{bio,data,lib}[foss/2020b,fosscuda/2020b] AlphaPulldown v0.30.4, cctbx-base v2020.8, Kalign v2.0.4 w/ Python 3.8.6 by deniskristak · Pull Request #17774 · easybuilders/easybuild-easyconfigs

deniskristak · 2023-04-20T21:36:34Z

(created using eb --new-pr)

…22.8-foss-2020b.eb, Kalign-2.0.4-GCCcore-11.2.0.eb and patches: AlphaPulldown-0.30.4_fix-deps.patch

Micket · 2023-04-21T14:45:29Z

@@ -0,0 +1,34 @@
+# making AlphaPulldown's dependencies less strict


some of these are making it a lot less strict. Especially TF from 2.9 to 2.4. Is this known to still work correctly?

well, we need the 2020b toolchain, as the cctbx-base binary is built for Python 3.8 and there are no alternatives...
when you brought it up, I actually checked the usage and differences between versions.
I've found that all the usages of tensorflow appear to begin with import tensorflow.compat.v1, which suggests that there is no reason to keep the deps this strict.

I looked into this with Denis, and unfortunately we indeed are forced to stick to Python 3.8 here, unless a lot more effort is made to figure out how to get a from-source install of cctbx-base to work (which doesn't seem trivial).

So we're proceeding under the assumption that the version requirements here are a bit too strict.
If problems emerge when using AlphaPullDown because of older dependency versions, we'll revisit this then

removed unnecessary Kalign

messed up version, removing this one as it uses the wrong version

deniskristak · 2023-05-05T18:07:17Z

@boegel repaired, thanks for all the feedback. Along the way, I realised I've messed up the version of the original file (even though the file downloaded was correct so apart from easyconfig name, all is good) so I had to delete the original one and replace it with the correctly named one.

boegel · 2023-05-10T08:23:43Z

@boegelbot please test @ generoso

boegelbot · 2023-05-10T08:25:11Z

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

PR test command 'EB_PR=17774 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17774 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10771

Test results coming soon (I hope)...

Details

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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).

boegelbot · 2023-05-10T08:30:24Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/6cf9e8a15e8333fd90dd2abac0bdd156 for a full test report.

boegel · 2023-05-16T19:52:19Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3110.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/0b37ba0dc2bfb4c2ae9ac16e6abaa788 for a full test report.

boegel · 2023-05-23T09:09:08Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-05-23T09:12:09Z

@boegel: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=17774 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17774 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2649

Test results coming soon (I hope)...

Details

- notification for comment with ID 1558868696 processed

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).

boegelbot · 2023-05-23T12:19:21Z

Test report by @boegelbot
FAILED
Build succeeded for 12 out of 14 (2 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/2c7ff18f4b921ccbb25434797695e868 for a full test report.

edit (by @boegel):

FATAL: corrupt installation: file '/home/boegelbot/.cache/bazel/_bazel_boegelbot/install/cb67963ea69cfe717114718f22c9a96d/A-server.jar' is missing or modified.  Please remove '/home/boegelbot/.cache/bazel/_bazel_boegelbot/install/cb67963ea69cfe717114718f22c9a96d' and try again.

I've removed ~/.cache/bazel on jsc-zen2, trying again...

boegel · 2023-05-31T15:15:31Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-05-31T15:17:08Z

@boegel: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=17774 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17774 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2678

Test results coming soon (I hope)...

Details

- notification for comment with ID 1570431415 processed

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).

boegelbot · 2023-05-31T15:21:21Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (2 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/68f87be4afb51b08dc2e648ec10f42bb for a full test report.

boegel · 2023-06-02T16:01:28Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3307.joltik.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz (cascadelake), 1 x NVIDIA Tesla V100-SXM2-32GB, 530.30.02, Python 3.6.8
See https://gist.github.com/boegel/f7c5eb2758fe11761d1fc341d0325287 for a full test report.

remark answered

boegel

lgtm

boegel · 2023-06-02T16:12:18Z

Going in, thanks @deniskristak!

adding easyconfigs: AlphaPulldown-0.30.4-foss-2020b.eb, cctbx-base-20…

7459490

…22.8-foss-2020b.eb, Kalign-2.0.4-GCCcore-11.2.0.eb and patches: AlphaPulldown-0.30.4_fix-deps.patch

deniskristak added new update labels Apr 20, 2023

code style checks

afed07f

Micket previously requested changes Apr 21, 2023

View reviewed changes

deniskristak and others added 2 commits May 2, 2023 13:30

Delete Kalign-2.0.4-GCCcore-11.2.0.eb

44666e9

removed unnecessary Kalign

style improvements

69dc591

boegel requested changes May 4, 2023

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deniskristak and others added 3 commits May 5, 2023 19:57

review updates

6ccedd9

review updates

ff37876

Delete cctbx-base-2022.8-foss-2020b.eb

02112be

messed up version, removing this one as it uses the wrong version

fixing gh errors

76f17dd

easybuilders deleted a comment from boegelbot May 10, 2023

boegel added this to the 4.x milestone May 10, 2023

deniskristak mentioned this pull request May 15, 2023

AlphaPullDown vscentrum/vsc-software-stack#39

Closed

minor code cleanup in easyconfigs for cctbx-base and AlphaPullDown

97c16ab

boegel changed the title ~~{bio,data,lib}[foss/2020b] AlphaPulldown v0.30.4, cctbx-base v2022.8, Kalign v2.0.4 w/ Python 3.8.6~~ {bio,data,lib}[foss/2020b] AlphaPulldown v0.30.4, cctbx-base v2020.8, Kalign v2.0.4 w/ Python 3.8.6 May 23, 2023

adding CUDA toolchains

ae982b6

boegel changed the title ~~{bio,data,lib}[foss/2020b] AlphaPulldown v0.30.4, cctbx-base v2020.8, Kalign v2.0.4 w/ Python 3.8.6~~ {bio,data,lib}[foss/2020b,fosscuda/2020b] AlphaPulldown v0.30.4, cctbx-base v2020.8, Kalign v2.0.4 w/ Python 3.8.6 Jun 2, 2023

boegel approved these changes Jun 2, 2023

View reviewed changes

boegel merged commit 0de139b into easybuilders:develop Jun 2, 2023

boegel modified the milestones: 4.x, next release (4.7.3?) Jun 23, 2023

		@@ -0,0 +1,34 @@
		# making AlphaPulldown's dependencies less strict

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