Comments (5)
marcus-ludwig
commented on June 3, 2024
Hi Huali,
sorry for the late response. Seems that this is an unpleasant native library error when using the CLP ILP solver.
Is this still error still persisting with latest SIRIUS version 4.9.5?
Best regards,
Marcsu
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jeep3
commented on June 3, 2024
Hello, Marcsu,
I just tried it on several servers, and the Linux version 4.95 GUI still has errors (Please see screenshot below). I am now using the Windows version as an alternative in processing the MS data, but it is very slow.
Kind regards,
Huali
At 2021-10-08 19:41:25, "marcus-ludwig" ***@***.***> wrote:
Hi Huali,
sorry for the late response. Seems that this is an unpleasant native library error when using the CLP ILP solver.
Is this still error still persisting with latest SIRIUS version 4.9.5?
Best regards,
Marcsu
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You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub, or unsubscribe.
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marcus-ludwig
commented on June 3, 2024
Hi Huali,
unfortunately, there is no screenshot attached. Hence, I do not completely understand the issue. But ...
- the GUI version is not meant for servers (which usually do not have a display server), for these we have a headless version of SIRIUS.
- SIRIUS should not be much slower on Windows.
Best regards,
Marcus
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jeep3
commented on June 3, 2024
Hi Marcus,
You should be able to see it in the attachment now. I embedded the image in the email just now, so there may have been a problem. Thanks for clarifying these. Perhaps because of the larger size in the sample, now I don't run all of them, but target to identify a particular metabolite of interest
Best,
Huali
At 2021-10-08 20:56:10, "marcus-ludwig" ***@***.***> wrote:
Hi Huali,
unfortunately, there is no screenshot attached. Hence, I do not completely understand the issue. But ...
the GUI version is not meant for servers (which usually do not have a display server), for these we have a headless version of SIRIUS.
SIRIUS should not be much slower on Windows.
Best regards,
Marcus
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub, or unsubscribe.
Triage notifications on the go with GitHub Mobile for iOS or Android.
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marcus-ludwig
commented on June 3, 2024
Emailing an attached image seems not to work to upload it to the GitHub comment.
If you are still encountering this native library error: The CLP solver is using some native libraries on your system. This may cause issues on some systems. Initially, we only supported commercial ILP solvers. Now, we ship CLP so users can run fragmentation tree computation (molecular formula assignment) out-of-the-box. But as you see, there may still be some issues with this.
There are 2 workarounds:
- only run heuristic fragmentation tree computations. This gives no guarantee to calculate the "optimal" tree that best matches the data, but it usually works quite well.
- install a commercial ILP solver. This may be a good option for academic users because you can apply for a free, academic license. These commercial solvers are also faster. See: https://boecker-lab.github.io/docs.sirius.github.io/install/#installing-gurobi-andor-cplex
I'll close this issue for now. Feel free to re-open if this does not answer your question.
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