Hi Kristen,
at the moment would be pretty sure that I am running bedpostx in parallel.
Before my processors were loaded modestly, and I could see only one
xfibres process. Now there are two processes and the processors throttle
on a full load. I am not familiar with sge, so I can not check what's in
the queues. Regarding the sge installation on the mac, I mostly accepted
default options just to get it simple and working as fast as possible.
When the installation was compete I added fsl specific queues (short,
veryshort, long, verylong), which was the most tricky part, but after some
reading of the sge documentation I was successful. Except for the
processors and slots, as Dave mentioned.
I am going to run an analysis over night, so I'll have an idea about
execution time in the morning.
Martin
On Thu, 13 Sep 2007, Lindgren, Kristen, Ann wrote:
> Is there any way to check if bedpostx is actually running in parallel
> correctly? I thought I followed the directions properly, but I'm not
> entirely sure it's set up properly. Any help you could provide would be
> greatly appreciated. Thanks!
>
>
>
> Kristen
>
>
>
> ________________________________
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Dave Flitney
> Sent: Thursday, September 13, 2007 8:11 AM
> To: [log in to unmask]
> Subject: Re: [FSL] bedpostx in parallel on MAC
>
>
>
> Okay, try "processors" and "slots" both equal to 2.
>
>
>
> "processors=1,2" seems to be interpreted as "processors=1" - this needs
> to reflect the number of cores available so that SGE can calculate loads
> correctly.
>
> "slots=1" means only 1 managed long.q process at a time - and you would
> like 2 presumably.
>
>
>
> On 13 Sep 2007, at 12:53, Martin Kavec wrote:
>
>
>
>
>
> Hi Dave,
>
>
>
> have you been able to find anything wrong in my settings? Thanks a lot.
>
>
>
> Martin
>
>
>
> On Wednesday 12 September 2007 12:53:24 Martin Kavec wrote:
>
> Hi Dave,
>
>
>
> the outputs are below. Thanks.
>
>
>
> Martin
>
>
>
> On Wednesday 12 September 2007 12:02:31 Dave Flitney wrote:
>
> Could you send me the output of the following commands:
>
>
>
> qconf -sconf
>
>
>
> $ qconf -sconf
>
> global:
>
> execd_spool_dir /opt/SGE/default/spool
>
> mailer /usr/bin/mail
>
> xterm /usr/X11R6/bin/xterm
>
> load_sensor none
>
> prolog none
>
> epilog none
>
> shell_start_mode posix_compliant
>
> login_shells sh,ksh,csh,tcsh
>
> min_uid 0
>
> min_gid 0
>
> user_lists none
>
> xuser_lists none
>
> projects none
>
> xprojects none
>
> enforce_project false
>
> enforce_user auto
>
> load_report_time 00:00:40
>
> max_unheard 00:05:00
>
> reschedule_unknown 00:00:00
>
> loglevel log_warning
>
> administrator_mail [log in to unmask]
>
> set_token_cmd none
>
> pag_cmd none
>
> token_extend_time none
>
> shepherd_cmd none
>
> qmaster_params none
>
> execd_params none
>
> reporting_params accounting=true reporting=false \
>
> flush_time=00:00:15
> joblog=false
>
> sharelog=00:00:00
>
> finished_jobs 100
>
> gid_range 20000-20100
>
> qlogin_command telnet
>
> qlogin_daemon /usr/libexec/telnetd
>
> rlogin_daemon /usr/libexec/rlogind
>
> max_aj_instances 2000
>
> max_aj_tasks 75000
>
> max_u_jobs 0
>
> max_jobs 0
>
> auto_user_oticket 0
>
> auto_user_fshare 0
>
> auto_user_default_project none
>
> auto_user_delete_time 86400
>
> delegated_file_staging false
>
> reprioritize 0
>
>
>
> qconf -sq long.q
>
>
>
> $ qconf -sq long.q
>
> qname long.q
>
> hostlist erasme52185.erasme.ulb.ac.be
>
> seq_no 0
>
> load_thresholds np_load_avg=1.75
>
> suspend_thresholds NONE
>
> nsuspend 1
>
> suspend_interval 00:05:00
>
> priority 0
>
> min_cpu_interval 24:00:00
>
> processors 1,2
>
> qtype BATCH INTERACTIVE
>
> ckpt_list NONE
>
> pe_list make
>
> rerun FALSE
>
> slots 1
>
> tmpdir /tmp
>
> shell /bin/sh
>
> prolog NONE
>
> epilog NONE
>
> shell_start_mode posix_compliant
>
> starter_method NONE
>
> suspend_method NONE
>
> resume_method NONE
>
> terminate_method NONE
>
> notify 00:00:60
>
> owner_list NONE
>
> user_lists NONE
>
> xuser_lists NONE
>
> subordinate_list NONE
>
> complex_values NONE
>
> projects NONE
>
> xprojects NONE
>
> calendar NONE
>
> initial_state default
>
> s_rt INFINITY
>
> h_rt INFINITY
>
> s_cpu INFINITY
>
> h_cpu INFINITY
>
> s_fsize INFINITY
>
> h_fsize INFINITY
>
> s_data INFINITY
>
> h_data INFINITY
>
> s_stack INFINITY
>
> h_stack INFINITY
>
> s_core INFINITY
>
> h_core INFINITY
>
> s_rss INFINITY
>
> h_rss INFINITY
>
> s_vmem INFINITY
>
> h_vmem INFINITY
>
>
>
> qconf -ss
>
>
>
> $ qconf -ss
>
> erasme52185.erasme.ulb.ac.be
>
>
>
> qconf -sel
>
>
>
> $ qconf -sel
>
> erasme52185.erasme.ulb.ac.be
>
>
>
> --
>
> Cheers, Dave
>
>
>
> Dave Flitney, IT Manager
>
> Oxford Centre for Functional MRI of the Brain
>
> E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
>
> URL: http://www.fmrib.ox.ac.uk/~flitney
>
>
>
>
>
>
>
>
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