Hi Jack,
On 03/09/15 21:54, Jack Perdue wrote:
LOL.... it works... thanks Ken... I could've
spent hours tracking that one down.
I can imagine. :-)
Issue submitted:
https://github.com/hpcugent/easybuild-framework/issues/1380
In true Robert McLay-style:
https://github.com/hpcugent/easybuild-framework/pull/1381 should fix
your problem.
My officemate who scoffs of my pattern of slapping #EOF
at the end of all sources[*] will get a kick out this one.
jack
[*] I like them for when I do something like 'cat * | less'. It makes
it clear where files begin/end. Also, it provides reassurance
on file transfers that the complete file was transferred (and not
truncated). Yeah... I'm a little weird.
I must admit I haven't seen this a lot (or at all ;-)) before, but
EasyBuild definitely shouldn't go down like this over something trivial
as this.
As they say in French: les goûts et les couleurs ne se discutent pas. ;-)
regards,
Kenneth
On 09/03/2015 02:46 PM, Kenneth Hoste wrote:
Hi Jack,
On 03/09/15 21:35, Jack Perdue wrote:
Howdy Ken and all,
I'm seeing some problems with 2.3.0. Yesterday
it was IPython. Today its plain Python.
I threw the relevant files of the simpler test case here:
http://www.siliconslick.com/easybuild/230err/
Included are the logs from building with the -d option
and the .eb file itself. Easyconfigs for dependencies
(if needed) can be found in:
http://www.siliconslick.com/easybuild/ebfiles_repo_cleaned/ada/
So far I've only see it impact Python related packages.
I note that there is now a PYTHONPATH set in the EB/2.3.0
module that wasn't in the 2.2.0 module.
Any ideas whats going on?
At first sight, it's probably the '# EOF' comment you have as the
last line of your easyconfig file...
One of the things that EB v2.3.0 does (that v2.2.0 didn't do), is
extracting comments from easyconfig files, so it can restore them
when an easyconfig file is dumped again later (which only happens in
very specific situations).
Can you try if the problem disappears if you remove the '# EOF' line
at the end?
If it does, please open a issue to report this via
https://github.com/hpcugent/easybuild-framework/issues/new, shouldn't
be hard to fix.
regards,
Kenneth
Jack Perdue
Lead Systems Administrator
High Performance Research Computing
TAMU Division of Research
[email protected] http://sc.tamu.edu
SC Helpdesk: [email protected]
On 09/02/2015 12:51 PM, Kenneth Hoste wrote:
Dear EasyBuilders,
It is my pleasure to announce the release of EasyBuild v2.3.0 [1],
by far the best EasyBuild version up until now (surprise!).
Although I was initially planning a bugfix release (v2.2.1) early
August, things worked out differently because of a lack of time in
the last couple of weeks.
Since several minor enhancements have been merged since v2.2.0, it
made sense to me to promote it to a 'feature' release. I'm sure you
don't mind. ;-)
Nevertheless, most of the changes compared to v2.2.0 are bug fixes.
The most significant issue that was fixed is correcting the sanity
check being performed for software packages that are 'extensions'
(Python packages, R libraries, Perl modules, etc.). [2]
After avoiding that the sanity check paths/commands for the
'parent' software are rechecked for every extension (which resulted
in potentially very slow installation of for example R or Perl), it
turned out that the default sanity check paths (i.e., checking for
'bin' and 'lib' or 'lib64' sub-directories) were not being
considered for these type of installations.
Because of this, the fact that the installations of FPM (Ruby gem)
and SIP (Python package) were not being performed in the intended
installation prefix (but that of the parent) went undetected [3,
4], which highlights the importance of the seemingly excessive
sanity check step once again.
This indirectly affects a significant number of software packages,
since the default sanity check is not a valid fallback for these.
Software packages for which custom sanity check paths needed to be
added include mpi4py, scipy (via EB_scipy easyblock), and various
other R/Perl/Python extensions (a full list is available in the
release notes [5]).
Other bug fixes include:
- fix --package by making it pick up the installed module file,
rather than the (no longer existing) temporary 'fake' module [6]
- fix use of custom module naming scheme that was included via
--include-module-naming-schemes [7]
- fix problems with --job and (hidden) dependencies [8, 9]
- make sure hidden Lua modules are seen [10]
- fix and enhancements to the EasyConfig.dump method (relevant for
future work) [11, 12, 13]
A minor enhancement worth mentioning is the new configure option
--cleanup-tmpdir [14], which enables you to instruct EasyBuild to
retain its temporary directory rather than cleaning it up (using
--disable-cleanup-tmpdir). This is particularly useful together
with --dry-run/-D and --try-* .
Additionally, support for building and installing 19 new software
packages was added, including GlobalArrays and Molpro.
A complete and detailed overview of the changes is available in the
updated release notes [5].
Thanks to everyone who contributed to this release in one way or
another!
To upgrade to EasyBuild v2.3.0, there are several options:
(i) (re)bootstrap EasyBuild to obtain an EasyBuild/2.3.0 module
to load [15]
(ii) install EasyBuild v2.3.0 with a previous version of
EasyBuild, using the easyconfig file available in [16]
(iii) install EasyBuild v2.3.0 from PyPI, using one of the
standard Python installation tools (easy_install, pip, ...) [17]
(iv) update your Git working copies of the different EasyBuild
repositories;
note: the minimal required vsc-base version has been
bumped to 2.2.4, so you may need to update vsc-base as well with
this approach
Enjoy!
regards,
Kenneth
EasyBuild release manager
[1] http://pypi.python.org/pypi/easybuild
[2] https://github.com/hpcugent/easybuild-framework/pull/1366 # fix
sanity_check_step for extensions
[3] https://github.com/hpcugent/easybuild-easyblocks/pull/667 # fix
install prefix for Ruby gems
[4] https://github.com/hpcugent/easybuild-framework/pull/1888 # fix
install prefix for SIP
[5] http://easybuild.readthedocs.org/en/latest/Release_notes.html
[6] https://github.com/hpcugent/easybuild-framework/pull/1348 # fix
--package
[7] https://github.com/hpcugent/easybuild-framework/pull/1370 # fix
--include-module-naming-schemes
[8] https://github.com/hpcugent/easybuild-framework/pull/1356 #
install hidden deps as hidden with --job
[9] https://github.com/hpcugent/easybuild-framework/pull/1359 #
correctly specify job dependencies
[10] https://github.com/hpcugent/easybuild-framework/pull/1364 #
make sure hidden Lua modules are seen
[11] https://github.com/hpcugent/easybuild-framework/pull/1327 #
preserve comments with dump
[12] https://github.com/hpcugent/easybuild-framework/pull/1345 #
style formatting with dump
[13] https://github.com/hpcugent/easybuild-framework/pull/1354 #
correctly handle hidden dependencies in dump
[14] https://github.com/hpcugent/easybuild-framework/pull/1365 #
--cleanup-tmpdir
[15]
http://easybuild.readthedocs.org/en/latest/Installation.html#bootstrapping-easybuild
[16] https://github.com/hpcugent/easybuild-easyconfigs/pull/1940
[17]
http://easybuild.readthedocs.org/en/latest/Installation_Alternative.html#standard-installation-of-latest-release
