[Neurodebian-users] FSL parallelization with condor
Antti Korvenoja
antti.korvenoja at helsinki.fi
Fri Mar 30 21:37:00 UTC 2012
I have Debian wheezy AMD64 system and fsl is 4.1.9-2~nd70+1. Condor is
7.7.5~dfsg.1-2.
idle state outputs:
> condor_status
Name OpSys Arch State Activity LoadAv Mem
ActvtyTime
slot1@ LINUX X86_64 Owner Idle 0.060 1977 0
+00:30:04
slot2@ LINUX X86_64 Owner Idle 0.000 1977 0
+00:30:05
Total Owner Claimed Unclaimed Matched Preempting
Backfill
X86_64/LINUX 2 2 0 0 0 0
0
Total 2 2 0 0 0 0
0
> condor_q
-- Submitter: : <127.0.0.1:40757> : fmri9
ID OWNER SUBMITTED RUN_TIME ST PRI SIZE
CMD
1.0 antti 3/26 21:46 0+00:00:01 H 0 1.0
bash
2.0 antti 3/26 21:46 0+00:00:00 H 0 1.0
bash
3.0 antti 3/26 21:46 0+00:00:03 H 0 0.0
cluster2_sentinel.
4.0 antti 3/26 21:46 0+00:00:00 H 0 1.0
bash
5.0 antti 3/26 21:46 0+00:00:03 H 0 0.0
cluster4_sentinel.
6.0 antti 3/26 21:46 0+00:00:00 H 0 1.0
bash
7.0 antti 3/26 21:46 0+00:00:03 H 0 0.0
cluster6_sentinel.
8.0 antti 3/26 21:46 0+00:00:00 H 0 1.0
bash
9.0 antti 3/26 21:46 0+00:00:04 H 0 0.0
cluster8_sentinel.
10.0 antti 3/26 21:46 0+00:00:00 H 0 1.0
bash
11.0 antti 3/26 21:46 0+00:00:02 H 0 0.0
cluster10_sentinel
13.0 antti 3/26 22:00 0+00:00:00 H 0 1.0
bash
14.0 antti 3/26 22:00 0+00:00:03 H 0 0.0
cluster13_sentinel
15.0 antti 3/26 22:00 0+00:00:00 H 0 0.1
sh /home/antti/sto
16.0 antti 3/26 22:00 0+00:00:03 H 0 0.0
cluster15_sentinel
17.0 antti 3/26 22:00 0+00:00:00 H 0 1.0
bash
18.0 antti 3/26 22:00 0+00:00:02 H 0 0.0
cluster17_sentinel
19.0 antti 3/26 22:00 0+00:00:00 H 0 1.0
bash
20.0 antti 3/26 22:00 0+00:00:03 H 0 0.0
cluster19_sentinel
21.0 antti 3/26 22:00 0+00:00:00 H 0 1.0
bash
22.0 antti 3/26 22:00 0+00:00:03 H 0 0.0
cluster21_sentinel
23.0 antti 3/26 22:00 0+00:00:00 H 0 1.0
bash
24.0 antti 3/26 22:00 0+00:00:04 H 0 0.0
cluster23_sentinel
25.0 antti 3/26 23:30 0+00:00:00 I 0 1.0
bash
26.0 antti 3/26 23:30 0+00:00:00 H 0 1.0
bash
27.0 antti 3/26 23:30 0+00:00:02 H 0 0.0
cluster26_sentinel
28.0 antti 3/26 23:30 0+00:00:00 H 0 1.0
bash
29.0 antti 3/26 23:30 0+00:00:02 H 0 0.0
cluster28_sentinel
30.0 antti 3/26 23:30 0+00:00:00 H 0 1.0
bash
31.0 antti 3/26 23:30 0+00:00:02 H 0 0.0
cluster30_sentinel
32.0 antti 3/26 23:30 0+00:00:00 H 0 1.0
bash
33.0 antti 3/26 23:30 0+00:00:01 H 0 0.0
cluster32_sentinel
34.0 antti 3/26 23:30 0+00:00:00 H 0 1.0
bash
35.0 antti 3/26 23:30 0+00:00:01 H 0 0.0
cluster34_sentinel
36.0 antti 3/27 22:28 0+00:00:00 I 0 1.0
bash
37.0 antti 3/27 22:28 0+00:00:00 H 0 1.0
bash
38.0 antti 3/27 22:28 0+00:00:01 H 0 0.0
cluster37_sentinel
39.0 antti 3/27 22:28 0+00:00:00 H 0 1.0
bash
40.0 antti 3/27 22:28 0+00:00:01 H 0 0.0
cluster39_sentinel
41.0 antti 3/27 22:28 0+00:00:00 H 0 1.0
bash
42.0 antti 3/27 22:28 0+00:00:01 H 0 0.0
cluster41_sentinel
43.0 antti 3/27 22:28 0+00:00:00 H 0 1.0
bash
44.0 antti 3/27 22:28 0+00:00:01 H 0 0.0
cluster43_sentinel
45.0 antti 3/27 22:28 0+00:00:00 H 0 1.0
bash
46.0 antti 3/27 22:28 0+00:00:01 H 0 0.0
cluster45_sentinel
47.0 antti 3/29 19:13 0+00:00:00 I 0 1.0
bash
48.0 antti 3/29 19:13 0+00:00:00 H 0 1.0
bash
49.0 antti 3/29 19:13 0+00:00:02 H 0 0.0
cluster48_sentinel
50.0 antti 3/29 19:13 0+00:00:00 H 0 1.0
bash
51.0 antti 3/29 19:13 0+00:00:04 H 0 0.0
cluster50_sentinel
52.0 antti 3/29 19:13 0+00:00:00 H 0 1.0
bash
53.0 antti 3/29 19:13 0+00:00:04 H 0 0.0
cluster52_sentinel
54.0 antti 3/29 19:13 0+00:00:00 H 0 1.0
bash
55.0 antti 3/29 19:13 0+00:00:02 H 0 0.0
cluster54_sentinel
56.0 antti 3/29 19:13 0+00:00:00 H 0 1.0
bash
57.0 antti 3/29 19:13 0+00:00:04 H 0 0.0
cluster56_sentinel
58.0 antti 3/29 19:20 0+00:00:00 I 0 1.0
bash
59.0 antti 3/29 19:20 0+00:00:00 H 0 1.0
bash
60.0 antti 3/29 19:20 0+00:00:04 H 0 0.0
cluster59_sentinel
61.0 antti 3/29 19:20 0+00:00:00 H 0 1.0
bash
62.0 antti 3/29 19:20 0+00:00:02 H 0 0.0
cluster61_sentinel
63.0 antti 3/29 19:20 0+00:00:00 H 0 1.0
bash
64.0 antti 3/29 19:20 0+00:00:05 H 0 0.0
cluster63_sentinel
65.0 antti 3/29 19:20 0+00:00:00 H 0 1.0
bash
66.0 antti 3/29 19:20 0+00:00:02 H 0 0.0
cluster65_sentinel
67.0 antti 3/29 19:20 0+00:00:00 H 0 1.0
bash
68.0 antti 3/29 19:20 0+00:00:05 H 0 0.0
cluster67_sentinel
69.0 antti 3/29 19:42 0+00:00:00 I 0 1.0
bash
70.0 antti 3/29 19:42 0+00:00:00 H 0 1.0
bash
71.0 antti 3/29 19:42 0+00:00:04 H 0 0.0
cluster70_sentinel
72.0 antti 3/29 19:42 0+00:00:00 H 0 1.0
bash
73.0 antti 3/29 19:42 0+00:00:03 H 0 0.0
cluster72_sentinel
74.0 antti 3/29 19:42 0+00:00:00 H 0 1.0
bash
75.0 antti 3/29 19:42 0+00:00:04 H 0 0.0
cluster74_sentinel
76.0 antti 3/29 19:42 0+00:00:00 H 0 1.0
bash
77.0 antti 3/29 19:42 0+00:00:04 H 0 0.0
cluster76_sentinel
78.0 antti 3/29 19:42 0+00:00:00 H 0 1.0
bash
79.0 antti 3/29 19:42 0+00:00:03 H 0 0.0
cluster78_sentinel
and after fsl-seltest feat
> condor_status
Name OpSys Arch State Activity LoadAv Mem
ActvtyTime
slot1@ LINUX X86_64 Owner Idle 0.210 1977 0
+00:35:04
slot2@ LINUX X86_64 Owner Idle 0.000 1977 0
+00:35:05
Total Owner Claimed Unclaimed Matched Preempting
Backfill
X86_64/LINUX 2 2 0 0 0 0
0
Total 2 2 0 0 0 0
0
> condor_q
-- Submitter: : <127.0.0.1:40757> : fmri9
ID OWNER SUBMITTED RUN_TIME ST PRI SIZE
CMD
1.0 antti 3/26 21:46 0+00:00:01 H 0 1.0
bash
2.0 antti 3/26 21:46 0+00:00:00 H 0 1.0
bash
3.0 antti 3/26 21:46 0+00:00:03 H 0 0.0
cluster2_sentinel.
4.0 antti 3/26 21:46 0+00:00:00 H 0 1.0
bash
5.0 antti 3/26 21:46 0+00:00:03 H 0 0.0
cluster4_sentinel.
6.0 antti 3/26 21:46 0+00:00:00 H 0 1.0
bash
7.0 antti 3/26 21:46 0+00:00:03 H 0 0.0
cluster6_sentinel.
8.0 antti 3/26 21:46 0+00:00:00 H 0 1.0
bash
9.0 antti 3/26 21:46 0+00:00:04 H 0 0.0
cluster8_sentinel.
10.0 antti 3/26 21:46 0+00:00:00 H 0 1.0
bash
11.0 antti 3/26 21:46 0+00:00:02 H 0 0.0
cluster10_sentinel
13.0 antti 3/26 22:00 0+00:00:00 H 0 1.0
bash
14.0 antti 3/26 22:00 0+00:00:03 H 0 0.0
cluster13_sentinel
15.0 antti 3/26 22:00 0+00:00:00 H 0 0.1
sh /home/antti/sto
16.0 antti 3/26 22:00 0+00:00:03 H 0 0.0
cluster15_sentinel
17.0 antti 3/26 22:00 0+00:00:00 H 0 1.0
bash
18.0 antti 3/26 22:00 0+00:00:02 H 0 0.0
cluster17_sentinel
19.0 antti 3/26 22:00 0+00:00:00 H 0 1.0
bash
20.0 antti 3/26 22:00 0+00:00:03 H 0 0.0
cluster19_sentinel
21.0 antti 3/26 22:00 0+00:00:00 H 0 1.0
bash
22.0 antti 3/26 22:00 0+00:00:03 H 0 0.0
cluster21_sentinel
23.0 antti 3/26 22:00 0+00:00:00 H 0 1.0
bash
24.0 antti 3/26 22:00 0+00:00:04 H 0 0.0
cluster23_sentinel
25.0 antti 3/26 23:30 0+00:00:00 I 0 1.0
bash
26.0 antti 3/26 23:30 0+00:00:00 H 0 1.0
bash
27.0 antti 3/26 23:30 0+00:00:02 H 0 0.0
cluster26_sentinel
28.0 antti 3/26 23:30 0+00:00:00 H 0 1.0
bash
29.0 antti 3/26 23:30 0+00:00:02 H 0 0.0
cluster28_sentinel
30.0 antti 3/26 23:30 0+00:00:00 H 0 1.0
bash
31.0 antti 3/26 23:30 0+00:00:02 H 0 0.0
cluster30_sentinel
32.0 antti 3/26 23:30 0+00:00:00 H 0 1.0
bash
33.0 antti 3/26 23:30 0+00:00:01 H 0 0.0
cluster32_sentinel
34.0 antti 3/26 23:30 0+00:00:00 H 0 1.0
bash
35.0 antti 3/26 23:30 0+00:00:01 H 0 0.0
cluster34_sentinel
36.0 antti 3/27 22:28 0+00:00:00 I 0 1.0
bash
37.0 antti 3/27 22:28 0+00:00:00 H 0 1.0
bash
38.0 antti 3/27 22:28 0+00:00:01 H 0 0.0
cluster37_sentinel
39.0 antti 3/27 22:28 0+00:00:00 H 0 1.0
bash
40.0 antti 3/27 22:28 0+00:00:01 H 0 0.0
cluster39_sentinel
41.0 antti 3/27 22:28 0+00:00:00 H 0 1.0
bash
42.0 antti 3/27 22:28 0+00:00:01 H 0 0.0
cluster41_sentinel
43.0 antti 3/27 22:28 0+00:00:00 H 0 1.0
bash
44.0 antti 3/27 22:28 0+00:00:01 H 0 0.0
cluster43_sentinel
45.0 antti 3/27 22:28 0+00:00:00 H 0 1.0
bash
46.0 antti 3/27 22:28 0+00:00:01 H 0 0.0
cluster45_sentinel
47.0 antti 3/29 19:13 0+00:00:00 I 0 1.0
bash
48.0 antti 3/29 19:13 0+00:00:00 H 0 1.0
bash
49.0 antti 3/29 19:13 0+00:00:02 H 0 0.0
cluster48_sentinel
50.0 antti 3/29 19:13 0+00:00:00 H 0 1.0
bash
51.0 antti 3/29 19:13 0+00:00:04 H 0 0.0
cluster50_sentinel
52.0 antti 3/29 19:13 0+00:00:00 H 0 1.0
bash
53.0 antti 3/29 19:13 0+00:00:04 H 0 0.0
cluster52_sentinel
54.0 antti 3/29 19:13 0+00:00:00 H 0 1.0
bash
55.0 antti 3/29 19:13 0+00:00:02 H 0 0.0
cluster54_sentinel
56.0 antti 3/29 19:13 0+00:00:00 H 0 1.0
bash
57.0 antti 3/29 19:13 0+00:00:04 H 0 0.0
cluster56_sentinel
58.0 antti 3/29 19:20 0+00:00:00 I 0 1.0
bash
59.0 antti 3/29 19:20 0+00:00:00 H 0 1.0
bash
60.0 antti 3/29 19:20 0+00:00:04 H 0 0.0
cluster59_sentinel
61.0 antti 3/29 19:20 0+00:00:00 H 0 1.0
bash
62.0 antti 3/29 19:20 0+00:00:02 H 0 0.0
cluster61_sentinel
63.0 antti 3/29 19:20 0+00:00:00 H 0 1.0
bash
64.0 antti 3/29 19:20 0+00:00:05 H 0 0.0
cluster63_sentinel
65.0 antti 3/29 19:20 0+00:00:00 H 0 1.0
bash
66.0 antti 3/29 19:20 0+00:00:02 H 0 0.0
cluster65_sentinel
67.0 antti 3/29 19:20 0+00:00:00 H 0 1.0
bash
68.0 antti 3/29 19:20 0+00:00:05 H 0 0.0
cluster67_sentinel
69.0 antti 3/29 19:42 0+00:00:00 I 0 1.0
bash
70.0 antti 3/29 19:42 0+00:00:00 H 0 1.0
bash
71.0 antti 3/29 19:42 0+00:00:04 H 0 0.0
cluster70_sentinel
72.0 antti 3/29 19:42 0+00:00:00 H 0 1.0
bash
73.0 antti 3/29 19:42 0+00:00:03 H 0 0.0
cluster72_sentinel
74.0 antti 3/29 19:42 0+00:00:00 H 0 1.0
bash
75.0 antti 3/29 19:42 0+00:00:04 H 0 0.0
cluster74_sentinel
76.0 antti 3/29 19:42 0+00:00:00 H 0 1.0
bash
77.0 antti 3/29 19:42 0+00:00:04 H 0 0.0
cluster76_sentinel
78.0 antti 3/29 19:42 0+00:00:00 H 0 1.0
bash
79.0 antti 3/29 19:42 0+00:00:03 H 0 0.0
cluster78_sentinel
80.0 antti 3/31 00:34 0+00:00:00 I 0 1.0
bash
81.0 antti 3/31 00:34 0+00:00:00 H 0 1.0
bash
82.0 antti 3/31 00:34 0+00:01:16 R 0 0.0
cluster81_sentinel
83.0 antti 3/31 00:34 0+00:00:00 H 0 1.0
bash
84.0 antti 3/31 00:34 0+00:01:16 R 0 0.0
cluster83_sentinel
85.0 antti 3/31 00:34 0+00:00:00 H 0 1.0
bash
86.0 antti 3/31 00:34 0+00:01:16 R 0 0.0
cluster85_sentinel
87.0 antti 3/31 00:34 0+00:00:00 H 0 1.0
bash
88.0 antti 3/31 00:35 0+00:01:15 R 0 0.0
cluster87_sentinel
89.0 antti 3/31 00:35 0+00:00:00 H 0 1.0
bash
90.0 antti 3/31 00:35 0+00:01:15 R 0 0.0
cluster89_sentinel
Greetings,
Antti
to, 2012-03-29 kello 20:14 +0200, Michael Hanke kirjoitti:
> On Thu, Mar 29, 2012 at 07:48:16PM +0300, Antti Korvenoja wrote:
> > Hello Michael,
> >
> > Unfortunately the modification you suggested does not fix the problem.
> > fsl-seltest feat runs fine. FSLPARALLEL=condor fsl-selftest feat shows
> > no progress and cpu usage remains at baseline.
>
> Alright, at least we have a command that produces the failure. Can you
> please provide some details of the system your are running: OS, OS
> version, condor version, fsl version. And the output of
>
> condor_status
>
> and
>
> condor_q
>
> After you started the 'fsl-selfttest feat' command. We will narrow it
> down, and get it to work!
>
> Michael
>
>
More information about the Neurodebian-users
mailing list