Brain Imaging & Analysis Center

For tasks using concurrent processes, average times are reported. Individual process times are included in the Notes section for the task.

A brief description of this task including information about software and datasets (size, runs …) used.

a dataset from MIRECC with 10 runs (180 timepoints each), 23 copes … job includes slice-time correction, motion correction, coregistration and stats within FSL, using a bash script that i (chris) wrote (calls FEAT and uses SED for some replacements).

• run1 finished in 17minutes(node1) | 16minutes(node2), the entire job took 2hr36m (~15m6s per run)
• needed to replace the fsl distribution of gnuplot with the standard version supplied with linux
• data read/wrote from/to the linux cluster, it was never transfered across the network to a storage server

the completed dataset from “batch job 1”, was used for a second level FSL analysis … 10 runs were combined for a within subject average (for all 23 copes).

• also using a batch script written by me (chris)

a dataset from MIRECC with 5 runs (180 timepoints each), 23 copes … job includes slice-time correction, motion correction, coregistration and stats within FSL, using a bash script that i (chris) wrote (calls FEAT and uses SED for some replacements).

• node1 had 2 instances of the same job running concurrently, each job finished in 1h20min (~16m each)
• node2 had 4 instances of the same job running concurrently, each job finished in 1h23min (~16.6m each)
• data read/wrote from/to the linux cluster, it was never transfered across the network to a storage server

the completed dataset from “batch job 3”, was used for a second level FSL analysis … 5 runs were combined for a within subject average (for all 23 copes).

• also using a batch script written by me (chris)
• node1 had 2 instances of the same job running, all finished in ~36m
• node2 had 4 instances of the same job running, all finished in ~38m

Running a modified version of Jim's “runfreesurfer” on a 256x256x166 (1mm^3) T1 dataset. BIAC Scan ID 31816, series600. This script will run “recon-all” with all options “autorecon1”, “autorecon2” and “autorecon3”.

• Had to edit “runfreesurfer” to add the subject directory to the input arguments of “recon-all” (using the -sd flag).
• All data was processed locally on the node in /home/bizzell/freesurfer
• Time for biacnode1: 892m, 43.227s (14h,52m,43s)
• Time for biacnode2: 940m, 25.618s (15h,40m,26s)

Running the modified version of “runfreesurfer” described above on two datasets:

• Dataset #1: 256x256x166 (1mm^3) T1, BIAC scan ID 31812, series600
• Dataset #2: 256x256x166 (1mm^3) T1, BIAC scan ID 31885, series600

For biacnode1, I am running Freesurfer on both of these datasets in parallel. For biacnode2, I made one copy of each dataset, and am running Freesurfer on all 4 datasets (31812, 31885, 31812 copy, and 31885 copy) in parallel.

Time for biacnode1:

• One dataset took 1096m, 17.684s (18h,16m,18s)
• Other dataset took 1274m, 11.860s (21h,14m,12s)
• Average time 1185m (19h,45m)

Time for biacnode2 (I incorrectly used the command “time” for this one, so I had to get the processing time from the Freesurfer log files):

• Dataset1 31812: Start 4/6/07 12:08:28, End 4/7/07 12:05:46; 23h, 57m; 1437m
• Dataset2 31812 copy: Start 4/6/07 12:08:28, End 4/7/07 11:48:57; 23h, 40m; 1420m
• Dataset3 31885: Start 4/6/07 12:08:28, End 4/7/07 8:29:03; 20h, 21m; 1221m
• Dataset4 31885 copy: Start 4/6/07 12:08:28, End 4/7/07 8:25:28; 20h, 17m; 1217m
• Average 31812: ~1429m; 23h, 49m
• Average 31885: 1219m; 20h, 19m
• Average all: ~1324m; 22h, 4m

SENSE spiral recon on exam 32904, run #7 (spiral-in, 64×64, 30 slices, 168 time points)

• 1 process on biacnode1: 39m
• 1 process on biacnode2: 42m

same as Matlab Job 1

• 2 concurrent processes on biacnode1: 48m | 48m | average: 48m
• 4 concurrent processes on biacnode2: 53m | 55m | 54m | 54m | average: 54m

• processor : Intel(R) Xeon(R) CPU 3070 @ 2.66GHz
• cache size : 4096 KB
• cpu cores : 2
• memory : 3988948 kB

• processor 1 : Intel(R) Xeon(R) CPU 5150 @ 2.66GHz
• cache size : 4096 KB
• cpu cores : 2

• processor 2 : Intel(R) Xeon(R) CPU 5150 @ 2.66GHz
• cache size : 4096 KB
• cpu cores : 2

• memory : 8131428 kB