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Thursday, November 20, 2008

How to setup remote subversion server through ssh

This site provides an excellent tutorial.

Mounting remote file system using SSH

Using svn with iDisk is very disappointing although I am a real Mac fan. However, this solution of using sshfs (Secure Shell File System) give me a new solution of setting up SVN server.


SVN works perfect in Mac

See this site:

changing paper size in LaTex

Sometimes a certain specific class file does not support options of paper size.  Default is usually A4.  The following line in the very front of your LaTex file, just below, will allow you to generate letter-sized pdf file as an outcome.


ssh session alive

It is very frequently happening that a terminal with ssh session dies after a certain period of time by any reason.  It looks like a server setting should be modified, which cannot be done by an end-user.  But, there is one thing can be done by each user.

1. Go to your .ssh directory:
      cd ~/.ssh

2. Check whether you have "config" file.  Anyway, open/create it: 
      vi config

3. Put the following line in the file:
      KeepAlive yes

Bibtex capital letters

Edit your bibtex file and use {} for words that you want to keep the style.

   author  = "George D. Greenwade",        
   title   = "The {C}omprehensive {T}ex {A}rchive {N}etwork ({CTAN})",        
   year    = "1993",        
   journal = "TUGBoat",        
   volume  = "14",     
   number  = "3",     
   pages   = "342--351" 


Tuesday, November 18, 2008

The underscore symbol between C and FORTRAN

When a C function is called from FORTRAN routine, the C function should end with '_'.  In other words, a C function 'myfun_' should be called as 'myfun' in a FORTRAN code.  Actually this is an old paradigm between GNU C and FORTRAN compilers. Current GNU FORTRAN compiler, gfortran, does not follow this rule, and so does Intel compilers.   This is actually a serious problem in compiling BLACS and SCALAPACK libraries.

In compiling BLACS, file should have an option:


and in compiling SCALAPACK, should have:

CDEFS     = -DAdd_

This option depends on compliers.

BLACS 64bit compiling

It is theoretically impossible to compile BLACS to make it work in 64 bit computing environment.  BLACS package downloadable from works only on 32 bit OSs. Otherwise, all the libraries including BLAS, LAPACK, and SCALAPACK should be recomiled with 32 bit option.  A possible way to go around this bottleneck is to use Intel MKL library, specifically,


The latest version of openmpi-1.2.8 works well with Intel-BLACS and scalapack compiled using Intel FORTRAN compiler, ifort.

Private network setup guide

Sunday, November 16, 2008

Compile openmpi-1.2.8 using Intel Compilers

./configure --prefix=/opt/openmpi-1.2.8/intel   CC=icc   CXX=icpc   F77=ifort   FC=ifort

Saturday, November 15, 2008

Lapack compile script to save messages

./xlintstd <> dtest.out 2>&1

Friday, November 14, 2008

Kerberos configuration file

When I install Kerberos to connect MHPCC machine, krb5 configuration needs to be edited. The location of krb5.conf is by default /usr/local/krb5. However, I got an error message like:

kinit(v5): Configuration file does not specify default realm when parsing name ........

This error has been resolved by copying


Symbolic link did not work.

Tuesday, November 4, 2008

Not to show URLs in LaTex generated papers

When I prepare a manuscript using LaTex with Elsevier package, two reference styles are provided, elsart-num.bst and elsart-harv.bst, which generate reference lists ordered by citation number and author's name, respectively.  It often shows long URLs, which is absolutely not necessary for any purposes. 

Not to show URLs in my final manuscript, I did as follows:

1. Open .bst file.
2. Search "write.url" and replace it by "% write.url" within
  • FUNCTION {article}
  • FUNCTION {book}
  • FUNCTION {booklet}
  • FUNCTION {inbook}
  • FUNCTION {incollection}
  • FUNCTION {inproceedings}
  • FUNCTION {manual}
  • FUNCTION {masterthesis}
  • FUNCTION {misc}
  • FUNCTION {phdthesis}
  • FUNCTION {proceedings}
  • FUNCTION {techreport}
  • FUNCTION {unpublished}
But, do not make any changes where "write.url" is defined in FUNCTION {write.url}.

3. Another way is to redefine FUNCTION {write.url}, but I did not figure out how to yet.

Add a user in a sudoer list

In most Unix/Linux system, the suoder file is /etc/sudoers.

1. Login as a normal user.
2. Type/enter "su" followed by a root password.
3. Open /etc/sudoers using vi or any editor and include a line

freeman ALL=(ALL) ALL

which will provide all the administration authority of the system to the user, "freeman".


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