add R 4.1.0 with foss/2021a to EESSI pilot 2021.12 by smoretti · Pull Request #210 · EESSI/software-layer

smoretti · 2022-12-14T15:31:36Z

Add R-4.1.0-foss-2021a.eb in the EESSI 2021.12 pilot

edit: checklist:

boegel · 2022-12-20T15:15:57Z

+echo ">> Installing R 4.1.0 (better be patient)..."
+ok_msg="R installed, wow!"
+fail_msg="Installation of R failed, so sad..."
+$EB --from-pr 16386 R-4.1.0-foss-2021a.eb --robot --parallel-extensions-install --experimental


@smoretti Instructing EasyBuild to download the R easyconfig from easybuilders/easybuild-easyconfigs#16386 is problematic currently, it fails with:

ERROR: Couldn't find path to patched file /tmp/eb-90906wdf/files_pr16386/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb

That's a result of the large number of easyconfigs being touched in this PR, and the changes that were made in easybuilders/easybuild-easyconfigs#16697 (so hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb no longer exists in the develop branch).

To some extent, that's a bug in EasyBuild (maybe), but we'll need to work around it.

The most recent change to R-4.1.0-foss-2021a.eb that really matters was made in easybuilders/easybuild-easyconfigs#16011 (checksum fix), so let's use that instead?

I thought using a PR number and an eb filename should avoid using all the other eb files from the PR

For the installation, yes, but for the initial setup, EasyBuild will make sure all easyconfig files touched in a PR are set up in a temporary directory when using --from-pr (and when using a merged PR, it uses the easyconfigs from the develop branch)

boegel · 2022-12-20T15:25:15Z

With the current installations in EESSI pilot 2021.12:

57 out of 95 required modules missing

Details

* pixman/0.40.0-GCCcore-10.3.0 (pixman-0.40.0-GCCcore-10.3.0.eb)
* Bison/3.7.6-GCCcore-10.3.0 (Bison-3.7.6-GCCcore-10.3.0.eb)
* PCRE2/10.36-GCCcore-10.3.0 (PCRE2-10.36-GCCcore-10.3.0.eb)
* libunwind/1.4.0-GCCcore-10.3.0 (libunwind-1.4.0-GCCcore-10.3.0.eb)
* libpng/1.6.37-GCCcore-10.3.0 (libpng-1.6.37-GCCcore-10.3.0.eb)
* nettle/3.7.2-GCCcore-10.3.0 (nettle-3.7.2-GCCcore-10.3.0.eb)
* NASM/2.15.05-GCCcore-10.3.0 (NASM-2.15.05-GCCcore-10.3.0.eb)
* libjpeg-turbo/2.0.6-GCCcore-10.3.0 (libjpeg-turbo-2.0.6-GCCcore-10.3.0.eb)
* Brotli/1.0.9-GCCcore-10.3.0 (Brotli-1.0.9-GCCcore-10.3.0.eb)
* freetype/2.10.4-GCCcore-10.3.0 (freetype-2.10.4-GCCcore-10.3.0.eb)
* Ninja/1.10.2-GCCcore-10.3.0 (Ninja-1.10.2-GCCcore-10.3.0.eb)
* fontconfig/2.13.93-GCCcore-10.3.0 (fontconfig-2.13.93-GCCcore-10.3.0.eb)
* Mako/1.1.4-GCCcore-10.3.0 (Mako-1.1.4-GCCcore-10.3.0.eb)
* Meson/0.58.0-GCCcore-10.3.0 (Meson-0.58.0-GCCcore-10.3.0.eb)
* GLib/2.68.2-GCCcore-10.3.0 (GLib-2.68.2-GCCcore-10.3.0.eb)
* jbigkit/2.1-GCCcore-10.3.0 (jbigkit-2.1-GCCcore-10.3.0.eb)
* gzip/1.10-GCCcore-10.3.0 (gzip-1.10-GCCcore-10.3.0.eb)
* X11/20210518-GCCcore-10.3.0 (X11-20210518-GCCcore-10.3.0.eb)
* libdrm/2.4.106-GCCcore-10.3.0 (libdrm-2.4.106-GCCcore-10.3.0.eb)
* cairo/1.16.0-GCCcore-10.3.0 (cairo-1.16.0-GCCcore-10.3.0.eb)
* libglvnd/1.3.3-GCCcore-10.3.0 (libglvnd-1.3.3-GCCcore-10.3.0.eb)
* Tk/8.6.11-GCCcore-10.3.0 (Tk-8.6.11-GCCcore-10.3.0.eb)
* LLVM/11.1.0-GCCcore-10.3.0 (LLVM-11.1.0-GCCcore-10.3.0.eb)
* lz4/1.9.3-GCCcore-10.3.0 (lz4-1.9.3-GCCcore-10.3.0.eb)
* zstd/1.4.9-GCCcore-10.3.0 (zstd-1.4.9-GCCcore-10.3.0.eb)
* Mesa/21.1.1-GCCcore-10.3.0 (Mesa-21.1.1-GCCcore-10.3.0.eb)
* libGLU/9.0.1-GCCcore-10.3.0 (libGLU-9.0.1-GCCcore-10.3.0.eb)
* LibTIFF/4.2.0-GCCcore-10.3.0 (LibTIFF-4.2.0-GCCcore-10.3.0.eb)
* Xvfb/1.20.11-GCCcore-10.3.0 (Xvfb-1.20.11-GCCcore-10.3.0.eb)
* NLopt/2.7.0-GCCcore-10.3.0 (NLopt-2.7.0-GCCcore-10.3.0.eb)
* ICU/69.1-GCCcore-10.3.0 (ICU-69.1-GCCcore-10.3.0.eb)
* libogg/1.3.4-GCCcore-10.3.0 (libogg-1.3.4-GCCcore-10.3.0.eb)
* FLAC/1.3.3-GCCcore-10.3.0 (FLAC-1.3.3-GCCcore-10.3.0.eb)
* libvorbis/1.3.7-GCCcore-10.3.0 (libvorbis-1.3.7-GCCcore-10.3.0.eb)
* libsndfile/1.0.31-GCCcore-10.3.0 (libsndfile-1.0.31-GCCcore-10.3.0.eb)
* UDUNITS/2.2.28-GCCcore-10.3.0 (UDUNITS-2.2.28-GCCcore-10.3.0.eb)
* Szip/2.1.1-GCCcore-10.3.0 (Szip-2.1.1-GCCcore-10.3.0.eb)
* GSL/2.7-GCC-10.3.0 (GSL-2.7-GCC-10.3.0.eb)
* GLPK/5.0-GCCcore-10.3.0 (GLPK-5.0-GCCcore-10.3.0.eb)
* Ghostscript/9.54.0-GCCcore-10.3.0 (Ghostscript-9.54.0-GCCcore-10.3.0.eb)
* nodejs/14.17.0-GCCcore-10.3.0 (nodejs-14.17.0-GCCcore-10.3.0.eb)
* JasPer/2.0.28-GCCcore-10.3.0 (JasPer-2.0.28-GCCcore-10.3.0.eb)
* HDF5/1.10.7-gompi-2021a (HDF5-1.10.7-gompi-2021a.eb)
* LittleCMS/2.12-GCCcore-10.3.0 (LittleCMS-2.12-GCCcore-10.3.0.eb)
* ImageMagick/7.0.11-14-GCCcore-10.3.0 (ImageMagick-7.0.11-14-GCCcore-10.3.0.eb)
* GEOS/3.9.1-GCC-10.3.0 (GEOS-3.9.1-GCC-10.3.0.eb)
* PCRE/8.44-GCCcore-10.3.0 (PCRE-8.44-GCCcore-10.3.0.eb)
* libgit2/1.1.0-GCCcore-10.3.0 (libgit2-1.1.0-GCCcore-10.3.0.eb)
* PROJ/8.0.1-GCCcore-10.3.0 (PROJ-8.0.1-GCCcore-10.3.0.eb)
* libiconv/1.16-GCCcore-10.3.0 (libiconv-1.16-GCCcore-10.3.0.eb)
* Doxygen/1.9.1-GCCcore-10.3.0 (Doxygen-1.9.1-GCCcore-10.3.0.eb)
* netCDF/4.8.0-gompi-2021a (netCDF-4.8.0-gompi-2021a.eb)
* libgeotiff/1.6.0-GCCcore-10.3.0 (libgeotiff-1.6.0-GCCcore-10.3.0.eb)
* libtirpc/1.3.2-GCCcore-10.3.0 (libtirpc-1.3.2-GCCcore-10.3.0.eb)
* HDF/4.2.15-GCCcore-10.3.0 (HDF-4.2.15-GCCcore-10.3.0.eb)
* GDAL/3.3.0-foss-2021a (GDAL-3.3.0-foss-2021a.eb)
* R/4.1.0-foss-2021a (R-4.1.0-foss-2021a.eb)

… installation problem for libXfont2 component

boegel

@smoretti We need to install X11 via a PR too, or the installation fails due to a missing patch.

Fixed in smoretti#1

install X11 dependency for R 4.1.0 via PR to pick up patch that fixes installation problem for libXfont2 component

eessi-bot · 2023-01-14T15:09:06Z

New job on instance eessi-bot-citc-aws for architecture x86_64-intel-haswell in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.01/pr_210/3310

date	job status	comment
Jan 14 15:09:05 UTC 2023	submitted	job id `3310` awaits release by job manager
Jan 14 15:09:21 UTC 2023	released	job awaits launch by Slurm scheduler
Jan 14 15:10:33 UTC 2023	running	job 3310 is running
Jan 14 16:14:14 UTC 2023	finished	😢 FAILURE Found slurm output `slurm-3310.out` in job dir Slurm output lacks message "No missing modules!".

edit (@boegel): trouble during installation of Ghostscript dependency for R:

== FAILED: Installation ended unsuccessfully (build directory: /tmp/bot/easybuild/build/Ghostscript/9.54.0/GCCcore-10.3.0): build failed (first 300 chars): cmd "make so && make soinstall" exited with exit code 2 and output:

The problem can be reproduced on non-AWS nodes too, actual problem is:

mv: cannot overwrite directory '/cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/software/Ghostscript/9.54.0-GCCcore-10.3.0/share/man/./man1/dvipdf.1' with non-directory
mv: cannot overwrite directory '/cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/software/Ghostscript/9.54.0-GCCcore-10.3.0/share/man/de/man1/pdf2dsc.1' with non-directory
mv: cannot overwrite directory '/cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/software/Ghostscript/9.54.0-GCCcore-10.3.0/share/man/de/man1/ps2ascii.1' with non-directory
mkdir -p /cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/software/Ghostscript/9.54.0-GCCcore-10.3.0/lib/ghostscript/9.54.0
/bin/sh -c 'for obj in ./soobj/X11.so; do \
    ./base/instcopy -c -m 755 $obj /cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/software/Ghostscript/9.54.0-GCCcore-10.3.0/lib/ghostscript/9.54.0/; done'
for f in ./contrib/uniprint/*.upp; do \
    ./base/instcopy -c -m 644 $f /cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/software/Ghostscript/9.54.0-GCCcore-10.3.0/share/ghostscript/9.54.0/lib || exit 1; \
done
mv: cannot overwrite directory '/cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/software/Ghostscript/9.54.0-GCCcore-10.3.0/share/ghostscript/9.54.0/lib/Stc670pl.upp' with non-directory
make[1]: *** [contrib/contrib.mak:1243: extra-upp-install] Error 1
make[1]: Leaving directory '/tmp/easybuild/build/Ghostscript/9.54.0/GCCcore-10.3.0/ghostscript-9.54.0'
make: *** [base/unix-dll.mak:391: soinstall] Error 2

There are a lot more of these mv: cannot overwrite directory ... with non-directory errors above too.

Update: This problem doesn't seem to occur with the updated build container, so should be resolved once #219 gets merged.

Overview, build with previous (debian10) build container:

failed for: x86_64-generic, x86_64-amd-zen2 (all due to Ghostscript problem above)
succeeded for: aarch64-graviton2, x86_64-intel-skylake_avx512
not run correctly for: x86_64-amd-zen3, aarch64-graviton3 (cfr. bot build script should make sure correct CPU target is used eessi-bot-software-layer#140)

eessi-bot · 2023-01-16T08:15:32Z

New job on instance eessi-bot-citc-aws for architecture x86_64-generic in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.01/pr_210/3517

date	job status	comment
Jan 16 08:15:31 UTC 2023	submitted	job id `3517` awaits release by job manager
Jan 16 08:15:34 UTC 2023	released	job awaits launch by Slurm scheduler
Jan 16 08:16:49 UTC 2023	running	job 3517 is running
Jan 16 18:59:24 UTC 2023	finished	😁 SUCCESS tarball `eessi-2021.12-software-linux-x86_64-generic-1673880338.tar.gz` (1.740 GiB) in job dir

eessi-bot · 2023-01-16T08:15:34Z

New job on instance eessi-bot-citc-aws for architecture x86_64-intel-haswell in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.01/pr_210/3518

date	job status	comment
Jan 16 08:15:33 UTC 2023	submitted	job id `3518` awaits release by job manager
Jan 16 08:16:47 UTC 2023	released	job awaits launch by Slurm scheduler
Jan 16 08:18:01 UTC 2023	running	job 3518 is running
Jan 16 18:59:33 UTC 2023	finished	😁 SUCCESS tarball `eessi-2021.12-software-linux-x86_64-intel-haswell-1673878597.tar.gz` (1.394 GiB) in job dir
Jan 19 09:22:09 UTC 2023	not uploaded	transfer of `eessi-2021.12-software-linux-x86_64-intel-haswell-1673878597.tar.gz` to S3 bucket failed
Jan 19 09:33:12 UTC 2023	uploaded	transfer of `eessi-2021.12-software-linux-x86_64-intel-haswell-1673878597.tar.gz` to S3 bucket succeeded

eessi-bot · 2023-01-16T08:15:35Z

New job on instance eessi-bot-citc-aws for architecture x86_64-intel-skylake_avx512 in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.01/pr_210/3519

date	job status	comment
Jan 16 08:15:34 UTC 2023	submitted	job id `3519` awaits release by job manager
Jan 16 08:16:45 UTC 2023	released	job awaits launch by Slurm scheduler
Jan 16 08:17:59 UTC 2023	running	job 3519 is running
Jan 16 18:59:28 UTC 2023	finished	😁 SUCCESS tarball `eessi-2021.12-software-linux-x86_64-intel-skylake_avx512-1673876419.tar.gz` (1.766 GiB) in job dir

eessi-bot · 2023-01-16T08:15:37Z

New job on instance eessi-bot-citc-aws for architecture x86_64-amd-zen2 in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.01/pr_210/3520

date	job status	comment
Jan 16 08:15:36 UTC 2023	submitted	job id `3520` awaits release by job manager
Jan 16 08:16:43 UTC 2023	released	job awaits launch by Slurm scheduler
Jan 16 08:17:57 UTC 2023	running	job 3520 is running
Jan 16 18:59:30 UTC 2023	finished	😁 SUCCESS tarball `eessi-2021.12-software-linux-x86_64-amd-zen2-1673875033.tar.gz` (1.393 GiB) in job dir
Jan 19 09:21:23 UTC 2023	not uploaded	transfer of `eessi-2021.12-software-linux-x86_64-amd-zen2-1673875033.tar.gz` to S3 bucket failed
Jan 19 09:31:44 UTC 2023	uploaded	transfer of `eessi-2021.12-software-linux-x86_64-amd-zen2-1673875033.tar.gz` to S3 bucket succeeded

eessi-bot · 2023-01-16T08:15:39Z

New job on instance eessi-bot-citc-aws for architecture x86_64-amd-zen3 in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.01/pr_210/3521

date	job status	comment
Jan 16 08:15:38 UTC 2023	submitted	job id `3521` awaits release by job manager
Jan 16 08:16:40 UTC 2023	released	job awaits launch by Slurm scheduler
Jan 16 08:17:56 UTC 2023	running	job 3521 is running
Jan 16 18:59:37 UTC 2023	finished	😁 SUCCESS tarball `eessi-2021.12-software-linux-x86_64-amd-zen3-1673870604.tar.gz` (1.393 GiB) in job dir
Jan 19 09:22:56 UTC 2023	not uploaded	transfer of `eessi-2021.12-software-linux-x86_64-amd-zen3-1673870604.tar.gz` to S3 bucket failed
Jan 19 09:34:42 UTC 2023	uploaded	transfer of `eessi-2021.12-software-linux-x86_64-amd-zen3-1673870604.tar.gz` to S3 bucket succeeded

eessi-bot · 2023-01-16T08:15:40Z

New job on instance eessi-bot-citc-aws for architecture aarch64-graviton2 in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.01/pr_210/3522

date	job status	comment
Jan 16 08:15:39 UTC 2023	submitted	job id `3522` awaits release by job manager
Jan 16 08:16:38 UTC 2023	released	job awaits launch by Slurm scheduler
Jan 16 08:17:54 UTC 2023	running	job 3522 is running
Jan 16 18:59:26 UTC 2023	finished	😁 SUCCESS tarball `eessi-2021.12-software-linux-aarch64-graviton2-1673872273.tar.gz` (1.663 GiB) in job dir

eessi-bot · 2023-01-16T08:15:42Z

New job on instance eessi-bot-citc-aws for architecture aarch64-graviton3 in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.01/pr_210/3523

date	job status	comment
Jan 16 08:15:41 UTC 2023	submitted	job id `3523` awaits release by job manager
Jan 16 08:16:36 UTC 2023	released	job awaits launch by Slurm scheduler
Jan 16 08:17:52 UTC 2023	running	job 3523 is running
Jan 16 18:59:35 UTC 2023	finished	😁 SUCCESS tarball `eessi-2021.12-software-linux-aarch64-graviton3-1673868409.tar.gz` (1.663 GiB) in job dir
Jan 19 09:22:34 UTC 2023	not uploaded	transfer of `eessi-2021.12-software-linux-aarch64-graviton3-1673868409.tar.gz` to S3 bucket failed
Jan 19 09:33:59 UTC 2023	uploaded	transfer of `eessi-2021.12-software-linux-aarch64-graviton3-1673868409.tar.gz` to S3 bucket succeeded

eessi-bot · 2023-01-19T11:56:45Z

New job on instance eessi-bot-citc-aws for architecture aarch64-generic in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.01/pr_210/3532

date	job status	comment
Jan 19 11:56:44 UTC 2023	submitted	job id `3532` awaits release by job manager
Jan 19 11:57:15 UTC 2023	released	job awaits launch by Slurm scheduler
Jan 19 11:58:17 UTC 2023	running	job 3532 is running
Jan 19 16:05:36 UTC 2023	finished	😁 SUCCESS tarball `eessi-2021.12-software-linux-aarch64-generic-1674144097.tar.gz` (1.663 GiB) in job dir
Jan 19 20:18:23 UTC 2023	uploaded	transfer of `eessi-2021.12-software-linux-aarch64-generic-1674144097.tar.gz` to S3 bucket succeeded

boegel · 2023-01-22T07:56:55Z

(finally) built and ingested for all CPU targets, so merging

Add R 4.1.0

85e83e0

boegel changed the title ~~Add R 4.1.0~~ add R 4.1.0 with foss/2021a to EESSI pilot 2021.12 Dec 20, 2022

boegel requested changes Dec 20, 2022

View reviewed changes

smoretti and others added 2 commits December 20, 2022 16:34

Move to a less problematic R 4.1.0 PR

97af63b

install X11 dependency for R 4.1.0 via PR to pick up patch that fixes…

33a3420

… installation problem for libXfont2 component

boegel mentioned this pull request Dec 20, 2022

install X11 dependency for R 4.1.0 via PR to pick up patch that fixes installation problem for libXfont2 component smoretti/EESSI_software-layer#1

Merged

boegel requested changes Dec 20, 2022

View reviewed changes

smoretti and others added 2 commits December 21, 2022 08:46

Merge pull request #1 from boegel/add-R-4.1.0

fb50159

install X11 dependency for R 4.1.0 via PR to pick up patch that fixes installation problem for libXfont2 component

Merge branch 'main' into add-R-4.1.0

6f69171

boegel added pilot-2021.12 bot:build and removed bot:build labels Jan 12, 2023

EESSI deleted a comment from eessi-bot Bot Jan 13, 2023

boegel mentioned this pull request Jan 13, 2023

flesh out script for checking on missing installations + fix it + test it in CI #218

Merged

boegel added the bot:build label Jan 14, 2023

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boegel added bot:build and removed bot:build labels Jan 15, 2023

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boegel added bot:deploy Ask bot to deploy missing software installations to EESSI bot:build and removed bot:deploy Ask bot to deploy missing software installations to EESSI bot:build labels Jan 19, 2023

boegel added the bot:deploy Ask bot to deploy missing software installations to EESSI label Jan 19, 2023

Merge branch 'main' into add-R-4.1.0

c7d7597

boegel approved these changes Jan 22, 2023

View reviewed changes

boegel merged commit 2abd447 into EESSI:main Jan 22, 2023

smoretti deleted the add-R-4.1.0 branch January 23, 2023 06:26

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