afni: symbol lookup error:

AFNI Message Board
1

Hey everyone,

I’m trying to run afni on the cubic computing cluster at penn. When I install afni, most of the command line tools work, but I get the following error when I try to run the GUI. Any thoughts?

afni: symbol lookup error: /cbica/software/external/afni/17.2.10/plug_3dsvm.so: undefined symbol: mcw_malloc

Thanks!
-nick

2

Hi Nick,

What is the output of: afni_system_check.py -check_all

Thanks,

  • rick
3

Hey Rick,

Thanks for the help. Here’s the output.

[nbald@cubic-login3 SCRIPTS]$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: x86_64
system: Linux
release: 3.10.0-1160.21.1.el7.x86_64
version: #1 SMP Tue Mar 16 18:28:22 UTC 2021
distribution: CentOS Linux 7.9.2009 Core
number of CPUs: 40
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /cbica/home/nbald/software/afni/inuse/afni
afni version : Precompiled binary linux_openmp_64: Mar 1 2023
: AFNI_23.0.07 ‘Commodus’
AFNI_version.txt : AFNI_23.0.07, linux_openmp_64, Mar 01 2023
which python : /cbica/software/external/python/anaconda/3/bin/python
python version : 3.6.8
which R : /usr/bin/R
R version : R version 3.6.0 (2019-04-26) – “Planting of a Tree”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/gpfs/fs001/cbica/home/nbald/software/afni/inuse/afni)
R : 1 (/usr/bin/R)
python : 2
/gpfs/fs001/cbica/software/external/python/anaconda/3/bin/python3.6
/usr/bin/python2.7
python2 : 1 (/usr/bin/python2.7)
python3 : 2
/gpfs/fs001/cbica/software/external/python/anaconda/3/bin/python3.6
/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: afex!
    These packages are not installed on the computer: phia!
    These packages are not installed on the computer: lmerTest!
    These packages are not installed on the computer: psych!
    These packages are not installed on the computer: brms!
    These packages are not installed on the computer: metafor!

R RHOME : /usr/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 : /cbica/software/external/python/anaconda/3/lib/python3.6/site-packages/matplotlib/pyplot.py
matplotlib version : 3.1.2

-------------------------------- env vars --------------------------------
PATH = /cbica/home/nbald/miniconda3/condabin:/cbica/home/nbald/software/afni/inuse:/cbica/software/external/freesurfer/centos7/6.0.0/bin:/cbica/software/external/freesurfer/centos7/6.0.0/fsfast/bin:/cbica/software/external/freesurfer/centos7/6.0.0/tktools:/cbica/software/external/fsl/centos7/5.0.11/bin:/cbica/software/external/freesurfer/centos7/6.0.0/mni/bin:/cbica/software/external/freesurfer/centos7/6.0.0/mni/bin:/cbica/software/external/freesurfer/centos7/6.0.0/bin:/cbica/software/external/gcc/centos7/4.9.2/bin:/usr/lib64/qt-3.3/bin:/usr/lib64/ccache:/cbica/software/lab/bin:/cbica/software/external/bin:/usr/lib64/openmpi/bin:/cbica/software/lab/captk/centos7/1.7.2/bin:/cbica/software/external/python/anaconda/3/bin:/cbica/software/lab/MUSE/centos7/3.0.5/bin:/cbica/software/lab/MARS/centos7/2.2.2/bin:/cbica/software/external/imagej:/cbica/software/external/dcmtk/centos7/3.6.3/bin:/cbica/software/external/gdcm/centos7/2.6.1/bin:/cbica/software/lab/SCPLearn/centos7/1.0.0:/cbica/software/external/swig/centos7/3.0.5/bin:/cbica/software/lab/dramms/centos7/1.4.2/bin:/cbica/software/lab/odvba/centos7/3.0/bin:/cbica/software/external/mricron/7.7.12:/cbica/software/external/nifticlib/2.0.0/bin:/cbica/software/lab/sbiaDti/253/bin:/cbica/software/lab/sbiaUtilities/0.3.3/centos7/bin:/cbica/software/external/fsl/centos7/5.0.11/bin:/cbica/software/external/matlab/R2018A/bin:/cbica/software/external/camino/1176/bin:/cbica/software/external/mipav/7.2.0:/cbica/software/external/minc/2.0.13/bin:/cbica/software/lab/mass/1.1.1/bin:/cbica/software/external/dtk/0.6:/cbica/software/external/dicom3tools/1.00.snapshot.20110207/bin:/cbica/software/lab/libra/centos7/1.0.4:/cbica/software/external/dependency_bundle/centos7/3817/bin:/cbica/software/external/ANTs/centos7/2.3.1/bin:/cbica/software/external/qt/centos7/5.11.1/Tools/QtInstallerFramework/3.0/bin:/cbica/software/external/qt/centos7/5.11.1/Tools/QtInstallerFramework/2.0/bin:/cbica/software/external/qt/centos7/5.11.1/Tools/QtCreator/bin:/cbica/software/external/qt/centos7/5.11.1/5.11.1/gcc_64/bin:/cbica/software/external/doxygen/centos7/1.8.9.1/bin:/cbica/software/external/texlive/2016/bin/x86_64-linux:/cbica/software/external/texlive/2016/bin:/cbica/software/external/jython/centos7/2.5.3/bin:/cbica/software/external/sge/8.1.9-1/bin/lx-amd64:/cbica/software/external/sge/8.1.9-1/bin:/cbica/software/lab/mico/1.0.0/centos7/bin:/usr/local/cuda-11.2/bin:/cbica/software/external/slicer/centos7/4.8.1:/cbica/software/external/Modules/4.1.2/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/lpp/mmfs/bin:/opt/puppetlabs/bin:/opt/dell/srvadmin/bin:/cbica/home/nbald/bin:/data/jag/cnds/nbalderston/software/simnibs/inuse:/cbica/home/nbald/software/simnibs/inuse/bin:/cbica/home/nbald/software/simnibs/inuse/Bash_modules

PYTHONPATH = /cbica/software/lab/sbiaDti/253/bin:/cbica/software/lab/sbiaUtilities/0.3.3/centos7/bin

R_LIBS = /cbica/software/external/R:/usr/lib64/R/library:/usr/share/R/library

LD_LIBRARY_PATH = /cbica/software/external/freesurfer/centos7/6.0.0/lib:/cbica/software/external/gcc/centos7/4.9.2/lib64:/cbica/software/external/gcc/centos7/4.9.2/lib:/usr/lib64/mpich/lib:/usr/lib64/openmpi/lib:/cbica/software/lab/captk/centos7/1.7.2/lib:/cbica/software/lab/MUSE/centos7/3.0.5/lib:/cbica/software/lab/MARS/centos7/2.2.2/lib:/cbica/software/external/dcmtk/centos7/3.6.3/lib64:/cbica/software/external/gdcm/centos7/2.6.1/lib:/cbica/software/external/bct-cpp/centos7/396/lib:/cbica/software/lab/dramms/centos7/1.4.2/lib:/cbica/software/external/nifticlib/2.0.0/lib:/cbica/software/external/fsl/centos7/5.0.11/lib:/cbica/software/external/minc/2.0.13/lib:/cbica/software/lab/mass/1.1.1/lib:/cbica/software/external/dicom3tools/1.00.snapshot.20110207/lib:/cbica/software/external/dependency_bundle/centos7/3817/lib64:/cbica/software/external/dependency_bundle/centos7/3817/lib:/cbica/software/external/ANTs/centos7/2.3.1/lib:/cbica/software/external/qt/centos7/5.11.1/Tools/QtCreator/lib:/cbica/software/external/qt/centos7/5.11.1/5.11.1/gcc_64/lib:/cbica/software/external/sge/8.1.9-1/…/…/local/8.1.9-1/lib64:/cbica/software/external/sge/8.1.9-1/lib/lx-amd64:/cbica/software/external/cudnn/centos7/8.2.1/cuda-11.2/lib64:/usr/local/cuda-11.2/extras/CUPTI/lib64:/usr/local/cuda-11.2/lib64:/usr/lib64:/usr/lib:/lib64:/lib:/cbica/software/external/matlab/R2018A/bin/glnxa64:/cbica/software/external/matlab/R2018A/runtime/glnxa64:/cbica/software/external/matlab/R2018A/sys/os/glnxa64

DYLD_LIBRARY_PATH =
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)

no modifications needed across 3 dot files

------------------------------ 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 /cbica/home/nbald/software/afni/inuse

------------------------------ 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)
  • insufficient data for AFNI bootcamp
    (see “Prepare for Bootcamp” on install pages)
4

Hey Rick,

I think I solved the issue. I had the following line in my bashrc file, but it was commented out. I uncommented the line and it seems to be working now.

PATH=${PATH}:/usr/lib64

Not sure why it was commented, or what I broke by uncommenting, but I guess I’ll save that for a future post.

-n

5

That is odd, but good news.

One thing to note is that your initial error message seemed to reference AFNI version 17.2.10 (since the error came from afni/17.2.10/plug_3dsvm.so), and it is a system package of AFNI (available to all users). I am not even sure if that was a CentOS build package, probably not.

The system_check output shows a working personal version of AFNI (in your own abin).

It seems likely that the PATH might have had bigger problems that you fixed.

  • rick
6

Hey Rick,

I think the mismatch there actually arose from my troubleshooting efforts. I tried loading the default afni module on our to see if the issue was specific to my user install prior to posting. I had the issue with both versions, but must have posted the error before unloading the default afni module. Aside from the missing R packages (I’ll save that issue for a different post), I think I’m up and running.

Thanks for the help!
-n