foss/2017b toolchain definition (REVIEW) #4768

boegel · 2017-06-22T16:01:43Z

(created using eb --new-pr)

requires ~~#4794~~ for GCC 6.4.0

boegel · 2017-06-22T16:55:33Z

Test report by @boegel
SUCCESS
Build succeeded for 8 out of 8 (8 easyconfigs in this PR)
node2050.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/d9fd0aca3f846294b80dbbfbfd9ff141 for a full test report.

boegel · 2017-06-22T19:02:35Z

easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.eb

+
+skipsteps = ['configure']
+
+buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1'


should also add USE_OPENMP=1, see #4524

boegel · 2017-06-22T21:40:07Z

Test report by @boegel
SUCCESS
Build succeeded for 8 out of 8 (8 easyconfigs in this PR)
node2441.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/0fdb2da006a7c8b573ebaacac4b4da70 for a full test report.

boegel · 2017-06-23T06:11:59Z

easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.eb

+easyblock = 'ConfigureMake'
+
+name = 'OpenBLAS'
+version = '0.2.19'


This is the most recent, but relatively old, version (released Sept'16).

I reached out to the OpenBLAS maintainer (@xianyi), this was his reply: We will release OpenBLAS in one or two weeks.

So, probably worth waiting for...

boegel · 2017-06-26T20:13:12Z

easybuild/easyconfigs/f/foss/foss-2017b.eb

+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+gccver = '6.3.0-2.28'


GCC 6.4.0 is imminent: https://gcc.gnu.org/ml/gcc/2017-06/msg00101.html (hat tip @ocaisa)

boegel · 2017-06-28T15:34:55Z

note: installing Python 2.7.13 + all dependencies on top of foss/2017b as it is currently (using the GCC 6.4.0 release candidate and OpenBLAS 0.2.19) works like a charm:

$ ml show Python/2.7.13-foss-2017b
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
   /tmp/vsc40023/modules/all/Python/2.7.13-foss-2017b.lua:
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
help([[
Description
===========
Python is a programming language that lets you work more quickly and integrate your systems
 more effectively.


More information
================
 - Homepage: http://python.org/


Included extensions
===================
arff-2.1.0, bitstring-3.1.5, blist-1.3.6, cryptography-1.8.1, Cython-0.25.2,
dateutil-2.6.0, deap-1.0.2, decorator-4.0.11, docopt-0.6.2, ecdsa-0.13,
enum34-1.1.6, funcsigs-1.0.2, mock-2.0.0, mpi4py-2.0.0, netaddr-0.7.19,
netifaces-0.10.5, nose-1.3.7, numpy-1.12.1, pandas-0.19.2, paramiko-2.1.2,
paycheck-1.0.2, pbr-2.0.0, pip-9.0.1, pycrypto-2.6.1, pyparsing-2.2.0,
pytz-2017.2, scipy-0.19.0, setuptools-33.1.1, six-1.10.0, virtualenv-15.1.0
]])
whatis("Description: Python is a programming language that lets you work more quickly and integrate your systems
 more effectively.")
whatis("Homepage: http://python.org/")
whatis("Extensions: arff-2.1.0, bitstring-3.1.5, blist-1.3.6, cryptography-1.8.1, Cython-0.25.2, dateutil-2.6.0, deap-1.0.2, decorator-4.0.11, docopt-0.6.2, ecdsa-0.13, enum34-1.1.6, funcsigs-1.0.2, mock-2.0.0, mpi4py-2.0.0, netaddr-0.7.19, netifaces-0.10.5, nose-1.3.7, numpy-1.12.1, pandas-0.19.2, paramiko-2.1.2, paycheck-1.0.2, pbr-2.0.0, pip-9.0.1, pycrypto-2.6.1, pyparsing-2.2.0, pytz-2017.2, scipy-0.19.0, setuptools-33.1.1, six-1.10.0, virtualenv-15.1.0")
conflict("Python")
load("foss/2017b")
load("bzip2/1.0.6-GCCcore-6.4.0")
load("zlib/1.2.11-GCCcore-6.4.0")
load("libreadline/7.0-GCCcore-6.4.0")
load("ncurses/6.0-GCCcore-6.4.0")
load("SQLite/3.19.3-GCCcore-6.4.0")
load("GMP/6.1.2-GCCcore-6.4.0")
load("libffi/3.2.1-GCCcore-6.4.0")
prepend_path("CPATH","/tmp/vsc40023/software/Python/2.7.13-foss-2017b/include")
prepend_path("LD_LIBRARY_PATH","/tmp/vsc40023/software/Python/2.7.13-foss-2017b/lib")
prepend_path("LIBRARY_PATH","/tmp/vsc40023/software/Python/2.7.13-foss-2017b/lib")
prepend_path("MANPATH","/tmp/vsc40023/software/Python/2.7.13-foss-2017b/share/man")
prepend_path("PATH","/tmp/vsc40023/software/Python/2.7.13-foss-2017b/bin")
prepend_path("PKG_CONFIG_PATH","/tmp/vsc40023/software/Python/2.7.13-foss-2017b/lib/pkgconfig")
setenv("EBROOTPYTHON","/tmp/vsc40023/software/Python/2.7.13-foss-2017b")
setenv("EBVERSIONPYTHON","2.7.13")
setenv("EBDEVELPYTHON","/tmp/vsc40023/software/Python/2.7.13-foss-2017b/easybuild/Python-2.7.13-foss-2017b-easybuild-devel")
prepend_path("CPATH","/tmp/vsc40023/software/Python/2.7.13-foss-2017b/lib/python2.7/site-packages/numpy-1.12.1-py2.7-linux-x86_64.egg/numpy/core/include")
prepend_path("LD_LIBRARY_PATH","/tmp/vsc40023/software/Python/2.7.13-foss-2017b/lib/python2.7/site-packages/numpy-1.12.1-py2.7-linux-x86_64.egg/numpy/core/lib")
prepend_path("LIBRARY_PATH","/tmp/vsc40023/software/Python/2.7.13-foss-2017b/lib/python2.7/site-packages/numpy-1.12.1-py2.7-linux-x86_64.egg/numpy/core/lib")
setenv("EBEXTSLISTPYTHON","setuptools-33.1.1,pip-9.0.1,nose-1.3.7,numpy-1.12.1,scipy-0.19.0,blist-1.3.6,mpi4py-2.0.0,paycheck-1.0.2,pbr-2.0.0,Cython-0.25.2,six-1.10.0,dateutil-2.6.0,deap-1.0.2,decorator-4.0.11,arff-2.1.0,pycrypto-2.6.1,ecdsa-0.13,cryptography-1.8.1,paramiko-2.1.2,pyparsing-2.2.0,netifaces-0.10.5,netaddr-0.7.19,funcsigs-1.0.2,mock-2.0.0,pytz-2017.2,pandas-0.19.2,enum34-1.1.6,bitstring-3.1.5,virtualenv-15.1.0,docopt-0.6.2")

boegel · 2017-07-03T09:02:22Z

easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb

+easyblock = 'ConfigureMake'
+
+name = 'OpenBLAS'
+version = '0.2.19'


OpenBLAS 0.2.20 is expected to be released soon (see OpenMathLib/OpenBLAS#1223); I suggest we postpone setting foss/2017b in stone until it's available?

Seems like they screwed something up with the OpenBLAS 0.2.20 release. Another quick 0.2.21 release is planned, probably worth waiting for this? See OpenMathLib/OpenBLAS#1258.

Thoughts @easybuilders/easybuild-easyconfigs-maintainers?

Since the 0.2.21 release isn't happening, I went forward with using 0.2.20 and applying two patches on top of it, so we can finalise foss/2017b...

boegel · 2017-07-10T19:14:11Z

easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb

+skipsteps = ['configure']
+
+buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1'
+installopts = "USE_THREAD=1 PREFIX=%(installdir)s"


should also add USE_OPENMP=1, see #4524

...and remove NO_AFFINITY=1 too for the reasons given in #4524

Add a checksum?

adding USE_OPENMP=1 and dropping NO_AFFINITY=1 done, see 91fc9ed

verdurin

Minor typos and SLURM comment suggestion

verdurin · 2017-07-11T22:43:02Z

easybuild/easyconfigs/f/foss/foss-2017b.eb

+comp_mpi_tc_name = 'gompi'
+comp_mpi_tc = (comp_mpi_tc_name, version)
+
+# compiler toolchain depencies


dependencies

verdurin · 2017-07-11T22:43:17Z

easybuild/easyconfigs/f/foss/foss-2017b.eb

+
+# compiler toolchain depencies
+# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain
+# because of toolchain preperation functions


preparation

verdurin · 2017-07-11T22:49:06Z

easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb

+configopts += '--enable-mpirun-prefix-by-default '  # suppress failure modes in relation to mpirun path
+configopts += '--with-hwloc=$EBROOTHWLOC '  # hwloc support
+configopts += '--disable-dlopen '  # statically link component, don't do dynamic loading
+


Worth adding a commented out option here for SLURM integration?

E.g. configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr

as a reference?

@verdurin I think that should go in the documentation somewhere, e.g. how to site-customise OpenMPI?

@boegel yes, that's fine too

verdurin · 2017-08-07T09:01:09Z

easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017b.eb

+toolchainopts = {'usempi': True}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['http://www.netlib.org/benchmark/%(namelower)s']


Add a checksum?

verdurin · 2017-08-07T09:02:05Z

easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb

+skipsteps = ['configure']
+
+buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1'
+installopts = "USE_THREAD=1 PREFIX=%(installdir)s"


Add a checksum?

verdurin · 2017-08-07T09:02:37Z

easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb

+toolchainopts = {'pic': True}
+
+source_urls = [homepage]
+sources = [SOURCELOWER_TGZ]


Add a checksum here too?

JackPerdue · 2017-08-08T14:23:08Z

Y'all know, if you used GCCcore (vs. GCC) for hwloc and numactl they could be reused when building iompi/2017b

…core 6.4.0 suffices

boegel · 2017-08-09T17:23:03Z

easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb

+name = 'OpenBLAS'
+version = '0.2.19'
+
+lapackver = '3.7.0'


LAPACK 3.7.1 is out, so we should bump this too

Or not, we should probably stick with the shipped LAPACK instead, see OpenMathLib/OpenBLAS#1273...

…t patches

….2.20 (cfr. easybuilders#4524)

boegel · 2017-08-23T14:30:55Z

@JackPerdue good point, now using existing hwloc & numactl easyconfigs that use GCCcore/6.4.0 as toolchain

boegel · 2017-08-23T19:24:17Z

Test report by @boegel
SUCCESS
Build succeeded for 7 out of 7 (7 easyconfigs in this PR)
node2026.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/17f70b785b9b9ab0c96046dec2aaf95e for a full test report.

boegel · 2017-08-24T10:32:16Z

Test report by @boegel
SUCCESS
Build succeeded for 7 out of 7 (7 easyconfigs in this PR)
node2473.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/f97186acf505eba7188d74591a88b03c for a full test report.

verdurin · 2017-08-25T10:58:09Z

Test report by @verdurin
SUCCESS
Build succeeded for 9 out of 9 (7 easyconfigs in this PR)
ca003.camp.thecrick.org - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2640 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/3fdbd1c0977f971b773fc28bcffcbe4c for a full test report.

JackPerdue · 2017-08-25T11:39:14Z

Test report by @JackPerdue
SUCCESS
Build succeeded for 3 out of 3 (7 easyconfigs in this PR)
tlogin-0502.cluster - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz, Python 2.7.5
See https://gist.github.com/d3f3cbf58e3483ac64a36ae7a42c3e64 for a full test report.

wpoely86 · 2017-08-25T11:40:40Z

Test report by @wpoely86
FAILED
Build succeeded for 11 out of 17 (7 easyconfigs in this PR)
nic66 - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz, Python 2.7.5
See https://gist.github.com/5696cc2e38a5644548b3b82611bc5e69 for a full test report.

boegel · 2017-08-25T11:43:06Z

@wpoely86 Hmm...

/bin/grep: /usr/lib64/libmunge.la: No such file or directory
/bin/sed: can't read /usr/lib64/libmunge.la: No such file or directory
libtool:   error: '/usr/lib64/libmunge.la' is not a valid libtool archive

Any ideas? I don't have any libmunge.* installed either, works fine for me...

ocaisa · 2017-08-25T11:48:17Z

@akesandgren Looks like your stack isn't consistent with the new PR (two versions of M4), maybe disable searching in your local repos?

boegel · 2017-08-25T11:48:32Z

easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb

+    (large_src, '.'),
+    (timing_src, '.'),
+    'OpenBLAS-%(version)s_fix-Intel-L1-cache-size-detection.patch',
+    'OpenBLAS-%(version)s_revert-honor-cpuset.patch',


I checked with one of the OpenBLAS co-maintainers whether going forward with OpenBLAS 0.2.20 with these two patches on top makes sense w.r.t. stability, and he confirmed it was.

No need to keep stalling this and hope for a 'quick' OpenBLAS 0.2.21 that includes these fixes...

JackPerdue · 2017-08-25T12:43:25Z

Test report by @JackPerdue
SUCCESS
Build succeeded for 7 out of 7 (7 easyconfigs in this PR)
tlogin-0502.cluster - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz, Python 2.7.5
See https://gist.github.com/14fb0fc56fc334acb6a3e653496695bb for a full test report.

boegel · 2017-08-25T12:57:01Z

@ocaisa @akesandgren Hmm, no, it's something else... The M4/1.4.17 module it's trying to load as a dependency for Bison is there (it was installed just before according to the test report), but Lmod fails to load it even though EB checked it was indeed there.

However, the check was done using module avail Core/M4/1.4.17, which passes, but when trying to load the module we have this: Current MODULEPATH: /scratch/ake/eb-sandbox/modules/all .

It makes sense that M4/1.4.17 can't be loaded then, since <prefix>/modules/all/Core is not included in $MODULEPATH.

See also easybuilders/easybuild-framework#2186.

@akesandgren Please do a module use /scratch/ake/eb-sandbox/modules/all/Core, and try again?

wpoely86 · 2017-08-25T13:03:42Z

We don't have libmunge-devel installed on our nodes. It seems like openmpi needs/wants it.

akesandgren · 2017-08-25T13:03:58Z

Yeah, i finally managed to get a correct sandbox test setup.
It's running and will produce a report sooner or later. Takes a while to compile GCCcore on the laptop.

@ocaisa was just to fast and read a report i deleted.

JackPerdue · 2017-08-25T13:20:34Z

For my last test (7 of 7) I didn't see the munge issue. We have munge installed for slurm but I made sure to remove munge-devel (which doesn't seem to have a libmunge.la on RHEL7) beforehand.

wpoely86 · 2017-08-25T14:46:36Z

Test report by @wpoely86
SUCCESS
Build succeeded for 17 out of 17 (7 easyconfigs in this PR)
nic66 - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz, Python 2.7.5
See https://gist.github.com/e2d0dab54128695cd92d1c4eceae411e for a full test report.

JackPerdue · 2017-08-25T16:41:44Z

Was dropping LAPACK-3.7.0 intentional?

boegel · 2017-08-25T16:49:07Z

@JackPerdue Yes, see discussion in OpenMathLib/OpenBLAS#1273

akesandgren · 2017-08-25T18:32:07Z

Test report by @akesandgren
SUCCESS
Build succeeded for 24 out of 24 (7 easyconfigs in this PR)
janson.hpc2n.umu.se - Linux ubuntu 16.04, Intel(R) Core(TM) i7-5600U CPU @ 2.60GHz, Python 2.7.12
See https://gist.github.com/8972f95f71a32b5a1d4cf3721ca30e3f for a full test report.

Requested changes applied

vanzod · 2017-08-31T20:20:48Z

Going in, thanks @boegel!

(proposal for) foss/2017b toolchain definition

e7cb3e9

boegel added this to the 3.3.0 milestone Jun 22, 2017

boegel commented Jun 22, 2017

View reviewed changes

boegel commented Jun 23, 2017

View reviewed changes

boegel modified the milestones: 3.3.0, 3.3.1 Jun 25, 2017

boegel commented Jun 26, 2017

View reviewed changes

bump GCC to 6.4.0 for foss/2017b

6b46855

boegel commented Jul 3, 2017

View reviewed changes

easybuilders deleted a comment from boegelbot Jul 5, 2017

boegel modified the milestones: 3.3.1, 3.4.0 Jul 9, 2017

boegel commented Jul 10, 2017

View reviewed changes

verdurin requested changes Jul 11, 2017

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verdurin previously requested changes Aug 7, 2017

View reviewed changes

boegel added 3 commits August 9, 2017 09:13

Merge branch 'develop' into 20170622180135_new_pr_HPL22

5f5f1cd

remove easyconfig for hwloc 1.11.7 with GCC-6.4.0-2.28 toolchain, GCC…

f5563b9

…core 6.4.0 suffices

fix @verdurin's remarks

55a2995

boegel commented Aug 9, 2017

View reviewed changes

boegel added 3 commits August 9, 2017 20:17

add SHA256 checksums for foss/2017b components

0539726

bump OpenBLAS to 0.2.20 in foss/2017b, with inclusion of two importan…

a10eead

…t patches

don't specify NO_AFFINITY=1, also specify USE_OPENMP=1 for OpenBLAS 0…

91fc9ed

….2.20 (cfr. easybuilders#4524)

boegel added 2 commits August 23, 2017 16:38

add back accidentally removed OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch

719d650

fix too long line in OpenBLAS 0.2.20 easyconfig

4050d91

easybuilders deleted a comment from boegelbot Aug 23, 2017

boegel mentioned this pull request Aug 25, 2017

OpenBLAS seems to be configured wrong #4524

Closed

boegel commented Aug 25, 2017

View reviewed changes

boegel mentioned this pull request Aug 25, 2017

openblas (0.2.20) openhpc/ohpc#517

Closed

boegel mentioned this pull request Aug 30, 2017

bump version for various easyconfigs that use GCCcore/6.4.0 #5073

Merged

vanzod approved these changes Aug 31, 2017

View reviewed changes

vanzod merged commit 34e22c4 into easybuilders:develop Aug 31, 2017

boegel deleted the 20170622180135_new_pr_HPL22 branch September 1, 2017 07:47

boegel mentioned this pull request Sep 6, 2017

update common toolchains with 2017b versions easybuilders/easybuild#373

Merged


		skipsteps = ['configure']

		buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1'


		toolchain = {'name': 'dummy', 'version': 'dummy'}

		gccver = '6.3.0-2.28'

foss/2017b toolchain definition (REVIEW) #4768

foss/2017b toolchain definition (REVIEW) #4768

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boegel commented Jun 22, 2017 • edited Loading

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