and nohup means nothing can kill it? I also understand that using multi threaded not=8 makes mira sue another algorythm. On Thu, May 12, 2011 at 12:22 PM, John Nash <john.he.nash@xxxxxxxxx> wrote: > 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 >>> -- >>> You have received this mail because you are subscribed to the mira_talk >>> mailing list. For information on how to subscribe or unsubscribe, please >>> visit http://www.chevreux.org/mira_mailinglists.html >>> >> >> >> > >