Merge pull request #25 from gjbex/development

Bug fixes

Makefile.am

@@ -1 +1 @@
-SUBDIRS = bin conf lib reduce
+SUBDIRS = bin conf lib reduce tmpls

Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.15 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2014 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -131,7 +131,7 @@ am__recursive_targets = \
   $(RECURSIVE_CLEAN_TARGETS) \
   $(am__extra_recursive_targets)
 AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
-	cscope distdir dist dist-all distcheck
+	cscope distdir distdir-am dist dist-all distcheck
 am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
 # Read a list of newline-separated strings from the standard input,
 # and print each of them once, without duplicates.  Input order is
@@ -261,7 +261,6 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
-runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
@@ -270,7 +269,7 @@ target_alias = @target_alias@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-SUBDIRS = bin conf lib reduce
+SUBDIRS = bin conf lib reduce tmpls
 all: all-recursive
 
 .SUFFIXES:
@@ -295,8 +294,8 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	    echo ' $(SHELL) ./config.status'; \
 	    $(SHELL) ./config.status;; \
 	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__maybe_remake_depfiles)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__maybe_remake_depfiles);; \
 	esac;
 
 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -414,7 +413,10 @@ distclean-tags:
 	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
 	-rm -f cscope.out cscope.in.out cscope.po.out cscope.files
 
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+	$(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
 	$(am__remove_distdir)
 	test -d "$(distdir)" || mkdir "$(distdir)"
 	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
@@ -479,7 +481,7 @@ distdir: $(DISTFILES)
 	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
 	|| chmod -R a+r "$(distdir)"
 dist-gzip: distdir
-	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
+	tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz
 	$(am__post_remove_distdir)
 
 dist-bzip2: distdir
@@ -505,7 +507,7 @@ dist-shar: distdir
 	@echo WARNING: "Support for shar distribution archives is" \
 	               "deprecated." >&2
 	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
-	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
+	shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz
 	$(am__post_remove_distdir)
 
 dist-zip: distdir
@@ -523,7 +525,7 @@ dist dist-all:
 distcheck: dist
 	case '$(DIST_ARCHIVES)' in \
 	*.tar.gz*) \
-	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
+	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\
 	*.tar.bz2*) \
 	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
 	*.tar.lz*) \
@@ -533,7 +535,7 @@ distcheck: dist
 	*.tar.Z*) \
 	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
 	*.shar.gz*) \
-	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
+	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
 	esac

README.md

@@ -4,7 +4,7 @@
 
 `atools` is intended to facilitate working with job arrays, a feature
 supported by a resource manager such as PBS torque, or a scheduler such
-as Moab (Adaptive Computing) and SUN Grid Engine.
+as Moab (Adaptive Computing), SUN Grid Engine and Slurm workload manager.
 
 Although the job array concept is quite versatile, typically some
 tinkering is required for bookkeeping purposes.  `atools` aims to
@@ -45,8 +45,8 @@ cost by a large factor compared to using the
 `atools` requires at least Python 2.7.x, but only uses the standard
 library.
 
-Currently, PBS torque, Adaptive Computing Moab, and SUN Grid Engine are
-supported.
+Currently, PBS torque, Adaptive Computing Moab, SUN Grid Engine and
+Slurm workload manager are supported.
 
 
 ## Installing
@@ -69,3 +69,6 @@ In no particular order...
   * Bug report
 * Ward Poelmans, Vrije Universiteit Brussel
   * Fixes to the install process
+* Kurt Lust, Antwerp University
+  * Several bug reports and fixes
+  * Added Slurm compatibility

aclocal.m4

@@ -1,6 +1,6 @@
-# generated automatically by aclocal 1.15 -*- Autoconf -*-
+# generated automatically by aclocal 1.16.1 -*- Autoconf -*-
 
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.
 
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -20,7 +20,7 @@ You have another version of autoconf.  It may work, but is not guaranteed to.
 If you have problems, you may need to regenerate the build system entirely.
 To do so, use the procedure documented by the package, typically 'autoreconf'.])])
 
-# Copyright (C) 2002-2014 Free Software Foundation, Inc.
+# Copyright (C) 2002-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -32,10 +32,10 @@ To do so, use the procedure documented by the package, typically 'autoreconf'.])
 # generated from the m4 files accompanying Automake X.Y.
 # (This private macro should not be called outside this file.)
 AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.15'
+[am__api_version='1.16'
 dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
 dnl require some minimum version.  Point them to the right macro.
-m4_if([$1], [1.15], [],
+m4_if([$1], [1.16.1], [],
       [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
 ])
 
@@ -51,14 +51,14 @@ m4_define([_AM_AUTOCONF_VERSION], [])
 # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
 # This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
 AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.15])dnl
+[AM_AUTOMAKE_VERSION([1.16.1])dnl
 m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
 
 # AM_AUX_DIR_EXPAND                                         -*- Autoconf -*-
 
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -110,7 +110,7 @@ am_aux_dir=`cd "$ac_aux_dir" && pwd`
 
 # Do all the work for Automake.                             -*- Autoconf -*-
 
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -197,8 +197,8 @@ AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
 AC_REQUIRE([AC_PROG_MKDIR_P])dnl
 # For better backward compatibility.  To be removed once Automake 1.9.x
 # dies out for good.  For more background, see:
-# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
-# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
+# <https://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
+# <https://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
 AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
 # We need awk for the "check" target (and possibly the TAP driver).  The
 # system "awk" is bad on some platforms.
@@ -265,7 +265,7 @@ END
 Aborting the configuration process, to ensure you take notice of the issue.
 
 You can download and install GNU coreutils to get an 'rm' implementation
-that behaves properly: <http://www.gnu.org/software/coreutils/>.
+that behaves properly: <https://www.gnu.org/software/coreutils/>.
 
 If you want to complete the configuration process using your problematic
 'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
@@ -307,7 +307,7 @@ for _am_header in $config_headers :; do
 done
 echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
 
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -328,7 +328,7 @@ if test x"${install_sh+set}" != xset; then
 fi
 AC_SUBST([install_sh])])
 
-# Copyright (C) 2003-2014 Free Software Foundation, Inc.
+# Copyright (C) 2003-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -349,7 +349,7 @@ AC_SUBST([am__leading_dot])])
 
 # Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-
 
-# Copyright (C) 1997-2014 Free Software Foundation, Inc.
+# Copyright (C) 1997-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -388,7 +388,7 @@ fi
 
 # Helper functions for option handling.                     -*- Autoconf -*-
 
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -417,7 +417,7 @@ AC_DEFUN([_AM_SET_OPTIONS],
 AC_DEFUN([_AM_IF_OPTION],
 [m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
 
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -436,7 +436,7 @@ AC_DEFUN([AM_RUN_LOG],
 
 # Check to make sure that the build environment is sane.    -*- Autoconf -*-
 
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -517,7 +517,7 @@ AC_CONFIG_COMMANDS_PRE(
 rm -f conftest.file
 ])
 
-# Copyright (C) 2009-2014 Free Software Foundation, Inc.
+# Copyright (C) 2009-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -577,7 +577,7 @@ AC_SUBST([AM_BACKSLASH])dnl
 _AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
 ])
 
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -605,7 +605,7 @@ fi
 INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
 AC_SUBST([INSTALL_STRIP_PROGRAM])])
 
-# Copyright (C) 2006-2014 Free Software Foundation, Inc.
+# Copyright (C) 2006-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -624,7 +624,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
 
 # Check how to create a tarball.                            -*- Autoconf -*-
 
-# Copyright (C) 2004-2014 Free Software Foundation, Inc.
+# Copyright (C) 2004-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,

autogen.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+autoreconf --install

bin/Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.15 from Makefile.am.
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2014 Free Software Foundation, Inc.
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -212,7 +212,6 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
-runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
@@ -242,8 +241,8 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	  *config.status*) \
 	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
 	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
 	esac;
 
 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -296,7 +295,10 @@ ctags CTAGS:
 cscope cscopelist:
 
 
-distdir: $(DISTFILES)
+distdir: $(BUILT_SOURCES)
+	$(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
 	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
 	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
 	list='$(DISTFILES)'; \

bin/acreate

@@ -1,4 +1,4 @@
-#!/bin/bash -l
+#!/usr/bin/env bash
 #
 # Copyright (C) 2013 Geert Jan Bex <[email protected]>
 # 

bin/aenv

@@ -1,4 +1,4 @@
-#!/bin/bash -l
+#!/usr/bin/env bash
 #
 # Copyright (C) 2013 Geert Jan Bex <[email protected]>
 # 

bin/aload

@@ -1,4 +1,4 @@
-#!/bin/bash -l
+#!/usr/bin/env bash
 #
 # Copyright (C) 2013 Geert Jan Bex <[email protected]>
 # 

bin/alog

@@ -1,4 +1,4 @@
-#!/bin/bash -l
+#!/usr/bin/env bash
 #
 # Copyright (C) 2013 Geert Jan Bex <[email protected]>
 # 

bin/arange

@@ -1,4 +1,4 @@
-#!/bin/bash -l
+#!/usr/bin/env bash
 #
 # Copyright (C) 2013 Geert Jan Bex <[email protected]>
 # 

bin/areduce

@@ -1,4 +1,4 @@
-#!/bin/bash -l
+#!/usr/bin/env bash
 #
 # Copyright (C) 2013 Geert Jan Bex <[email protected]>
 #