{bio}[foss/2023a] EVidenceModeler v2.1.0, FASTA v36.3.8i, PASA v2.5.3, pblat v2.5.1 by laraPPr · Pull Request #21569 · easybuilders/easybuild-easyconfigs

laraPPr · 2024-10-07T10:23:02Z

(created using eb --new-pr)

…i-GCC-12.3.0.eb, GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb, PASA-2.5.3-foss-2023a.eb, pblat-2.5.1-foss-2023a.eb

laraPPr · 2024-10-07T13:10:05Z

I had not tested the sanity check command for EVidenceModeler yet. The one that is now included fails with this:

Sanity check failed: sanity check command $EVM_HOME/EVidenceModeler -h exited 

with code 255 (output: 

################# Evidence Modeler ##############################

#

#  parameters:

#

#  Required:

# 

#  --sample_id <str>           sample_id (for naming outputs)

#  --genome <str>              geno (took 36 secs)

The output looks correct, its just the exit code where EasyBuild fails over.

Shall I remove sanity_check_commands or is their a work around for this @boegel?

laraPPr · 2024-10-07T14:58:48Z

Test report by @laraPPr
FAILED
Build succeeded for 4 out of 5 (5 easyconfigs in total)
node4003.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.11.3
See https://gist.github.com/laraPPr/761ee2d50d4b491c40bcf163527a11ce for a full test report.

boegel · 2024-10-08T17:38:54Z

@laraPPr I would use "$EVM_HOME/EVidenceModeler -h | grep 'Evidence Modeler' " as sanity check command.

You may need to also redirect stderr to stdout, so: "$EVM_HOME/EVidenceModeler -h 2>&1 | grep 'Evidence Modeler' "

laraPPr · 2024-10-09T10:38:06Z

Test report by @laraPPr
SUCCESS
Build succeeded for 0 out of 0 (5 easyconfigs in total)
node4002.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.11.3
See https://gist.github.com/laraPPr/a73c462cd71cf1f59a235f57ca56bd6e for a full test report.

laraPPr · 2024-10-09T11:26:53Z

@boegelbot please test @ generoso

boegelbot · 2024-10-09T11:30:08Z

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

PR test command 'EB_PR=21569 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21569 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14429

Test results coming soon (I hope)...

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boegelbot · 2024-10-09T11:33:50Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 5 (5 easyconfigs in total)
cns2 - 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/b5f51d08f97c8deae3182ec29f6ae733 for a full test report.

laraPPr · 2024-10-09T12:04:19Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-10-09T12:10:13Z

@laraPPr: 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=21569 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21569 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5041

Test results coming soon (I hope)...

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boegelbot · 2024-10-09T12:13:50Z

Test report by @boegelbot
FAILED
Build succeeded for 4 out of 5 (5 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/510e5179f1af70ea01bf17369a6dd717 for a full test report.

laraPPr · 2024-10-10T07:33:35Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-10-10T07:40:10Z

@laraPPr: 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=21569 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21569 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5048

Test results coming soon (I hope)...

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boegelbot · 2024-10-10T07:44:28Z

Test report by @boegelbot
FAILED
Build succeeded for 4 out of 5 (5 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/941a0ad509310942c18bfeb123ea5186 for a full test report.

…True

laraPPr · 2024-10-10T08:01:50Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-10-10T08:10:09Z

@laraPPr: 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=21569 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21569 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5049

Test results coming soon (I hope)...

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boegelbot · 2024-10-10T08:13:51Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 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/116d0bee5b84a5e7d0215bcf2bf8fb1c for a full test report.

laraPPr · 2024-10-10T08:14:10Z

@boegelbot please test @ generoso

boegelbot · 2024-10-10T08:15:10Z

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

PR test command 'EB_PR=21569 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21569 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14438

Test results coming soon (I hope)...

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boegelbot · 2024-10-10T08:18:50Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 5 (5 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/4f656f26370c56266ee3972281ab4b0b for a full test report.

laraPPr · 2024-10-10T08:23:13Z

@boegel I don't understand why GMAP-GSNAP is failing on Generoso?

boegelbot · 2024-10-15T15:20:12Z

@laraPPr: 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=21569 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21569 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5078

Test results coming soon (I hope)...

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boegelbot · 2024-10-15T15:23:45Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 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/454c27bb147319f4269c41b39bd390fe for a full test report.

boegel · 2024-10-16T07:57:16Z

+]
+
+# Install ParaFly
+postinstallcmds = ["cd %(installdir)s && make"]


@laraPPr The Makefile has this:

CFLAGS="-fopenmp" CXXFLAGS="-fopenmp"

which should really be

CFLAGS="$CFLAGS -fopenmp" CXXFLAGS="$CXXFLAGS -fopenmp"

Without that, ParaFly will be built without any compiler optimizations (default is -O0), which makes it a very slow binary.

Let's add a patch for that?

We should probably report this upstream...

it fails with this when I try what you suggested configure: error: C++ compiler cannot create executables

We should also remove the pre-built binary:

Suggested change

postinstallcmds = ["cd %(installdir)s && make"]

postinstallcmds = ["cd %(installdir)s && rm plugins/ParaFly/bin/ParaFly && make"]

EVidenceModeler is no longer maintained so I report it upstream but it probably is not gonna be picked up

boegel · 2024-10-16T07:59:05Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3124.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/3a4abda5d00f2b1ab97acd06fb3193d1 for a full test report.

boegel · 2024-10-16T10:17:34Z

+]
+
+# Install ParaFly
+postinstallcmds = ["cd %(installdir)s && make"]


We should also remove the pre-built binary:

Suggested change

postinstallcmds = ["cd %(installdir)s && make"]

postinstallcmds = ["cd %(installdir)s && rm plugins/ParaFly/bin/ParaFly && make"]

laraPPr · 2024-10-16T11:35:28Z

Test report by @laraPPr
FAILED
Build succeeded for 3 out of 4 (4 easyconfigs in total)
node4012.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.11.3
See https://gist.github.com/laraPPr/138139ec2aaba78487232851e2982d44 for a full test report.

laraPPr · 2024-10-16T11:42:22Z

Test report by @laraPPr
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node4012.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.11.3
See https://gist.github.com/laraPPr/283f99cbe8e42c9aaf34dd18262a61e5 for a full test report.

boegel · 2024-10-16T17:22:20Z

+modextrapaths = {
+    'EVM_HOME': '',
+}
+
+sanity_check_commands = ["$EVM_HOME/EVidenceModeler -h 2>&1 | grep 'Evidence Modeler'"]


@laraPPr Shouldn't we add the top-level installation directory to $PATH?

Suggested change

modextrapaths = {

'EVM_HOME': '',

}

sanity_check_commands = ["$EVM_HOME/EVidenceModeler -h 2>&1 | grep 'Evidence Modeler'"]

modextrapaths = {

'EVM_HOME': '',

'PATH': ''.

}

sanity_check_commands = ["EVidenceModeler -h 2>&1 | grep 'Evidence Modeler'"]

I'm not sure funannotate only uses $EVM_HOME and that is also what their own documentation says. But in a sense their is no harm in adding it. I think.

laraPPr · 2024-10-18T08:51:39Z

Test report by @laraPPr
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node4012.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.11.3
See https://gist.github.com/laraPPr/aeb63bd183a002b35dcf33a31d6395a6 for a full test report.

laraPPr · 2024-10-18T10:56:53Z

@boegelbot please test @ generoso

boegelbot · 2024-10-18T11:00:06Z

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

PR test command 'EB_PR=21569 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21569 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14531

Test results coming soon (I hope)...

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boegelbot · 2024-10-18T11:03:54Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
cns2 - 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/e5fdac0b7b2a5d38b88459e9c9ef43ba for a full test report.

laraPPr · 2024-10-18T11:51:35Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-10-18T12:00:11Z

@laraPPr: 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=21569 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21569 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5126

Test results coming soon (I hope)...

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boegelbot · 2024-10-18T12:03:14Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 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/75d2ae2ff284afca59cdfdd17cb48479 for a full test report.

boegel · 2024-10-19T08:06:31Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3115.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/c9be57e99a9c84fa1262a3ebd15ff3cf for a full test report.

boegel

lgtm

adding easyconfigs: EVidenceModeler-2.1.0-foss-2023a.eb, FASTA-36.3.8…

5940aaa

…i-GCC-12.3.0.eb, GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb, PASA-2.5.3-foss-2023a.eb, pblat-2.5.1-foss-2023a.eb

laraPPr added new update labels Oct 7, 2024

laraPPr mentioned this pull request Oct 7, 2024

EVidenceModeler vscentrum/vsc-software-stack#414

Closed

2 tasks

add checksum and remove empty patches from GMAP

3ec9888

update the sanity check command

2bfc0cb

boegel added this to the 4.x milestone Oct 8, 2024

update sanity check command

97bba67

update checksum

8c81ac8

set checksum to None as done fort other source that use "recursive": …

dfc4bf0

…True

boegel changed the title ~~{bio}[foss/2023a] EVidenceModeler v2.1.0, FASTA v36.3.8i, ...~~ {bio}[foss/2023a] EVidenceModeler v2.1.0, FASTA v36.3.8i, PASA v2.5.3, pblat v2.5.1 Oct 16, 2024

boegel requested changes Oct 16, 2024

View reviewed changes

fix CFLAGS and add sanity check for ParaFly binary

00b0f0a

add patch

69c624d

boegel requested changes Oct 16, 2024

View reviewed changes

add sanitychecks

d3c9903

laraPPr commented Oct 17, 2024

View reviewed changes

Comment thread easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb

vsc46128 and others added 3 commits October 17, 2024 12:23

add extra paths and make CI happy

d92759e

make CI happy

7128e6f

change GMAP-GSNAP version

1a2c313

laraPPr mentioned this pull request Oct 18, 2024

{bio}[foss/2023a] funannotate v1.8.17 + required dependencies #21705

Merged

2 tasks

add missing description to patch file for EVidenceModeler

6e9519d

boegel approved these changes Oct 19, 2024

View reviewed changes

boegel merged commit 9227e1b into easybuilders:develop Oct 19, 2024

boegel modified the milestones: 4.x, 5.0.0 Mar 18, 2025

	postinstallcmds = ["cd %(installdir)s && make"]
	postinstallcmds = ["cd %(installdir)s && rm plugins/ParaFly/bin/ParaFly && make"]

Conversation

laraPPr commented Oct 7, 2024

Uh oh!

laraPPr commented Oct 7, 2024

Uh oh!

laraPPr commented Oct 7, 2024

Uh oh!

boegel commented Oct 8, 2024

Uh oh!

laraPPr commented Oct 9, 2024

Uh oh!

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Uh oh!

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