Expected Runtime for Test File

[Andrew]

I have installed SMufin on our computing cluster and have been trying to run the example provided at : http://cg.bsc.es/smufin/manual.php . However, it runs for over 100 hours and does not appear to be generating any results. I am wondering what a typical runtime would be and what the expected results are to indicate that the installation is successful.

The attempted run was executed on 8 compute nodes running Intel Xeon E5-2660 v3 cpus (each node has 40 mpi processing cores and 256 Gb of RAM) and the interconnect between the nodes is 40 Gb ethernet. We are running the latest version of Openmpi and other mpi based programs are able to run successfully. Looking at the logs I see nothing to indicate that the job fails (other than it exceeding alloted walltime) and I also see nothing to indicate that the job is progressing.

What is the expected output I should be seeing to indicate that the job is running successfully/failing ?

Thank you.

[SMuFin]

Dear Andrew,

In the error file you should see some lines like this ones:

idl 14:2
[bam_header_parse] missing LB tag in @RG lines.
[bam_header_parse] missing LB tag in @RG lines.
idl 15:2
idl 16:2
idl 17:2
idl 18:2
idl 19:2
idl 1:1 hs37d5 30000001 40000000
idl 2:1
idl 3:3
idl 4:3
idl 3:3
idl 4:3
idl 14:3
[bam_header_parse] missing LB tag in @RG lines.
[bam_header_parse] missing LB tag in @RG lines.
idl 15:3
idl 16:3
idl 17:3
idl 18:3
idl 19:3

If you are getting these kind of lines the execution is running propertly.