Hi,
Im running mother on a cluster (however not MPI) since the cluster is not fully set up. Im running on the master node using 6-12 processors (out of 72) having 80 GB of RAM. However, when Im running the shhh.flows cmd the process will eventually be killed due to memory shortage (see below).
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214700 56915 56678.4
214738 56934 56697.2
Total time: 56934 58048.9
Clustering flowgrams...
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************
Killed
Mar 12 03:40:23 biocluster kernel: sge_qmaster invoked oom-killer: gfp_mask=0x201da, order=0, oom_adj=0, oom_score_adj=0
Mar 12 03:40:23 biocluster kernel: [<ffffffff8111400a>] ? oom_kill_process+0x8a/0x2c0
Mar 12 03:40:23 biocluster kernel: Out of memory: Kill process 28047 (mothur) score 982 or sacrifice child
Mar 12 03:40:23 biocluster kernel: Killed process 28047, UID 509, (mothur) total-vm:134438668kB, anon-rss:81057244kB, file-rss:8kB
Is there a way to set the amount of memory usage? Or any advice would be appreciated. Thanks!