methylKit taking very long to run on Raven

[yaaminiv]

I feel like I encountered this issue years ago...but trying to use methylKit on the R Studio server on Raven has been very slow the past few days. Computationally-intensive steps cause the server to freeze/reboot after 15-20 minutes. I have been trying to load in a ~20G .RData file on and off all day. Earlier this week I was able to load in this same .RData file in ~5 min. Is this to be expected when others are also using Raven for other tasks? Is there a different workflow I should use instead?

[sr320]

It's likely related to others using Raven. Klone is probably better. I'm happy to run the code if you provide it here in this issue.

…

On Thu, Jul 9, 2026 at 3:07 PM Dr. Yaamini R. Venkataraman < ***@***.***> wrote: *yaaminiv* created an issue (RobertsLab/resources#2471) <https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/2471__;!!K-Hz7m0Vt54!kcaf25kk_Q3R5ySTfkS2zpbGDfOK6HgWh-LTKfoaAK20ptFgNxvB_8F47_oeEL22zr2nkTZrEZMLex8DlnDqz-M$> I feel like I encountered this issue years ago...but trying to use methylKit on the R Studio server on Raven has been very slow the past few days. Computationally-intensive steps cause the server to freeze/reboot after 15-20 minutes. I have been trying to load in a ~20G .RData file on and off all day. Earlier this week I was able to load in this same .RData file in ~5 min. Is this to be expected when others are also using Raven for other tasks? Is there a different workflow I should use instead? — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/2471?email_source=notifications&email_token=ABB4PN6RQP4GVCWX4GNY3IT5EAJRTA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NBYGUYDENJRGAZDPJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L__;!!K-Hz7m0Vt54!kcaf25kk_Q3R5ySTfkS2zpbGDfOK6HgWh-LTKfoaAK20ptFgNxvB_8F47_oeEL22zr2nkTZrEZMLex8DlYxrdto$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABB4PN2RJBBS33QPKEVZY2L5EAJRTAVCNFSNUABEKJSXA33TNF2G64TZHM4TSNRZHA3DQOB3JFZXG5LFHM2DQNJQGI2TCMBSG6QXMAQ__;!!K-Hz7m0Vt54!kcaf25kk_Q3R5ySTfkS2zpbGDfOK6HgWh-LTKfoaAK20ptFgNxvB_8F47_oeEL22zr2nkTZrEZMLex8DF086w6k$> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[kubu4]

@yaaminiv might be onto something.

I can't get into Raven at all - login times out. Usually, I can at least SSH in.

Aaaand, I'm unable to ping Raven.

I have Husky OnNet active, so that's no an issue.

I'm wondering if it's turned off? Or, ethernet cable is disconnected or switch isn't working or something?

[kubu4]

@yaaminiv - We've rebooted Raven and that has at least fixed remote access. I'm guessing this should help with this issue, however, Hyak is faster, so you may just want to go with @sr320's proposed solution of running there.