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Fix boost runtime issue on Ubuntu16.04 with gcc 5.4 #92

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merged 8 commits into from
Aug 7, 2019

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shssf
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@shssf shssf commented Jul 15, 2019

  • boost::regex cause runtime symbol resolution issue.
  • several build time warnings resolved (unused variables, signed\unsigned comparison, etc.).

@shssf shssf requested a review from fschlimb July 15, 2019 18:38
@shssf shssf added the bug label Jul 15, 2019
@@ -309,14 +309,14 @@ static PyObject* csv_chunk_reader(std::istream * f, size_t fsz, bool is_parallel
std::vector<size_t> line_offset = count_lines(f, hpat_dist_get_node_portion(fsz, nranks, rank));
size_t no_lines = line_offset.size();
// get total number of lines using allreduce
size_t tot_no_lines(0);
int64_t tot_no_lines = 0;
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why?

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Code readability and consistence. I think this is more common way to initialize variables. From the compiler point of view, in this particular place, they are equal.

size_t byte_first_line = hpat_dist_exscan_i8(no_lines);
size_t byte_last_line = byte_first_line + no_lines;
int64_t byte_first_line = hpat_dist_exscan_i8(no_lines);
int64_t byte_last_line = byte_first_line + no_lines;
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why do change to signed?

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Because later it participated in comparison with signed input argument. In this case tne compiler show the warning.

@@ -377,8 +370,6 @@ void decode_utf8(const char *s, Py_ssize_t size, int* kind, int *is_ascii, int*
goto End;
}
errmsg = "invalid continuation byte";
startinpos = s - starts;
endinpos = startinpos + ch - 1;
break;
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How close is this code to the original CPython version?

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Not sure about CPython but these variables used nowhere.

@fschlimb
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Could you please describe the bug this is fixing? We have binaries using boost which seem to work. How can I reproduce the bug?

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shssf commented Jul 16, 2019

On Ubuntu 16.04 with default GCC 5.4 in newly installed Anaconda 3 I see following:

sshalnov@fxsatlin01:/localdisk/work/sshalnov/HPAT/hpat$ python ./setup.py test
running test
running egg_info
writing hpat.egg-info/PKG-INFO
writing dependency_links to hpat.egg-info/dependency_links.txt
writing requirements to hpat.egg-info/requires.txt
writing top-level names to hpat.egg-info/top_level.txt
reading manifest file 'hpat.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'hpat.egg-info/SOURCES.txt'
running build_ext
copying build/lib.linux-x86_64-3.7/hpat/hdist.cpython-37m-x86_64-linux-gnu.so -> hpat
copying build/lib.linux-x86_64-3.7/hpat/chiframes.cpython-37m-x86_64-linux-gnu.so -> hpat
copying build/lib.linux-x86_64-3.7/hpat/hdict_ext.cpython-37m-x86_64-linux-gnu.so -> hpat
copying build/lib.linux-x86_64-3.7/hpat/hset_ext.cpython-37m-x86_64-linux-gnu.so -> hpat
copying build/lib.linux-x86_64-3.7/hpat/hstr_ext.cpython-37m-x86_64-linux-gnu.so -> hpat
copying build/lib.linux-x86_64-3.7/hpat/quantile_alg.cpython-37m-x86_64-linux-gnu.so -> hpat
copying build/lib.linux-x86_64-3.7/hpat/hdatetime_ext.cpython-37m-x86_64-linux-gnu.so -> hpat
copying build/lib.linux-x86_64-3.7/hpat/hio.cpython-37m-x86_64-linux-gnu.so -> hpat
copying build/lib.linux-x86_64-3.7/hpat/parquet_cpp.cpython-37m-x86_64-linux-gnu.so -> hpat
hpat (unittest.loader._FailedTest) ... ERROR

======================================================================
ERROR: hpat (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: hpat
Traceback (most recent call last):
  File "/localdisk/work/sshalnov/anaconda3/lib/python3.7/unittest/loader.py", line 470, in _find_test_path
    package = self._get_module_from_name(name)
  File "/localdisk/work/sshalnov/anaconda3/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name
    __import__(name)
  File "/localdisk/work/sshalnov/HPAT/hpat/hpat/__init__.py", line 8, in <module>
    import hpat.dict_ext
  File "/localdisk/work/sshalnov/HPAT/hpat/hpat/dict_ext.py", line 12, in <module>
    from hpat.str_ext import string_type, gen_unicode_to_std_str, gen_std_str_to_unicode
  File "/localdisk/work/sshalnov/HPAT/hpat/hpat/str_ext.py", line 22, in <module>
    from . import hstr_ext
ImportError: /localdisk/work/sshalnov/HPAT/hpat/hpat/hstr_ext.cpython-37m-x86_64-linux-gnu.so: undefined symbol: _ZNK5boost16re_detail_10670031cpp_regex_traits_implementationIcE9transformEPKcS4_


----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)
Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
error: Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
sshalnov@fxsatlin01:/localdisk/work/sshalnov/HPAT/hpat$

This symbol boost::re_detail_106700::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const came from Boost library.

@shssf shssf merged commit 732a93a into master Aug 7, 2019
Vyacheslav-Smirnov pushed a commit to Vyacheslav-Smirnov/sdc that referenced this pull request Aug 7, 2019
Vyacheslav-Smirnov added a commit to Vyacheslav-Smirnov/sdc that referenced this pull request Aug 7, 2019
Vyacheslav-Smirnov added a commit to Vyacheslav-Smirnov/sdc that referenced this pull request Aug 7, 2019
shssf pushed a commit that referenced this pull request Aug 8, 2019
* Remove spark dependency (#102)

Remove spark dependency from HPA; use pre-generated sdf_dt.pq

* explicitly adding data-file (#104)

* HPAT Build: Code style check for C and Python sources (#103)

* HPAT Build: Code style check for C and Python sources

* PR103. Comments partially addressed

* Code style change part 1 (#106)

* Style check config fo pystyle (#105)

* Fix for pandas.merge wrong overload handling of 'on' args (#99)

Problem description: merge_overload and merge_asof_overload functions
use 'on' argument value to compute 'left_on' and 'right_on' arguments
in a way that breaks type stability, causing compilation failure
when 'on' is assigned a StringLiteral value.

Error:
  File "../hpat/hiframes/dataframe_pass.py", line 202, in _run_assign
    return self._run_call(assign, lhs, rhs)
  File "../hpat/hiframes/dataframe_pass.py", line 522, in _run_call
    return self._run_call_join(assign, lhs, rhs)
  File "../hpat/hiframes/dataframe_pass.py", line 1488, in
_run_call_join
    left_on = self._get_const_or_list(left_on_var)
  File "../hpat/hiframes/dataframe_pass.py", line 2135, in
_get_const_or_list
    raise ValueError(err_msg)
ValueError: Failed in hpat mode pipeline (step: typed dataframe pass)
None

Following tests should be fixed with this commit:
    test_join_cat1 (hpat.tests.test_join.TestJoin)
    test_join_cat2 (hpat.tests.test_join.TestJoin)
    test_join_cat_parallel1 (hpat.tests.test_join.TestJoin)
    test_join_datetime_seq1 (hpat.tests.test_join.TestJoin)
    test_join_left_seq1 (hpat.tests.test_join.TestJoin)
    test_join_left_seq2 (hpat.tests.test_join.TestJoin)
    test_join_outer_seq1 (hpat.tests.test_join.TestJoin)
    test_join_right_seq1 (hpat.tests.test_join.TestJoin)
    test_merge_asof_seq1 (hpat.tests.test_join.TestJoin)

* [STL] PEP8 code style for 'test_strings.py', 'test_utils.py', 'test_series.py' (#97)

* pep8 style for 'test_strings.py'; flake8 check successful

* pep8 style for 'test_utils.py'

* pep8 style for 'test_series.py'; more readable

* fixed 'test_string_series'

* removed extra white spaces

* deleted mention of flake8

* trigger build

* Code style change part 2 (#107)

* code_style_change_part_2

* Add more check in style configuration (#108)

* code_style_part_3 (#109)

* Fix boost runtime issue on Ubuntu16.04 with gcc 5.4 (#92)

* Code style change part 4 (#110)

* Revert "Code style change part 4 (#110)"

This reverts commit dfc54ee.

* Revert "Fix boost runtime issue on Ubuntu16.04 with gcc 5.4 (#92)"

This reverts commit 231a76c.

* Revert "code_style_part_3 (#109)"

This reverts commit 4070ce3.

* Revert "Add more check in style configuration (#108)"

This reverts commit abf5bd0.

* Revert "Code style change part 2 (#107)"

This reverts commit 9076493.

* Revert "[STL] PEP8 code style for 'test_strings.py', 'test_utils.py', 'test_series.py' (#97)"

This reverts commit 8641f7a.

* Revert "Fix for pandas.merge wrong overload handling of 'on' args (#99)"

This reverts commit a2a8ee5.

* Revert "Style check config fo pystyle (#105)"

This reverts commit 551c0e3.

* Revert "Code style change part 1 (#106)"

This reverts commit 6dae0b3.

* Revert "HPAT Build: Code style check for C and Python sources (#103)"

This reverts commit 1a30e4f.

* Revert "explicitly adding data-file (#104)"

This reverts commit 34a2260.

* Revert "Remove spark dependency (#102)"

This reverts commit 9e77fde.

* Unskip passing dataframe tests

Actually, following tests in test_dataframe.py are pass and can be unskipped:
test_create1
test_len1
test_column_getitem1
test_df_apply
test_df_apply_branch
test_df_describe
test_count1
test_append1

At the same time, test_sort_parallel and test_sort_parallel_single_col
has some problems with __pycache__:
 - They are passed if execute the suite with -B
 - They are passed if execute them separate
 - They and failed when some tests above are unskipped.
So, decide to skip them.
@shssf shssf deleted the compilation_varning_ubuntu16 branch August 10, 2019 13:52
shssf pushed a commit that referenced this pull request Aug 13, 2019
* Remove spark dependency (#102)

Remove spark dependency from HPA; use pre-generated sdf_dt.pq

* explicitly adding data-file (#104)

* HPAT Build: Code style check for C and Python sources (#103)

* HPAT Build: Code style check for C and Python sources

* PR103. Comments partially addressed

* Code style change part 1 (#106)

* Style check config fo pystyle (#105)

* Fix for pandas.merge wrong overload handling of 'on' args (#99)

Problem description: merge_overload and merge_asof_overload functions
use 'on' argument value to compute 'left_on' and 'right_on' arguments
in a way that breaks type stability, causing compilation failure
when 'on' is assigned a StringLiteral value.

Error:
  File "../hpat/hiframes/dataframe_pass.py", line 202, in _run_assign
    return self._run_call(assign, lhs, rhs)
  File "../hpat/hiframes/dataframe_pass.py", line 522, in _run_call
    return self._run_call_join(assign, lhs, rhs)
  File "../hpat/hiframes/dataframe_pass.py", line 1488, in
_run_call_join
    left_on = self._get_const_or_list(left_on_var)
  File "../hpat/hiframes/dataframe_pass.py", line 2135, in
_get_const_or_list
    raise ValueError(err_msg)
ValueError: Failed in hpat mode pipeline (step: typed dataframe pass)
None

Following tests should be fixed with this commit:
    test_join_cat1 (hpat.tests.test_join.TestJoin)
    test_join_cat2 (hpat.tests.test_join.TestJoin)
    test_join_cat_parallel1 (hpat.tests.test_join.TestJoin)
    test_join_datetime_seq1 (hpat.tests.test_join.TestJoin)
    test_join_left_seq1 (hpat.tests.test_join.TestJoin)
    test_join_left_seq2 (hpat.tests.test_join.TestJoin)
    test_join_outer_seq1 (hpat.tests.test_join.TestJoin)
    test_join_right_seq1 (hpat.tests.test_join.TestJoin)
    test_merge_asof_seq1 (hpat.tests.test_join.TestJoin)

* [STL] PEP8 code style for 'test_strings.py', 'test_utils.py', 'test_series.py' (#97)

* pep8 style for 'test_strings.py'; flake8 check successful

* pep8 style for 'test_utils.py'

* pep8 style for 'test_series.py'; more readable

* fixed 'test_string_series'

* removed extra white spaces

* deleted mention of flake8

* trigger build

* Code style change part 2 (#107)

* code_style_change_part_2

* Add more check in style configuration (#108)

* code_style_part_3 (#109)

* Fix boost runtime issue on Ubuntu16.04 with gcc 5.4 (#92)

* Code style change part 4 (#110)

* Cahnge tests execution

Actually test suite should be executed via hpat.runtests:
python -u -m hpat.runtests -v
This resolve the issue with doulbe test suite execution
which occurs due to the "python -u -m unittest -v" command
import all files in tree including runtests.py and runtests.py
triggers 1-st suite execution. Then unittest triggers 2-d.

Add decorator to execute some tests (mostly parallel)
2 or more times (depending on existance of REPEAT_TEST_NUMBER
environment variable)
This should highlight issues like the test fails if executed twice
because is corrupts memory during first execution
(like test_series_head_index_parallel1)

Skip test_series_head_index_parallel1 because it triggers memory
corruption. This should be fixed.

* Revert "Code style change part 4 (#110)"

This reverts commit dfc54ee.

* Revert "Fix boost runtime issue on Ubuntu16.04 with gcc 5.4 (#92)"

This reverts commit 231a76c.

* Revert "code_style_part_3 (#109)"

This reverts commit 4070ce3.

* Revert "Add more check in style configuration (#108)"

This reverts commit abf5bd0.

* Revert "Code style change part 2 (#107)"

This reverts commit 9076493.

* Revert "[STL] PEP8 code style for 'test_strings.py', 'test_utils.py', 'test_series.py' (#97)"

This reverts commit 8641f7a.

* Revert "Fix for pandas.merge wrong overload handling of 'on' args (#99)"

This reverts commit a2a8ee5.

* Revert "Style check config fo pystyle (#105)"

This reverts commit 551c0e3.

* Revert "Code style change part 1 (#106)"

This reverts commit 6dae0b3.

* Revert "HPAT Build: Code style check for C and Python sources (#103)"

This reverts commit 1a30e4f.

* Revert "explicitly adding data-file (#104)"

This reverts commit 34a2260.

* Revert "Remove spark dependency (#102)"

This reverts commit 9e77fde.

* Wrap functions to be executed twice in runtests.py

* Update runtests.py

Execute every test specified times, which is set via
the REPEAT_TEST_NUMBER environment variable.

Skip test_series_list_str_unbox1 because is fails on the second
launch with Segmentation fault

* Apply comments from review

Rename REPEAT_TEST_NUMBER to HPAT_REPEAT_TEST_NUMBER
Use os.getenv to get value for HPAT_REPEAT_TEST_NUMBER
kozlov-alexey pushed a commit to kozlov-alexey/sdc that referenced this pull request Oct 4, 2019
kozlov-alexey pushed a commit to kozlov-alexey/sdc that referenced this pull request Oct 4, 2019
* Remove spark dependency (IntelPython#102)

Remove spark dependency from HPA; use pre-generated sdf_dt.pq

* explicitly adding data-file (IntelPython#104)

* HPAT Build: Code style check for C and Python sources (IntelPython#103)

* HPAT Build: Code style check for C and Python sources

* PR103. Comments partially addressed

* Code style change part 1 (IntelPython#106)

* Style check config fo pystyle (IntelPython#105)

* Fix for pandas.merge wrong overload handling of 'on' args (IntelPython#99)

Problem description: merge_overload and merge_asof_overload functions
use 'on' argument value to compute 'left_on' and 'right_on' arguments
in a way that breaks type stability, causing compilation failure
when 'on' is assigned a StringLiteral value.

Error:
  File "../hpat/hiframes/dataframe_pass.py", line 202, in _run_assign
    return self._run_call(assign, lhs, rhs)
  File "../hpat/hiframes/dataframe_pass.py", line 522, in _run_call
    return self._run_call_join(assign, lhs, rhs)
  File "../hpat/hiframes/dataframe_pass.py", line 1488, in
_run_call_join
    left_on = self._get_const_or_list(left_on_var)
  File "../hpat/hiframes/dataframe_pass.py", line 2135, in
_get_const_or_list
    raise ValueError(err_msg)
ValueError: Failed in hpat mode pipeline (step: typed dataframe pass)
None

Following tests should be fixed with this commit:
    test_join_cat1 (hpat.tests.test_join.TestJoin)
    test_join_cat2 (hpat.tests.test_join.TestJoin)
    test_join_cat_parallel1 (hpat.tests.test_join.TestJoin)
    test_join_datetime_seq1 (hpat.tests.test_join.TestJoin)
    test_join_left_seq1 (hpat.tests.test_join.TestJoin)
    test_join_left_seq2 (hpat.tests.test_join.TestJoin)
    test_join_outer_seq1 (hpat.tests.test_join.TestJoin)
    test_join_right_seq1 (hpat.tests.test_join.TestJoin)
    test_merge_asof_seq1 (hpat.tests.test_join.TestJoin)

* [STL] PEP8 code style for 'test_strings.py', 'test_utils.py', 'test_series.py' (IntelPython#97)

* pep8 style for 'test_strings.py'; flake8 check successful

* pep8 style for 'test_utils.py'

* pep8 style for 'test_series.py'; more readable

* fixed 'test_string_series'

* removed extra white spaces

* deleted mention of flake8

* trigger build

* Code style change part 2 (IntelPython#107)

* code_style_change_part_2

* Add more check in style configuration (IntelPython#108)

* code_style_part_3 (IntelPython#109)

* Fix boost runtime issue on Ubuntu16.04 with gcc 5.4 (IntelPython#92)

* Code style change part 4 (IntelPython#110)

* Revert "Code style change part 4 (IntelPython#110)"

This reverts commit dfc54ee.

* Revert "Fix boost runtime issue on Ubuntu16.04 with gcc 5.4 (IntelPython#92)"

This reverts commit 231a76c.

* Revert "code_style_part_3 (IntelPython#109)"

This reverts commit 4070ce3.

* Revert "Add more check in style configuration (IntelPython#108)"

This reverts commit abf5bd0.

* Revert "Code style change part 2 (IntelPython#107)"

This reverts commit 9076493.

* Revert "[STL] PEP8 code style for 'test_strings.py', 'test_utils.py', 'test_series.py' (IntelPython#97)"

This reverts commit 8641f7a.

* Revert "Fix for pandas.merge wrong overload handling of 'on' args (IntelPython#99)"

This reverts commit a2a8ee5.

* Revert "Style check config fo pystyle (IntelPython#105)"

This reverts commit 551c0e3.

* Revert "Code style change part 1 (IntelPython#106)"

This reverts commit 6dae0b3.

* Revert "HPAT Build: Code style check for C and Python sources (IntelPython#103)"

This reverts commit 1a30e4f.

* Revert "explicitly adding data-file (IntelPython#104)"

This reverts commit 34a2260.

* Revert "Remove spark dependency (IntelPython#102)"

This reverts commit 9e77fde.

* Unskip passing dataframe tests

Actually, following tests in test_dataframe.py are pass and can be unskipped:
test_create1
test_len1
test_column_getitem1
test_df_apply
test_df_apply_branch
test_df_describe
test_count1
test_append1

At the same time, test_sort_parallel and test_sort_parallel_single_col
has some problems with __pycache__:
 - They are passed if execute the suite with -B
 - They are passed if execute them separate
 - They and failed when some tests above are unskipped.
So, decide to skip them.
kozlov-alexey pushed a commit to kozlov-alexey/sdc that referenced this pull request Oct 4, 2019
* Remove spark dependency (IntelPython#102)

Remove spark dependency from HPA; use pre-generated sdf_dt.pq

* explicitly adding data-file (IntelPython#104)

* HPAT Build: Code style check for C and Python sources (IntelPython#103)

* HPAT Build: Code style check for C and Python sources

* PR103. Comments partially addressed

* Code style change part 1 (IntelPython#106)

* Style check config fo pystyle (IntelPython#105)

* Fix for pandas.merge wrong overload handling of 'on' args (IntelPython#99)

Problem description: merge_overload and merge_asof_overload functions
use 'on' argument value to compute 'left_on' and 'right_on' arguments
in a way that breaks type stability, causing compilation failure
when 'on' is assigned a StringLiteral value.

Error:
  File "../hpat/hiframes/dataframe_pass.py", line 202, in _run_assign
    return self._run_call(assign, lhs, rhs)
  File "../hpat/hiframes/dataframe_pass.py", line 522, in _run_call
    return self._run_call_join(assign, lhs, rhs)
  File "../hpat/hiframes/dataframe_pass.py", line 1488, in
_run_call_join
    left_on = self._get_const_or_list(left_on_var)
  File "../hpat/hiframes/dataframe_pass.py", line 2135, in
_get_const_or_list
    raise ValueError(err_msg)
ValueError: Failed in hpat mode pipeline (step: typed dataframe pass)
None

Following tests should be fixed with this commit:
    test_join_cat1 (hpat.tests.test_join.TestJoin)
    test_join_cat2 (hpat.tests.test_join.TestJoin)
    test_join_cat_parallel1 (hpat.tests.test_join.TestJoin)
    test_join_datetime_seq1 (hpat.tests.test_join.TestJoin)
    test_join_left_seq1 (hpat.tests.test_join.TestJoin)
    test_join_left_seq2 (hpat.tests.test_join.TestJoin)
    test_join_outer_seq1 (hpat.tests.test_join.TestJoin)
    test_join_right_seq1 (hpat.tests.test_join.TestJoin)
    test_merge_asof_seq1 (hpat.tests.test_join.TestJoin)

* [STL] PEP8 code style for 'test_strings.py', 'test_utils.py', 'test_series.py' (IntelPython#97)

* pep8 style for 'test_strings.py'; flake8 check successful

* pep8 style for 'test_utils.py'

* pep8 style for 'test_series.py'; more readable

* fixed 'test_string_series'

* removed extra white spaces

* deleted mention of flake8

* trigger build

* Code style change part 2 (IntelPython#107)

* code_style_change_part_2

* Add more check in style configuration (IntelPython#108)

* code_style_part_3 (IntelPython#109)

* Fix boost runtime issue on Ubuntu16.04 with gcc 5.4 (IntelPython#92)

* Code style change part 4 (IntelPython#110)

* Cahnge tests execution

Actually test suite should be executed via hpat.runtests:
python -u -m hpat.runtests -v
This resolve the issue with doulbe test suite execution
which occurs due to the "python -u -m unittest -v" command
import all files in tree including runtests.py and runtests.py
triggers 1-st suite execution. Then unittest triggers 2-d.

Add decorator to execute some tests (mostly parallel)
2 or more times (depending on existance of REPEAT_TEST_NUMBER
environment variable)
This should highlight issues like the test fails if executed twice
because is corrupts memory during first execution
(like test_series_head_index_parallel1)

Skip test_series_head_index_parallel1 because it triggers memory
corruption. This should be fixed.

* Revert "Code style change part 4 (IntelPython#110)"

This reverts commit dfc54ee.

* Revert "Fix boost runtime issue on Ubuntu16.04 with gcc 5.4 (IntelPython#92)"

This reverts commit 231a76c.

* Revert "code_style_part_3 (IntelPython#109)"

This reverts commit 4070ce3.

* Revert "Add more check in style configuration (IntelPython#108)"

This reverts commit abf5bd0.

* Revert "Code style change part 2 (IntelPython#107)"

This reverts commit 9076493.

* Revert "[STL] PEP8 code style for 'test_strings.py', 'test_utils.py', 'test_series.py' (IntelPython#97)"

This reverts commit 8641f7a.

* Revert "Fix for pandas.merge wrong overload handling of 'on' args (IntelPython#99)"

This reverts commit a2a8ee5.

* Revert "Style check config fo pystyle (IntelPython#105)"

This reverts commit 551c0e3.

* Revert "Code style change part 1 (IntelPython#106)"

This reverts commit 6dae0b3.

* Revert "HPAT Build: Code style check for C and Python sources (IntelPython#103)"

This reverts commit 1a30e4f.

* Revert "explicitly adding data-file (IntelPython#104)"

This reverts commit 34a2260.

* Revert "Remove spark dependency (IntelPython#102)"

This reverts commit 9e77fde.

* Wrap functions to be executed twice in runtests.py

* Update runtests.py

Execute every test specified times, which is set via
the REPEAT_TEST_NUMBER environment variable.

Skip test_series_list_str_unbox1 because is fails on the second
launch with Segmentation fault

* Apply comments from review

Rename REPEAT_TEST_NUMBER to HPAT_REPEAT_TEST_NUMBER
Use os.getenv to get value for HPAT_REPEAT_TEST_NUMBER
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