[GE users] Integration of the MPICH2 and SGE

reuti reuti at staff.uni-marburg.de
Sat May 29 20:55:06 BST 2010


Hi,

Am 29.05.2010 um 16:59 schrieb gqc606:

> Hi reuti:
>   According to your tips,I entered this command "ps -e f" after
> submit a job:

please quote ALWAYS the original post. By doing so, it is easier for
me to follow different threads (for you it's only one thread, for me
there are plenty of them), and for you it will have the effect that
you reread the question when you post your answers below. Then you
would have easily spotted out, that I asked for something different.
And please answer all questions.

-- Reuti


> [test at cluster ~]$ ps -e f
>  PID TTY      STAT   TIME COMMAND
>    1 ?        Ss     0:00 init [5]
>    2 ?        S<     0:00 [migration/0]
>    3 ?        SN     0:00 [ksoftirqd/0]
>    4 ?        S<     0:00 [watchdog/0]
>    5 ?        S<     0:00 [migration/1]
>    6 ?        SN     0:00 [ksoftirqd/1]
>    7 ?        S<     0:00 [watchdog/1]
>    8 ?        S<     0:00 [migration/2]
>    9 ?        SN     0:00 [ksoftirqd/2]
>   10 ?        S<     0:00 [watchdog/2]
>   11 ?        S<     0:00 [migration/3]
>   12 ?        SN     0:00 [ksoftirqd/3]
>   13 ?        S<     0:00 [watchdog/3]
>   14 ?        S<     0:00 [events/0]
>   15 ?        S<     0:00 [events/1]
>   16 ?        S<     0:00 [events/2]
>   17 ?        S<     0:00 [events/3]
>   18 ?        S<     0:00 [khelper]
>   19 ?        S<     0:00 [kthread]
>   25 ?        S<     0:00  \_ [kblockd/0]
>   26 ?        S<     0:00  \_ [kblockd/1]
>   27 ?        S<     0:00  \_ [kblockd/2]
>   28 ?        S<     0:00  \_ [kblockd/3]
>   29 ?        S<     0:00  \_ [kacpid]
>  133 ?        S<     0:00  \_ [cqueue/0]
>  134 ?        S<     0:00  \_ [cqueue/1]
>  135 ?        S<     0:00  \_ [cqueue/2]
>  136 ?        S<     0:00  \_ [cqueue/3]
>  139 ?        S<     0:00  \_ [khubd]
>  141 ?        S<     0:00  \_ [kseriod]
>  214 ?        S      0:00  \_ [pdflush]
>  215 ?        S      0:00  \_ [pdflush]
>  216 ?        S<     0:00  \_ [kswapd0]
>  217 ?        S<     0:00  \_ [aio/0]
>  218 ?        S<     0:00  \_ [aio/1]
>  219 ?        S<     0:00  \_ [aio/2]
>  220 ?        S<     0:00  \_ [aio/3]
>  377 ?        S<     0:00  \_ [kpsmoused]
>  424 ?        S<     0:00  \_ [ata/0]
>  425 ?        S<     0:00  \_ [ata/1]
>  426 ?        S<     0:00  \_ [ata/2]
>  427 ?        S<     0:00  \_ [ata/3]
>  428 ?        S<     0:00  \_ [ata_aux]
>  434 ?        S<     0:00  \_ [scsi_eh_0]
>  435 ?        S<     0:00  \_ [scsi_eh_1]
>  446 ?        S<     0:00  \_ [kstriped]
>  467 ?        S<     0:00  \_ [kjournald]
>  494 ?        S<     0:00  \_ [kauditd]
> 1656 ?        S<     0:00  \_ [kmpathd/0]
> 1657 ?        S<     0:00  \_ [kmpathd/1]
> 1658 ?        S<     0:00  \_ [kmpathd/2]
> 1659 ?        S<     0:00  \_ [kmpathd/3]
> 1660 ?        S<     0:00  \_ [kmpath_handlerd]
> 1691 ?        S<     0:00  \_ [kjournald]
> 1693 ?        S<     0:00  \_ [kjournald]
> 1893 ?        S<     0:00  \_ [kondemand/0]
> 1894 ?        S<     0:00  \_ [kondemand/1]
> 1895 ?        S<     0:00  \_ [kondemand/2]
> 1896 ?        S<     0:00  \_ [kondemand/3]
> 1938 ?        S<     0:00  \_ [ib_addr]
> 1955 ?        S<     0:00  \_ [ib_mcast]
> 1956 ?        S<     0:00  \_ [ib_inform]
> 1957 ?        S<     0:00  \_ [local_sa]
> 1962 ?        S<     0:00  \_ [iw_cm_wq]
> 1969 ?        S<     0:00  \_ [ib_cm/0]
> 1970 ?        S<     0:00  \_ [ib_cm/1]
> 1971 ?        S<     0:00  \_ [ib_cm/2]
> 1972 ?        S<     0:00  \_ [ib_cm/3]
> 1978 ?        S<     0:00  \_ [rdma_cm]
> 2655 ?        S<     0:00  \_ [rpciod/0]
> 2656 ?        S<     0:00  \_ [rpciod/1]
> 2657 ?        S<     0:00  \_ [rpciod/2]
> 2658 ?        S<     0:00  \_ [rpciod/3]
> 2976 ?        S<     0:00  \_ [nfsd4]
>  526 ?        S<s    0:00 /sbin/udevd -d
> 1549 ?        Ss     0:00 /sbin/change_console -f
> 1988 ?        Ss     0:00 iscsid
> 1989 ?        S<Ls   0:00 iscsid
> 2389 ?        S<sl   0:00 auditd
> 2391 ?        S<sl   0:00  \_ /sbin/audispd
> 2512 ?        Sl     0:08 /opt/rocks/bin/python /opt/rocks/bin/
> greceptor
> 2523 ?        Ss     0:00 syslogd -r -m 0
> 2526 ?        Ss     0:00 klogd -x
> 2538 ?        Ss     0:00 irqbalance
> 2572 ?        Ssl    0:00 /usr/sbin/named -u named
> 2595 ?        Ss     0:00 portmap
> 2620 ?        Ss     0:00 rpc.statd
> 2666 ?        Ss     0:00 rpc.idmapd
> 2686 ?        Ss     0:05 dbus-daemon --system
> 2736 ?        Ssl    0:00 automount
> 2756 ?        Ss     0:00 /usr/sbin/acpid
> 2857 ?        Sl     0:22 /opt/gridengine/bin/lx26-x86/sge_qmaster
> 2888 ?        Sl     0:08 /usr/sbin/snmpd -Lsd -Lf /dev/null -p /var/
> run/snmpd.pid -a
> 2903 ?        Ss     0:00 /usr/sbin/sshd
> 2915 ?        Ss     0:00 xinetd -stayalive -pidfile /var/run/
> xinetd.pid
> 2943 ?        Ss     0:00 rpc.rquotad
> 2977 ?        S      0:00 [lockd]
> 2978 ?        S      0:00 [nfsd]
> 2979 ?        S      0:00 [nfsd]
> 2980 ?        S      0:00 [nfsd]
> 2981 ?        S      0:00 [nfsd]
> 2982 ?        S      0:00 [nfsd]
> 2983 ?        S      0:00 [nfsd]
> 2984 ?        S      0:00 [nfsd]
> 2985 ?        S      0:00 [nfsd]
> 2988 ?        Ss     0:00 rpc.mountd
> 3023 ?        S      0:00 /bin/sh /opt/rocks/bin/mysqld_safe --
> defaults-file=/opt/rocks/etc/my.cnf --datadir=/var/opt/rocks/
> 3096 ?        Sl     0:00  \_ /opt/rocks/libexec/mysqld --defaults-
> file=/opt/rocks/etc/my.cnf --basedir=/opt/rocks --datadir
> 3117 ?        Ss     0:00 /usr/sbin/dhcpd eth0
> 3172 ?        Ss     0:00 /usr/libexec/postfix/master
> 3182 ?        S      0:00  \_ qmgr -l -t fifo -u
> 23623 ?        S      0:00  \_ pickup -l -t fifo -u
> 3186 ?        Ss     0:00 /usr/sbin/httpd
> 3247 ?        S      0:00  \_ /usr/sbin/httpd
> 3248 ?        S      0:00  \_ /usr/sbin/httpd
> 3249 ?        S      0:00  \_ /usr/sbin/httpd
> 3250 ?        S      0:00  \_ /usr/sbin/httpd
> 3251 ?        S      0:00  \_ /usr/sbin/httpd
> 3253 ?        S      0:00  \_ /usr/sbin/httpd
> 3254 ?        S      0:00  \_ /usr/sbin/httpd
> 3256 ?        S      0:00  \_ /usr/sbin/httpd
> 3197 ?        Ss     0:00 crond
> 3228 ?        Ss     0:00 xfs -droppriv -daemon
> 3257 ?        Ss     0:00 /usr/sbin/atd
> 3279 ?        Ss     0:06 hald
> 3280 ?        S      0:00  \_ hald-runner
> 3287 ?        S      0:00      \_ hald-addon-acpi: listening on
> acpid socket /var/run/acpid.socket
> 3293 ?        S      0:00      \_ hald-addon-keyboard: listening on /
> dev/input/event0
> 3376 ?        S      0:02 /opt/rocks/bin/python /opt/rocks/
> bittorrent/bttrack.py --port 7625 --dfile /tmp/dstate
> 3402 ?        S      0:00 /usr/sbin/smartd -q never
> 3407 tty1     Ss+    0:00 /sbin/mingetty tty1
> 3408 tty2     Ss+    0:00 /sbin/mingetty tty2
> 3409 tty3     Ss+    0:00 /sbin/mingetty tty3
> 3411 tty4     Ss+    0:00 /sbin/mingetty tty4
> 3413 tty5     Ss+    0:00 /sbin/mingetty tty5
> 3418 tty6     Ss+    0:00 /sbin/mingetty tty6
> 3484 ?        Ss     0:00 /usr/sbin/gdm-binary -nodaemon
> 3600 ?        S      0:00  \_ /usr/sbin/gdm-binary -nodaemon
> 3605 tty7     Ss+    1:50      \_ /usr/bin/Xorg :0 -br -audit 0 -
> auth /var/gdm/:0.Xauth -nolisten tcp vt7
> 3625 ?        Ss     0:00      \_ /usr/bin/gnome-session
> 3664 ?        Ss     0:00          \_ /usr/bin/ssh-agent /bin/sh -c
> exec -l /bin/bash -c "/usr/bin/dbus-launch --exit-with-s
> 3602 ?        S      0:00 /usr/libexec/gdm-rh-security-token-helper
> 3768 ?        S      0:00 /usr/bin/dbus-launch --exit-with-session /
> etc/X11/xinit/Xclients
> 3769 ?        Ss     0:00 /bin/dbus-daemon --fork --print-pid 4 --
> print-address 6 --session
> 3775 ?        S      0:00 /usr/libexec/gconfd-2 5
> 3778 ?        S      0:00 /usr/bin/gnome-keyring-daemon
> 3780 ?        Sl     0:01 /usr/libexec/gnome-settings-daemon
> 3795 ?        Ss     0:22 metacity --sm-client-id=default1
> 3799 ?        Ss     0:06 gnome-panel --sm-client-id default2
> 3801 ?        Ssl    1:08 nautilus --no-default-window --sm-client-
> id default3
> 3805 ?        Ssl    0:00 /usr/libexec/bonobo-activation-server --ac-
> activate --ior-output-fd=16
> 3808 ?        Ss     0:00 eggcups --sm-client-id default4
> 3809 ?        Ss     0:00 gnome-volume-manager --sm-client-id default5
> 3811 ?        S      0:00 /usr/libexec/gnome-vfs-daemon
> 3827 ?        Ss     0:00 bt-applet --sm-disable
> 3829 ?        S      0:00 /usr/libexec/gam_server
> 3831 ?        Ss     0:00 nm-applet --sm-disable
> 3840 ?        S      0:16 /usr/libexec/wnck-applet --oaf-activate-
> iid=OAFIID:GNOME_Wncklet_Factory --oaf-ior-fd=19
> 3842 ?        S      0:00 /usr/libexec/trashapplet --oaf-activate-
> iid=OAFIID:GNOME_Panel_TrashApplet_Factory --oaf-ior-fd=22
> 3851 ?        Ss     0:00 pam-panel-icon --sm-client-id default0
> 3853 ?        S      0:00  \_ /sbin/pam_timestamp_check -d root
> 3854 ?        Ss     0:02 gnome-power-manager
> 3857 ?        S      0:00 ./escd --key_Inserted="/usr/bin/esc" --
> on_Signal="/usr/bin/esc"
> 3865 ?        S      0:00 /usr/sbin/nm-system-settings --config /etc/
> NetworkManager/nm-system-settings.conf
> 3875 ?        S      0:00 /usr/libexec/mapping-daemon
> 3880 ?        S      0:00 /usr/libexec/notification-area-applet --
> oaf-activate-iid=OAFIID:GNOME_NotificationAreaApplet_Facto
> 3882 ?        S      0:00 /usr/libexec/clock-applet --oaf-activate-
> iid=OAFIID:GNOME_ClockApplet_Factory --oaf-ior-fd=29
> 3884 ?        Sl     0:00 /usr/libexec/mixer_applet2 --oaf-activate-
> iid=OAFIID:GNOME_MixerApplet_Factory --oaf-ior-fd=24
> 3890 ?        Rl     0:12 gnome-terminal
> 3891 ?        S      0:00  \_ gnome-pty-helper
> 11812 pts/2    Ss     0:00  \_ bash
> 16637 pts/2    S+     0:00  |   \_ ssh compute-0-0
> 14186 pts/1    Ss     0:00  \_ bash
> 14277 pts/1    S      0:00  |   \_ su test
> 14278 pts/1    S      0:00  |       \_ bash
> 23779 pts/1    R+     0:00  |           \_ ps -e f
> 16642 pts/3    Ss     0:00  \_ bash
> 16734 pts/3    S+     0:00      \_ ssh compute-0-1
> 4085 ?        Ss     0:02 gnome-screensaver
> 4540 ?        SLs    0:00 ntpd -A -u ntp:ntp -p /var/run/ntpd.pid -g
> 4545 ?        S      0:00  \_ ntpd -A -u ntp:ntp -p /var/run/
> ntpd.pid -g
> [test at cluster ~]$ qstat -f
> queuename                      qtype resv/used/tot. load_avg
> arch          states
> ---------------------------------------------------------------------------------
> all.q at compute-0-0.local        BIP   0/3/4          0.00     lx26-x86
>    258 0.55500 flat_aireb test         dr    05/29/2010 14:42:56     3
> ---------------------------------------------------------------------------------
> all.q at compute-0-1.local        BIP   0/3/4          0.00     lx26-x86
>    258 0.55500 flat_aireb test         dr    05/29/2010 14:42:56     3
>
> I don't know how to analysis it;Can you give me some tips?Thanks!
>
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