[mira_talk] Re: Mira says "killed" as last word after being almost done
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 12 May 2011 11:58:16 -0400
I have had mira crash a few times on my 12 CPU 64-bit Dell server running SLES
(yuk), 32 GB RAM.
Looking at dmesg, it appears that each time it was a RAM resources issue. It
turned out that somebody else was running a huge job on the server at night,
which caused problems. Are you the only user? Are there other automated jobs
which are RAM intensive which could be causing the crash? Have you tried
changing kpmf to 20? Do you use all 8 processors?
FWIW, I run mira as "nohup mira etc... &" after some uh-oh moments.
John
On 2011-05-12, at 11:28 AM, Adrian Pelin wrote:
> The & is a neet idea. However commenting on:
>
> > - Maybe you killed it by error when connecting... does the time of creating
> > of your log corresponds to the time you connected remotely?
>
> Likely not since the last modification done to any of the listed files was 1
> h before i connected. And to kill you need to ctrl+c it, and it does not say
> killed, I have killed it with ctrl + c many times and it never said Killed.
> Likely got killed by something and the only culprit is the OS. I think it has
> to do with OOM Killer which kills stuff when it goes crazy. I told Mira to
> leave 15% of memory free but who knows, maybe it went crazy on the CPU and
> that is why it got killed, or maybe it is the running time that you mentioned.
>
> This is a 32 GB server with 2 quad core cpus.
>
>
>
> On Thu, May 12, 2011 at 11:21 AM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote:
>
> On 12 May 2011, at 17:12 , Adrian Pelin wrote:
>
> > - I did not do it since i was home and connected remotly to find out it is
> > dead
>
> Maybe you killed it by error when connecting... does the time of creating of
> your log corresponds to the time you connected remotely?
>
> > - That means that only the OS could of killed because of exceeded resource
> > usage or max run time, which it is I have no idea:(
>
> I doubt it, it would have been in the case where you were running things on a
> cluster with a queuing system. Not on y standard desktop box.
>
> I'd just run it again (try to run it in the background to avoid logging off
> problems)
>
> mira --fastq --project=gigaspora -proout=gigaspora_denovo
> --job=denovo,genome,accurate,454,solexa SOLEXA_SETTINGS
> -GE:tismin=50:tismax=350;tpbd=1 > log_hybdn.txt &
>
> (note the "&" at the far end of the command)
> Lionel
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