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EDIT: Here's an output of the top command. Same story. All % CPU under System is unnaccounted for in top, as well as in activity monitor. I have 12 physical cores (24 with hyper threading) on the machine, so 8 forked R processes each taking 100% cpu only accounts for 33% of CPU (what's under User).

Processes: 202 total, 10 running, 9 stuck, 183 sleeping, 845 threads                                                                                                                                                      16:40:46
Load Avg: 16.81, 14.89, 11.47  CPU usage: 32.97% user, 35.27% sys, 31.74% idle  SharedLibs: 10M resident, 3332K data, 0B linkedit. MemRegions: 74215 total, 8797M resident, 35M private, 14G shared.
PhysMem: 45G used (5360M wired), 12G unused. VM: 770G vsize, 1043M framework vsize, 905949(0) swapins, 1927120(0) swapouts.  Networks: packets: 786361/1025M in, 669041/904M out. Disks: 1780468/188G read, 1536871/30G written.

PID    COMMAND      %CPU  TIME     #TH    #WQ  #PORT #MREG MEM    RPRVT  PURG   CMPRS  VPRVT  VSIZE  PGRP  PPID  STATE    UID  FAULTS     COW      MSGSENT    MSGRECV    SYSBSD    SYSMACH   CSW        PAGEINS KPRVT  KSHRD
27694  R            101.5 07:26.65 1/1    0    7     3055+ 7116M+ 812M+  0B     0B     822M+  22G+   10309 15033 running  502  2429348+   138079+  36         16         11676+    11415+    29506+     0       23M+   231K+
27693  R            101.1 07:26.79 1/1    0    7     2917+ 7049M+ 751M+  0B     0B     763M+  21G+   10309 15033 running  502  2326962+   136821+  34         14         11259+    10022+    23910+     0       23M+   201K+
27692  R            101.0 07:26.73 1/1    0    7     2850- 7132M- 781M-  0B     0B     797M-  21G-   10309 15033 running  502  2404303+   141462+  35         15         11751+    11105+    27449+     0       23M-   182K-
27691  R            100.8 07:26.77 1/1    0    7     3310+ 7291M+ 957M+  0B     0B     977M+  22G+   10309 15033 running  502  2374283+   139669+  34         15         11202+    10358+    25394+     0       23M+   284K+
27689  R            100.8 07:26.70 1/1    0    7     3155+ 7195M+ 881M+  0B     0B     892M+  22G+   10309 15033 running  502  2449497+   139793+  37+        17+        11943+    11515+    29045+     0       23M+   251K+
27695  R            100.5 07:26.70 1/1    0    7     3401+ 7320M+ 988M+  0B     0B     1007M+ 22G+   10309 15033 running  502  2472322+   144544+  42         17         13105+    11710+    29017+     0       23M+   304K+
27690  R            100.1 07:26.71 1/1    0    7     3052+ 7261M+ 893M+  0B     0B     913M+  22G+   10309 15033 running  502  2432181+   140952+  36         16         12080+    11257+    27092      0       23M+   229K+
27688  R            99.5  07:26.66 1/1    0    7     3307+ 7366M+ 1013M+ 0B     0B     1036M+ 22G+   10309 15033 running  502  2482511+   139454+  36         16         11331+    11598+    29773+     0       23M+   289K+
27720  top          20.2  00:15.51 1/1    0    22    74+   3808K+ 3576K+ 0B     0B     207M+  2566M+ 27720 470   running  0    83438+     111      9267209+   4633523+   36139+    4744288+  1870+      12      329K+  138K+
133    WindowServer 3.7   24:37.23 4      0    435   2734  41M-   46M    51M+   57M    479M   4043M  133   1     sleeping 88   1106029    3616     71798681+  33280535+  293955    47953977+ 13597819+  2379    10M-   44M+
327    Terminal     2.3   27:26.62 8      1    198   1578  96M    90M    0B     271M   1805M  4258M  327   265   sleeping 502  3826356    17691    7388415+   181612     42406285+ 15097554+ 9358587+   2176    10M    57M+
26685  R            1.9   14:22.11 3      0    45    2434  35M    35M    0B     4682M  4988M  7395M  26685 472   sleeping 502  44308891   75552    1177048+   1055       12394750+ 9626458+  3543849+   0       28M    16M

I am running a job in R that forks multiple processes. Every once in a while it seems that when the forked processes return and the next job starts, the previously forked processes terminate, but the CPU for those processes moves from 'User' to 'System'. So my activity monitor looks like this:

How can I debug this? How can I determine what processes are using the 'System' section in the screenshot? They do not show up if I sort by CPU in activity monitor. Only the 'User' processes show up, no matter how I sort it, or which tab (CPU, memory) I use.

My activity monitor is showing 'all processes', so I do see running processes for the root user. However, all of the 'System' CPU is unaccounted for in activity monitor.

The R use case may not be relevant. Or it may be. But generally, what I'd like to know is how to determine what is using the 'System' portion of the CPU load in OS X Mavericks.

I am running a job in R that forks multiple processes. Every once in a while it seems that when the forked processes return and the next job starts, the previously forked processes terminate, but the CPU for those processes moves from 'User' to 'System'. So my activity monitor looks like this:

How can I debug this? How can I determine what processes are using the 'System' section in the screenshot? They do not show up if I sort by CPU in activity monitor, or on another tab (e.g., memory).

My activity monitor is showing 'all processes', so I do see running processes for the root user. However, all of the 'System' CPU is unaccounted for in activity monitor. And I tried showing 'system processes', but nothing with high cpu shows up there (which makes sense since these processes also show up for 'all processes').

The R use case may not be relevant. Or it may be. But generally, what I'd like to know is how to determine what is using the 'System' portion of the CPU load in OS X Mavericks.