flto gcc flag only for data.table by jangorecki · Pull Request #3880 · Rdatatable/data.table

jangorecki · 2019-09-16T19:55:46Z

follow up of #3878

jangorecki · 2019-09-16T19:58:49Z

.gitlab-ci.yml

    - mkdir -p ~/.R
-    - echo 'CFLAGS=-g0'> ~/.R/Makevars   # No -g because -g increases datatable.so size from 0.5MB to 1.5MB and breaches 'installed package size <= 5MB' note
-    - echo 'CXXFLAGS=-g0' >> ~/.R/Makevars
+    - echo 'CFLAGS=-g0 -O2 -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2'> ~/.R/Makevars # -g0 because -g increases datatable.so size from 0.5MB to 1.5MB and breaches 'installed package size <= 5MB' note


these are the defaults flags, they were disabled when writing just -g0 to Makevars so adding them now

.gitlab-ci.yml

mattdowle · 2019-09-16T20:06:03Z

I added the 1.12.4 milestone, but then removed it because this isn't the package. So it might be wasteful to pollute the tag with non-package tasks. On the other hand we're using the milestone tag to mark what's going ahead now, or not. Maybe the rule should be if it's tagged CI then we shouldn't mark the milestone.

codecov · 2019-09-16T20:08:03Z

Codecov Report

Merging #3880 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #3880   +/-   ##
=======================================
  Coverage   99.42%   99.42%           
=======================================
  Files          72       72           
  Lines       13498    13498           
=======================================
  Hits        13421    13421           
  Misses         77       77

Continue to review full report at Codecov.

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jangorecki · 2019-09-16T20:08:08Z

I think it is fine to tag milestone for stuff that is in .Rbuildignore

jangorecki · 2019-09-16T20:09:15Z

Even when having such a rule, there is no way to ensure we align to it always. It is easier to have a rule the other way around.

jangorecki · 2019-09-16T20:38:43Z

PR fixed previous flto issue: https://gitlab.com/Rdatatable/data.table/-/jobs/296558457

failure state is now due to grep, for some reason, ci yaml line

! grep "warning:" data.table.Rcheck/00install.out

is run in a job without leading !

grep "warning:" data.table.Rcheck/00install.out

OK, ! is reserved in yaml: https://stackoverflow.com/q/52145224/2490497

00install.log

* installing *source* package ‘data.table’ ...
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c assign.c -o assign.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c between.c -o between.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c bmerge.c -o bmerge.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c chmatch.c -o chmatch.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c cj.c -o cj.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c coalesce.c -o coalesce.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c dogroups.c -o dogroups.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fastmean.c -o fastmean.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fcast.c -o fcast.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fifelse.c -o fifelse.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fmelt.c -o fmelt.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c forder.c -o forder.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c frank.c -o frank.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fread.c -o fread.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c freadR.c -o freadR.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c froll.c -o froll.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c frollR.c -o frollR.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c frolladaptive.c -o frolladaptive.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fsort.c -o fsort.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fwrite.c -o fwrite.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fwriteR.c -o fwriteR.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c gsumm.c -o gsumm.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c ijoin.c -o ijoin.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c init.c -o init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c inrange.c -o inrange.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c nafill.c -o nafill.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c nqrecreateindices.c -o nqrecreateindices.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c openmp-utils.c -o openmp-utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c quickselect.c -o quickselect.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c rbindlist.c -o rbindlist.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c reorder.c -o reorder.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c shift.c -o shift.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c subset.c -o subset.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c transpose.c -o transpose.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c types.c -o types.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c uniqlist.c -o uniqlist.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c vecseq.c -o vecseq.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O3 -flto -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c wrappers.c -o wrappers.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -lz -L/usr/lib/R/lib -lR
mv data.table.so datatable.so
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/assign.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/between.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/bmerge.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/chmatch.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/cj.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/coalesce.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/dogroups.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/fastmean.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/fcast.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/fifelse.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/fmelt.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/forder.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/frank.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/fread.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/freadR.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/froll.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/frollR.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/frolladaptive.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/fsort.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/fwrite.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/fwriteR.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/gsumm.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/ijoin.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/init.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/inrange.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/nafill.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/nqrecreateindices.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/openmp-utils.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/quickselect.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/rbindlist.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/reorder.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/shift.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/subset.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/transpose.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/types.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/uniqlist.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/utils.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/vecseq.o: plugin needed to handle lto object
/usr/bin/nm: /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00_pkg_src/data.table/src/wrappers.o: plugin needed to handle lto object
installing to /builds/Rdatatable/data.table/bus/test-rel-lin/data.table.Rcheck/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)

flto gcc flag only for data.table

3641656

jangorecki added the ci label Sep 16, 2019

jangorecki commented Sep 16, 2019

View reviewed changes

.gitlab-ci.yml Show resolved Hide resolved

jangorecki requested a review from mattdowle September 16, 2019 20:00

mattdowle modified the milestone: 1.12.4 Sep 16, 2019

mattdowle merged commit 84623f8 into master Sep 16, 2019

mattdowle deleted the lto-dt-only branch September 16, 2019 20:12

jangorecki mentioned this pull request Sep 16, 2019

yaml fix for reserved char #3881

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flto gcc flag only for data.table#3880

flto gcc flag only for data.table#3880
mattdowle merged 1 commit intomasterfrom
lto-dt-only

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