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GEMMA version 0.98
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@pjotrp pjotrp released this 29 Sep 09:37
· 182 commits to master since this release
v0.98
fe9bceb

With the v0.98 release GEMMA has stabilized, is faster than ever, and
contains extensive error checking. This release contains quite a few
bug fixes, hardware-based floating point checking and speedups.

  • GEMMA is faster than ever #136
  • Fixes log standing 'GSL ERROR: matrix is singular in lu.c at line
    266' mvlmm regression with correlated phenotypes #179 with
    9952786 -
    (thank you @HannahVMeyer and @xiangzhou)
  • Adds x86 hardware based floating point error checking #161, see 70f4196
  • Provide a static release of GEMMA again for Linux #162
  • Fixes clang++ build on MacOS #160
  • Enforce failed for 0.00 in src/io.cpp at line 1431 in BimbamKin #149
  • -no-check is default now
  • Force SIGINT on error so debuggers can get a stack trace
  • Improved CalcPab functions to not break on division by zero
    genenetwork@8010061
    (thank you @xiangzhou)
  • Add Windows MingW compilation support (thanks @DannyArends)
  • Fully utilizing GNU Guix containers for a build system (see INSTALL.md)
  • Updated manual by @xiangzhou)

Note: This is the last purely C/C++ compilable release because we are
integrating faster-lmm-d code for new functionality in the next
version. Also we are working on a Python and R interface.

To install the image, download and

md5sum gemma-0.98.gz
875cde6d37fb96014356b15dc77ebf93  gemma-0.98.gz
gzip -d gemma-0.98.gz
chmod a+x gemma-0.98
./gemma-0.98

GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018

type ./gemma -h [num] for detailed help

The binary images were reproducibly built on x86_64 with

guix pull -l
Generation 4    Sep 25 2018 10:16:39    (current)
  guix 932839f
    repository URL: https://git.savannah.gnu.org/git/guix.git
    branch: origin/master
    commit: 932839ff124ff3b0dd3070914fb1c5beec69bf32

guix environment -C guix --ad-hoc gcc gdb gfortran:lib gsl eigen openblas zlib bash ld-wrapper perl
make clean && make -j 16 && make fast-check
for x in `ldd bin/gemma|cut -d ' ' -f 3` ; do realpath $x ; done
  /gnu/store/kf8pva0pgwg6yrcpa52iri293j8fc56q-gsl-2.5/lib/libgsl.so.23.1.0
  /gnu/store/fxiwj2wpp11sif613axdax7gmwzsg6kp-zlib-1.2.11/lib/libz.so.1.2.11
  /gnu/store/zpm494j02m6snmvcjxcdqxkgwx43nkmj-openblas-0.3.2/lib/libopenblasp-r0.3.2.so
  /gnu/store/4ik1aw34nxs4372xlimvnaq2ilhclwpw-gfortran-8.2.0-lib/lib/libgfortran.so.5.0.0
  /gnu/store/bmaxmigwnlbdpls20px2ipq1fll36ncd-gcc-8.2.0-lib/lib/libquadmath.so.0.0.0
  /gnu/store/bmaxmigwnlbdpls20px2ipq1fll36ncd-gcc-8.2.0-lib/lib/libstdc++.so.6.0.25
  /gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libm-2.27.so
  /gnu/store/bmaxmigwnlbdpls20px2ipq1fll36ncd-gcc-8.2.0-lib/lib/libgcc_s.so.1
  /gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libpthread-2.27.so
  /gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libc-2.27.so
  /gnu/store/1yym4xrvnlsvcnbzgxy967cg6dlb19gq-gfortran-5.5.0-lib/lib/libgfortran.so.3.0.0

# build static image
make clean && make FORCE_STATIC=1 -j 16 && make check
Assets 3
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