msPurity.filterFragSpectra Memory Issue

Workflow4Metabolomics Instance
1

Bonjour support,

An issue occurs while running MSMS pipeline. At the msPurity.filterFragSpectra step I have the following error
"This job was terminated because it used more memory than it was allocated.
Please click the bug icon to report this problem if you need help."

Can you set the memory threshold a bit higher for that step please? It was done formerly for the createDatabase step and worked fine so maybe you can put the same parameters. see issue

Maybe for @gildaslecorguille or an other admin

Thanks
Yann

2

Ping @team.galaxy

3

J'ai fait passer la mémoire de 12Go à 24Go.
Normalement ça devrait être bon.

2 « J'aime »
4

Merci Beaucoup je test ça de suite
Yann

5

Bonjour @team.galaxy, je réouvre le ticket désolé...

Merci @Lain J'ai testé et msPurity.FilterFrag Spectra est passé ... Mais du coup ce sont les briques d'après qui beug..avec le même soucis mémoire

Est-il possible de paramétrer les autres outils msPurity pour qu'ils testent itérativement avec 8 Go puis 12 Go puis 24 Go en cas d'erreur?

Les outils seraient
msPurity.averageFragSpectra
msPurity.createDatabase
msPurity.createMSP
msPurity.spectralMatching

Merci pour votre aide
Yann

6

Hello!
Les outils:

  • msPurity.averageFragSpectra
  • msPurity.createDatabase
  • msPurity.createMSP
  • msPurity.spectralMatching
  • msPurity.filterFragSpectra

ont tous une mémoire dispo' de base de 8Go, puis de 12Go, puis de 24 en cas de limite de mémoire disponible atteinte.

Lain

2 « J'aime »
7

Hi @Lain

Thanks for all that, But I still have RAM issues ...Do you think possible to investigate a bit more my jobs to find where exactly is the issue?
Thanks for your help
Yann

8

Hello Yann,
I don't have the access to the clusters, and I will not be able to run these jobs on my own computer to find where the issue comes from.
Perhaps someone in the @team.galaxy can do it?

9

If you got the same message about the memory, we don't need to investigate.
It's mean that this tool need more memory.

Which tool(s)?

10

Hi @gildaslecorguille, @Lain

The last error is on
msPurity.averageFragSpectra tool, but after that i will run
msPurity.createDatabase
msPurity.createMSP
msPurity.spectralMatching

and i guess that those tools will need RAM extension too.

What is the maximum RAM amount that can be given to a tool ?

Thanks for your help
Yann

11

You can't be sure that the whole suite will request the same among of memory.

I will ask to Ralf their settings!

1 « J'aime »
12

Hi @gildaslecorguille

did you find the time to increase the RAM of the msPurity.createDatabase module?
I have retried this morning but it failed again

Thanks for the help Yann

13

Hi @gildaslecorguille , Hi @Lain

Tom from msPurity team just send me an email. He is asking for an update of the msPurity Galaxy Tools on W4M. Can you do that?

Thanks

Hi all,

Is it possible to update the msPurity Galaxy tools on W4M to the latest versions please.

Could I also check what the current memory and cpu's that are assigned to the msPurity tools on W4M as well? And what max memory you are able to use.

[..]

Kind regards,

Tom

14

Bonjour, c'est encore moi je réouvre le sujet

Car sur un nouveau projet j'ai encore un RAM limit reached ici sur msPurity.filterFragSpectra

peut-on mettre 64 Go au lieu de 48 Go ?
Merci

15

Bonjour @yguitton,

msPurity.filterFragSpectra n'avait que 8Go de RAM.
Je l'ai passé à 48 Go.
Faites nous savoir si c'est suffisant.

Thomas

1 « J'aime »