PGI: add pomkl-2016.03 toolchain + imkl-11.3.2.181-pompi + HPL by bartoldeman · Pull Request #2900 · easybuilders/easybuild-easyconfigs

bartoldeman · 2016-04-15T14:04:17Z

This depends on a lot of other PRs:
~~easybuilders/easybuild-framework#1342~~
~~easybuilders/easybuild-framework#1664~~
~~easybuilders/easybuild-easyblocks#866~~
~~#2879~~
~~#2899~~

I need -ldl in HPL to compile this:

mpicc -O2 -Mflushz -L/software/CentOS-6/eb/software/Toolchain/pompi/2016.03/imkl/11.3.2.181/lib -L/software/CentOS-6/eb/software/Toolchain/pompi/2016.03/imkl/11.3.2.181/mkl/lib/intel64 -L/software/CentOS-6/eb/software/Toolchain/pompi/2016.03/imkl/11.3.2.181/lib  -o /dev/shm/HPL/2.1/pomkl-2016.03/hpl-2.1//bin/UNKNOWN/xhpl HPL_pddriver.o         HPL_pdinfo.o           HPL_pdtest.o /dev/shm/HPL/2.1/pomkl-2016.03/hpl-2.1//lib/UNKNOWN/libhpl.a  -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_pgi_thread -lmkl_core -Wl,--end-group -Wl,-Bdynamic 
/software/CentOS-6/eb/software/Toolchain/GCCcore/4.9.3/binutils/2.25/bin/ld: /software/CentOS-6/eb/software/Toolchain/pompi/2016.03/imkl/11.3.2.181/mkl/lib/intel64/libmkl_core.a(mkl_memory_patched.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5'
//lib64/libdl.so.2: error adding symbols: DSO missing from command line

my workaround is ugly. There ought to be a better solution.

hpcugentbot · 2016-04-15T14:04:18Z

Automatic reply from Jenkins: Can I test this?

boegel · 2016-05-02T18:44:10Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in this PR)
node2523.golett.os - Linux centos linux 7.2.1511, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/d67ad5ce38fecdf92349d93d8356ad80 for a full test report.

boegel · 2016-05-02T18:44:32Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in this PR)
node2159.delcatty.os - Linux SL 6.7, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/dff263264468de4834cbc4e095d8971d for a full test report.

boegel · 2016-05-11T06:30:11Z

Jenkins: ok to test

hpcugentbot · 2016-05-11T06:49:42Z

Easyconfigs unit test suite FAILed.

See https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/7974/console for more details.

Please fix the reported issues by pushing additional commits to the branch corresponding with this pull request; contact @boegel if you're not sure what to do.

boegel · 2016-05-11T13:36:32Z

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in this PR)
node2159.delcatty.os - Linux SL 6.7, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/7746f8cb41829e0431ac67b98bdec839 for a full test report.

boegel · 2016-05-11T14:38:40Z

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in this PR)
node2434.golett.os - Linux centos linux 7.2.1511, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/a429c80ce093b5732503a23781e7eacd for a full test report.

boegel · 2016-05-11T14:52:12Z

@Bart-VUB do you mind merging bartoldeman#3, mainly to trigger Travis testing this PR?

sync with develop

hpcugentbot · 2016-05-11T16:25:57Z

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/7991/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

boegel · 2016-05-11T19:17:24Z

all good to go, thanks @bartoldeman!

boegel · 2016-05-11T19:49:34Z

+# needs to include -ldl or else we get
+# .../libmkl_core.a(mkl_memory_patched.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5'
+import os
+os.environ['LIBS'] = '-ldl'


ah, crap, only noticed this now...

this is a hack at best, no @bartoldeman?

it actually indicates that something is missing in the toolchain support somewhere?

@geimer is this the problem you mentioned during today's conf call?

bartoldeman · 2016-05-11T21:01:10Z

Yes, as I mentioned during in the very first comment here, there ought to be a better way.
I'll manually compile HPL and see what happens.

boegel · 2016-05-11T21:15:56Z

@bartoldeman maybe we should define LIB_MATH = ['dl'] in toolchains/compiler/pgi.py, similar to what we do for Clang, cfr. https://github.com/hpcugent/easybuild-framework/blob/d9016c2e22a6b0c6eb3763251e8790fb4bdea85e/easybuild/toolchains/compiler/clang.py#L102.

This will be picked up by the toolchain mechanism and added to $LIBS, cfr. https://github.com/hpcugent/easybuild-framework/blob/master/easybuild/tools/toolchain/compiler.py#L216

bartoldeman · 2016-05-11T21:32:30Z

I suspect it should be fixed in the MKL support for PGI.

bartoldeman · 2016-05-11T21:42:03Z

The link line advisor says this:

-Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_sequential.a -Wl,--end-group -lpthread -lm -ldl

https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor

note this includes the -ldl. So it should be a change to intelmkl.py.

bartoldeman · 2016-05-11T22:02:43Z

Link line advisor adds -ldl for MKL 11.0 and higher for all compilers (PGI, GCC, Intel), not for 10.3.

bartoldeman · 2016-05-11T22:03:06Z

I need to leave soon but will have a further look tomorrow.

geimer · 2016-05-12T08:19:25Z

@boegel: My issue with PGI was different, see easybuilders/easybuild#217.

PGI: add pomkl-2016.03 toolchain + imkl-11.3.2.181-pompi + HPL

a6b0c16

boegel mentioned this pull request Apr 15, 2016

PGI support (roadmap) easybuilders/easybuild#211

Closed

10 tasks

boegel added this to the v2.8.0 milestone Apr 15, 2016

This was referenced May 11, 2016

Add PGI support to imkl easyblock easybuilders/easybuild-easyblocks#866

Merged

Add PGI support to MKL easybuilders/easybuild-framework#1664

Merged

PGI: add pompi and pomkl toolchains (similar to iompi and iomkl). easybuilders/easybuild-framework#1724

Merged

Merge branch 'develop' into pomkl

4b1995e

boegel mentioned this pull request May 11, 2016

sync with develop bartoldeman/easybuild-easyconfigs#3

Merged

Merge pull request #3 from boegel/pomkl

44c63b7

sync with develop

boegel merged commit 277e516 into easybuilders:develop May 11, 2016

boegel reviewed May 11, 2016
View reviewed changes

boegel mentioned this pull request May 11, 2016

{toolchain}[pomkl/2016.04] HPL 2.1 (REVIEW) #3044

Merged

boegel mentioned this pull request May 12, 2016

remove hack in HPL pomkl easyconfig for linking with -ldl #3046

Merged

boegel mentioned this pull request May 12, 2016

include '-ldl' in $LIBBLAS*/* & co when linking with Intel MKL 11.x or newer easybuilders/easybuild-framework#1761

Merged

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bartoldeman commented Apr 15, 2016 •

edited by boegel

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