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March 03, 2021 10:03PM
Here is everything that you requested. I do not see slow performance with the data from the bootcamp. You can download the data I am using from here: https://utexas.box.com/s/7penj3t5k5w3p4ah6ipfxxlfbdbp9lgx (it is from FCP-INDI/CoRR)


afni_system_check.py -check_all

-------------------------------- general ---------------------------------
architecture:         64bit ELF
system:               Linux
release:              5.4.0-66-generic
version:              #74-Ubuntu SMP Wed Jan 27 22:54:38 UTC 2021
distribution:         Ubuntu 20.04.2 LTS
number of CPUs:       24
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /home/cameron/abin/afni
afni version         : Precompiled binary linux_ubuntu_16_64: Feb 25 2021 
                     : AFNI_21.0.12 'Titus'
AFNI_version.txt     : AFNI_21.0.12, linux_ubuntu_16_64, Feb 25 2021
which python         : /home/cameron/venvs/cpac/bin/python
python version       : 3.8.5
which R              : /usr/bin/R
R version            : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh           : /usr/bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/home/cameron/abin/afni)
    R       : 1   (/usr/bin/R)
    python  : 1   (/usr/bin/python3.8)
    python2 : 1   (/usr/bin/python2.7)
    python3 : 1   (/usr/bin/python3.8)


testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    uber_subject.py      : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success
    3dMVM                : success

checking for R packages...
    rPkgsInstall -pkgs ALL -check : FAILURE
        
        oo Warning: 
           These packages are not installed on the computer: afex!
        These packages are not installed on the computer: phia!
        These packages are not installed on the computer: snow!
        These packages are not installed on the computer: lmerTest!
        These packages are not installed on the computer: paran!
        These packages are not installed on the computer: brms!
        These packages are not installed on the computer: corrplot!
        These packages are not installed on the computer: metafor!
        

R RHOME : /usr/lib/R

checking for $HOME files...
    .afnirc                   : found
    .sumarc                   : found
    .afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
   module file : /home/cameron/venvs/cpac/lib/python3.8/site-packages/matplotlib/pyplot.py

-------------------------------- env vars --------------------------------
PATH = /home/cameron/venvs/cpac/bin:/home/cameron/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/cameron/abin

PYTHONPATH = 
R_LIBS = 
LD_LIBRARY_PATH = 
DYLD_LIBRARY_PATH = 
DYLD_FALLBACK_LIBRARY_PATH = 

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas    : found TT_N27+tlrc  under /home/cameron/abin

------------------------------ OS specific -------------------------------
which apt-get        : /usr/bin/apt-get
apt-get version      : apt 2.0.4 (amd64)

have Ubuntu system: Ubuntu 20.04.2 LTS
have Ubuntu afni  : Precompiled binary linux_ubuntu_16_64: Feb 25 2021 

=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  missing R packages (see rPkgsInstall)
*  insufficient data for AFNI bootcamp

afni -no_detach -q -VAFNI_COMPRESSOR=
<BLANK>

afni -no_detach -q -VAFNI_DONT_USE_PIGZ=
<BLANK>

Still seeing the problem:
time ~/abin/3dROIstats -mask mask2.nii.gz func.nii.gz 
File	Sub-brick	Mean_1  
func.nii.gz	0[?]	9957.563410
func.nii.gz	1[?]	9947.920665
func.nii.gz	2[?]	9938.978018
func.nii.gz	3[?]	9942.901682
...
func.nii.gz	334[?]	10085.826948
func.nii.gz	335[?]	10079.657652
func.nii.gz	336[?]	10037.459720
func.nii.gz	337[?]	10058.559225

real	2m35.273s
user	2m21.209s
sys	0m13.998s

Now trying with bootcamp data ...
++ Compile date = Feb 25 2021 {AFNI_21.0.12:linux_ubuntu_16_64}

time ~/abin/3dROIstats -mask mask.auto.nii.gz epi_r1+orig.HEAD
File	Sub-brick	Mean_1  
epi_r1+orig.HEAD	0[#0]	1541.724452
epi_r1+orig.HEAD	1[#1]	1380.877077
epi_r1+orig.HEAD	2[#2]	1340.660904
epi_r1+orig.HEAD	3[#3]	1339.089622
...
epi_r1+orig.HEAD	148[#148]	1334.726368
epi_r1+orig.HEAD	149[#149]	1333.623429
epi_r1+orig.HEAD	150[#150]	1332.642166
epi_r1+orig.HEAD	151[#151]	1334.085370

real	0m0.114s
user	0m0.065s
sys	0m0.049s

time ~/abin/3dROIstats -mask mask.auto.nii.gz LONG.nii.gz
File	Sub-brick	Mean_1  
LONG.nii.gz	0[#0]	1541.724452
LONG.nii.gz	1[#1]	1380.877077
LONG.nii.gz	2[#2]	1340.660904
LONG.nii.gz	3[#3]	1339.089622
...
LONG.nii.gz	605[#149]	1333.623429
LONG.nii.gz	606[#150]	1332.642166
LONG.nii.gz	607[#151]	1334.085370

real	0m1.466s
user	0m1.398s
sys	0m0.068s


3dinfo epi_r1+orig.HEAD 
++ 3dinfo: AFNI version=AFNI_21.0.12 (Feb 25 2021) [64-bit]

Dataset File:    epi_r1+orig
Identifier Code: AFN_1obeBrbaja6u2HfupnCFbA  Creation Date: Thu Mar 18 14:28:42 2010
Template Space:  ORIG
Dataset Type:    Echo Planar (-epan)
Byte Order:      LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode:    BRIK
Storage Space:   64,204,800 (64 million) bytes
Geometry String: "MATRIX(2.75,0,0,-112.6622,0,2.75,0,-122.7787,0,0,3,-17.65058):80,80,33"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Right-to-Left
  second (y) = Anterior-to-Posterior
  third  (z) = Inferior-to-Superior   [-orient RAI]
R-to-L extent:  -112.662 [R] -to-   104.588 [L] -step-     2.750 mm [ 80 voxels]
A-to-P extent:  -122.779 [A] -to-    94.471 [P] -step-     2.750 mm [ 80 voxels]
I-to-S extent:   -17.651  -to-    78.349 [S] -step-     3.000 mm [ 33 voxels]
Number of time steps = 152  Time step = 2.00000s  Origin = 0.00000s  Number time-offset slices = 33  Thickness = 3.000
  -- At sub-brick #0 '#0' datum type is short:            0 to          3272
  -- At sub-brick #1 '#1' datum type is short:            0 to          2924
  -- At sub-brick #2 '#2' datum type is short:            0 to          2841
** For info on all 152 sub-bricks, use '3dinfo -verb' **

----- HISTORY -----
[rickr@manwe.nimh.nih.gov: Thu Mar 18 11:19:14 2010] 3dcopy epi_r1.nii FT_epi_r1
[rickr@manwe.nimh.nih.gov: Thu Mar 18 14:28:42 2010] 3dcopy FT_epi_r1+orig epi_r1


++ 3dinfo: AFNI version=AFNI_21.0.12 (Feb 25 2021) [64-bit]

Dataset File:    func.nii.gz
Identifier Code: NII_hDcnbsY6k2aQQvVLdGzh0w  Creation Date: Wed Mar  3 20:39:20 2021
Template Space:  ORIG
Dataset Type:    Echo Planar (-epan)
Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:    NIFTI
Storage Space:   160,595,968 (161 million) bytes
Geometry String: "MATRIX(3.4375,0,0,-119.0361,0,-3.4375,0,65.85879,0,0,3.959766,-91.56892):64,64,29"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Right-to-Left
  second (y) = Posterior-to-Anterior
  third  (z) = Inferior-to-Superior   [-orient RPI]
R-to-L extent:  -119.036 [R] -to-    97.526 [L] -step-     3.438 mm [ 64 voxels]
A-to-P extent:  -150.704 [A] -to-    65.859 [P] -step-     3.437 mm [ 64 voxels]
I-to-S extent:   -91.569  -to-    19.305 [S] -step-     3.960 mm [ 29 voxels]
Number of time steps = 338  Time step = 1.75000s  Origin = 0.00000s
  -- At sub-brick #0 '?' datum type is float
  -- At sub-brick #1 '?' datum type is float
  -- At sub-brick #2 '?' datum type is float
** For info on all 338 sub-bricks, use '3dinfo -verb' **


Other than voxel size and number of TRs the main different in datasets is the data type and the range of values, lets make epi_r1 match func.nii.gz for those and see if it changes anything:

3dcalc -prefix epi_r1_float.nii.gz -a epi_r1 -expr '10000*a/2962' -datum float

time 3dROIstats -mask mask.auto.nii.gz epi_r1_float.nii.gz 
File	Sub-brick	Mean_1  
epi_r1_float.nii.gz	0[#0]	5205.011654
epi_r1_float.nii.gz	1[#1]	4661.975278
epi_r1_float.nii.gz	2[#2]	4526.201565
epi_r1_float.nii.gz	3[#3]	4520.896766
...

epi_r1_float.nii.gz	148[#148]	4506.165995
epi_r1_float.nii.gz	149[#149]	4502.442365
epi_r1_float.nii.gz	150[#150]	4499.129527
epi_r1_float.nii.gz	151[#151]	4504.001923

real	0m0.481s
user	0m0.457s
sys	0m0.024s

When I try to convert func.nii.gz to float, I get:
3dcalc -prefix func_short.nii.gz -a func.nii.gz -exp 'a' -datum short
++ 3dcalc: AFNI version=AFNI_21.0.12 (Feb 25 2021) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: varying brick factors, writing NIfTI as float
++ Output dataset ./func_short.nii.gz

Could that be related to the problem

Thanks again for the help!

=cc
Subject Author Posted

AFNI_21.0.12 Slow performance on Ubuntu 16.04 and 20.04

cameron February 26, 2021 04:49PM

Re: AFNI_21.0.12 Slow performance on Ubuntu 16.04 and 20.04

ptaylor February 26, 2021 05:12PM

Re: AFNI_21.0.12 Slow performance on Ubuntu 16.04 and 20.04

Daniel Glen February 28, 2021 01:05AM

Re: AFNI_21.0.12 Slow performance on Ubuntu 16.04 and 20.04

cameron March 01, 2021 01:05PM

Re: AFNI_21.0.12 Slow performance on Ubuntu 16.04 and 20.04

cameron March 01, 2021 01:02PM

Re: AFNI_21.0.12 Slow performance on Ubuntu 16.04 and 20.04

ptaylor March 02, 2021 09:49AM

Re: AFNI_21.0.12 Slow performance on Ubuntu 16.04 and 20.04

cameron March 03, 2021 10:03PM

Re: AFNI_21.0.12 Slow performance on Ubuntu 16.04 and 20.04

rick reynolds March 04, 2021 10:10AM

Re: AFNI_21.0.12 Slow performance on Ubuntu 16.04 and 20.04

rick reynolds March 04, 2021 11:58AM

Re: AFNI_21.0.12 Slow performance on Ubuntu 16.04 and 20.04

cameron March 04, 2021 02:08PM



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