[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 12:22:42 -0400
When I run mira, I include:
nohup mira --project=whatever --job=denovo,genome,accurate,454
-GE:not=8:kpmf=15 >&log_assembly.txt &
not=8 uses 8 processors in some of the assembly stages. kpmf=15 (depending on
which server I use, I change it from 10-20 according to experience) is the
command to "keep percent memory free"
Hth
John
On 2011-05-12, at 12:13 PM, Adrian Pelin wrote:
> No, this was done on VMware, me being the only root/user, no other person
> knows the passwd. No other jobs have been running.
>
> Qhat do you mean change kpmf to 20?
>
> On Thu, May 12, 2011 at 11:58 AM, John Nash <john.he.nash@xxxxxxxxx> wrote:
> 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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