Initial support for specifying stdin file in execopts
Using execopts stdin file for knucleotide
Using execopts stdin file for reverse-complement
Merge branch 'master' into stdin-in-execopts
Produce an error if a .stdin file exists and one is specified in execopts
Adding lustre
Merge remote-tracking branch 'origin' into lustre
moving lustre support to sys.c
Merge branch 'master' into lustre
Merging ChapelRangeBase.chpl into ChapelRange.chpl
adding -Qunused for lustre
Comment changes following Tom's review, plus removing two lines of useless code.
Merged chapel-lang/master
One more test adjustment, unrelated to Tom's review.
Merge pull request #90 from vasslitvinov/mergeChapelRangeBase

Merged ChapelRangeBase.chpl into ChapelRange.chpl.

[reviewed by Tom]

ChapelRangeBase.chpl was split out from ChapelRange.chpl (SVN r18549)
when ambiguous alignment was introduced, via range._aligned.

As part of the split, the fields _low, _high, _stride, _alignment,
plus a lot of the code to handle them, were moved to the record 'rangeBase'
and to the file ChapelRangeBase.chpl.
The record 'range', instead of these four fields directly, got a single
field _base that was a rangeBase.

Given our experiences with this arrangement since then, we would like
to revert it. We expect that having _base's fields directly in 'range'
would simplify the generated code. Also for a given functionality on
'range', we expect it to be easier to examine/maintain when it is
in a single function instead of being split into two.

IMPLEMENTATION STRATEGY

Primarily I inlined by hand each 'rangeBase' function into the
corresponding 'range' function. Some helper functions moved
from ChapelRangeBase.chpl to ChapelRange.chpl verbatim.

While there, I simplified some things where it looked easy enough.

-----------------------------------------------------------------------------
DETAILED NOTES

<pre>

* Simplified interior(), exterior() by merging the stridable and
  unstridable cases.

  For that, I introduced _effAlmt(), which is admittedly not very elegant.

* Fixed a bug in exterior().

* In general, paren-less member functions cannot be called without
  specifying the receiver, i.e. cannot omit the implicit "this.".
  So I made my new function paren-ful:
    _effAlmt

  and added explicit "this." for the following existing functions:
    first
    length

* Simplified this function:

    proc rangeBase.translate(i: integral)
    {
      if _isSignedType(i.type) then
        return this + i:idxType;
      else if i >= 0 then return this + i:idxType;
      else return this - abs(i):idxType;
    }

  down to the seemingly equivalent:

    return this + i:idxType;

* Merged the two separate ==(rangeBase*2) functions
  (one was for bounded ranges and the other was "else")
  into a single ==(range*2), separating them by "if isBoundedRange(r1)".

* Removed the range constructor that took rangeBase as argument,
  and a couple of other rangeBase functions that are now unused.

* In former chpl__count(), now chpl_count_help(),
  when the degenerate range is returned,
  I changed _alignment from 1 to 0 and _aligned from r._aligned with false.

  As a result, a couple of empty ranges now print without "align 1" in:

    types/range/hilde/count.chpl

* Some library and test code references range fields directly.
  I removed _base there:

    modules/dists/BlockDist.chpl
    modules/dists/dims/BlockCycDim.chpl
    test/arrays/vass/slices-with-negative-strides-1.chpl
    test/release/examples/benchmarks/miniMD/helpers/StencilDist.chpl

* Removed this test (approved by Sung):

    test/types/records/sungeun/chapelTypes/record_rangeBase.chpl

  It would break because it relies on 'rangeBase' from the modules,
  which is no longer there.

  A similiar test that uses 'range' instead of 'rangeBase',
  still exists and passes:

    (unchanged) test/types/records/sungeun/chapelTypes/record_range.chpl

* ChapelRangeBase is no longer mentioned in:

    test/modules/sungeun/init/printModuleInitOrder.good

* Tom notes that the following functions are pretty long
  and warrant refactoring:

    range.this
    chpl_count_help
    range.these (leader)
    range.these (follower)

  They were already worth refactoring prior to this change,
  and are more so now. However I am leaving refactoring as future work.

* There is one fewer instantiation of _unknown in the test
  explainInstantiation.chpl. I am assuming that it is an artifact of
  how --explain-instantiation works and not an issue with my changes:

    test/classes/hilde/explainInstantiation.good
Update prediff-for-aprun-with-moab to filter more generally.

Removes absolute filepath and line number from grep filter. This came about when we moved testing from one system to another.
minor cleanup of glob iterator
Using execopts stdin for regex-dna
Merge pull request #97 from tzakian/parallel-glob

Minor cleanup of glob iterator
Merge pull request #98 from benharsh/stdin-in-execopts

This patch modifies sub_test to support specifying the stdin file inside an *execopts file.

Three shootout benchmarks (k-nucleotide, regex-dna, and reverse-complement) use the output of the fasta benchmark as input.

The size of the input files we need for performance testing is far too large to keep in the repository (50MB to 250MB). A later patch will support the generation and cleanup of these files during testing.

However, once we have these generated files, we would still need to create .stdin files so our test scripts would use them as standard input. Making copies of these files would take up a lot of space, and using links is unattractive. Both might be difficult to clean up.

The solution here is to allow for the stdin file to be specified inside an *execopts file. If the second-to-last argument is '<', then this patch will attempt to use the last argument as the stdin file.

Another benefit of this change is that we can have just one correctness input file per shootout, instead of one per .chpl test.

This change has passed paratest.

Reviewed by lydia-duncan