Cannot execute binary files

AFNI Message Board
1

Hi AFNI connoisseurs,

I feel this is really basic, so I apologize for my naivety.

I’m attempting to download AFNI onto my personal account within the ComputeCanada cluster.

The main issue I get when checking if the installation ran successfully is that the AFNI binaries cannot be executed.

For installation i followed instructions from here: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_admins/steps_mac_reg.html#install-afni-binaries

Is the issue that I am operating via linux and the isntructions were specific to Mac?

Any pointers would be greatly appreciated

p.s. here is the output from afni_system_check.py -check_all :

-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type:
system: Linux
release: 3.10.0-1160.76.1.el7.x86_64
version: #1 SMP Wed Aug 10 16:21:17 UTC 2022
distribution: CentOS Linux 7 (Core)
number of CPUs: 40
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/coopapap/AFNIbin/afni
afni version : /bin/sh: /home/coopapap/AFNIbin/afni: cannot execute binary file
:
AFNI_version.txt : AFNI_23.0.04, macos_10.12_local, Feb 13 2023
which python : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin/python
python version : 3.8.10
which R : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.0.2/bin/R
R version : R version 4.0.2 (2020-06-22) – “Taking Off Again”
which tcsh : /cvmfs/soft.computecanada.ca/gentoo/2020/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/coopapap/AFNIbin/afni)
R : 1 (/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.0.2/bin/R)
python : 3
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin/python3.8
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/python-exec2c
/usr/bin/python2.7
python2 : 2
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/python-exec2c
/usr/bin/python2.7
python3 : 3
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin/python3.8
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/python-exec2c
/usr/bin/python3.6

testing ability to start various programs…
afni : FAILURE
/bin/sh: /home/coopapap/AFNIbin/afni: cannot execute binary file
suma : FAILURE
/bin/sh: /home/coopapap/AFNIbin/suma: cannot execute binary file
3dSkullStrip : FAILURE
/bin/sh: /home/coopapap/AFNIbin/3dSkullStrip: cannot execute binary file
uber_subject.py : success
3dAllineate : FAILURE
/bin/sh: /home/coopapap/AFNIbin/3dAllineate: cannot execute binary file
3dRSFC : FAILURE
/bin/sh: /home/coopapap/AFNIbin/3dRSFC: cannot execute binary file
SurfMesh : FAILURE
/bin/sh: /home/coopapap/AFNIbin/SurfMesh: cannot execute binary file
3dClustSim : FAILURE
/bin/sh: /home/coopapap/AFNIbin/3dClustSim: cannot execute binary file
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object ‘/home/coopapap/AFNIbin/R_io.so’:
/home/coopapap/AFNIbin/R_io.so: invalid ELF header
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Execution halted

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

R RHOME : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.0.2/lib64/R

checking for $HOME files…
.afnirc : found
.sumarc : missing
.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 : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/scipy-stack/2020a/lib/python3.8/site-packages/matplotlib/pyplot.py
matplotlib version : 3.2.1

-------------------------------- env vars --------------------------------
PATH = /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.0.2/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/scipy-stack/2020a/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/ipykernel/2020a/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/gcc9/cuda11.0/fsl/6.0.3/fsl/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/wxwidgets/3.1.4/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/expat/2.2.9/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/jbigkit/2.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/qt/5.12.8/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/gsl/2.6/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/vtk/8.2.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/libgd/2.3.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/gcc9/cuda11.0/openmpi/4.0.3/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/cuda11.0/libfabric/1.10.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/cuda11.0/ucx/1.8.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/cuda11.0/gdrcopy/2.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.0.2:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.0.2/nvvm/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.0.2/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/tktools:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/mni/bin:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/fsfast/bin:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/bin:/cvmfs/restricted.computecanada.ca/easybuild/software/2020/Core/matlab/2021a.5:/cvmfs/restricted.computecanada.ca/easybuild/software/2020/Core/matlab/2021a.5/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/mii/1.1.2/bin:/cvmfs/soft.computecanada.ca/easybuild/bin:/cvmfs/soft.computecanada.ca/custom/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/bin:/cvmfs/soft.computecanada.ca/custom/bin/computecanada:/home/coopapap/AFNIbin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.0.2/bin/R:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/coopapap/.local/bin:/home/coopapap/bin

PYTHONPATH = /cvmfs/soft.computecanada.ca/easybuild/python/site-packages:/cvmfs/soft.computecanada.ca/custom/python/site-packages

R_LIBS = /home/coopapap/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

DYLD_FALLBACK_LIBRARY_PATH =

----------------------------- eval dot files -----------------------------

– good: .tcshrc seems to contain ‘source .cshrc’
– considered opertaions: path, flatdir, apsearch
(not on a mac, should skip flatdir)

– note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)

dot file test : want 2 modifications across 3 files:

  file             path  flatdir  apsearch        follower
  ---------------  ----  -------  --------        --------
  .cshrc           1     0        1               0
  .tcshrc          0     0        0               1
  .bashrc          0     0        0               0

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (109595431M Avail)
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: …ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
data dir : found suma_demo under $HOME
top history: …s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /home/coopapap/AFNIbin

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3

========================= summary, please fix: =========================

  • just be aware: login shell ‘bash’, but our code examples use ‘tcsh’
  • AFNI programs show FAILURE
  • please run: “suma -update_env” for .sumarc
  • dot file test : want 2 modifications across 3 files:
2

Yes, this output is very helpful. You are working on a CentOS 7 system there. We actually have binaries for that particular system (which might possibly need libraries, we can see). But change to those binaries and please post the afni_system_check.py output again. So run this first:

@update.afni.binaries -package linux_centos_7_64

Then please post the updated system_check output.

Thanks,

  • rick
3

Thanks a lot Rick!

Now the issue seems to be a lack of libXm.so.4 libraries.

I’m trying to solve this, but if I haven’t posted an update by the time you see this, and you know an easy solution, please share :slight_smile:

Till next time,
Austin

p.s. here’s the output text:

-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type:
system: Linux
release: 3.10.0-1160.76.1.el7.x86_64
version: #1 SMP Wed Aug 10 16:21:17 UTC 2022
distribution: CentOS Linux 7 (Core)
number of CPUs: 40
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/coopapap/AFNIbin/afni
afni version : afni: error while loading shared libraries: libXm.so.4: cannot open shared object file: No such file or directory
:
AFNI_version.txt : AFNI_23.0.04, linux_centos_7_64, Feb 13 2023
which python : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin/python
python version : 3.8.10
which R : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.0.2/bin/R
R version : R version 4.0.2 (2020-06-22) – “Taking Off Again”
which tcsh : /cvmfs/soft.computecanada.ca/gentoo/2020/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/coopapap/AFNIbin/afni)
R : 1 (/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.0.2/bin/R)
python : 3
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin/python3.8
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/python-exec2c
/usr/bin/python2.7
python2 : 2
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/python-exec2c
/usr/bin/python2.7
python3 : 3
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin/python3.8
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/python-exec2c
/usr/bin/python3.6

testing ability to start various programs…
afni : FAILURE
afni: error while loading shared libraries: libXm.so.4: cannot open shared object file: No such file or directory
suma : FAILURE
suma: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory
uber_subject.py : success
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
SurfMesh : FAILURE
SurfMesh: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory
3dClustSim : success
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object ‘/home/coopapap/AFNIbin/R_io.so’:
libpng15.so.15: cannot open shared object file: No such file or directory
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Execution halted

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

R RHOME : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.0.2/lib64/R

checking for $HOME files…
.afnirc : found
.sumarc : missing
.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 : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/scipy-stack/2020a/lib/python3.8/site-packages/matplotlib/pyplot.py
matplotlib version : 3.2.1

-------------------------------- env vars --------------------------------
PATH = /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.0.2/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/scipy-stack/2020a/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/ipykernel/2020a/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/gcc9/cuda11.0/fsl/6.0.3/fsl/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/wxwidgets/3.1.4/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/expat/2.2.9/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/jbigkit/2.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/qt/5.12.8/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/gsl/2.6/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/vtk/8.2.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/libgd/2.3.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/gcc9/cuda11.0/openmpi/4.0.3/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/cuda11.0/libfabric/1.10.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/cuda11.0/ucx/1.8.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/cuda11.0/gdrcopy/2.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.0.2:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.0.2/nvvm/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.0.2/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/tktools:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/mni/bin:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/fsfast/bin:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/bin:/cvmfs/restricted.computecanada.ca/easybuild/software/2020/Core/matlab/2021a.5:/cvmfs/restricted.computecanada.ca/easybuild/software/2020/Core/matlab/2021a.5/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/mii/1.1.2/bin:/cvmfs/soft.computecanada.ca/easybuild/bin:/cvmfs/soft.computecanada.ca/custom/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/bin:/cvmfs/soft.computecanada.ca/custom/bin/computecanada:/home/coopapap/AFNIbin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.0.2/bin/R:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/coopapap/.local/bin:/home/coopapap/bin

PYTHONPATH = /cvmfs/soft.computecanada.ca/easybuild/python/site-packages:/cvmfs/soft.computecanada.ca/custom/python/site-packages

R_LIBS = /home/coopapap/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

DYLD_FALLBACK_LIBRARY_PATH =

----------------------------- eval dot files -----------------------------

– good: .tcshrc seems to contain ‘source .cshrc’
– considered opertaions: path, flatdir, apsearch
(not on a mac, should skip flatdir)

– note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)

dot file test : want 2 modifications across 3 files:

  file             path  flatdir  apsearch        follower
  ---------------  ----  -------  --------        --------
  .cshrc           1     0        1               0     
  .tcshrc          0     0        0               1     
  .bashrc          0     0        0               0

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (109595468M Avail)
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: …ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
data dir : found suma_demo under $HOME
top history: …s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /home/coopapap/AFNIbin

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3

========================= summary, please fix: =========================

  • just be aware: login shell ‘bash’, but our code examples use ‘tcsh’
  • AFNI programs show FAILURE
  • please run: “suma -update_env” for .sumarc
  • dot file test : want 2 modifications across 3 files:
4

That is great and somewhat expected. To be sure, is this a system that is maintained by separate administrators? If so, you will probably need to ask them to install any needed libraries. The install instructions for CentOS 7 include these packages (yum install commands):

sudo yum install epel-release
sudo yum install gcc motif gsl libXpm
sudo yum install mesa-libGLw mesa-libGLU libXi glib2
sudo yum install python R PyQt4

If you could forward that to as system administrator and ask them to install the packages, that would be great.

  • rick
5

Thank you kindly Rick!

I have made some progress, though are still some problems, and i presume they are to do with a lack of installed packages.

I wonder if the 1 missing R package is substantial?

I wish to use the @SSwarper command in addition to:
“afni_proc.py
-subj_id # enter your subject and directory of it here
-out_dir # enter your output directory… for the results here
-dsets
# enter EPI/functional raw scan here
-blocks despike tshift align tlrc volreg mask blur regress
-copy_anat $directory_sswarper_1/anatSS.$subject.nii
-anat_has_skull no
-tcat_remove_first_trs 4
-align_opts_aea -cost lpc+ZZ \ # lpc+ZZ is a standard… you can try this first
-volreg_align_e2a
-volreg_align_to MIN_OUTLIER
-volreg_tlrc_warp -tlrc_base MNI152_2009_template_SSW.nii.gz
-tlrc_NL_warp
-tlrc_NL_warped_dsets
$directory_sswarper_1/anatQQ.$subject.nii \ # please enter the specific subject files here…
$directory_sswarper_1/anatQQ.$subject.aff12.1D
$directory_sswarper_1/anatQQ.${subject}_WARP.nii
-volreg_post_vr_allin yes
-volreg_pvra_base_index MIN_OUTLIER
-mask_segment_anat yes
-mask_segment_erode yes
-regress_anaticor
-regress_ROI WMe CSFe
-regress_apply_mot_types demean deriv
-regress_motion_per_run
-regress_censor_motion 0.2 \ # please adjust… (0.2 is standard in afni for resting-state, but its up to you)
-regress_censor_outliers 0.05 \ # please adjust… (0.05 is standard in afni for resting-state, but its up to you)
-blur_size 8.0 \ # please adjust…
-regress_est_blur_epits
-regress_est_blur_errts
-html_review_style pythonic
-execute”

Here is the current output from afni_system_check.py -check_all:

[coopapap@beluga1 ~]$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type:
system: Linux
release: 3.10.0-1160.76.1.el7.x86_64
version: #1 SMP Wed Aug 10 16:21:17 UTC 2022
distribution: CentOS Linux 7 (Core)
number of CPUs: 40
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/coopapap/AFNIbin/afni
afni version : Precompiled binary linux_centos_7_64: Feb 13 2023
: AFNI_23.0.04 ‘Commodus’
AFNI_version.txt : AFNI_23.0.04, linux_centos_7_64, Feb 13 2023
which python : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin/python
python version : 3.8.10
which R : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.2.1/bin/R
R version : R version 4.2.1 (2022-06-23) – “Funny-Looking Kid”
which tcsh : /cvmfs/soft.computecanada.ca/gentoo/2020/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/coopapap/AFNIbin/afni)
R : 2
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.2.1/bin/R
/home/coopapap/R
python : 3
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin/python3.8
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/python-exec2c
/usr/bin/python2.7
python2 : 2
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/python-exec2c
/usr/bin/python2.7
python3 : 3
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin/python3.8
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/python-exec2c
/usr/bin/python3.6

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: brms!

R RHOME : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.2.1/lib64/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 : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/scipy-stack/2020a/lib/python3.8/site-packages/matplotlib/pyplot.py
matplotlib version : 3.2.1

-------------------------------- env vars --------------------------------
PATH = /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/gsl/1.16/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.2.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/scipy-stack/2020a/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/ipykernel/2020a/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/gcc9/cuda11.0/fsl/6.0.3/fsl/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/wxwidgets/3.1.4/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/expat/2.2.9/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/jbigkit/2.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/qt/5.12.8/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/vtk/8.2.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/libgd/2.3.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/gcc9/cuda11.0/openmpi/4.0.3/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/cuda11.0/libfabric/1.10.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/cuda11.0/ucx/1.8.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/cuda11.0/gdrcopy/2.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.0.2:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.0.2/nvvm/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.0.2/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/tktools:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/mni/bin:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/fsfast/bin:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/bin:/cvmfs/restricted.computecanada.ca/easybuild/software/2020/Core/matlab/2021a.5:/cvmfs/restricted.computecanada.ca/easybuild/software/2020/Core/matlab/2021a.5/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/mii/1.1.2/bin:/cvmfs/soft.computecanada.ca/easybuild/bin:/cvmfs/soft.computecanada.ca/custom/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/bin:/cvmfs/soft.computecanada.ca/custom/bin/computecanada:/home/coopapap:/home/coopapap/AFNIbin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.0.2/bin/R:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/coopapap/.local/bin:/home/coopapap/bin

PYTHONPATH = /cvmfs/soft.computecanada.ca/easybuild/python/site-packages:/cvmfs/soft.computecanada.ca/custom/python/site-packages

R_LIBS = /home/coopapap/R

LD_LIBRARY_PATH = /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/gsl/1.16/lib

DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

DYLD_FALLBACK_LIBRARY_PATH =

----------------------------- eval dot files -----------------------------

– good: .tcshrc seems to contain ‘source .cshrc’
– considered opertaions: path, flatdir, apsearch
(not on a mac, should skip flatdir)

– note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)

dot file test : want 2 modifications across 3 files:

  file             path  flatdir  apsearch        follower
  ---------------  ----  -------  --------        --------
  .cshrc           1     0        1               0
  .tcshrc          0     0        0               1
  .bashrc          0     0        0               0

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (109595417M Avail)
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: …ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
data dir : found suma_demo under $HOME
top history: …s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /home/coopapap/AFNIbin

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3

========================= summary, please fix: =========================

  • just be aware: login shell ‘bash’, but our code examples use ‘tcsh’
  • missing R packages (see rPkgsInstall)
  • dot file test : want 2 modifications across 3 files:
6

Hi Austin,

This looks pretty good!
The R packages are needed for Gang’s group analysis programs. Fixing that won’t be important until you want those programs.

Oh, for that I should have suggested installing R-devel instead of R. You might need to ask for that.

Have you tried installing anything under ~/R? Is that directory empty? populated? old?

  • rick
7

Hey Rick!

Yup that’s where I downloaded R packages to. I attached a photo of all the contents in it.

I’m running into a new issue now. things worked well for @SSwarper which was my first goal. But when i add the option
-SSopt ‘-blur_fwhm 2’
I get
-SSopt: command not found

Is it obvious why this command would work:
xvfb-run vglrun -d egl @SSwarper
-input $work/control_$1/t1_hr.nii
-base /home/coopapap/AFNIbin/MNI152_2009_template_SSW.nii.gz
-subid control_$1
-odir $directory_sswarper

but not this one:
xvfb-run vglrun -d egl @SSwarper
-input $work/control_$1/t1_hr.nii
-base /home/coopapap/AFNIbin/MNI152_2009_template_SSW.nii.gz
-subid control_$1
-odir $directory_sswarper
-SSopt ‘-blur_fwhm 2’

R.png
R.png1866×390 34.6 KB

8

Great!

Sure, a command not found error is from the OS when you try to run a command that is not in your path. It usually means either a misspelling of the command, or as in this case, a missing line continuation character () on the previous line. The ‘-odir’ line does not have a '' at the end.

  • rick