH: . PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/zlib_1.2.6/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/hdf5_1.8.9/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/graphviz_2.28.0/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/db_4.7.25/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/tcltk8.5.9/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/emacs_24.5/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/subversion_1.7.2/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/neon_0.29.3/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/sqlite_3.7.17/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/hmmer_3.1/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/mysql_5.6.20/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/coreutils_8.22/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/git_1.8.5.6/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/jdk1.8.0_121/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/ncbi-blast_2.2.30+-x86_64/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/perl_5.8.9/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/dbd-oracle_1.23-perl-5.8.9-oracle-instantclient-10.2.0.4.0/bin PATH: /broad/software/nonfree/Linux/redhat_6_x86_64/pkgs/oracle_instantclient-10.2.0.4.0/instantclient_10_2 PATH: /broad/uge/8.5.3/bin/lx-amd64 PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/imagemagick_6.9.0-5/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/genetorrent_download-3.8.7/cghub/bin PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/netcdf_4.0.1/bin PATH: /home/unix/bhaas/utilities PATH: /home/unix/bhaas/GITHUB/pasapipeline/misc_utilities/ PATH: /home/unix/bhaas/bin PATH: /seq/regev_genome_portal/SOFTWARE/SRA_TOOLKIT/sratoolkit.2.5.1-centos_linux64/bin PATH: /usr/local/bin PATH: /bin PATH: /usr/bin PATH: /usr/local/sbin PATH: /usr/sbin PATH: /sbin PATH: /seq/regev_genome_portal/SOFTWARE/OpenMPI/openmpi-1.6.5/bin PATH: /home/unix/bhaas/GITHUB/Trinity_CTAT/fusion PATH: /home/unix/bhaas/GITHUB/trinityrnaseq PATH: /home/unix/bhaas/.firecloud-cli/ubin ## ----------- ## ## Core tests. ## ## ----------- ## configure:1831: checking for a BSD-compatible install configure:1899: result: /broad/software/free/Linux/redhat_6_x86_64/pkgs/coreutils_8.22/bin/install -c configure:1910: checking whether build environment is sane configure:1970: result: yes configure:2111: checking for a thread-safe mkdir -p configure:2150: result: /broad/software/free/Linux/redhat_6_x86_64/pkgs/coreutils_8.22/bin/mkdir -p configure:2163: checking for gawk configure:2179: found /bin/gawk configure:2190: result: gawk configure:2201: checking whether make sets $(MAKE) configure:2223: result: yes configure:2369: checking for g++ configure:2385: found /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/bin/g++ configure:2396: result: g++ configure:2423: checking for C++ compiler version configure:2431: g++ --version >&5 g++ (GCC) 5.1.0 Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:2435: $? = 0 configure:2442: g++ -v >&5 Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/libexec/gcc/x86_64-redhat-linux/5.1.0/lto-wrapper Target: x86_64-redhat-linux Configured with: /tmp/redhat_6_x86_64/build/tmp/gcc-5.1.0/configure --prefix=/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0 --enable-lto --with-cloog --enable-plugins --enable-languages=c,c++,objc,obj-c++,fortran --build=x86_64-redhat-linux --disable-multilib --with-gmp=/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0 --with-mpfr=/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0 Thread model: posix gcc version 5.1.0 (GCC) configure:2446: $? = 0 configure:2453: g++ -V >&5 g++: error: unrecognized command line option '-V' g++: fatal error: no input files compilation terminated. configure:2457: $? = 1 configure:2480: checking for C++ compiler default output file name configure:2502: g++ conftest.cpp >&5 configure:2506: $? = 0 configure:2544: result: a.out configure:2563: checking whether the C++ compiler works configure:2573: ./a.out configure:2577: $? = 0 configure:2596: result: yes configure:2603: checking whether we are cross compiling configure:2605: result: no configure:2608: checking for suffix of executables configure:2615: g++ -o conftest conftest.cpp >&5 configure:2619: $? = 0 configure:2645: result: configure:2651: checking for suffix of object files configure:2677: g++ -c conftest.cpp >&5 configure:2681: $? = 0 configure:2706: result: o configure:2710: checking whether we are using the GNU C++ compiler configure:2739: g++ -c conftest.cpp >&5 configure:2746: $? = 0 configure:2763: result: yes configure:2772: checking whether g++ accepts -g configure:2802: g++ -c -g conftest.cpp >&5 configure:2809: $? = 0 configure:2910: result: yes configure:2944: checking for style of include used by make configure:2972: result: GNU configure:2997: checking dependency style of g++ configure:3107: result: gcc3 configure:3134: checking for library containing cos configure:3175: g++ -o conftest -g -O2 conftest.cpp >&5 configure:3182: $? = 0 configure:3213: result: none required configure:3349: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by Parafly config.status 0.1, which was generated by GNU Autoconf 2.63. 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/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/algorithm: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/utility: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_relops.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_algo.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/algorithmfwd.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_heap.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_tempbuf.h: /usr/include/signal.h: /usr/include/bits/signum.h: /usr/include/bits/siginfo.h: /usr/include/bits/sigaction.h: /usr/include/bits/sigcontext.h: /usr/include/bits/sigstack.h: /usr/include/sys/ucontext.h: /usr/include/bits/sigthread.h: /usr/include/sys/wait.h: /usr/include/sys/resource.h: /usr/include/bits/resource.h: argProcessor.hpp: ParaFly-0.1.0/src/.deps/argProcessor.Po000066400000000000000000000302101315300572300176120ustar00rootroot00000000000000argProcessor.o: argProcessor.cpp argProcessor.hpp \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/map \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_tree.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_algobase.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/c++config.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/os_defines.h \ /usr/include/features.h /usr/include/sys/cdefs.h \ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ /usr/include/gnu/stubs-64.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/cpu_defines.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/functexcept.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/exception_defines.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/cpp_type_traits.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/ext/type_traits.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/ext/numeric_traits.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_pair.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/move.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/concept_check.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_iterator_base_types.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_iterator_base_funcs.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/debug/debug.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_iterator.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/ptr_traits.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/predefined_ops.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/allocator.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/c++allocator.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/ext/new_allocator.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/new \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/exception \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/atomic_lockfree_defines.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/memoryfwd.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_function.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/backward/binders.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/ext/alloc_traits.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_map.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_multimap.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/range_access.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/string \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stringfwd.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/char_traits.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/postypes.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/cwchar \ /usr/include/wchar.h /usr/include/stdio.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/lib/gcc/x86_64-redhat-linux/5.1.0/include/stdarg.h \ /usr/include/bits/wchar.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/lib/gcc/x86_64-redhat-linux/5.1.0/include/stddef.h \ /usr/include/xlocale.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/localefwd.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/c++locale.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/clocale \ /usr/include/locale.h /usr/include/bits/locale.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/iosfwd \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/cctype \ /usr/include/ctype.h /usr/include/bits/types.h \ /usr/include/bits/typesizes.h /usr/include/endian.h \ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/ostream_insert.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/cxxabi_forced.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/basic_string.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/ext/atomicity.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/gthr.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/gthr-default.h \ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ /usr/include/bits/sched.h /usr/include/bits/time.h \ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/atomic_word.h \ /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/basic_string.tcc \ /usr/include/stdlib.h /usr/include/bits/waitflags.h \ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ /usr/include/sys/select.h /usr/include/bits/select.h \ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ /usr/include/alloca.h argProcessor.hpp: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/map: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_tree.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_algobase.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/c++config.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: /usr/include/sys/cdefs.h: /usr/include/bits/wordsize.h: /usr/include/gnu/stubs.h: /usr/include/gnu/stubs-64.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/cpu_defines.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/functexcept.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/exception_defines.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/cpp_type_traits.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/ext/type_traits.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/ext/numeric_traits.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_pair.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/move.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/concept_check.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_iterator_base_types.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_iterator_base_funcs.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/debug/debug.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_iterator.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/ptr_traits.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/predefined_ops.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/allocator.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/c++allocator.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/ext/new_allocator.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/new: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/exception: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/atomic_lockfree_defines.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/memoryfwd.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_function.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/backward/binders.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/ext/alloc_traits.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_map.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stl_multimap.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/range_access.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/string: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/stringfwd.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/char_traits.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/postypes.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/cwchar: /usr/include/wchar.h: /usr/include/stdio.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/lib/gcc/x86_64-redhat-linux/5.1.0/include/stdarg.h: /usr/include/bits/wchar.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/lib/gcc/x86_64-redhat-linux/5.1.0/include/stddef.h: /usr/include/xlocale.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/localefwd.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/x86_64-redhat-linux/bits/c++locale.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/clocale: /usr/include/locale.h: /usr/include/bits/locale.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/iosfwd: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/cctype: /usr/include/ctype.h: /usr/include/bits/types.h: /usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: /usr/include/bits/byteswap.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/ostream_insert.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/cxxabi_forced.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/bits/basic_string.h: /broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.1.0/include/c++/5.1.0/ext/atomicity.h: 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using namespace std; static int VERBOSE_LEVEL = 0; int main(int argc, char* argv[]) { /* This program executes commands in Parallel using C++, the program is a wrapper designed for the orignal Trinity Program for seemless parallel OPENMP execution, Authors of this wrapper are MB Couger (mbcouger(AT Symbol)gmail.com, Matt Stowe mstowe(AT Symbol)okstate.edu*/ // code modified by bhaas for general cmd-line processing ArgProcessor args(argc, argv); bool shuffle_flag = false; int max_retries = 10; if (args.isArgSet("-help") || ! (args.isArgSet("-c") ) || ! (args.isArgSet("-CPU") ) ) { cerr << usage() << endl << endl; return(1); } if (args.isArgSet("-v")) { VERBOSE_LEVEL = 1; } else if (args.isArgSet("-vv")) { VERBOSE_LEVEL = 2; } if (args.isArgSet("-shuffle")) { shuffle_flag = true; } if (args.isArgSet("-max_retry")) { max_retries = args.getIntVal("-max_retry"); } string commands_file = args.getStringVal("-c"); int num_cpus = args.getIntVal("-CPU"); string failed_commands_filename = "FailedCommands"; if (args.isArgSet("-failed_cmds")) { failed_commands_filename = args.getStringVal("-failed_cmds"); } //declare variables start input stream ifstream in; // Create an input file stream. in.open(commands_file.c_str()); // Use it to read from a file named data.txt. if ( ! in ) { stringstream errstr; errstr << "Error, cannot open file : " << commands_file << endl; cerr << errstr.str(); exit(1); } // check to see if any commands had completed map previously_completed_commands; bool have_previously_completed_commands = false; ofstream successfully_completed_fh; { ifstream prev_completed_fh; stringstream completed_commands_filename_ss; completed_commands_filename_ss << commands_file << ".completed"; string completed_commands_filename = completed_commands_filename_ss.str(); prev_completed_fh.open(completed_commands_filename.c_str()); if (prev_completed_fh) { have_previously_completed_commands = true; string command_line; getline(prev_completed_fh, command_line); while(! prev_completed_fh.eof()) { previously_completed_commands[command_line] = true; getline(prev_completed_fh, command_line); } prev_completed_fh.close(); } successfully_completed_fh.open(completed_commands_filename.c_str(), ios_base::app); // open for append } long int NumberofCommands; NumberofCommands=0; vector commandsArray; string line; getline(in,line); int count_skip = 0; int max_report_skip = 10; while (! in.eof()) { if (have_previously_completed_commands && previously_completed_commands.find(line) != previously_completed_commands.end()) { // this command has been run before successfully, not running it again. if (VERBOSE_LEVEL and count_skip < max_report_skip) { cerr << "warning, command: " << line << " has successfully completed from a previous run. Skipping it here." << endl; count_skip++; if (count_skip >= max_report_skip) { cerr << "-reached max skip warning, turning off warnings for this." << endl; } } } else { NumberofCommands++; commandsArray.push_back(line); } getline(in,line); } if (VERBOSE_LEVEL) { cerr << "Number of Commands: " << NumberofCommands << endl; } //Parrell Execution of Individual Commands vector failedCommands; int num_failed_commands = 0; int num_succeeded_commands = 0; if (shuffle_flag) { random_shuffle(commandsArray.begin(), commandsArray.end()); } omp_set_dynamic(0); omp_set_num_threads(num_cpus); #pragma omp parallel for schedule (dynamic) for (long int i=0;i 0) { ss << ", failed(" << num_failed_commands << ")"; } int total_executed = num_succeeded_commands + num_failed_commands; float percent_done = (float)total_executed/NumberofCommands * 100; ss << " " << percent_done << "% completed. "; #pragma omp critical (standard_error) cerr << ss.str(); } } successfully_completed_fh.close(); //ErrorCheckingOut if (num_failed_commands != 0) { ofstream outdata(failed_commands_filename.c_str()); for (int t=0;t :filename containing list of bash-style commands to execute." << endl << "# -CPU :number_of_threads" << endl << "#" << endl << "# Optional:" << endl << "# -max_retry :number of times to retry a command if it fails. (default: 10)" << endl << "# -shuffle :randomly shuffles the command order. " << endl << "# -failed_cmds :filename to capture failed commands. default(\"FailedCommands\")" << endl << "# -v :simple progress monitoring." << endl << "# -vv :increased verbosity in progress monitoring." << endl << "#" << endl << "##########################################################" << endl << endl; ss << "Note: This process creates a file named based on your commands filename with a .completed extension." << endl << "This enables a resume functionality, where if rerun, only those commands not completed successfully will be reprocessed." << endl << endl; return(ss.str()); } ParaFly-0.1.0/src/argProcessor.cpp000077500000000000000000000016721315300572300170220ustar00rootroot00000000000000#include "argProcessor.hpp" #include // #include ArgProcessor::ArgProcessor(int argc, char* argv[]) { for (int i=1; i < argc; i++) { char* arg = argv[i]; string myArg (arg); if (arg[0] == '-') { argSet[myArg] = true; // see if next argument is another arg or value: if (i != argc-1) { // value: string nextArg (argv[i+1]); argVal[myArg] = nextArg; } } } } bool ArgProcessor::isArgSet(string arg) { map::const_iterator it; it = argSet.find(arg); if (it != argSet.end()) { return(true); } else { return(false); } } int ArgProcessor::getIntVal(string arg) { return(atoi(argVal[arg].c_str())); } long ArgProcessor::getLongVal(string arg) { return(atol(argVal[arg].c_str())); } float ArgProcessor::getFloatVal(string arg) { return(atof(argVal[arg].c_str())); } string ArgProcessor::getStringVal(string arg) { return(argVal[arg]); } ParaFly-0.1.0/src/argProcessor.hpp000077500000000000000000000006561315300572300170300ustar00rootroot00000000000000#ifndef __argProcessor__ #define __argProcessor__ #include #include using namespace std; class ArgProcessor { public: ArgProcessor(int argc, char* argv[]); bool isArgSet(string arg); int getIntVal(string arg); long getLongVal(string arg); float getFloatVal(string arg); string getStringVal(string arg); private: map argSet; map argVal; }; #endif ParaFly-0.1.0/stamp-h1000066400000000000000000000000271315300572300144210ustar00rootroot00000000000000timestamp for config.h ParaFly-0.1.0/test/000077500000000000000000000000001315300572300140245ustar00rootroot00000000000000ParaFly-0.1.0/test/Makefile000066400000000000000000000001371315300572300154650ustar00rootroot00000000000000test: ../bin/ParaFly -c cmds.txt -vv -CPU 2 clean: rm -f FailedCommands cmds.txt.completed ParaFly-0.1.0/test/cmds.txt000066400000000000000000000002531315300572300155130ustar00rootroot00000000000000./rand_exit.pl 1 ./rand_exit.pl 2 ./rand_exit.pl 3 ./rand_exit.pl 4 ./rand_exit.pl 5 ./rand_exit.pl 6 ./rand_exit.pl 7 ./rand_exit.pl 8 ./rand_exit.pl 9 ./rand_exit.pl 10 ParaFly-0.1.0/test/rand_exit.pl000077500000000000000000000001051315300572300163350ustar00rootroot00000000000000#!/usr/bin/env perl use strict; use warnings; exit(int(rand(3)));