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Add Biopython#3
casparvl wants to merge 7 commits into
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add_cowsay2

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bot: build repo:eessi.io-2025.06-software instance:surf-hpcv-bot for:arch=x86_64/amd/zen2

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surf-hpcv-bot Bot commented May 11, 2026

New job on instance surf-hpcv-bot for repository eessi.io-2025.06-software
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /projects/surf-hpcv-bot/surf-hpcv-bot/jobs/2026.05/pr_3/22637713

date job status comment
May 11 11:28:37 UTC 2026 submitted job id 22637713 will be eligible to start in about 20 seconds

Caspar van Leeuwen added 2 commits May 11, 2026 14:59
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bot: build repo:eessi.io-2025.06-software instance:surf-hpcv-bot for:arch=x86_64/amd/zen2

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surf-hpcv-bot Bot commented May 11, 2026

New job on instance surf-hpcv-bot for repository eessi.io-2025.06-software
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /projects/surf-hpcv-bot/surf-hpcv-bot/jobs/2026.05/pr_3/22639817

date job status comment
May 11 13:16:59 UTC 2026 submitted job id 22639817 will be eligible to start in about 20 seconds
May 11 13:17:12 UTC 2026 received job awaits launch by Slurm scheduler
May 11 13:17:26 UTC 2026 running job 22639817 is running

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bot:cancel job:22637713

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bot: build repo:eessi.io-2025.06-software instance:surf-hpcv-bot for:arch=x86_64/amd/zen2

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surf-hpcv-bot Bot commented May 11, 2026

New job on instance surf-hpcv-bot for repository eessi.io-2025.06-software
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /projects/surf-hpcv-bot/surf-hpcv-bot/jobs/2026.05/pr_3/22639852

date job status comment
May 11 13:18:51 UTC 2026 submitted job id 22639852 will be eligible to start in about 20 seconds
May 11 13:19:46 UTC 2026 received job awaits launch by Slurm scheduler
May 11 13:19:49 UTC 2026 running job 22639852 is running
May 12 08:18:31 UTC 2026 finished job id 22639852 was cancelled
May 12 08:18:44 UTC 2026 finished
🤷 UNKNOWN (click triangle for detailed information)
  • Job results file _bot_job22639852.result does not exist in job directory, or parsing it failed.
  • No artefacts were found/reported.
May 12 08:18:44 UTC 2026 test result
🤷 UNKNOWN (click triangle for detailed information)
  • Job test file _bot_job22639852.test does not exist in job directory, or parsing it failed.

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bot: build repo:eessi.io-2025.06-software instance:surf-hpcv-bot for:arch=x86_64/amd/zen2

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surf-hpcv-bot Bot commented May 11, 2026

New job on instance surf-hpcv-bot for repository eessi.io-2025.06-software
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /projects/surf-hpcv-bot/surf-hpcv-bot/jobs/2026.05/pr_3/22640012

date job status comment
May 11 13:28:37 UTC 2026 submitted job id 22640012 will be eligible to start in about 20 seconds
May 11 13:28:45 UTC 2026 received job awaits launch by Slurm scheduler
May 11 13:29:00 UTC 2026 running job 22640012 is running
May 12 08:18:43 UTC 2026 finished job id 22640012 was cancelled
May 12 08:18:57 UTC 2026 finished
🤷 UNKNOWN (click triangle for detailed information)
  • Job results file _bot_job22640012.result does not exist in job directory, or parsing it failed.
  • No artefacts were found/reported.
May 12 08:18:57 UTC 2026 test result
🤷 UNKNOWN (click triangle for detailed information)
  • Job test file _bot_job22640012.test does not exist in job directory, or parsing it failed.

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bot: build repo:software.surf.nl-2025 instance:surf-hpcv-bot for:arch=x86_64/amd/zen2

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Both jobs are hanging, because CVMFS isn't cleaning up. htop shows:

1382689 surf-hpcv-  20   0  3628  1024  1024 S   0.0  0.0  0:00.00 119 │     └─ bwrap --clearenv --seccomp 7 --args 8 --info-fd 11 --block-fd 12 --unshare-pid -- /bin/sleep infinity
1382690 surf-hpcv-  20   0  3628  1024  1024 S   0.0  0.0  0:00.00 123 │        └─ bwrap --clearenv --seccomp 7 --args 8 --info-fd 11 --block-fd 12 --unshare-pid -- /bin/sleep infinity
1382691 surf-hpcv-  20   0  2644  1024  1024 S   0.0  0.0  0:00.00 127 │           └─ /bin/sleep infinity
1382788 surf-hpcv-  20   0  217M  2048  2048 S   0.0  0.0  0:00.00 100 │  └─ bash /var/spool/slurm/slurmd/job22640012/slurm_script
1382802 surf-hpcv-  20   0  217M  3072  3072 S   0.0  0.0  0:00.00 101 │     └─ bash bot/build.sh
1382873 surf-hpcv-  20   0  217M  2048  2048 S   0.0  0.0  0:00.03 102 │        └─ bash software-layer-scripts/bot/build.sh
1383123 surf-hpcv-  20   0  216M  1024  1024 S   0.0  0.0  0:00.03  99 │           └─ tee -a build.outerr.q250
1383937 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.04  97 ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384004 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.00 104 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384005 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.00 110 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384006 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.05  96 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384007 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.01 100 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384008 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:10.64  97 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384009 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.00 104 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384010 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.00 110 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384011 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.00 100 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384012 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.00 104 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384013 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.00 100 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384014 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.66  97 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384015 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.69 109 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384020 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.68 106 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384022 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.69 105 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384029 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.72  99 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384032 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.67 102 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384040 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.70  98 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384061 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.66 105 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384457 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.54 111 │  ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1384540 surf-hpcv-  20   0 1125M 44760  7168 S   0.0  0.0  0:00.50 107 │  └─ cvmfs2 software.eessi.io /dev/fd/3 -f
1383989 surf-hpcv-  20   0 16680  1024  1024 S   0.0  0.0  0:00.00  98 ├─ cvmfs2 software.eessi.io /dev/fd/3 -f
1383991 surf-hpcv-  20   0 22320  6144  5120 S   0.0  0.0  0:01.17 110 ├─ cvmfs2 __cachemgr__ . 10 11 10485760000 5242880000 1 3 -1 :
1383996 surf-hpcv-  20   0 22320  6144  5120 S   0.0  0.0  0:00.00 104 │  └─ cvmfs2 __cachemgr__ . 10 11 10485760000 5242880000 1 3 -1 :
1383995 surf-hpcv-  20   0 16432  1024  1024 S   0.0  0.0  0:00.00  97 ├─ cvmfs2 __cachemgr__ . 10 11 10485760000 5242880000 1 3 -1 :

And this is keeping the job running, even though the container run has finished.

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I'll kill it manually...

bot:cancel jobid:22639852

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bot:cancel jobid:22640012

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bot: build repo:software.surf.nl-2025 instance:surf-hpcv-bot for:arch=x86_64/amd/zen2

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bot:show_config

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surf-hpcv-bot Bot commented May 12, 2026

Instance surf-hpcv-bot is configured to build on:

  • Node type cpu_zen2:

    • OS: linux
    • CPU architecture: x86_64/amd/zen2
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software']
  • Node type cpu_zen4:

    • OS: linux
    • CPU architecture: x86_64/amd/zen4
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software']
  • Node type gpu_a100:

    • OS: linux
    • CPU architecture: x86_64/intel/icelake
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software']
    • Accelerators: nvidia/cc80
  • Node type gpu_h100:

    • OS: linux
    • CPU architecture: x86_64/amd/zen4
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software']
    • Accelerators: nvidia/cc90

@casparvl casparvl changed the title Add cowsay Add Biopython May 12, 2026
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bot:show_config

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surf-hpcv-bot Bot commented May 12, 2026

Instance surf-hpcv-bot is configured to build on:

  • Node type cpu_zen2:

    • OS: linux
    • CPU architecture: x86_64/amd/zen2
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software', 'software.surf.nl-2025']
  • Node type cpu_zen4:

    • OS: linux
    • CPU architecture: x86_64/amd/zen4
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software', 'software.surf.nl-2025']
  • Node type gpu_a100:

    • OS: linux
    • CPU architecture: x86_64/intel/icelake
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software', 'software.surf.nl-2025']
    • Accelerators: nvidia/cc80
  • Node type gpu_h100:

    • OS: linux
    • CPU architecture: x86_64/amd/zen4
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software', 'software.surf.nl-2025']
    • Accelerators: nvidia/cc90

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bot: build repo:software.surf.nl-2025 instance:surf-hpcv-bot for:arch=x86_64/amd/zen2

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surf-hpcv-bot Bot commented May 12, 2026

New job on instance surf-hpcv-bot for repository software.surf.nl-2025
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /projects/surf-hpcv-bot/surf-hpcv-bot/jobs/2026.05/pr_3/22667343

date job status comment
May 12 09:38:54 UTC 2026 submitted job id 22667343 will be eligible to start in about 20 seconds
May 12 09:39:07 UTC 2026 received job awaits launch by Slurm scheduler
May 12 09:39:51 UTC 2026 running job 22667343 is running
May 12 09:40:12 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-22667343.out
❌ found message matching FATAL:
✅ no message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
Details
No artefacts were created or found.
May 12 09:40:12 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
Failed for unknown reason
Details
✅ job output file slurm-22667343.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@casparvl
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Weird...

INFO:    Environment variable SINGULARITY_TMPDIR is set, but APPTAINER_TMPDIR is preferred
INFO:    Environment variable SINGULARITY_CACHEDIR is set, but APPTAINER_CACHEDIR is preferred
FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://ghrc.io/eessi/build-node:debian12: pinging container registry ghrc.io: StatusCode: 404, "<ht
ml>\r\n<head><title>404 Not Found</title></head>\r..."
CONTAINER=docker://ghrc.io/eessi/build-node:debian12
EESSI_CVMFS_VAR_LIB=/tmp/surf-hpcv-bot/EESSI/eessi_job.opkLnasLcm/eessi.eKKtHSkxK8/var-lib-cvmfs

I don't understand why it would matter what repo I'm targetting for pulling the container - that should always work?

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Let's see if this was just a hickup:

bot: build repo:software.surf.nl-2025 instance:surf-hpcv-bot for:arch=x86_64/amd/zen2

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surf-hpcv-bot Bot commented May 12, 2026

New job on instance surf-hpcv-bot for repository software.surf.nl-2025
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /projects/surf-hpcv-bot/surf-hpcv-bot/jobs/2026.05/pr_3/22669154

date job status comment
May 12 10:19:47 UTC 2026 submitted job id 22669154 will be eligible to start in about 20 seconds
May 12 10:20:11 UTC 2026 received job awaits launch by Slurm scheduler
May 12 10:20:25 UTC 2026 running job 22669154 is running

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surf-hpcv-bot Bot commented May 12, 2026

New job on instance surf-hpcv-bot for repository software.surf.nl-2025
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /projects/surf-hpcv-bot/surf-hpcv-bot/jobs/2026.05/pr_3/22669154

date job status comment
May 12 10:19:47 UTC 2026 submitted job id 22669154 will be eligible to start in about 20 seconds
May 12 10:20:47 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-22669154.out
❌ found message matching FATAL:
✅ no message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
Details
No artefacts were created or found.
May 12 10:20:47 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
Failed for unknown reason
Details
✅ job output file slurm-22669154.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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bot: build repo:software.surf.nl-2025 instance:surf-hpcv-bot for:arch=x86_64/amd/zen2

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The deploy seems to have worked (see #3 (comment) with the succesful upload message), though I don't really know what to expect on the bucket side:

[casparl@int6 eessi-bot-software-layer]$ aws s3 ls s3://surf_hpcv_casparl_software_test
                           PRE 2025.06/

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casparvl commented May 27, 2026

Ignoring the failing test step for now, I've created a script to handle automated ingestion. It fakes checking the signature (for now):

#!/usr/bin/env bash
# ------------------------------------------------------------
# ingest‑tarballs.sh
#   - Lists .tar.zst objects in an S3 bucket (excluding “archive/”)
#   - Downloads each tarball + its .meta.txt file
#   - Verifies the tarball with `check_signature`
#   - On success, ingests the tarball into CVMFS
#   - Removes local copies after ingest
#   - Moves the processed objects to <bucket>/archive
#
# Requirements:
#   * aws CLI (v2) configured with access to the bucket
#   * `check_signature` executable in $PATH
#   * cvmfs_server command available (root / sudo rights)
#   * Destination directory must be writable
#
# Author: EduGenAI (2026‑05‑27)
# ------------------------------------------------------------

set -euo pipefail   # strict mode
IFS=$'\n\t'         # sane field splitting

# -------------------- Configuration -------------------------
BUCKET="surf_hpcv_casparl_software_test"
DOWNLOAD_DIR="/data/cvmfs_s0_storage/staged_tarballs"
REPO_NAME="software.casparl.nl"
ARCHIVE_PREFIX="archive"
BASEDIR="versions"

# Ensure the download directory exists
mkdir -p "${DOWNLOAD_DIR}"

# -------------------- Step 1: Get the list ------------------
# Store the keys in a Bash array called `tar_keys`
mapfile -t tar_keys < <(
    aws s3api list-objects-v2 \
        --bucket "${BUCKET}" \
        --query 'Contents[?ends_with(Key, `.tar.zst`) && !contains(Key, `archive/`)].Key' \
        --output text
)

# If no keys were found, exit early
if [[ ${#tar_keys[@]} -eq 0 ]]; then
    echo "No tarballs found in bucket '${BUCKET}' (excluding archive/)."
    exit 0
fi

echo "Found ${#tar_keys[@]} tarball(s) to process."

# -------------------- Step 2: Loop & process ----------------
for key in "${tar_keys[@]}"; do
    # Extract the base filename (e.g. 17798741550.tar.zst)
    filename=$(basename "${key}")

    # Derive the meta‑file name (same basename with .meta.txt suffix)
    meta_file="${filename}.meta.txt"

    # Full local paths
    local_tar="${DOWNLOAD_DIR}/${filename}"
    local_meta="${DOWNLOAD_DIR}/${meta_file}"

    echo "=== Processing ${filename} ==="

    # ---- Download tarball ----
    echo "Downloading tarball..."
    aws s3 cp "s3://${BUCKET}/${key}" "${local_tar}" || {
        echo "ERROR: Failed to download ${key}" >&2
        continue
    }

    # ---- Download meta file (if it exists) ----
    # The meta file is expected to sit next to the tarball in S3
    echo "Downloading meta file..."
    if aws s3 cp "s3://${BUCKET}/${key}.meta.txt" "${local_meta}" 2>/dev/null; then
        echo "Meta file downloaded."
    else
        echo "WARNING: No meta file found for ${filename}. Continuing without it."
        # Remove the variable so we don't pass a non‑existent file later
        local_meta=""
    fi

    # ---- Verify signature ----
    echo "Running check_signature..."
    if check_signature "${local_tar}"; then
        echo "Signature OK."
    else
        echo "ERROR: Signature verification failed for ${filename}. Skipping ingest." >&2
        # Optionally clean up the bad files
        rm -f "${local_tar}" "${local_meta}"
        continue
    fi

    # ---- Ingest into CVMFS ----
    echo "Ingesting into CVMFS (${REPO_NAME})..."
    if zstd -c -d "${local_tar}" | cvmfs_server ingest --tar_file - --base_dir "${BASEDIR}" "${REPO_NAME}"; then
        echo "Ingest succeeded for ${filename}."
    else
        echo "ERROR: cvmfs_server ingest failed for ${filename}." >&2
        # Keep the files for troubleshooting
        continue
    fi

    # ---- Clean up local copies ----
    echo "Removing local files..."
    rm -f "${local_tar}" "${local_meta}"

    # ---- Archive the objects in S3 ----
    # Destination key = archive/<original‑key>
    archive_key="${ARCHIVE_PREFIX}/${key}"
    echo "Archiving S3 object to s3://${BUCKET}/${archive_key} ..."
    if ! aws s3 mv "s3://${BUCKET}/${key}" "s3://${BUCKET}/${archive_key}"; then
        echo "ERROR: Failed to move tarball to archive." >&2
    else
        echo "Tarball archived."
    fi

    # Archive the metadata file (if it existed)
    if [[ -n "${meta_file}" && -n "${local_meta}" ]]; then
        archive_meta_key="${ARCHIVE_PREFIX}/${key}.meta.txt"
        echo "Archiving metadata to s3://${BUCKET}/${archive_meta_key} ..."
        if ! aws s3 mv "s3://${BUCKET}/${key}.meta.txt" "s3://${BUCKET}/${archive_meta_key}"; then
            echo "ERROR: Failed to move metadata to archive." >&2
        else
            echo "Metadata archived."
        fi
    fi

done

echo "All done."

With that, and my S3 credentials set up at the Stratum 0:

cvanleeuwe@cvmfss0:~$ ./ingest_script.sh
Found 1 tarball(s) to process.
=== Processing eessi-2025.06-software-linux-x86_64-amd-zen2-17798741550.tar.zst ===
Downloading tarball...
download: s3://surf_hpcv_casparl_software_test/2025.06/software/linux/x86_64/amd/zen2/17798741550.tar.zst/eessi-2025.06-software-linux-x86_64-amd-zen2-17798741550.tar.zst to ../../data/cvmfs_s0_storage/staged_tarballs/eessi-2025.06-software-linux-x86_64-amd-zen2-17798741550.tar.zst
Downloading meta file...
download: s3://surf_hpcv_casparl_software_test/2025.06/software/linux/x86_64/amd/zen2/17798741550.tar.zst/eessi-2025.06-software-linux-x86_64-amd-zen2-17798741550.tar.zst.meta.txt to ../../data/cvmfs_s0_storage/staged_tarballs/eessi-2025.06-software-linux-x86_64-amd-zen2-17798741550.tar.zst.meta.txt
Meta file downloaded.
Running check_signature...
FAKING A SIGNATURE CHECK
Signature OK.
Ingesting into CVMFS (software.casparl.nl)...
Info: transaction on repository software.casparl.nl
Using auto tag 'generic-2026-05-27T11:15:35Z'
Swissknife Ingest: Processing changes...
...........
Waiting for upload of files before committing...
Committing file catalogs...
Swissknife Ingest: Wait for all uploads to finish
Swissknife Ingest: Exporting repository manifest
Statistics stored at: /var/spool/cvmfs/software.casparl.nl/stats.db
Tagging software.casparl.nl
Flushing file system buffers
Signing new manifest
Remounting newly created repository revision
Ingest succeeded for eessi-2025.06-software-linux-x86_64-amd-zen2-17798741550.tar.zst.
Removing local files...
Archiving S3 object to s3://surf_hpcv_casparl_software_test/archive/2025.06/software/linux/x86_64/amd/zen2/17798741550.tar.zst/eessi-2025.06-software-linux-x86_64-amd-zen2-17798741550.tar.zst ...
move: s3://surf_hpcv_casparl_software_test/2025.06/software/linux/x86_64/amd/zen2/17798741550.tar.zst/eessi-2025.06-software-linux-x86_64-amd-zen2-17798741550.tar.zst to s3://surf_hpcv_casparl_software_test/archive/2025.06/software/linux/x86_64/amd/zen2/17798741550.tar.zst/eessi-2025.06-software-linux-x86_64-amd-zen2-17798741550.tar.zst
Tarball archived.
Archiving metadata to s3://surf_hpcv_casparl_software_test/archive/2025.06/software/linux/x86_64/amd/zen2/17798741550.tar.zst/eessi-2025.06-software-linux-x86_64-amd-zen2-17798741550.tar.zst.meta.txt ...
move: s3://surf_hpcv_casparl_software_test/2025.06/software/linux/x86_64/amd/zen2/17798741550.tar.zst/eessi-2025.06-software-linux-x86_64-amd-zen2-17798741550.tar.zst.meta.txt to s3://surf_hpcv_casparl_software_test/archive/2025.06/software/linux/x86_64/amd/zen2/17798741550.tar.zst/eessi-2025.06-software-linux-x86_64-amd-zen2-17798741550.tar.zst.meta.txt
Metadata archived.
All done.

Note that rerunning prints:

$ ./ingest_script.sh
No tarballs found in bucket 'surf_hpcv_casparl_software_test' (excluding archive/).

On the stratum 0:

cvanleeuwe@cvmfss0:~$ ls -al /cvmfs/software.casparl.nl/versions/2025.06/software/linux/x86_64/amd/zen2/software/Biopython/1.86-gfbf-2025b/
total 19
dr-xr-xr-x 4 cvanleeuwe rsc_co_201397 4096 May 27 11:28 .
drwxr-xr-x 3 cvanleeuwe rsc_co_201397 4096 May 27 13:15 ..
dr-xr-xr-x 3 cvanleeuwe rsc_co_201397 4096 May 27 11:28 easybuild
dr-xr-xr-x 3 cvanleeuwe rsc_co_201397 4096 May 27 11:27 lib
lrwxrwxrwx 1 cvanleeuwe rsc_co_201397    3 May 27 11:27 lib64 -> lib

On the client:

cvanleeuwe@debugcvmfs:~$ ls -al /cvmfs/software.casparl.nl/versions/2025.06/software/linux/x86_64/amd/zen2/software/Biopython/1.86-gfbf-2025b/total 19
dr-xr-xr-x 4 cvmfs cvmfs 4096 May 27 11:28 .
drwxr-xr-x 3 cvmfs cvmfs 4096 May 27 13:15 ..
dr-xr-xr-x 3 cvmfs cvmfs 4096 May 27 11:28 easybuild
dr-xr-xr-x 3 cvmfs cvmfs 4096 May 27 11:27 lib
lrwxrwxrwx 1 cvmfs cvmfs    3 May 27 11:27 lib64 -> lib

Then:

cvanleeuwe@debugcvmfs:~$ export EESSI_SITE_SOFTWARE_PREFIX=/cvmfs/software.casparl.nl
cvanleeuwe@debugcvmfs:~$ source /cvmfs/software.eessi.io/versions/2025.06/init/lmod/bash
Module for EESSI/2025.06 loaded successfully
EESSI has selected x86_64/amd/zen2 as the compatible CPU target for EESSI/2025.06
EESSI did not identify an accelerator on the system
(for debug information when loading the EESSI module, set the environment variable EESSI_MODULE_DEBUG_INIT)
{EESSI/2025.06} cvanleeuwe@debugcvmfs:~$ module av Biopython

------------------------------------------------------------------------------------------------- /cvmfs/software.casparl.nl/versions/2025.06/software/linux/x86_64/amd/zen2/modules/all --------------------------------------------------------------------------------------------------
   Biopython/1.86-gfbf-2025b (D)

-------------------------------------------------------------------------------------------------- /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen2/modules/all ---------------------------------------------------------------------------------------------------
   Biopython/1.85-gfbf-2025a

  Where:
   D:  Default Module

If the avail list is too long consider trying:

"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

{EESSI/2025.06} cvanleeuwe@debugcvmfs:~$ module load Biopython/1.86-gfbf-2025b

{EESSI/2025.06} cvanleeuwe@debugcvmfs:~$ python -c 'import Bio.motifs; print(Bio.motifs.__path__)'
['/cvmfs/software.casparl.nl/versions/2025.06/software/linux/x86_64/amd/zen2/software/Biopython/1.86-gfbf-2025b/lib/python3.13/site-packages/Bio/motifs']

Not bad at all! :)

@casparvl
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bot: build repo:software.casparl.nl-2025 instance:caspar-hpcv-bot for:arch=x86_64/amd/zen2

@hpcv-bot-casparvl
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hpcv-bot-casparvl Bot commented May 28, 2026

New job on instance caspar-hpcv-bot for repository software.casparl.nl-2025
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /home/casparl/HPCV_Software/bot-instance/jobs/2026.05/pr_3/23175779

date job status comment
May 28 10:32:41 UTC 2026 submitted job id 23175779 will be eligible to start in about 10 seconds
May 28 10:32:50 UTC 2026 received job awaits launch by Slurm scheduler
May 28 10:33:03 UTC 2026 running job 23175779 is running
May 28 10:35:16 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-23175779.out
✅ no message matching FATAL:
✅ no message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
✅ found message(s) matching No missing installations
✅ found message matching .tar.* created!
Artefacts
Details
No artefacts were created or found.
May 28 10:35:16 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite was not run, test step itself failed to execute.
Details
✅ job output file slurm-23175779.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@casparvl
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bot:show_config

@surf-hpcv-bot
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surf-hpcv-bot Bot commented May 28, 2026

Instance surf-hpcv-bot is configured to build on:

  • Node type cpu_zen2:

    • OS: linux
    • CPU architecture: x86_64/amd/zen2
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software', 'software.surf.nl-2025']
  • Node type cpu_zen4:

    • OS: linux
    • CPU architecture: x86_64/amd/zen4
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software', 'software.surf.nl-2025']
  • Node type gpu_a100:

    • OS: linux
    • CPU architecture: x86_64/intel/icelake
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software', 'software.surf.nl-2025']
    • Accelerators: nvidia/cc80
  • Node type gpu_h100:

    • OS: linux
    • CPU architecture: x86_64/amd/zen4
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software', 'software.surf.nl-2025']
    • Accelerators: nvidia/cc90

@hpcv-bot-casparvl
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Instance caspar-hpcv-bot is configured to build on:

  • Node type cpu_zen2:

    • OS: linux
    • CPU architecture: x86_64/amd/zen2
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software', 'software.surf.nl-2025', 'software.casparl.nl-2025']
  • Node type cpu_zen4:

    • OS: linux
    • CPU architecture: x86_64/amd/zen4
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software', 'software.surf.nl-2025', 'software.casparl.nl-2025']
  • Node type gpu_a100:

    • OS: linux
    • CPU architecture: x86_64/intel/icelake
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software', 'software.surf.nl-2025', 'software.casparl.nl-2025']
    • Accelerators: nvidia/cc80
  • Node type gpu_h100:

    • OS: linux
    • CPU architecture: x86_64/amd/zen4
    • Repositories: ['eessi.io-2023.06-compat', 'eessi.io-2023.06-software', 'eessi.io-2025.06-compat', 'eessi.io-2025.06-software', 'software.surf.nl-2025', 'software.casparl.nl-2025']
    • Accelerators: nvidia/cc90

@casparvl
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bot: build repo:software.casparl.nl-2025 instance:caspar-hpcv-bot for:arch=x86_64/amd/zen2

@hpcv-bot-casparvl
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hpcv-bot-casparvl Bot commented May 28, 2026

New job on instance caspar-hpcv-bot for repository software.casparl.nl-2025
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /home/casparl/HPCV_Software/bot-instance/jobs/2026.05/pr_3/23175958

date job status comment
May 28 10:38:46 UTC 2026 submitted job id 23175958 will be eligible to start in about 10 seconds
May 28 10:38:56 UTC 2026 received job awaits launch by Slurm scheduler
May 28 10:39:09 UTC 2026 running job 23175958 is running
May 28 10:41:16 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-23175958.out
✅ no message matching FATAL:
✅ no message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
✅ found message(s) matching No missing installations
✅ found message matching .tar.* created!
Artefacts
Details
No artefacts were created or found.
May 28 10:41:16 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite was not run, test step itself failed to execute.
Details
✅ job output file slurm-23175958.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@casparvl
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bot: build repo:software.caspar.nl-2025 instance:caspar-hpcv-bot for:arch=x86_64/amd/zen2

1 similar comment
@casparvl
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bot: build repo:software.caspar.nl-2025 instance:caspar-hpcv-bot for:arch=x86_64/amd/zen2

@casparvl
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Restarted the bot to know about the new software.caspar.nl-2025 repo

@casparvl
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bot: build repo:software.caspar.nl-2025 instance:caspar-hpcv-bot for:arch=x86_64/amd/zen2

@hpcv-bot-casparvl
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hpcv-bot-casparvl Bot commented May 28, 2026

New job on instance caspar-hpcv-bot for repository software.caspar.nl-2025
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /home/casparl/HPCV_Software/bot-instance/jobs/2026.05/pr_3/23176283

date job status comment
May 28 10:51:13 UTC 2026 submitted job id 23176283 will be eligible to start in about 10 seconds
May 28 10:51:24 UTC 2026 received job awaits launch by Slurm scheduler
May 28 10:51:37 UTC 2026 running job 23176283 is running
May 28 10:51:49 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-23176283.out
❌ found message matching FATAL:
✅ no message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
Details
No artefacts were created or found.
May 28 10:51:49 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
Failed for unknown reason
Details
✅ job output file slurm-23176283.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@casparvl
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Fixed repos config

@casparvl
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bot: build repo:software.caspar.nl-2025 instance:caspar-hpcv-bot for:arch=x86_64/amd/zen2

@hpcv-bot-casparvl
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hpcv-bot-casparvl Bot commented May 28, 2026

New job on instance caspar-hpcv-bot for repository software.caspar.nl-2025
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /home/casparl/HPCV_Software/bot-instance/jobs/2026.05/pr_3/23176329

date job status comment
May 28 10:53:14 UTC 2026 submitted job id 23176329 will be eligible to start in about 10 seconds
May 28 10:53:24 UTC 2026 received job awaits launch by Slurm scheduler
May 28 10:53:37 UTC 2026 running job 23176329 is running
May 28 10:57:45 UTC 2026 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-23176329.out
✅ no message matching FATAL:
✅ no message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
✅ found message(s) matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-amd-zen2-17799658480.tar.zstsize: 4 MiB (4462208 bytes)
entries: 1112
modules under 2025.06/software/linux/x86_64/amd/zen2/modules/all
Biopython/1.86-gfbf-2025b.lua
software under 2025.06/software/linux/x86_64/amd/zen2/software
Biopython/1.86-gfbf-2025b
reprod directories under 2025.06/software/linux/x86_64/amd/zen2/reprod
Biopython/1.86-gfbf-2025b/20260528_105623UTC
other under 2025.06/software/linux/x86_64/amd/zen2
no other files in tarball
May 28 10:57:45 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite was not run, test step itself failed to execute.
Details
✅ job output file slurm-23176329.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case
May 28 11:38:14 UTC 2026 uploaded transfer of eessi-2025.06-software-linux-x86_64-amd-zen2-17799658480.tar.zst to S3 bucket succeeded

@casparvl
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bot: build repo:software.caspar.nl-2025 instance:caspar-hpcv-bot for:arch=x86_64/amd/zen2

@hpcv-bot-casparvl
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hpcv-bot-casparvl Bot commented May 28, 2026

New job on instance caspar-hpcv-bot for repository software.caspar.nl-2025
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /home/casparl/HPCV_Software/bot-instance/jobs/2026.05/pr_3/23189243

date job status comment
May 28 15:50:43 UTC 2026 submitted job id 23189243 will be eligible to start in about 10 seconds
May 28 15:50:52 UTC 2026 received job awaits launch by Slurm scheduler
May 28 15:51:06 UTC 2026 running job 23189243 is running
May 28 16:01:43 UTC 2026 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-23189243.out
✅ no message matching FATAL:
✅ no message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
✅ found message(s) matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-amd-zen2-17799840880.tar.zstsize: 4 MiB (4462339 bytes)
entries: 1112
modules under 2025.06/software/linux/x86_64/amd/zen2/modules/all
Biopython/1.86-gfbf-2025b.lua
software under 2025.06/software/linux/x86_64/amd/zen2/software
Biopython/1.86-gfbf-2025b
reprod directories under 2025.06/software/linux/x86_64/amd/zen2/reprod
Biopython/1.86-gfbf-2025b/20260528_160005UTC
other under 2025.06/software/linux/x86_64/amd/zen2
no other files in tarball
May 28 16:01:43 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite was not run, test step itself failed to execute.
Details
✅ job output file slurm-23189243.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@casparvl
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Before, it would still build from easystacks/software.eessi.io. That's awkward for site builds. Now, it should check the EESS_CVMFS_REPO_OVERRIDE repo name first, in this case software.caspar.nl. We thus expect that rebuilding this 'as is' will fail. Let's see:

bot: build repo:software.caspar.nl-2025 instance:caspar-hpcv-bot for:arch=x86_64/amd/zen2

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hpcv-bot-casparvl Bot commented May 29, 2026

New job on instance caspar-hpcv-bot for repository software.caspar.nl-2025
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /home/casparl/HPCV_Software/bot-instance/jobs/2026.05/pr_3/23207905

date job status comment
May 29 07:03:23 UTC 2026 submitted job id 23207905 will be eligible to start in about 10 seconds
May 29 07:03:32 UTC 2026 received job awaits launch by Slurm scheduler
May 29 07:03:46 UTC 2026 running job 23207905 is running
May 29 07:06:55 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-23207905.out
✅ no message matching FATAL:
✅ no message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-amd-zen2-17800383970.tar.zstsize: 0 MiB (22 bytes)
entries: 0
modules under 2025.06/software/linux/x86_64/amd/zen2/modules/all
no module files in tarball
software under 2025.06/software/linux/x86_64/amd/zen2/software
no software packages in tarball
reprod directories under 2025.06/software/linux/x86_64/amd/zen2/reprod
no reprod directories in tarball
other under 2025.06/software/linux/x86_64/amd/zen2
no other files in tarball
May 29 07:06:55 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite was not run, test step itself failed to execute.
Details
✅ job output file slurm-23207905.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@casparvl
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Check if error is now more clear:

bot: build repo:software.caspar.nl-2025 instance:caspar-hpcv-bot for:arch=x86_64/amd/zen2

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bot: build repo:software.caspar.nl-2025 instance:caspar-hpcv-bot for:arch=x86_64/amd/zen2

@hpcv-bot-casparvl
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hpcv-bot-casparvl Bot commented May 29, 2026

New job on instance caspar-hpcv-bot for repository software.caspar.nl-2025
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /home/casparl/HPCV_Software/bot-instance/jobs/2026.05/pr_3/23221404

date job status comment
May 29 13:43:50 UTC 2026 submitted job id 23221404 will be eligible to start in about 10 seconds
May 29 13:44:02 UTC 2026 received job awaits launch by Slurm scheduler
May 29 13:44:15 UTC 2026 running job 23221404 is running
May 29 13:45:02 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-23221404.out
✅ no message matching FATAL:
✅ no message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-amd-zen2-17800622830.tar.zstsize: 0 MiB (22 bytes)
entries: 0
modules under 2025.06/software/linux/x86_64/amd/zen2/modules/all
no module files in tarball
software under 2025.06/software/linux/x86_64/amd/zen2/software
no software packages in tarball
reprod directories under 2025.06/software/linux/x86_64/amd/zen2/reprod
no reprod directories in tarball
other under 2025.06/software/linux/x86_64/amd/zen2
no other files in tarball
May 29 13:45:02 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite was not run, test step itself failed to execute.
Details
✅ job output file slurm-23221404.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@casparvl
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bot: build repo:software.caspar.nl-2025 instance:caspar-hpcv-bot for:arch=x86_64/amd/zen2

@hpcv-bot-casparvl
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hpcv-bot-casparvl Bot commented May 29, 2026

New job on instance caspar-hpcv-bot for repository software.caspar.nl-2025
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /home/casparl/HPCV_Software/bot-instance/jobs/2026.05/pr_3/23221494

date job status comment
May 29 13:47:31 UTC 2026 submitted job id 23221494 will be eligible to start in about 10 seconds
May 29 13:47:44 UTC 2026 received job awaits launch by Slurm scheduler
May 29 13:48:00 UTC 2026 running job 23221494 is running
May 29 13:48:43 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-23221494.out
✅ no message matching FATAL:
✅ no message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-amd-zen2-17800625060.tar.zstsize: 0 MiB (22 bytes)
entries: 0
modules under 2025.06/software/linux/x86_64/amd/zen2/modules/all
no module files in tarball
software under 2025.06/software/linux/x86_64/amd/zen2/software
no software packages in tarball
reprod directories under 2025.06/software/linux/x86_64/amd/zen2/reprod
no reprod directories in tarball
other under 2025.06/software/linux/x86_64/amd/zen2
no other files in tarball
May 29 13:48:43 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite was not run, test step itself failed to execute.
Details
✅ job output file slurm-23221494.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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