SuFin_0.9.3_mpi_beta failed with MPI error

[Chen Bill]

We are runing SuFin_0.9.3_mpi_beta with Openmpi 1.6.5. The example data works fine.

But when we try to run another data, it failed with the following error: 

... 

num_targets: 25 

num_targets: 25 

num_targets: 25 

num_targets: 25 

num_targets: 25 

=================================================================================== 

[node2:43134] *** An error occurred in MPI_Send

[node2:43134] *** on communicator MPI_COMM_WORLD

[node2:43134] *** MPI_ERR_COUNT: invalid count argument

[node2:43134] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort

--------------------------------------------------------------------------

mpirun has exited due to process rank 0 with PID 43134 on

node node2 exiting improperly. There are two reasons this could occur:

1. this process did not call "init" before exiting, but others in

the job did. This can cause a job to hang indefinitely while it waits

for all processes to call "init". By rule, if one process calls "init",

then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".

By rule, all processes that call "init" MUST call "finalize" prior to

exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be

terminated by signals sent by mpirun (as reported here).

Any suggestions will be appreciate!

Many thanks,

Bill

[elizabeth...@gmail.com]

Hi,


I have a similar problem (posted Apr 22nd about it)

Did you find any solution that worked for you?

Authors: any idea what this could be due to?

Thanks!!

Elizabeth

[SMufin]

Hi Chen Bill,

Can you provide more information about your execution? In particular we will need:

- The exact command you are running in your job.
- The total amount of resources you are using: number of nodes, memory available in each node, number of threads per node, etc.
- The main characteristics of your analysis: Human whole genome sequencing? Which coverage ? Are you running SMUFIN from BAM files or directly from FASTQ files?

Thx,

Santi