{lib}[system/system] Circuitscape v5.12.3 #16720

ItIsI-Orient · 2022-11-23T15:06:14Z

(created using eb --new-pr)

ItIsI-Orient · 2022-11-23T15:18:50Z

@lexming I have finished with the dependency tree for this one, but I am hitting an error that I am not sure how to resolve. Do you have any idea of how should I proceed? I will be grateful for any insight you could have on this.

Error: Hash Mismatch!
   Expected sha256:   66ea28cff2833d9417a082fb3e4fc23ee8fb393f6ff282462f1b213f41d5d989
   Calculated sha256: 444268a49548a199d471769bd2d6438fd43b61597c2511249d34b300d19ecff2
 @ Pkg.PlatformEngines /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/Pkg/src/PlatformEngines.jl:629
ERROR: Unable to automatically install 'libpng' from '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/haswell-ib/software/Circuitscape/5.11.2-Julia-1.7.2/packages/libpng_jll/Artifacts.toml'
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] ensure_artifact_installed(name::String, meta::Dict{String, Any}, artifacts_toml::String; platform::Base.BinaryPlatforms.Platform, verbose::Bool, quiet_download::Bool, io::Base.PipeEndpoint)
    @ Pkg.Artifacts /kyukon/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/haswell-ib/software/Julia/1.7.2-linux-x86_64/share/julia/stdlib/v1.7/Pkg/src/Artifacts.jl:441
  [3] download_artifacts(env::Pkg.Types.EnvCache; platform::Base.BinaryPlatforms.Platform, julia_version::VersionNumber, verbose::Bool, io::Base.PipeEndpoint)
    @ Pkg.Operations /kyukon/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/haswell-ib/software/Julia/1.7.2-linux-x86_64/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:617
  [4] develop(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform)
    @ Pkg.Operations /kyukon/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/haswell-ib/software/Julia/1.7.2-linux-x86_64/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1201
  [5] develop(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; shared::Bool, preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Pairs{Symbol, Base.PipeEndpoint, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.PipeEndpoint}}})
    @ Pkg.API /kyukon/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/haswell-ib/software/Julia/1.7.2-linux-x86_64/share/julia/stdlib/v1.7/Pkg/src/API.jl:215
  [6] develop(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API /kyukon/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/haswell-ib/software/Julia/1.7.2-linux-x86_64/share/julia/stdlib/v1.7/Pkg/src/API.jl:149
  [7] develop(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API /kyukon/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/haswell-ib/software/Julia/1.7.2-linux-x86_64/share/julia/stdlib/v1.7/Pkg/src/API.jl:144
  [8] #develop#14
    @ /kyukon/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/haswell-ib/software/Julia/1.7.2-linux-x86_64/share/julia/stdlib/v1.7/Pkg/src/API.jl:141 [inlined]
  [9] develop(pkg::Pkg.Types.PackageSpec)
    @ Pkg.API /kyukon/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/haswell-ib/software/Julia/1.7.2-linux-x86_64/share/julia/stdlib/v1.7/Pkg/src/API.jl:141
 [10] top-level scope
    @ none:1
 (at easybuild/easybuild-framework/easybuild/tools/run.py:618 in parse_cmd_output)

easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb

ItIsI-Orient · 2023-03-17T00:30:49Z

@boegelbot please test @ generoso

boegelbot · 2023-03-17T00:35:08Z

@ItIsI-Orient: Request for testing this PR well received on login1

PR test command 'EB_PR=16720 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_16720 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10496

Test results coming soon (I hope)...

- notification for comment with ID 1472938005 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 · 2023-03-17T00:47:39Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns2 - 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/5905ec0a0fb4403908acd38c438a7830 for a full test report.

ItIsI-Orient · 2023-03-17T10:57:28Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-03-17T11:02:09Z

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

PR test command 'EB_PR=16720 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_16720 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2377

Test results coming soon (I hope)...

- notification for comment with ID 1473656920 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 · 2023-03-17T11:12:22Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/af079d67be6a79cd20dca26ec14fa913 for a full test report.

boegel · 2023-03-22T10:26:40Z

easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb

+easyblock = 'Bundle'
+
+name = 'Circuitscape'
+version = '5.11.2'


@ItIsI-Orient How painful would it be to update to 5.11.3 (cfr. https://github.com/Circuitscape/Circuitscape.jl/releases/tag/v5.12.3)?

Is that just about Circuitscape itself, or would other Julia Packages need to be updated too? Can you check?

Running the build now, hopefully nothing breaks

… 5.12.3

boegel · 2023-03-29T16:22:31Z

@boegelbot please test @ generoso

boegelbot · 2023-03-29T16:25:09Z

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

PR test command 'EB_PR=16720 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_16720 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10555

Test results coming soon (I hope)...

- notification for comment with ID 1488918178 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 · 2023-03-29T16:40:21Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/b513d912531462fed4184ff37d5de482 for a full test report.

boegel · 2023-03-29T17:04:31Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node3127.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/5a48d3645b74ea976668c1749c23aa8b for a full test report.

ERROR: expected package `ImageCore [a09fc81d]` to exist at path `/software/Circuitscape/5.12.3-Julia-1.7.2/packages/ImageCore`

boegel · 2023-04-21T07:18:49Z

@ItIsI-Orient Any idea what the error I'm hitting is about? I'm still hitting it now...

ItIsI-Orient · 2023-04-21T15:08:34Z

Test report by @ItIsI-Orient
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4009.donphan.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 530.30.02, Python 3.6.8
See https://gist.github.com/ItIsI-Orient/7c4b4d27273587070436b4dda5b894c8 for a full test report.

boegel · 2023-05-23T08:51:57Z

Probably caused by this?

$ grep -A 4 deps.ImageCore ~/.julia/environments/v1.7/Manifest.toml
[[deps.ImageCore]]
deps = ["AbstractFFTs", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Graphics", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "Reexport"]
path = "/user/gent/400/vsc40023/eb_arcaninescratch/RHEL8/skylake-ib/software/Circuitscape/5.12.3-Julia-1.7.2/packages/ImageCore"
uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534"
version = "0.9.4"

@lexming Any idea how we can prevent that stuff from .julia is picked up (or even created in the first place)?

boegel · 2023-05-23T08:55:36Z

Maybe we need to set $JULIA_PKGDIR to an empty directory to prevent stuff from $HOME/.julia being picked up?

boegel · 2023-05-23T08:57:02Z

easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb

@@ -0,0 +1,420 @@
+easyblock = 'Bundle'


@ItIsI-Orient Let's use JuliaBundle?

boegel · 2023-05-23T08:57:15Z

easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb

+exts_filter = ("LD_LIBRARY_PATH="" julia -e 'using %(ext_name)s'", "")
+exts_default_options = {
+    'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+}


This whole block can be removed when using JuliaBundle

boegel · 2023-05-23T08:59:39Z

easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb

+sanity_check_paths = {
+    'files': [],
+    'dirs': ['packages'],
+}


This whole block can be removed when using JuliaBundle

boegel · 2023-05-23T08:59:42Z

easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb

+
+modextrapaths = {
+    'JULIA_DEPOT_PATH': '',
+}


This whole block can be removed when using JuliaBundle

easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb

boegel · 2023-05-23T09:06:13Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3133.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/1fb00477e07bb97bd5fa07ab79cff5cc for a full test report.

lexming · 2023-05-23T09:26:06Z

@boegel that's a shared environment which was probably manually created, in the sense that something else made it not related to EasyBuild. I'll check if there is any way to ignore those during installation.

lexming · 2023-05-25T14:21:16Z

@boegel please test with easybuilders/easybuild-easyblocks#2935

ItIsI-Orient · 2023-06-06T15:53:04Z

@boegelbot please test @ generoso

boegelbot · 2023-06-06T15:55:09Z

@ItIsI-Orient: Request for testing this PR well received on login1

PR test command 'EB_PR=16720 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_16720 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10947

Test results coming soon (I hope)...

- notification for comment with ID 1579029053 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 · 2023-06-20T08:32:30Z

@boegelbot please test @ generoso

boegelbot · 2023-06-20T08:35:09Z

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

PR test command 'EB_PR=16720 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_16720 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11027

Test results coming soon (I hope)...

- notification for comment with ID 1598349030 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 · 2023-06-20T12:58:36Z

test on generoso worked fine, but test report failed to make it back due to known problem, see easybuilders/easybuild-framework#3934

boegel · 2023-06-20T12:58:40Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-06-20T13:02:08Z

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

PR test command 'EB_PR=16720 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_16720 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2800

Test results coming soon (I hope)...

- notification for comment with ID 1598723122 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 · 2023-06-20T13:14:18Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/1f63e34bc737ff71c25a84cc838939a8 for a full test report.

boegel · 2023-06-20T13:14:42Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3143.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/3d98f80132a01190d9ba02379fb1f5a3 for a full test report.

boegel

lgtm

boegel · 2023-06-20T13:32:40Z

Going in, thanks @ItIsI-Orient!

adding easyconfigs: Circuitscape-5.11.2-Julia-1.7.2.eb

92fc270

ItIsI-Orient marked this pull request as draft November 23, 2022 15:07

lexming reviewed Dec 10, 2022

View reviewed changes

easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb Outdated Show resolved Hide resolved

easybuilders deleted a comment from boegelbot Dec 10, 2022

boegel added the new label Dec 13, 2022

boegel added this to the 4.x milestone Dec 13, 2022

boegel mentioned this pull request Mar 14, 2023

ResistanceGA vscentrum/vsc-software-stack#29

Closed

1 task

Fixed version mismatch

d22d9af

ItIsI-Orient marked this pull request as ready for review March 16, 2023 23:15

boegel reviewed Mar 22, 2023

View reviewed changes

Orient and others added 4 commits March 22, 2023 18:11

Changed to latest version of Circuitscape

859be3b

Added checksum for Circuitscape

f05d5fd

Added sanity check command to run unit tests

493ee8e

remove easyconfig for Circuitscape 5.11.2, replaced with Circuitscape…

dca1235

… 5.12.3

boegel changed the title ~~{lib}[system/system] Circuitscape v5.11.2~~ {lib}[system/system] Circuitscape v5.12.3 Mar 29, 2023

boegel requested changes May 23, 2023

View reviewed changes

lexming mentioned this pull request May 23, 2023

Remove user directory from JULIA_DEPOT_PATH during installation #17961

Closed

Changed easyblock to JuliaBundle

c89adda

boegel approved these changes Jun 20, 2023

View reviewed changes

boegel merged commit 8ac8b57 into easybuilders:develop Jun 20, 2023
5 checks passed

boegel modified the milestones: 4.x, next release (4.7.3?) Jun 20, 2023

{lib}[system/system] Circuitscape v5.12.3 #16720

{lib}[system/system] Circuitscape v5.12.3 #16720

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ItIsI-Orient commented Nov 23, 2022

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