Hardware requirements

[mvisani]

Hi !

We've trying to develop a wrapper around Sirius CLI in Rust for our project. My problem is that the tests work on some machines but not on others.

On my machine (MB Pro 4 CPUs - 16GB memory) and on GitHub actions (Ubuntu, 4 CPUs - 16 GB memory) Sirius gets stuck here :

WARNING: <590>[TwoPhaseGibbsSampling-590] The graph seems to be badly connected. You might want to enforce more connections using local edge thresholds
STEP 1
STEP 2
STEP 3
STEP 4
heuristic: 9 / 28 ( 32.143 %)
PREPARING INNER EDGE SCORER TOOK 4 milliseconds
Sampling TOOK 291 milliseconds
number of badly connected compounds 8
number of compounds with more than 15 neighbours 0
Feb 12, 2024 4:26:19 PM de.unijena.bioinf.jjobs.JJob lambda$logWarn$5
WARNING: <590>[TwoPhaseGibbsSampling-590] The graph seems to be badly connected. You might want to enforce more connections using local edge thresholds
Feb 12, 2024 4:26:22 PM de.unijena.bioinf.jjobs.JJob lambda$logWarn$5
WARNING: <688>[FingerprintPreprocessingJJob-688 | [email protected]/z] Ignore fragmentation tree for C10H13N5O4 because it contains less than 3 vertices.
Feb 12, 2024 4:26:22 PM de.unijena.bioinf.jjobs.JJob lambda$logWarn$5
WARNING: <688>[FingerprintPreprocessingJJob-688 | [email protected]/z] Ignore fragmentation tree for C9H17NO8 because it contains less than 3 vertices.
Feb 12, 2024 4:26:22 PM de.unijena.bioinf.jjobs.JJob lambda$logWarn$5
WARNING: <688>[FingerprintPreprocessingJJob-688 | [email protected]/z] Ignore fragmentation tree for C8H18N3O5P because it contains less than 3 vertices.
Feb 12, 2024 4:26:22 PM de.unijena.bioinf.jjobs.JJob lambda$logWarn$5
WARNING: <688>[FingerprintPreprocessingJJob-688 | [email protected]/z] No suitable fragmentation tree left.
Feb 12, 2024 4:26:22 PM de.unijena.bioinf.jjobs.JJob lambda$logWarn$5
WARNING: <695>[FingerprintJJob-695 | [email protected]/z] No suitable input trees found.
Feb 12, 2024 4:26:22 PM de.unijena.bioinf.jjobs.JJob lambda$logWarn$5
WARNING: <701>[FingerblastJJob-701 | [email protected]/z] No suitable input fingerprints found.
Feb 12, 2024 4:26:22 PM de.unijena.bioinf.rest.ProxyManager decorateWithPoolSettings
INFO: Starting http Client with MaxPerRoute=1 / maxTotal=1 (CPU-Threads=2).
Feb 12, 2024 4:26:23 PM de.unijena.bioinf.rest.ProxyManager decorateWithPoolSettings
INFO: Starting http Client with MaxPerRoute=1 / maxTotal=1 (CPU-Threads=2).

After running this command :

sirius -i tests/data/input_sirius.mgf --output tests/data/output_sirius_default --maxmz=800.0 formula zodiac fingerprint structure canopus write-summaries

On other machines (also MacBook Pro and Linux) with more CPUs or RAM, Sirius works like a charm. We've been using the same input file, the same logins, and the same parameters.

I was wondering then if this could be a hardware requirement problem.

Thanks in advance !