{bio}[foss/2016a] RepastHPC 2.2.0 by mboisson · Pull Request #4395 · easybuilders/easybuild-easyconfigs

mboisson · 2017-03-24T19:30:14Z

Added a recipe for the RepastHPC package.

boegel

minor style remarks

boegel · 2017-03-27T17:51:47Z

+
+homepage = 'https://repast.github.io/'
+description = """The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years:
+Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers."""


@mboisson Lines are too line, please wrap to lines with <= 120 chars.

boegel · 2017-03-27T17:52:07Z

+source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%s' % version]
+
+dependencies = [
+    ('netCDF-C++','4.2'),


style nitpicking: space after ,

boegel · 2017-03-27T17:52:40Z

+toolchainopts = {'usempi': True}
+
+sources = ["repast_hpc-%s.tgz" % version]
+source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%s' % version]


please use %(version)s:

sources = ["repast_hpc-%(version)s.tgz"] source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%(version)s']

boegel · 2017-03-27T17:53:39Z

+configopts = '--with-boost=$EBROOTBOOST --with-netcdf=$EBROOTNETCDFMINCPLUSPLUS'
+
+sanity_check_paths = {
+    'files': ['lib/librepast_hpc-%s.so' % version, 'lib/librelogo-%s.so' % version],


please use %(version)s, and avoid hardcoding .so, use SHLIB_EXT constant:

'files': ['lib/librepast_hpc-%%(version)s.%s' % SHLIB_EXT, 'lib/librelogo-%%(version)s.%s' % SHLIB_EXT],

boegel · 2017-03-27T17:54:03Z

+
+sanity_check_paths = {
+    'files': ['lib/librepast_hpc-%s.so' % version, 'lib/librelogo-%s.so' % version],
+    'dirs': ['include','lib','bin/zombie', 'bin/rumor'],


please sort alphabetically, include space after , in the list

boegel · 2017-03-27T18:53:58Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node2028.delcatty.os - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/18091d7e41857c3e2ccb65a797abbba1 for a full test report.

mboisson · 2017-03-27T19:27:47Z

I think I addressed all of the remarks in the latest commit.

boegelbot · 2017-03-27T19:52:59Z

Travis test report: 8/8 runs failed - see https://travis-ci.org/hpcugent/easybuild-easyconfigs/builds/215661862

Only showing partial log for 1st failed test suite run 4122.1;
full log at https://travis-ci.org/hpcugent/easybuild-easyconfigs/jobs/215661863

...
ERROR: Test for parsing of easyconfig RepastHPC-2.2.0-foss-2016a.eb
----------------------------------------------------------------------
Traceback (most recent call last):
  File "<string>", line 1, in innertest
  File "/home/travis/build/hpcugent/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 201, in template_easyconfig_test
    ecs = process_easyconfig(spec)
  File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/easybuild_framework-3.2.0.dev0-py2.6.egg/easybuild/framework/easyconfig/easyconfig.py", line 1261, in process_easyconfig
    ec = EasyConfig(spec, build_specs=build_specs, validate=validate, hidden=hidden)
  File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/easybuild_framework-3.2.0.dev0-py2.6.egg/easybuild/framework/easyconfig/easyconfig.py", line 323, in __init__
    auto_convert_value_types=auto_convert_value_types)
  File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/easybuild_framework-3.2.0.dev0-py2.6.egg/easybuild/framework/easyconfig/parser.py", line 105, in __init__
    self._set_formatter(filename)
  File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/easybuild_framework-3.2.0.dev0-py2.6.egg/easybuild/framework/easyconfig/parser.py", line 196, in _set_formatter
    self._formatter.parse(self.rawcontent)
  File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/easybuild_framework-3.2.0.dev0-py2.6.egg/easybuild/framework/easyconfig/format/one.py", line 125, in parse
    super(FormatOneZero, self).parse(txt, strict_section_markers=True)
  File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/easybuild_framework-3.2.0.dev0-py2.6.egg/easybuild/framework/easyconfig/format/pyheaderconfigobj.py", line 134, in parse
    self.parse_pre_section(txt[:start_section])
  File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/easybuild_framework-3.2.0.dev0-py2.6.egg/easybuild/framework/easyconfig/format/pyheaderconfigobj.py", line 165, in parse_pre_section
    self.parse_pyheader('\n'.join(txt_list))
  File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/easybuild_framework-3.2.0.dev0-py2.6.egg/easybuild/framework/easyconfig/format/pyheaderconfigobj.py", line 186, in parse_pyheader
    exec(pyheader, global_vars, local_vars)
  File "<string>", line 26, in <module>
TypeError: format requires a mapping

----------------------------------------------------------------------
Ran 6755 tests in 117.439s

FAILED (errors=1)
ERROR: Not all tests were successful.

4122.2 - errored => https://travis-ci.org/hpcugent/easybuild-easyconfigs/jobs/215661864
4122.3 - errored => https://travis-ci.org/hpcugent/easybuild-easyconfigs/jobs/215661865
4122.4 - errored => https://travis-ci.org/hpcugent/easybuild-easyconfigs/jobs/215661866
4122.5 - errored => https://travis-ci.org/hpcugent/easybuild-easyconfigs/jobs/215661867
4122.6 - errored => https://travis-ci.org/hpcugent/easybuild-easyconfigs/jobs/215661868
4122.7 - errored => https://travis-ci.org/hpcugent/easybuild-easyconfigs/jobs/215661869
4122.8 - errored => https://travis-ci.org/hpcugent/easybuild-easyconfigs/jobs/215661870
(bleep, bloop, I'm just a bot, please talk to my owner @boegel if you notice you me acting stupid)

mboisson · 2017-03-27T20:40:06Z

not sure how to fix that. I don't know the %(version)s easybuild special syntax (which is why I used pure Python syntax in the first place).

boegel · 2017-03-28T07:02:02Z

+configopts = '--with-boost=$EBROOTBOOST --with-netcdf=$EBROOTNETCDFMINCPLUSPLUS'
+
+sanity_check_paths = {
+    'files': ['lib/librelogo-%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%(version)s.%s' % SHLIB_EXT ],


@mboisson You need to use %%(version)s here (i.e. escape the %), to ensure that you have %(version)s in the string after string templating with % SHLIB_EXT is done

boegel · 2017-03-28T07:03:00Z

+
+sanity_check_paths = {
+    'files': ['lib/librelogo-%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%(version)s.%s' % SHLIB_EXT ],
+    'dirs': ['bin/rumor', 'bin/zombie', 'include', 'lib'],


Are bin/rumor and bin/zombie subdirectories with binaries in them? If so, should we add them to $PATH?

mboisson · 2017-03-28T11:19:10Z

They are, but I don't think they should be added to the paths. They are demo programs that are compiled automatically. I just take them as proof that The libraries are correctly compiled and can be linked against.

boegel · 2017-03-28T14:37:01Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node2124.delcatty.os - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/a56a4ad1b8f5782baa753a6695b05b8e for a full test report.

boegel · 2017-03-28T14:45:23Z

Test report by @boegel
FAILED
Build succeeded for 8 out of 15 (1 easyconfigs in this PR)
node2428.golett.os - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/848dd0b7937344388dea6f679333791d for a full test report.

mboisson · 2017-03-28T14:47:50Z

Seems like what is failing is building dependencies that are already in the develop branch, not what is included in this PR.

boegel · 2017-03-28T15:46:12Z

+    'dirs': ['bin/rumor', 'bin/zombie', 'include', 'lib'],
+}
+
+moduleclass = 'bio'


@mboisson This just caught my eye, is this correct?

I was not sure what moduleclass to put (and I have no clue what is the impact of that value on anything).

RepastHPC is typically used to do agent based modeling, which our researcher use to perform simulations on animal population dynamics. Could also be used for simulations about spreading of diseases. But of course it can also be used to simulate non-biological related stuff like transport dynamics....

OK, let's leave it then.

The impact isn't very big, but some sites rely on moduleclass for example to group modules per domain.

boegel · 2017-03-28T15:46:52Z

@mboisson Something is wrong with my GCCcore/4.9.3 installation, I'll look into fixing it and submitting a working test report.

boegel · 2017-03-29T08:53:24Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node2609.swalot.os - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/68e268368a587145ccd3d5c4e147eb60 for a full test report.

boegel · 2017-03-29T08:53:32Z

lgtm

boegel · 2017-03-29T08:53:44Z

Going in, thanks @mboisson!

added recipe for repasthpc

8f63e32

boegel requested changes Mar 27, 2017

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boegel added this to the 3.2.0 milestone Mar 27, 2017

cosmetic changes

1af6f17

boegel requested changes Mar 28, 2017

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boegel reviewed Mar 28, 2017

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escaped %

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boegel changed the title ~~added recipe for repasthpc~~ {bio}[foss/2016a] RepastHPC 2.2.0 Mar 28, 2017

boegel requested changes Mar 28, 2017

View reviewed changes

boegel approved these changes Mar 29, 2017

View reviewed changes

boegel merged commit daad11e into easybuilders:develop Mar 29, 2017

mboisson deleted the repasthpcd branch March 29, 2017 12:04

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mboisson commented Mar 28, 2017 via email •

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