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add patch for AmberTools 23.6 to fix infinite loop of for mdgx on aarch64#25193

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branfosj merged 1 commit intoeasybuilders:developfrom
Crivella:fix-ambertools_aarch64
Feb 2, 2026
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add patch for AmberTools 23.6 to fix infinite loop of for mdgx on aarch64#25193
branfosj merged 1 commit intoeasybuilders:developfrom
Crivella:fix-ambertools_aarch64

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For a detailed description on the issue see:

@Crivella Crivella added bug fix EESSI Related to EESSI project aarch64 Related to Arm 64-bit (aarch64) labels Jan 30, 2026
@Crivella Crivella removed the change label Jan 30, 2026
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@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath=/tmp/pr-25193"

Check that the patch does not affect behavior on non aarch64 machines (should not since they have the same code in Amber 25)

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@Crivella: 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=25193 EB_ARGS="--installpath=/tmp/pr-25193" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25193 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 9535

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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Crivella commented Jan 30, 2026

Test report by @Crivella

SUCCESS
Build succeeded MANUAL REPORT (unrelated failure in uploading the report file).
crivella-desktop - Linux Ubuntu 22.04.5 LTS (Jammy Jellyfish), x86_64, 13th Gen Intel(R) Core(TM) i9-13900K (skylake), Python 3.11.14
See https://gist.github.com/Crivella/cbcb06c388f2d9d8afa37c7573e8ecc9 for a full test report.

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Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (total: 1 hour 34 mins 15 secs) (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/122def4b580fa0b98ddf89ae638cd9a7 for a full test report.

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Was also able to perform a manual build on top of EESSI on a neoverse_v1 node

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branfosj commented Feb 2, 2026

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (total: 3 hours 31 mins 46 secs) (1 easyconfigs in total)
bear-pg0210u03a - Linux RHEL 8.10, x86_64, Intel(R) Xeon(R) Platinum 8480CL (sapphirerapids), Python 3.6.8
See https://gist.github.com/branfosj/2cdc491446eb2306773f1537e9108a76 for a full test report.

@branfosj branfosj added this to the next release (5.2.1?) milestone Feb 2, 2026
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branfosj commented Feb 2, 2026

Going in, thanks @Crivella!

@branfosj branfosj merged commit 4ee0b32 into easybuilders:develop Feb 2, 2026
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@Crivella Crivella deleted the fix-ambertools_aarch64 branch February 2, 2026 22:30
@boegel boegel changed the title AmberTools: fix infinite loop of for mdgx on aarch64 add patch for AmberTools 23.6 to fix infinite loop of for mdgx on aarch64 Feb 19, 2026
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