running mpirun, mpirun noticed that process rank 0 with PID 5835 on node localhost exited on signal 11 (Segmentation fault).

[huic...@gmail.com]

[root@localhost br]# mpirun --allow-run-as-root /tools/setup/smufin_0.9.3_mpi_beta/SMuFin --ref /ref/gatkhg19/hg19 --normal_bam /br/sfl_y.bam --tumor_bam /br/sfm_y.bam --min_sup_reads 4 --cpus_per_node 1 --patient_id br
Checking input data files...
BWT index found for /ref/gatkhg19/hg19
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 5835 on node localhost exited on signal 11 (Segmentation fault).

my server's cpu is 8 Intel(R) Xeon(R) CPU E5-2407 v2 @ 2.40GHz

cpu core too less?

thanks

[huic...@gmail.com]

one bam file is 400M，from Human whole genome bam 50Gb,use samtools view chrY.
>40x is 91%.
running about 12 seconds SMuFin before an error.
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
6346 root 20 0 288m 6716 4140 R 37.2 0.0 0:01.12 SMuFin
6347 root 20 0 3280m 1.3g 4188 R 37.2 1.1 0:01.12 SMuFin
6348 root 20 0 3280m 1.9g 4176 R 37.2 1.5 0:01.12 SMuFin
6349 root 20 0 3280m 1.4g 4184 R 37.2 1.1 0:01.12 SMuFin
6351 root 20 0 3280m 1.9g 4184 R 36.8 1.5 0:01.11 SMuFin
6352 root 20 0 3280m 1.4g 4180 R 36.8 1.1 0:01.11 SMuFin
6353 root 20 0 3280m 1.8g 4184 R 36.8 1.5 0:01.11 SMuFin
6355 root 20 0 3280m 1.4g 4176 R 36.8 1.1 0:01.11 SMuFin
6344 root 20 0 154m 3752 2436 S 1.0 0.0 0:00.03 mpirun

mpirun version is 0.9.3.
thanks.

[SMuFin]

Hi,

You should change your mpi. To run SMuFin is required the OpenMPI >= 1.5.X.

Regards