That is cool Future Shopping! --- sent by Tom *_* Thanks for sharing.

How to kill program processes running behind the system in fedora 13?

#ps -ef | more
find the PID number

#kill -9 PID

Novell Groupwise installation under Fedora 13.

#rpm -ivh novell-groupwise-client-8.0.2-90388.i586.rpm

error: Failed dependencies:
    libXm.so.3 is needed by novell-groupwise-client-8.0.2-90388.i586

#cd /usr/lib
#ln -s libXm.so.4 libXm.so.3

#rpm -Uhv novell-groupwise-client-8.0.2-90388.i586.rpm --nodeps

SELinux error, use the following command to solve this problem.

#chcon -t textrel_shlib_t '/opt/novell/groupwise/client/java/lib/i386/client/libjvm.so'

Bingo!  Groupwise works well!

Well, I have to uninstall this version and install a lower version since CCHMC doesn't support this higher version.  Oops...

If you get errors like:

Error: Failed to load /home/dunnj/.novell/groupwise/.webrenderer/linux/corecomponents/libgtksuperwin.so
Error: Failed to load /home/dunnj/.novell/groupwise/.webrenderer/linux/corecomponents/libgtkxtbin.so
Error: Failed to load /home/dunnj/.novell/groupwise/.webrenderer/linux/corecomponents/libgtkembedmoz.so
Error: Failed to load /home/dunnj/.novell/groupwise/.webrenderer/linux/corecomponents/libgtkxtbin.so
Error: Failed to load.
Exception in thread “ControlQueue” java.lang.UnsatisfiedLinkError: com.webrenderer.linux.NativeMozillaLibrary.setMozPath(Ljava/lang/String;Z)V
at com.webrenderer.linux.NativeMozillaLibrary.setMozPath(Native Method)
at com.webrenderer.linux.NativeMozillaLibrary.a(NativeMozillaLibrary.java)
at com.webrenderer.linux.k.task(k.java)
at com.webrenderer.linux.ControlQueue.run(ControlQueue.java)

it means you didn’t install gtk+, glib and gdk-pixbuf, JRE.

If the html view is still not supported, use the following command:

#/opt/novell/groupwise/client/bin/groupwise.sh -jvm=-Dawt.toolkit=sun.awt.motif.MToolkit

The error messages are still be there, you can try the following commands:


become superuser: su

#setsebool -P allow_execmod 1


or

#semanage fcontext -a -t textrel_shlib_t /home/yyw/.novell/groupwise/.webrenderer/linux/libwebrenderer.so0

#restorecon -v /home/yyw/.novell/groupwise/.webrenderer/linux

#semanage fcontext -a -t textrel_shlib_t /home/yyw/.novell/groupwise/.webrenderer/linux/libwebrenderer.so1

#restorecon -v /home/yyw/.novell/groupwise/.webrenderer/linux


#semanage fcontext -a -t textrel_shlib_t /home/yyw/.novell/groupwise/.webrenderer/linux/libwebrenderer.so2

#restorecon -v /home/yyw/.novell/groupwise/.webrenderer/linux

#semanage fcontext -a -t textrel_shlib_t /home/yyw/.novell/groupwise/.webrenderer/linux/libwebrenderer.so3

#restorecon -v /home/yyw/.novell/groupwise/.webrenderer/linux


#semanage fcontext -a -t textrel_shlib_t /home/yyw/.novell/groupwise/.webrenderer/linux/libwebrenderer.so4

#restorecon -v /home/yyw/.novell/groupwise/.webrenderer/linux

#semanage fcontext -a -t textrel_shlib_t /home/yyw/.novell/groupwise/.webrenderer/linux/libwebrenderer.so5

#restorecon -v /home/yyw/.novell/groupwise/.webrenderer/linux


#semanage fcontext -a -t textrel_shlib_t /home/yyw/.novell/groupwise/.webrenderer/linux/libwebrenderer.so6

#restorecon -v /home/yyw/.novell/groupwise/.webrenderer/linux

#semanage fcontext -a -t textrel_shlib_t /home/yyw/.novell/groupwise/.webrenderer/linux/libwebrenderer.so7

#restorecon -v /home/yyw/.novell/groupwise/.webrenderer/linux

Bingo!

The error messages are gone!

Install AFNI and CTF software packages on Fedora 13 system

MEG CTF software packages work under Linux system.  Fedora is free to use.  Also I learned how to install Fedora from Dr. Tom who is a very good teacher and scientist at NIMH.  Here I wrote down the basic steps for installation.

First, I installed Fedora 13 using installation DVD made myself.  (The content is downloaded from http://fedoraproject.org/)  The procedure is quite straightforward.  Follow the instruction on the screen.  The system was successfully installed.

Second, I installed AFNI using following steps (adapted from AFNI website).

Step 0: enter these commands to prepare for the installation:
      
        cd
        mkdir abin
      

        The first command, 'cd', is used just to make sure the user is in
        their home directory, before issuing further commands.

        The second command, 'mkdir abin' is used to create the directory
        which will be used to store the actual programs from the AFNI
        package.  The main reason that 'abin' (for "AFNI binaries") is
        chosen for a name is to allow the descriptions to be more generic,
        and less dependent upon which operating system is in use.

Step 1: enter these commands to get and unpack the AFNI binary package:
      
        wget http://afni.nimh.nih.gov/pub/dist/tgz/linux_gcc32.tgz
        tar xvfz linux_gcc32.tgz
        mv linux_gcc32/* abin
        rmdir linux_gcc32
      

        The first command, 'wget http://...' is used to actually download
        the AFNI package.  The user may use their browser, pointed to
        pub/dist/tgz to find the linux_gcc32.tgz package, also.

        The second command, 'tar xvfz linux_gcc32.tgz' is used to
        extract the contents (the programs) of the compressed package.
        The options used with this tar command are:
            x - to extract the contents of the archive
            v - verbose, to display files as they are extracted
            f - file, the next argument is the tar file to expand
            z - uncompress the file before extracting its contents
        See 'man tar' for more details.

        The third command, 'mv linux_gcc32/* abin' moves everything from
        the newly extracted linux_gcc32 directory into the abin directory.

        The final command, 'rmdir linux_gcc32' is used to remove the
        empty linux_gcc32 directory, now that its contents have been
        moved to abin.

        Note: this linux_gcc32.tgz package includes SUMA.

Step 2: enter these commands to get and unpack some sample data:
      
        wget http://afni.nimh.nih.gov/pub/dist/edu/data/AFNI_data1.tgz
        tar xvfz AFNI_data1.tgz
      

        The first command, 'wget http://...' is used to download the
        AFNI_data1.tgz sample data package.  This package contains
        SPGR anatomy, EPI time-series data, and an 'afni' directory,
        with datasets made from that raw data.  The user may also use
        their browser to download AFNI_data1.tgz.

        The 'tar xvfz ...' command is to extract the AFNI_data1
        directory from the compressed archive.  The tar options are
        the same as in Step 1.

Step 3: enter this command to add the directory ~/abin to your PATH:
    gedit ~/.bash_profile
    Then you will see a file open and change it to the following contents:

    # .bash_profile

    # Get the aliases and functions
    if [ -f ~/.bashrc ]; then
    . ~/.bashrc
    fi

    # User specific environment and startup programs

    PATH=$PATH:$HOME/abin

    export PATH
  
    Save it.

Step 4: log out and log back in

        This is done to invoke the change to the .cshrc file, meaning
        that any new terminal window would have a command shell with
        ~/abin in the PATH.  It also has the effect of using the
        'rehash' command, which tells the shell (T-shell) to make note
        of all executables in the PATH.

Step 5: open a new terminal window, and start playing!
      
        cd AFNI_data1/afni
        afni
      

        Note that if the 'afni' command fails, you may want to review the
        steps that have been taken.  There are two commands that may help
        resolve any problems:
      
        echo $PATH

It worked.  You might need to install netpbm rpm packages for supporting different image formats. (warning message might look like this)

Initializing: X11.
++++++++ IMAGE SAVE SETUP WARNINGS ++++++++
++ Can't find program ppmtogif AND/OR ppmquant for Save to GIF
++ Can't find program ppm2tiff OR pnmtotiff for Save to TIFF
++ Can't find program ppmtobmp for Save to BMP
++ Can't find program pnmtops for Save to EPS
++ Can't find program pnmtopng for Save to PNG
++ Some of the missing image Save programs are in
++  the netpbm software package, which is freeware.
++  Netpbm can be found at http://netpbm.sourceforge.net/
++ To disable these warnings, set environment
++  variable AFNI_IMSAVE_WARNINGS to 'NO'.
+++++++++++++++++++++++++++++++++++++++++++


Third, I installed CTF software package.

[root@localhost Downloads]# mkdir /tmp/mnt
[root@localhost Downloads]# mount -o loop,ro -t iso9660 ctf-5.4.0CD_20061212.iso /tmp/mnt
[root@localhost Downloads]# cd /tmp/mnt
[root@localhost mnt]# ./CTF.install
(c) Copyright VSM MedTech Ltd. All Rights Reserved.
Description:
This script updates or installs the CTF_MEG MEG/EEG Software suite.
If a current installation is not found, then a "complete install" is performed
otherwise, an upgrade is performed. An upgrade copies all executable and script
files from the distribution CD-ROM to the CTF_MEG software directory.
The CTF.install will then copy any configuration files that are on the CD-ROM
but are missing in the CTF_MEG directory. The user is given the option of
copying all configuration files, as well as creating backups of all
existing files that are over written.

If necessary, CTF.install will install acroread ( PDF file reader ) and
openmotif, ghostscript, Python, Xdialog, Xprint, a set of pixmap conversion
programs, and a set of postscript conversion programs.

Checking current installation....
The directory /opt/ctf does not exist
Is this a new installation? [ , n ]y  
Please enter a destination path for the installation? [ ]

Please enter path of the source directory for the install? [ ]/tmp/mnt

Select which electronics system is in use.

CTF_MEG2000 -- Contains  DSQ-2041/DSQ-2043 DSP bank with DSQ-2010 SQUID Channel Units
               and rack mounted ADC/Trigger units
CTF_MEG2005 -- Contains  DSQ-2041/DSQ-2043 based DSP bank with DSQ-2010 SQUID Channel Units
               and desktop Electronic Control Console

Select "Skip" to skip installation of electronics specific files.

1) CTF_MEG2000
2) CTF_MEG2005
3) Skip
Select electronics system version :3
Checking for required libraries ...

Dynamically shared library file libXm.so.3 needed by CTF software is missing
Please insure that you are installing the software on RedHat Enterprise 3.0 or higher

Installation of the CTF_MEG MEG/EEG Software has failed prematurely.
Do you want to continue [ y, ]?n

solve libXm.so.3 problem:
#cd /usr/lib
#ln -s libXm.so.4 libXm.so.3

Then you will get another error: libstdc++.so.5
#yum install compat-libstdc++-33-3.2.3-68.i686

Reference:  http://kurage.nimh.nih.gov/meglab/Meg/CTFSoftwareInstallation

If you have specific problems, feel free to contact me.

It is a big challenging to go back to school.

2009.9.23

I officially quit my job at Children's hospital and started my full-time study at UC.  The timing worked perfectly for me.  I am really thankful for God's provision and I always believe that he has a plan for my life.

  

I started to work at Children's in June of 2006.  My title was research assistant III.  Basically, I helped Dr. Xiang with MEG data collection, analysis and recruitment and published one first-author paper, etc (Pubmed).  Since I never studied in U.S.A, I always wanted to get my highest degree in the U.S.A.  I started to prepare for the TOEFL and GRE exams in 2008.  I got a great TOEFL score but not an ideal GRE score, but I did not want to wait any more.  So I applied to UC anyway using my current TOEFL and GRE score.

  

I need a change and a challenge after working as a RA for three years.

  

In the beginning of 2009, I got interview calls.  Dr. Christy Holland, the graduate program director of the BME department at UC decided to give me an interview chance.  Fortunately, It turned out that I knew two of the three professors who interviewed me.  One professor is Dr. Douglas Mast.  I took his class in my spare time when I was still working at Children's.  He is a real nice person.  I liked his biomedical image processing class, which directly led me to apply for the BME program at UC.  The other professor is Dr. Scott Holland.  I knew him through my work.  Dr. Holland is a world famous researcher in fMRI neuroimaging field.  When I worked at Children's, I often met him at various meetings.  Although I did not work with him directly, his articulation and great leadership left me with a deep impression.  He has amazing personal charms which unite people together and work for him.  I dreamed that one day I could work for him and sharpen my skills.  (Well, now my dream came true)  Although I did not know Dr. Christy Holland who interviewed me, she is Dr. Scott Holland's wife.  How small the world is!  All three interviews went well.  However, the poor economic situation made the funding budget very tight, I was concerned that I might not get into the program in 2009.  I did not get the official offer letter till the end of June, 2010.  (I did get an oral offer from Dr. Scott Holland in March, 2010)  During the waiting period, my friends were praying for me and myself too.  Eventually, everything worked out fine.  Thank you, my LORD.

  

From H1-B to F-1

I had to get my visa changed which involves fees, documentations and etc.  My visa status was officially changed to F-1 from H1-B on September.11.2009.  Some of my friends thought I was too crazy to do that.  That is life.  When you make a decision, you might lose some benefits.

  

2009-9-23 --- 2010-6-12

During this time period, I successfully finished all the courses required for Ph.D candidacy exam.  This summer, I have to discipline myself and write the proposal for qualification exam in October.