Hi Ole,
On 29/09/16 11:14, Ole Holm Nielsen wrote:
I have to correct myself: Building Python-3.5.2 like this bombs out
with an error message:
$ eb Python-3.5.2-foss-2016.04.eb --try-toolchain=foss,2016.09 -r
== temporary log file in case of crash
/tmp/eb-vxeoSA/easybuild-fB_HiJ.log
== resolving dependencies ...
== processing EasyBuild easyconfig
/tmp/eb-vxeoSA/tweaked_easyconfigs/Python-3.5.2-foss-2016.09.eb
== building and installing Python/3.5.2-foss-2016.09...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== FAILED: Installation ended unsuccessfully (build directory:
/home/opt/modules/xeonv4/build/Python/3.5.2/foss-2016.09): build
failed (first 300 chars): cmd " make -j 48 " exited with exitcode 2
and output:
gcc -c -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC -O2 -march=native -fPIC -O2 -march=native
-Werror=declaration-after-statement -I. -IInclude -I./Include
-I/home/opt/modules/xeonv4/software/OpenBL
== Results of the build can be found in the log file(s)
/tmp/eb-vxeoSA/easybuild-Python-3.5.2-20160929.110801.gGcTN.log
ERROR: Build of
/tmp/eb-vxeoSA/tweaked_easyconfigs/Python-3.5.2-foss-2016.09.eb failed
(err: 'build failed (first 300 chars): cmd " make -j 48 " exited with
exitcode 2 and output:\ngcc -c -Wno-unused-result -Wsign-compare
-DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -O2
-march=native -fPIC -O2 -march=native
-Werror=declaration-after-statement -I. -IInclude -I./Include
-I/home/opt/modules/xeonv4/software/OpenBL')
In the logfile there are other error messages as well.
This is exactly what I mean, this may be an (unknown) issue with using
the latest & greatest GCC that is part of foss/2016.09...
Can you share a full (debug, i.e. also using --debug) log of this
failing build with us?
I'm beginning to wonder if I should go back to an older foss toolchain?
Unless you have a good reason to go with the latest & greatest 'foss'
toolchain, it's probably wise to stick to the 'common' toolchain
versions like foss/2016b, which get a lot more testing (and for which
more easyconfigs are readily available).
I still need to put together a page in the documentation on the common
toolchains too...
regards,
Kenneth
Thanks for any advice,
Ole
On 09/29/2016 11:07 AM, Ole Holm Nielsen wrote:
Pablo, Kenneth: Thanks a lot! The --try-toolchain works correctly.
Question: Is --try-toolchain just a hack for testing out something new,
or is it supposed to be used also for production modules?
If used for production, how may we remember/document the requirement for
--try-toolchain with some older easyconfig? Documentation would seem to
become an issue.
Thanks,
Ole
On 09/29/2016 10:48 AM, Kenneth Hoste wrote:
Hi Ole,
On 29/09/16 10:37, Pablo Escobar Lopez wrote:
have you tried "eb Python-3.5.2-foss-2016.04.eb
--try-toolchain=foss,2016.09 -r" ?
+1 on this, the problem is that there are no easyconfigs available for
the dependencies of Python 3.5.2 with foss/2016.09.
If you combine --try-toolchain (or --try-toolchain-version) with
--robot, EasyBuild will first construct the full dependency graph using
the foss/2016.04, and then generate easyconfigs (in a temp dir) for
each
of the components using foss/2016.09, and then proceed to building and
installing everything.
regards,
Kenneth
2016-09-29 8:55 GMT+02:00 Ole Holm Nielsen <[email protected]
<mailto:[email protected]>>:
I need to build Python 3.5 for the EB 2.9.0 toolchain
foss-2016.09.
I copied the file Python-3.5.2-foss-2016.04.eb and replaced 04 by
09.
Unfortunately, irresolvable dependencies are found:
# eb Python-3.5.2-foss-2016.09.eb -r
== temporary log file in case of crash
/tmp/eb-mvPeVH/easybuild-tixAOo.log
== resolving dependencies ...
ERROR: Irresolvable dependencies encountered:
bzip2/1.0.6-foss-2016.09,
zlib/1.2.8-foss-2016.09, libreadline/6.3-foss-2016.09,
ncurses/6.0-foss-2016.09, SQLite/3.13.0-foss-2016.09,
Tk/8.6.5-foss-2016.09, GMP/6.1.1-foss-2016.09,
XZ/5.2.2-foss-2016.09,
libffi/3.2.1-foss-2016.09
I suppose that these dependencies could be built independently of
the
foss toolchain.
Question: Does anyone have a working EB file
Python-3.5.2-foss-2016.09.eb?
Thanks a lot,
Ole
--
Pablo Escobar López
HPC systems engineer
sciCORE, University of Basel
SIB Swiss Institute of Bioinformatics
http://scicore.unibas.ch
