3dClustSim issue

Zhihao_Li · October 12, 2016, 5:24am

Hi AFNI experts,
I have 2 versions of 3dClustSim, one goes with AFNI_16.2.07 (older, Aug.2,16) and the other goes with AFNI_16.2.19 (newer, Sep.28,16).
I was trying to run it with “-acf” and with identical inputs. However, the old version works but the new version hangs.
The initial outputs are the same for the 2 versions except after “Startup clock time”, the old version begins “Simulating” while the new versions says “Using 15 OpenMP threads” and then followed by “Simulating”.

I am not sure why the new version hangs on “Simulating”; meanwhile, the process viewer of “top” does not see it either.

rwcox · October 13, 2016, 5:25pm

What kind of system are you running on? This does not happen on my Mac.

Zhihao_Li · October 14, 2016, 12:44am

I am showing you the output of “lscpu”, but please let me know if you need any specific information.

The new version of 3dClustSim is running on this system:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 64
On-line CPU(s) list: 0-63
Thread(s) per core: 2
Core(s) per socket: 8
Socket(s): 4
NUMA node(s): 4
Vendor ID: GenuineIntel
CPU family: 6
Model: 62
Stepping: 4
CPU MHz: 2600.175
BogoMIPS: 5199.79
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 20480K

Thel older version of 3dClustSim is running on this system:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 8
On-line CPU(s) list: 0-7
Thread(s) per core: 1
Core(s) per socket: 4
Socket(s): 2
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 23
Stepping: 6
CPU MHz: 2500.127
BogoMIPS: 5000.03
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 6144K

rickr · October 14, 2016, 1:43am

If you would not mind, please post the output from:

afni_system_check.py -check_all

Thanks,

rick

Zhihao_Li · October 14, 2016, 1:31pm

Thank you Rick, please the output of afni_system_check.py:

system with 3dClustSim hangs:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 2.6.32-573.el6.x86_64
version: #1 SMP Wed Jul 1 18:23:37 EDT 2015
distribution: Red Hat Enterprise Linux Server 6.7 Santiago
number of CPUs: 64
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni_linux_openmp_64/afni
afni version : Precompiled binary linux_openmp_64: Sep 28 2016
AFNI_version.txt : AFNI_16.2.19, linux_openmp_64, Sep 28 2016
which python : /usr/bin/python
python version : 2.6.6
which R : /usr/bin/R
R version : R version 3.3.1 (2016-06-21) – “Bug in Your Hair”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/usr/local/afni_linux_openmp_64/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python)

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libgsl.so.0: 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 : success

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

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

------------------------------ python libs -------------------------------
** python module not found: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/lzh/bin:/usr/local/afni_linux_openmp_64:/home/lzh/bin:/usr/local/afni_linux_openmp_64

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
data dir : missing FATCAT_DEMO
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /usr/local/afni_linux_openmp_64

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.2.29

============================ summary comments ============================

login shell ‘bash’, trusting user to translate from ‘tcsh’
AFNI programs show FAILURE
consider running “suma -update_env” for .sumarc
consider running: apsearch -update_all_afni_help
insufficient data for AFNI bootcamp
consider running: yum install PyQt4

System with 3dClustSim worked
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 2.6.32-504.el6.x86_64
version: #1 SMP Wed Oct 15 04:27:16 UTC 2014
distribution: CentOS 6.6 Final
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/AFNI/linux_xorg7_64/afni
afni version : Precompiled binary linux_xorg7_64: Aug 2 2016
AFNI_version.txt : AFNI_16.2.07, linux_xorg7_64, Aug 02 2016
which python : /usr/bin/python
python version : 2.6.6
which R : /usr/bin/R
R version : R version 3.1.1 (2014-07-10) – “Sock it to Me”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/usr/local/AFNI/linux_xorg7_64/afni)
R : 1 (/usr/bin/R)
python : 2
/usr/bin/python
/data/home3/lzh/libsvm-3.20/python

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

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

    oo Warning: 
       These packages are not installed on the computer: paran!
    These packages are not installed on the computer: psych!

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

------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /usr/lib64/python2.6/site-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /home/lzh/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/home/lzh/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/sge/bin/lx24-amd64:/usr/lib64/qt-3.3/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/4dfp:/usr/local/AFNI/linux_xorg7_64:/usr/lib64/alliance/bin:/usr/local/caret/bin_linux64:/usr/local/fsl/bin:/usr/local/MITK:/usr/local/mrtrix3/bin:/usr/local/Slicer4:/home/lzh/bin:/home/lzh/libsvm-3.20

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /usr/lib64/alliance/lib

DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
data dir : missing FATCAT_DEMO
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /usr/local/AFNI/linux_xorg7_64

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.2.29

============================ summary comments ============================

login shell ‘bash’, trusting user to translate from ‘tcsh’
missing R packages (see rPkgsInstall)
consider running: cp /usr/local/AFNI/linux_xorg7_64/AFNI.afnirc ~/.afnirc
consider running “suma -update_env” for .sumarc
consider running: apsearch -update_all_afni_help
insufficient data for AFNI bootcamp

rwcox · October 14, 2016, 6:08pm

I am running linux_openmp_64 on the Linux box in my office right now – at build Oct 13 2016 (Version AFNI_16.3.03). The command

3dClustSim -acf 0.5 7 9 -mask askull+orig

is working well. If I do ‘top -U rwcox’ it shows up.

Perhaps you need to update your AFNI binaries? I don’t know what else to suggest.

Zhihao_Li · November 24, 2016, 5:06am

afni -ver
Precompiled binary linux_openmp_64: Nov 23 2016 (Version AFNI_16.3.13)

The option of “-Clustsim” of 3dttest++ does work after saying “Using 15 OpenMP threads”.
However, my 3dClustSim still hangs exactly there. Weird.

rickr · November 27, 2016, 2:59pm

It seems there may be a problem with OpenMP on those
Red Hat systems. So it might be helpful to try other
packages.

One possibility is linux_fedora_21_64. The advantage
of that package is that it is still built for OpenMP.
But it is possible that OpenMP would still not work.
That might be worth testing though. Another possible
problem is that some of the linked libraries might be
newer that what is on your system, in which case, they
would not work.

The other option would be to fall back to the same
xorg7_64 package that is working on your other system.

To get a new package, consider either of these commands
(maybe by your system administrator):

@update.afni.binaries -package linux_fedora_21_64
@update.afni.binaries -package linux_xorg7_64

Please let us know how that goes. Thanks!

rick