Process quits with message "Killed" about carnival HOT 4 CLOSED

Hi @laylagerami,

Are there any errors in the log file from the server? This may be related to the memory issues, what is the limit for you on the server? The jobs can be killed by the server when exceeding a time limit set by admins.

What I would try first is to decrease Omnipath to e.g. only the edges with one or two confirmed sources and run again to see if it's able to finish.

from carnival.

Hi @ivanovaos, no log is produced by the server. We do not have per-user memory limits, the limit is basically dictated by the memory available (out of 252G). And we also don't have a time limit!

I will try to reduce the network and see if I can run it. I'll let you know what the outcome is.

from carnival.

Hi,

Can it be because you need to set additionally solver="cplex"? Maybe CARNIVAL is still running the matrix formulation (which is very memory exhausting) although you have set path to the executable cplex.

Cheers,

from carnival.

@enio23 that worked, thank you so much!

r1 = runCARNIVAL(inputObj=NULL, 
                   weightObj = progenylist$`1`,
                   measObj = measObj, 
                   netObj = netfilefull,
                   solverPath = "../../../ibm/ILOG/CPLEX_Studio1210/cplex/bin/x86-64_linux/cplex",
                   solver = 'cplex',
                   threads = 10,
                   dir_name="../Results/Test")

from carnival.