{bio}[foss/2020b] AlphaFold v2.0.0 w/ Python 3.8.6 #13744

boegel · 2021-08-14T04:39:00Z

(created using eb --new-pr)
requires ~~#13622~~ (jax)

~~marked as WIP because I haven't tested the installation yet...~~

boegel · 2021-08-14T04:46:43Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3503.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/d2b2a4dba3e5ee1729a043f9f37cf215 for a full test report.

branfosj

That is from a quick test - I'm downloading the data...

easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb

…ndencies, also install scripts and 'alphafold' command

… take into account $ALPHAFOLD_DATA_DIR, fix sanity check command

…lphafold.py script

easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch

… of cores to use

…, switch to installing AlphaFold via 'components' because it now requires multiple source files

…o avoid hardcoding core count for jackhmmer and hhblits

… defined

SebastianAchilles · 2021-08-24T21:58:08Z

Test report by @SebastianAchilles
FAILED
Build succeeded for 0 out of 2 (2 easyconfigs in total)
jwvis00.juwels - Linux centos linux 8.4.2105, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, Python 3.6.8
See https://gist.github.com/a9b4c8daf6aa1c435d3385b513496532 for a full test report.

SebastianAchilles · 2021-08-25T21:40:23Z

Test report by @SebastianAchilles
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
jwvis00.juwels - Linux centos linux 8.4.2105, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, Python 3.6.8
See https://gist.github.com/a038f890871b5ddfa873d0a7f7aee9a1 for a full test report.

…asyconfigs into 20210814063853_new_pr_AlphaFold200

boegel · 2021-08-28T08:48:31Z

@boegelbot please test @ generoso

boegelbot · 2021-08-30T09:31:35Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 2 (2 easyconfigs in total)
generoso-c1-s-6 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/5bb811df976a99275ed73ebe4134f35b for a full test report.

edit (by @boegel): the installation of PDBFixer failed after a successful installation of AlphaFold, because the setup.py script for the OpenMM Python bindings happily uninstalls existing OpenMM Python bindings (regardless of where they are installed), see https://github.com/openmm/openmm/blob/master/wrappers/python/setup.py#L252.

I'll add a fix to prevent that...

…run_alphafold.py script

boegel · 2021-08-30T10:24:41Z

@boegelbot please test @ generoso
CORE_CNT=16
EB_ARGS="OpenMM-7.5.1-foss-2020b.eb PDBFixer-1.7-foss-2020b.eb AlphaFold-2.0.0-foss-2020b.eb"

boegelbot · 2021-08-30T10:25:07Z

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

PR test command 'EB_PR=13744 EB_ARGS="OpenMM-7.5.1-foss-2020b.eb PDBFixer-1.7-foss-2020b.eb AlphaFold-2.0.0-foss-2020b.eb" /apps/slurm/default/bin/sbatch --job-name test_PR_13744 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 18238

Test results coming soon (I hope)...

- notification for comment with ID 908227778 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).

boegel · 2021-08-30T10:32:44Z

Test report by @boegel
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
node3582.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/c226db76e002c79c3001eaf5f0ed8754 for a full test report.

boegelbot · 2021-08-30T10:36:20Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (3 easyconfigs in total)
generoso-x-1 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/fe954d2bf6da1b5c7824345419e7b5d3 for a full test report.

…a directory)

boegel · 2021-08-30T11:47:43Z

@boegelbot please test @ generoso

boegelbot · 2021-08-30T11:50:08Z

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

PR test command 'EB_PR=13744 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_13744 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 18239

Test results coming soon (I hope)...

- notification for comment with ID 908274823 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).

boegel · 2021-08-30T11:55:34Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3582.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/8d3b56dcfa5a2441f8984d00d62a3f3a for a full test report.

boegelbot · 2021-08-30T12:00:00Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
generoso-c1-s-6 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/f0cc2ce8c63550075e993d04d70b2746 for a full test report.

boegel · 2021-08-30T12:00:20Z

@boegelbot please test @ generoso

boegelbot · 2021-08-30T12:05:12Z

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

PR test command 'EB_PR=13744 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_13744 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 18240

Test results coming soon (I hope)...

- notification for comment with ID 908281752 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 · 2021-08-30T12:14:14Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
generoso-c1-s-6 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/cde546c296d9b86ab6b3e8492e493bc2 for a full test report.

easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb

easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-scp-path.patch

easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb

…to avoid depending on two variants of OpenMM

branfosj · 2021-08-30T13:42:38Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u08b.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/48ff12810162dcf4433884f2bbbdd4f5 for a full test report.

branfosj · 2021-08-30T13:44:55Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0212u15b.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz (broadwell), Python 3.6.8
See https://gist.github.com/d4e87dfa2c57debc995db4561f1775d9 for a full test report.

akesandgren · 2021-08-30T13:52:39Z

Test report by @akesandgren
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
b-an02.hpc2n.umu.se - Linux Ubuntu 20.04, x86_64, Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, Python 3.8.5
See https://gist.github.com/b02e790e062bb0d64aeffe25889e61a8 for a full test report.

akesandgren · 2021-08-30T13:56:01Z

Might be worth adding a modlua/tclfooter that adds a conflicts('OpenMM') of the right kind to the resulting modulefile.

boegel · 2021-08-30T14:00:10Z

Might be worth adding a modlua/tclfooter that adds a conflicts('OpenMM') of the right kind to the resulting modulefile.

That implies making assumptions about the module naming scheme though? It may be openmm rather than OpenMM...

akesandgren · 2021-08-30T14:09:45Z

mmm, we can probably benefit from a function to do this correctly.

branfosj · 2021-08-30T14:26:17Z

Going in, thanks @boegel!

branfosj · 2021-08-30T14:27:35Z

We have easybuilders/easybuild-framework#221 filed for adding the module conflicts feature to framework.

adding easyconfigs: AlphaFold-2.0.0-foss-2020b.eb

4ce31c1

boegel added the new label Aug 14, 2021

boegel changed the title ~~{bio}[foss/2020b] AlphaFold v2.0.0 w/ Python 3.8.6~~ {bio}[foss/2020b] AlphaFold v2.0.0 w/ Python 3.8.6 (WIP) Aug 14, 2021

boegel marked this pull request as draft August 14, 2021 04:41

boegel added this to the 4.x milestone Aug 14, 2021

stick to TensorFlow 2.4.1 dependency for AlphaFold 2.0.0 with foss/2020b

4d65a50

branfosj requested changes Aug 15, 2021

View reviewed changes

easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb Show resolved Hide resolved

easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb Show resolved Hide resolved

boegel added 4 commits August 16, 2021 09:48

add patch for AlphaFold to fix setup.py, add OpenMM and PDBFixer depe…

75b034f

…ndencies, also install scripts and 'alphafold' command

add missing dependencies for AlphaFold + patch to pick up on them and…

9fb09ee

… take into account $ALPHAFOLD_DATA_DIR, fix sanity check command

avoid warnigns about non-default values for required options to run_a…

7ecf851

…lphafold.py script

fix default value for template_mmcif_dir based on \ALPHAFOLD_DATA_DIR

b7b1ccd

branfosj reviewed Aug 16, 2021

View reviewed changes

easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch Outdated Show resolved Hide resolved

boegel mentioned this pull request Aug 16, 2021

{bio}[foss-2020b] pdbfixer-1.7 required for alphahelix created #13464

Closed

boegel added 2 commits August 16, 2021 12:21

add patch for HHBlits and JackHmmer scripts to avoid hardcoded number…

c032e63

… of cores to use

include stereo_chemical_props.txt in AlphaFold installaiton directory…

08d2902

…, switch to installing AlphaFold via 'components' because it now requires multiple source files

This was referenced Aug 16, 2021

Python modules for Alphafold: currently not working! WIP #13572

Closed

Python modules for Alphafold: working. WIP #13571

Closed

boegel added 4 commits August 16, 2021 17:19

include patched OpenMM as component in AlphaFold installation

e82389d

don't pick up on \SLURM_CPUS_ON_NODE, only add environment variable t…

6cf72d7

…o avoid hardcoding core count for jackhmmer and hhblits

fix default paths to downloaded AlphaFold data

0342cb8

Merge branch 'develop' into 20210814063853_new_pr_AlphaFold200

0d5795d

branfosj mentioned this pull request Aug 16, 2021

{bio}[gompic/2020b] HMMER v3.3.2, HH-suite v3.3.0 w/ Python 3.8.6 #13752

Merged

make run_alphafold.py print a warning when $ALPHAFOLD_DATA_DIR is not…

1784637

… defined

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

e380a8c

…asyconfigs into 20210814063853_new_pr_AlphaFold200

boegel marked this pull request as ready for review August 28, 2021 08:48

boegel changed the title ~~{bio}[foss/2020b] AlphaFold v2.0.0 w/ Python 3.8.6 (WIP)~~ {bio}[foss/2020b] AlphaFold v2.0.0 w/ Python 3.8.6 Aug 28, 2021

avoid that existing OpenMM Python bindings get wiped + run tests for …

0dd5ba0

…run_alphafold.py script

fix AlphaFold sanity check (stereo_chemical_props.txt is a file, not …

a53f6c8

…a directory)

branfosj requested changes Aug 30, 2021

View reviewed changes

easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb Outdated Show resolved Hide resolved

easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-scp-path.patch Show resolved Hide resolved

easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb Outdated Show resolved Hide resolved

boegel added 2 commits August 30, 2021 15:13

collapse PDBFixer easyconfig as extension into AlphaFold easyconfig, …

bf7ab99

…to avoid depending on two variants of OpenMM

consistently use %(version)s template in list of patches for AlphaFold

f9c5efa

branfosj approved these changes Aug 30, 2021

View reviewed changes

branfosj modified the milestones: 4.x, next release (4.4.2?) Aug 30, 2021

branfosj merged commit 92d2265 into easybuilders:develop Aug 30, 2021

boegel deleted the 20210814063853_new_pr_AlphaFold200 branch August 31, 2021 09:31

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{bio}[foss/2020b] AlphaFold v2.0.0 w/ Python 3.8.6 #13744

{bio}[foss/2020b] AlphaFold v2.0.0 w/ Python 3.8.6 #13744

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{bio}[foss/2020b] AlphaFold v2.0.0 w/ Python 3.8.6 #13744

{bio}[foss/2020b] AlphaFold v2.0.0 w/ Python 3.8.6 #13744

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