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Conference call notes 20160622

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Kenneth Hoste edited this pageJun 22, 2016· 8 revisions

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Notes on the 54th EasyBuild conference call, Wednesday June 22nd 2016 (5pm - 5.30pm CET)

Attendees

Alphabetical list of attendees (4):

  • Fotis Georgatos (Illumina, UK)
  • Kenneth Hoste (HPC-UGent)
  • Adam Huffman (Francis Crick Institute, UK)
  • Alan O'Cais (JSC, Germany)

Agenda

  • outlook to future EasyBuild releases: v2.8.2 (July'16), v2.9.0 (Sept'16), v3.0.0 (Nov'16)

  • discuss test results for candidates for foss/2016b and intel/2016b common toolchain candidates

  • Q&A

Notes

outlook to future EasyBuild releases

  • EasyBuild v2.8.2: (mostly) bug fix release before summer holidays

  • EasyBuild v2.9.0: feature release, preparing for v3.0.0

    • planned for Sept'16
    • make sure behaviour that will be broken in v3.0.0 is deprecated
    • alternatives are available for evaluation

  • EasyBuild v3.0.0: major new releases, breaking backwards compatibility in minor ways

    • Nov'16 (?)
    • hopefully incl. support for RPATH linking
2016b toolchain candidates: testing results

  • foss/2016.06 as prime candidate for foss/2016b:

    • GCC 5.4 + binutils 2.26
    • OpenMPI 1.10.3
    • OpenBLAS 0.2.18 + LAPACK 3.6.0 + ScaLAPACK 2.0.2
    • FFTW 3.3.4
    • note: all latest & greatest, except for GCC 6.1

  • intel/2016.03-GCC-5.4 as prime candidate for intel/2016b:

    • GCC 5.4 + binutils 2.26
    • icc & ifort 2016.3.210
    • impi 5.1.13
    • imkl 11.3.3.210
    • note: all latest & greatest

  • test results, rebuilding all 2016a easyconfigs via naive --try-toolchain:

    • foss/2016.06: success for 278/279 easyconfigs

      • OK: BioPerl; Boost; BWA; GMP; GROMACS; GSL; HDF5; IPython; LLVM; libX; MariaDB; Mesa; netCDF*; Perl 5.22.1 w/ extensions; Python 2.7.11 & 3.5.1 w/ numpy/scipy/pandas/...; R 3.2.3 w/ extensions; QT 4.8.7 & 5.6.0; SAMtools; etc.

      • only RMBlast failed due to a hard check on the GCC version

    • intel/2016.03-GCC-5.4: success for 384/413 easyconfigs

      • OK: BioPerl; BWA; Boost; CLHEP; FSL; GAMESS-US; GATE 6.2 & 7.1; GMP; GROMACS; GSL; Geant4; HDF5; IPython; LLVM; libX; MariaDB; Mesa; NGS; netCDF*; OpenFOAM 2.2.2 & OpenFOAM-Extend 3.2; Perl 5.20.3 & 5.22.2; Python 2.7.11 & 3.5.1 w/ numpy/scipy/pandas/scikit-learn/...; Qt 4.8.7; R 3.2.3 w/ extensions; ROOT; SAMtools; WRF; etc.

      • 11 failed builds + 18 more due to missing deps:

        • HISAT2: failed due to linking with g++ to Intel-built libraries (easy fix?)
        • Amber: failed due to hard check on GCC version (by CUDA)
          • GCC 5 compat fixed in next release of CUDA 8.x?
        • mysqlclient & MySQL-Python: weird symbol issue with libmysqlclient library (ld.gold issue?)
        • PCMSolver: error: namespace "std" has no member "nullptr_t"
        • GATE 7.2: error: no operator "<<" matches these operands (missing "#include <string>" ?)
        • Qt 5.6.0: error #809: exception specification for virtual function ... is incompatible with that of overridden function
        • HarfBuzz & GST-plugins: error: identifier "__builtin_uadd_overflow" is undefined (not implemented by Intel)

      • will be pushed to ML for further feedback

      • Alan: CUDA is not (officially) compatible yet with GCC 5.x

      • Fotis: overview of software (versions) vs toolchains in a 'matrix' online: what (doesn't) work, etc?

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