pdf to eps conversion

Currently, I need to convert pdf files to eps so that they can be included in latex files.

1. Use Acrobat Pro open the pdf file. 
   Click File -> export -> PostScript -> Encapsulated PostScript or use "Save As" and change "Save As Type"
   However, the bounding box is NOT correctly calculated.
   You can use gsview to correct it.  Use gsview open the eps file, click "File -> PS to EPS", select "Automatically calculate Bounding Box" and save the output file.

2. Use ghostscript.  Execute following command:
   gswin32 -sDEVICE=epswrite -sOutputFile=<filename>.eps <filename>.pdf
   This works well and bounding box is correctly calculated.

3. Use Xpdf (http://www.foolabs.com/xpdf/download.html)
   pdftops -eps <filename>.pdf <filename>.eps
   However, the bounding box is NOT correctly calculated.

Brief Latex notes for equations

In-line: $…$

Single line, without equation number: \[ … \] or \begin{equation*} … \end{equation*}

Single line, with equation number: \begin{equation} … \end{equation}

Multi-line, without equation number: \begin{align*} ... \end{align*}

Multi-line, with equation number: \begin{align} ... \end{align}

"a double backslash (\\) is used to separate the lines, and an ampersand symbol (&) is used to indicate the place at which the formulas should be aligned."

For align, \label must be put in front of each equation. For equation, it does not matter you put it in front or in the end.

Make vim-latex to generate output in a specified directory

Recently I started to use latex to write papers.  I want to edit latex in my favorite editor - vim. I found the project vim-latex: http://vim-latex.sourceforge.net/.  It is powerful and convenient to use. 

However, one feature I want is to generate output files (.div, .ps, .log, etc) into a separate directory rather than the same directory as tex files.  It turns out that vim-latex does not support it natively.  So I hacked into the source code to make it work on Windows.

1. Edit file ~/vimfiles/ftplugin/tex.vim

   Add following config:

     set iskeyword+=: 
     let g:Tex_Outdir='out' 
     let g:Tex_ViewRule_pdf='"Foxit Reader.exe" ' 
     let g:Tex_CompileRule_dvi='mkdir '.g:Tex_Outdir.' & latex -output-directory='.g:Tex_Outdir.' -src-specials --interaction=nonstopmode $*' 
     let g:Tex_CompileRule_pdf=g:Tex_CompileRule_dvi.' & cd '.g:Tex_Outdir.' & dvipdfm $*.dvi'

   Basically above config specifies

   1. output directory of latex compilation
   2. How to view PDF files (if you don't give full path, the command needs to be in env variable PATH)
   3. How to compile dvi: create the output directory and put output there
   4. How to compile pdf: first compile tex to dvi, and then call dvipdfm to generate pdf

2. Change ~/vimfiles/ftplugin/latex-suite/compiler.vim

   Change line 252 to (this line adds the full path of output directory):
     let execString = 'start '.s:viewer.' "'.expand('%:p:h').'/'.g:Tex_Outdir.'/$*.'.s:target.'"'

   Change line 405 to (this line adds the full path of output directory):
   let execString = 'silent! !'.viewer.' "'.expand('%:p:h').'/'.g:Tex_Outdir.'/'.mainfnameRoot.'.'.s:target.'" '.line('.').' "'.expand('%').'"'

   Note: the text in blue is what I added (diff against the original code)

Use command 'TTarget' to switch amont dvi, ps, pdf, etc.

How to publish artifacts to ivy local repository and use it in another project

Build artifacts that are required by another project

ivy.xml: Attributes organisation, module and revision of element ivy-module/info.

1) Add a new resolver to ivy by adding following snippet to ivysettings.xml:

<filesystem name="gerald-local-ivy" m2compatible="false" force="false" local="true">
    <artifact pattern="${ivy.default.ivy.user.dir}/local/[organisation]/[module]/[type]s/[artifact]-[revision](-[classifier]).[ext]"/>
</filesystem>

This will create a directory local under <user.home>/.ivy2/.

2) Add following snippet to your build.xml:

<target name="publish" depends="jar" description="Publish">
    <!-- following property defines the version to publish -->
    <property name="ivy.deliver.revision" value="${version}"/>
    <ivy:publish resolver="gerald-local-ivy" forcedeliver="true"
    	 settingsRef="${ant.project.name}.ivy.settings" overwrite="true">
    	<artifacts pattern="${build.dir}/[artifact]-[revision](-[classifier]).[ext]" />
    </ivy:publish>
</target>

The resolver attribute of ivy:publish must match name attribute specified in step 1). Change pattern attribute for artifacts element to match where you put the artifact.

3) Use command ant publish to publish your jar.

Build main project that depends on the artifacts built above.

1) Add the same resolver to ivy by adding following snippet to ivysettings.xml:

<filesystem name="gerald-local-ivy" m2compatible="false" force="false" local="true">
    <artifact pattern="${ivy.default.ivy.user.dir}/local/[organisation]/[module]/[type]s/[artifact]-[revision](-[classifier]).[ext]"/>
</filesystem>

2) Add it to your effective resolver chain.

3) Add dependency declaration to ivy.xml

<dependency org="<organization>" name="<module>" 

            rev="<version>" conf="<common->master>">

The attributes org, name, rev must match the values specified when you built the dependency jar.

4) Manually remove the artifacts that exist in local cache (<user.home>/.ivy2/cache).

5) Build your project

Resources

http://ant.apache.org/ivy/history/2.2.0/use/publish.html
http://ant.apache.org/ivy/history/latest-milestone/resolver/chain.html
http://stackoverflow.com/questions/353336/how-does-ivypublish-work
http://mail-archives.apache.org/mod_mbox/ant-ivy-user/201002.mbox/%3C27714488.post@talk.nabble.com%3E

Configure ivy to use local Maven repository

This post shows how to configure ivy to use specific local Maven repository.

1) Add following config as a child element of tag "resolvers" in you ivy settings file:

    <filesystem name="local-maven-2" m2compatible="true" force="false" local="true">
       <artifact pattern="${gerald.repo.dir}/[organisation]/[module]/[revision]/[module]-[revision].[ext]"/>
       <ivy pattern="${gerald.repo.dir}/[organisation]/[module]/[revision]/[module]-[revision].pom"/>
    </filesystem>

2) Then add it to your chain resolver config. Example: 

    <chain name="internal" dual="true">
      <resolver ref="local-maven-2"/>
      <resolver ref="apache-snapshot"/> 
      <resolver ref="maven2"/>
    </chain>

If you have multiple resolver chain, make sure that the correct one, which is effective for you build, is changed.

3) After ivy caches the artifacts in its own local repo (the first time the dependency is resolved), it will not pick changes you made to the artifacts in the original Maven repository.  In other words, if you use "mvn clean install" to re-publish the artifact, the new version will NOT propagate to ivy.
You can change the default behavior by tweaking parameters:
    checkmodified, changingPattern,  changingMatcher, alwaysCheckExactRevision
Read this article for details: http://ant.apache.org/ivy/history/trunk/settings/resolvers.html
One example:

    <chain name="default" dual="true" 
	     checkmodified="true" changingPattern=".*SNAPSHOT">
     ......
    </chain>

Resources:

http://mail-archives.apache.org/mod_mbox/ant-ivy-user/200807.mbox/raw/%3C94bda3fa0807202250y446a818eodb527dba96c8ac93@mail.gmail.com%3E/

Vdbench notes

Two types of supported testings.  Following table shows the configuration groups for these testings.

Storage device testing	File system testing
General - optional	General - optional
Host Definition(HD) - optional	Host Definition (HD) - optional
Storage Definition(SD)	File System Definition (FSD)
Workload Definition(WD)	File System Workload Definition(FSWD)
Run Definition (RD)	Run Definition (RD)

Different configuration groups may be specified in one single file or multiple files (use multiple -f options to specify all of them).

Comments: a line starting with '/', '#', or '*' is a comment.
Continuation: end a line with a comma plus a whitespace.

Output file
-o dirname+   # if dirname has existed, use dirname001.
-o dirname.tod    # the directory name will be dirname.yymmdd.hhmmss

General parameters

Host definition

Storage definition

Workload definition

Run definition

File System Definition

File System Workload Definition

Run definition for file system testing

Resources:
Official doc: http://downloads.sourceforge.net/project/vdbench/vdbench502.pdf?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fvdbench%2Ffiles%2F&ts=1315925901&use_mirror=superb-sea2

R notes

Construct a list of lists

a = c(1,2,3)
b = c(4,5,6)
c = list(a, b)
d = list(c, list(a))    # different from list(c, a)
e = list(d, name="gerald")

Append to a list:

mylist[[length(mylist) + 1]] = obj

Append to a vector:

append(vec, val)

 

Type information

typeof(var),  class(var)

Resources

• http://www.statmethods.net/input/datatypes.html

How to get network information in Linux

Following files/dirs can be directly read:

/proc/net/dev
/sys/class/net/<if_name>/
/sys/class/net/<if_name>/statistics

Tool netstat is your friend to get network-related information:

netstat -I  # display interface info
netstat -s  # display statistics info
netstat -r  # display routing info
netstat -tlnp  # display TCP listening info

Other tools: sar, ifconfig, iftop

How to see network card and disk speed

Sometimes, you may want to know the hardware speed limit for network interface cards and disks.

Network Interface Card

I use commands

dmesg | grep -i ethernet
dmesg | grep -i infiniband

The output looks like

Intel(R) Gigabit Ethernet Network Driver - version 2.1.0-k2-1
igb 0000:0b:00.0: Intel(R) Gigabit Ethernet Network Connection
igb 0000:0b:00.1: Intel(R) Gigabit Ethernet Network Connection

and

mlx4_ib: Mellanox ConnectX InfiniBand driver v1.0 (April 4, 2008)
Registered RDS/infiniband transport

I also use command

/sbin/lspci

The output has following useful information

0b:00.0 Ethernet controller: Intel Corporation 82575EB Gigabit Network Connection (rev 02)
0b:00.1 Ethernet controller: Intel Corporation 82575EB Gigabit Network Connection (rev 02)
10:00.0 InfiniBand: Mellanox Technologies MT26418 [ConnectX VPI PCIe 2.0 5GT/s - IB DDR / 10GigE] (rev a0)

Disk

/sbin/lspci | grep -i ata

Other useful tools

mii-tools
hdparm

They need root privilege usually.

java.lang.LinkageError in Tomcat 6

Usually the cause of this error is you may unintentionally include following two jars into your war file. 
    el-api.jar jasper-el.jar
They are provided by tomcat 6.

In Tomcat 6, you will get following error:

java.lang.LinkageError: loader constraint violation: loader …

You can solve the problem by adding following snippet into your pom file.

<dependency>
        <groupId>org.apache.tomcat</groupId>
        <artifactId>el-api</artifactId>
        <version>[1,)</version>
        <scope>provided</scope>
</dependency>
<dependency>
        <groupId>org.apache.tomcat</groupId>
        <artifactId>jasper-el</artifactId>
        <version>[1,)</version>
        <scope>provided</scope>
</dependency>

Read this post for more information.