cannot reintegrate branch

I created a branch from another branch, and after I am ready to merge, I encounter this problem:

$ cd photon-branch; svn update

$ svn merge –reintegrate
svn: Cannot reintegrate from ‘’ yet:
Some revisions have been merged under it that have not been merged into the reintegration target; merge them first, then retry.

It turns out to be a problem in subversion 1.5. I found a blog that speaks about this problem. And then, in one of the forum, someone gave a clear explanation on how to do it. So basically what I need to do is to go back to my other branch, in this case “photon-recursive”, and delete the merge info of the files except the “.” merge info.

$ cd photon-recursive

$ svn propget svn:merge info –depth=infinity

you will many list, the term before “-” is the file. You will find one for “.” and maybe some other files. Mine is like this:

. – /branches/photon-branch:115-181
src/parallel – /branches/photon-branch/src/parallel:115-181
src/globalconst.h – /branches/photon-branch/src/globalconst.h:115-181
src/parallel/deviceinfo.h – /branches/photon-branch/src/parallel/deviceinfo.h:11
src/negf.cpp – /branches/photon-branch/src/negf.cpp:115-181
src/output – /branches/photon-branch/src/output:115-181
src/deviceinfo.h – /branches/photon-branch/src/deviceinfo.h:115-181
src/main.cpp – /branches/photon-branch/src/main.cpp:115-181
src/negf.h – /branches/photon-branch/src/negf.h:115-181
src/solvebias.cpp – /branches/photon-branch/src/solvebias.cpp:115-181
src/devrtd.cpp – /branches/photon-branch/src/devrtd.cpp:115-181
src/poisson.cpp – /branches/photon-branch/src/poisson.cpp:115-181
src/itppmath.h – /branches/photon-branch/src/itppmath.h:115-181
src/solvebias.h – /branches/photon-branch/src/solvebias.h:115-181
src/Makefile – /branches/photon-branch/src/Makefile:115-181
src/finvhalff77h.f – /branches/photon-branch/src/finvhalff77h.f:115-181
src/DevRTD.h – /branches/photon-branch/src/DevRTD.h:115-181
src/finvhalf.cpp – /branches/photon-branch/src/finvhalf.cpp:115-181
src/output.log – /branches/photon-branch/src/output.log:115-181
src/poisson.h – /branches/photon-branch/src/poisson.h:115-181

So now what I need to do is to delete the merge info from all other files except the “.” (root). To do this :

$ svn propdel svn:merge info ./src/globalconst.h

$ svn propdel svn:mergeinfo ./src/parallel/deviceinfo.h

Once it is done, it will only leave the merge info for “.”

$ svn propget svn:mergeinfo –depth=infinity
. – /branches/photon-branch:115-181

and we can commit

$ svn commit -m “Removed bogus merge info.”

After this, I went back to the main branch (in my case photon-branch) and do a merge –reintegrate. it turns out to solve the problem 🙂


Kubuntu Jaunty 9.04 md5sums

a292c1caaedb481db56462f16453c408 *kubuntu-9.04-alternate-amd64.iso
a846a8059ebd37730f8b803e6cae9311 *kubuntu-9.04-alternate-i386.iso
798b8789af2f13bb9687b2ce57f25f9c *kubuntu-9.04-desktop-amd64.iso
537a22de1342d5671b7e0070f66a6076 *kubuntu-9.04-desktop-i386.iso

Error in starting firefox: no XBL binding

Somehow after I upgrade my firefox to 3.0.9 in Kubuntu 8.04, I couldn’t run it, it gives an error message “no XBL binding” and then another error message and then it closes down. Then after searching the forum, the solution is simply to kill the firefox. So it seems the firefox still runs at the back and this causes problem.
do a “ps aux | grep ‘firefox’ ” and find the PID, then after that kill the program. This solves my problem.

Compiling ARPACK++

I have had difficulties in compiling the examples code provided by ARPACK++. After some googling, it turns out that ARPACK++ is not compatible with newer version of GCC. Luckily, I found a page that provide a patch. So let me provide the steps to compile ARPACK++ .

1. First you have to install ARPACK, UMFPACK, and SuperLU.

2. To install ARPACK, download the files from ( make sure to download the “patch” file as well. Then simply extract the two files:

        zcat arpack96.tar.gz | tar -xvf -
        zcat patch.tar.gz    | tar -xvf -
3. In the ARPACK folder, modify It is better to use the BLAS and LAPACK provided by ARPACK. Sometimes using other libraries creates problem. And for my case, I need to modify the location of the ARPACK source tree and the location for "make" program.
4. type make lib. This should compile arpack for your platform, copy the library to your local library locations. You should test also the EXAMPLES codes provided to make sure everything went well.
5. Now install SuperLU, downlaod the source code from (
6. Modify This is the one that I use:
SuperLUroot     = /scratch/kurniawano/Download/SuperLU_3.1
SUPERLULIB      = $(SuperLUroot)/lib/libsuperlu_3.1.a
BLASLIB         = /usr/lib64/libblas.a
TMGLIB          = libtmglib.a
LIBS            = $(SUPERLULIB) $(BLASLIB)
CDEFS        = -DAdd_
with "one" underscore after "-DAdd"
7. Then type make, if there is an error due to the timer, just type make again and it will continue compiling.
8. Now UMFPACK is installed from the SuiteSparse package. I have written some other posts on this package installation. Just search on this blog.
9. So now download Arpack++ from (, and its patch from (
10. extract Arpack++ and copy the patch file to the arpack++ folder, and type 
patch -p1 < arpack++1.2.patch.diff
11. After that modify, especially the path to the Arpack++ and the following libraries:

ARPACK_LIB   = /scratch/kurniawano/local/lib/libarpack.a
LAPACK_LIB   = -llapack
UMFPACK_LIB  = /scratch/kurniawano/local/lib/libumfpack.a
SUPERLU_LIB  = /scratch/kurniawano/local/lib/libsuperlu.a
BLAS_LIB     = -lblas
FORTRAN_LIBS = /scratch/kurniawano/local/lib/libg2c.a

Changing Eclipse keyboard shortcut

I am using Eclipse 3.4.1, and somehow after I install some plugin, some of the shortcuts were modified. The most annoying thing is that CTRL+X is no longer to cut text but to exit eclipse.

If you want to change back the shortcut:

click Tab “General” -> Keys
from there you can modify or simply unbind certain shortcut keys