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remove --with-64 from configopts for recent BLAST+ versions#20784

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boegel merged 1 commit intoeasybuilders:developfrom
bedroge:blast+_arm_configopts
Jun 10, 2024
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remove --with-64 from configopts for recent BLAST+ versions#20784
boegel merged 1 commit intoeasybuilders:developfrom
bedroge:blast+_arm_configopts

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@bedroge bedroge commented Jun 10, 2024

Compiling BLAST+ on Arm fails in the configure step:

checking whether this system supports --with(out)-64... no
configure: error: cannot continue; please try different options

The --with-64 adds -m64 to the compiler flags, and this is not supported on Arm (and neither on for instance RISC-V). Without the flag, it just doesn't add -m64 (which should be fine too) and I preferred that over having to add if statements for distinguishing between the different architectures.

@bedroge bedroge added bug fix aarch64 Related to Arm 64-bit (aarch64) labels Jun 10, 2024
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bedroge commented Jun 10, 2024

For reference, I checked the BLAST+ binary tarballs, they contain a file ncbi_package_info that describes how it was built. For both 2.14.1 and 2.15.0 they use the following for x86_64:

PACKAGE_CONFIG: Linux64-Centos : gcc : ./c++/compilers/unix/GCC.sh --with-static --without-dll --with-bin-release --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-experimental=Int8GI --without-gnutls --without-gcrypt --with-vdb=/panfs/traces01.be-md.ncbi.nlm.nih.gov/trace_software/vdb --with-static-vdb --with-build-root-sfx=--Linux64-Centos-gcc --with-flat-makefile --with-ncbi-public --without-ccache --without-caution --without-runpath --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal

So they don't use --with-64 either.

@bedroge bedroge added the EESSI Related to EESSI project label Jun 10, 2024
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bedroge commented Jun 10, 2024

Test report by @bedroge
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 22.04, x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.10.12
See https://gist.github.com/bedroge/fdbe6bac17d01c000a5c0b10aa8c491b for a full test report.

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bedroge commented Jun 10, 2024

Successfully tested with the EESSI bot on an Arm node: EESSI/software-layer#599 (comment)

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bedroge commented Jun 10, 2024

Test report by @bedroge
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
interactive1 - Linux Rocky Linux 8.9, x86_64, AMD EPYC-Milan Processor (zen2), Python 3.6.8
See https://gist.github.com/bedroge/cb8fb299ef61f2910409800c0f75ab00 for a full test report.

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bedroge commented Jun 10, 2024

@boegelbot please test @ generoso

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boegelbot commented Jun 10, 2024

@bedroge: Request for testing this PR well received on login1

PR test command 'EB_PR=20784 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20784 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 13702

Test results coming soon (I hope)...

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bedroge commented Jun 10, 2024

@boegelbot please test @ jsc-zen3

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boegelbot commented Jun 10, 2024

@bedroge: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=20784 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20784 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 4352

Test results coming soon (I hope)...

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boegel approved these changes Jun 10, 2024
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lgtm

@boegel boegel added this to the 4.9.2 milestone Jun 10, 2024
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boegelbot commented Jun 10, 2024

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (3 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/0af3eb77c8c293e4175933b39cf8abd8 for a full test report.

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boegelbot commented Jun 10, 2024

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (3 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/ae00171ba521ddfc6918f4501bd3aae8 for a full test report.

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boegel commented Jun 10, 2024

Test report by @boegel
SUCCESS
Build succeeded for 7 out of 7 (3 easyconfigs in total)
node3132.skitty.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/boegel/2a56457397c1bc517511628eec24ef41 for a full test report.

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boegel commented Jun 10, 2024

failed test reports are fallout due to overlapped testing of #20794

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boegel commented Jun 10, 2024

@boegelbot please test @ jsc-zen3
EB_ARGS="BLAST+-2.14.1-gompi-2023a.eb"

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boegelbot commented Jun 10, 2024

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=20784 EB_ARGS="BLAST+-2.14.1-gompi-2023a.eb" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20784 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 4358

Test results coming soon (I hope)...

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boegel commented Jun 10, 2024 •
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@boegelbot please test @ generoso
EB_ARGS="BLAST+-2.14.1-gompi-2023a.eb"
CORE_CNT=16

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boegelbot commented Jun 10, 2024

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=20784 EB_ARGS="BLAST+-2.14.1-gompi-2023a.eb" EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20784 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 13710

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

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boegelbot commented Jun 10, 2024

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/523f1d3161677e32c9f5f5e2f2490341 for a full test report.

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boegelbot commented Jun 10, 2024

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cnx1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/e539e06cd83bd11c927d1734d1e1fac6 for a full test report.

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boegel commented Jun 10, 2024

Going in, thanks @bedroge!

@boegel boegel merged commit b2cb652 into easybuilders:develop Jun 10, 2024
@bedroge bedroge deleted the blast+_arm_configopts branch June 10, 2024 20:59
@bedroge bedroge mentioned this pull request Jul 23, 2024
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aarch64 Related to Arm 64-bit (aarch64) bug fix EESSI Related to EESSI project

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