GNU Plot and SVG: Change the terminal size and font

Again, not really a dev related issue, but I did not find much info online regarding this.

When using gnuplot to create SVG files, one use the set term svg command that sets the following defaults:

gnuplot> set term svg
Terminal type set to 'svg'
Options are 'size 640 480 fixed fname 'Arial' fsize 12 butt '

One can speficy custom parameters to get the desired output:

gnuplot> set term svg size 640,350 fname 'Times New Roman' fsize 10
Terminal type set to 'svg'
Options are 'size 640 350 fixed fname 'Times New Roman' fsize 10 butt '

Ossim on Ubuntu causes error on missing llampi++

When compiling Ossim with lam mpi on Ubuntu 9, you might receive this error:

/usr/bin/ld: cannot find -llammpi++

The easiest way to fix this is to ensure liblam4 and openmpi is installed (via the Synaptic Package Manager) and to edit the Makefile.common in the ossim directory ($OSSIM_HOME), changing the MPI_LIB_PATH.

# Open the Makefile.common
gedit $OSSIM_HOME/Makefile.common

# Locate the following line and set its path to /usr/lib/lam/lib
MPI_LIB_PATH         = -L/usr/lib/lam/lib

Compile GDAL with GeoTiff support

I've been running Ubuntu on my personal machine for a while now and just realized that the gdal synaptic package does not enable support for GeoTiffs. This is where Gentoo has one up, but its not the end of the world. You can 'simply' build GDAL from source with the correct flags.

Here's what I did:
1. Install the Tiff, GeotTiff, Png and OpenJpeg dev packages and their dependencies (libtiff4-dev, libgeotiff-dev, libpng12-dev and libopenjpeg-dev). Also be sure to install g++ and subversion.
2. Fire up a terminal and checkout the GDAL subversion repository anywhere in your home directory:

svn co http://svn.osgeo.org/gdal/trunk/gdal

3. Go into the GDAL directory and run configure:

cd gdal
./configure --with-geotiff=/usr --with-jpeg=/usr --with-libtiff=/usr --without-libtool

4. In theory you should be able to run make now, but the configure script missed the geotiff header files directory so I had to set these manually. This is the error I received:

make -C gtiff install-obj
make[2]: Entering directory `/home/andreh/workspace/project-ossim_dev/gdal/frmts/gtiff'
/bin/sh /home/andreh/workspace/project-ossim_dev/gdal/libtool --mode=compile --tag=CXX g++ -g -O2  -Wall  -I/home/andreh/workspace/project-ossim_dev/gdal/port -I/home/andreh/workspace/project-ossim_dev/gdal/gcore -I/home/andreh/workspace/project-ossim_dev/gdal/alg -I/home/andreh/workspace/project-ossim_dev/gdal/ogr -I/home/andreh/workspace/project-ossim_dev/gdal/ogr/ogrsf_frmts   -DOGR_ENABLED -I/home/andreh/workspace/project-ossim_dev/gdal/port -I/usr/lib/include -I -I/include  -c -o ../o/geotiff.lo geotiff.cpp
libtool: compile:  g++ -g -O2 -Wall -I/home/andreh/workspace/project-ossim_dev/gdal/port -I/home/andreh/workspace/project-ossim_dev/gdal/gcore -I/home/andreh/workspace/project-ossim_dev/gdal/alg -I/home/andreh/workspace/project-ossim_dev/gdal/ogr -I/home/andreh/workspace/project-ossim_dev/gdal/ogr/ogrsf_frmts -DOGR_ENABLED -I/home/andreh/workspace/project-ossim_dev/gdal/port -I/usr/lib/include -I -I/include -c geotiff.cpp  -fPIC -DPIC -o ../o/.libs/geotiff.o
geotiff.cpp:34:21: error: xtiffio.h: No such file or directory
geotiff.cpp:35:21: error: geotiff.h: No such file or directory
geotiff.cpp:36:27: error: geo_normalize.h: No such file or directory
geotiff.cpp:37:23: error: geovalues.h: No such file or directory
geotiff.cpp:46: error: 'GTIF' was not declared in this scope
geotiff.cpp:46: error: expected primary-expression before ',' token
geotiff.cpp:46: error: 'GTIFDefn' was not declared in this scope
geotiff.cpp:46: error: expected primary-expression before ')' token
geotiff.cpp:46: error: initializer expression list treated as compound expression
geotiff.cpp:47: error: 'GTIF' was not declared in this scope
geotiff.cpp:47: error: expected primary-expression before ',' token
geotiff.cpp:47: error: expected primary-expression before 'const'
geotiff.cpp:47: error: initializer expression list treated as compound expression
geotiff.cpp: In destructor 'virtual GTiffDataset::~GTiffDataset()':
geotiff.cpp:2249: error: 'XTIFFClose' was not declared in this scope
geotiff.cpp: In member function 'void GTiffDataset::WriteGeoTIFFInfo()':
geotiff.cpp:3336: error: 'TIFFTAG_GEOPIXELSCALE' was not declared in this scope
geotiff.cpp:3346: error: 'TIFFTAG_GEOTIEPOINTS' was not declared in this scope
geotiff.cpp:3363: error: 'TIFFTAG_GEOTRANSMATRIX' was not declared in this scope
geotiff.cpp:3393: error: 'TIFFTAG_GEOTIEPOINTS' was not declared in this scope
geotiff.cpp:3404: error: 'GTIF' was not declared in this scope
geotiff.cpp:3404: error: 'psGTIF' was not declared in this scope
geotiff.cpp:3413: error: 'TIFFTAG_GEOKEYDIRECTORY' was not declared in this scope
geotiff.cpp:3420: error: 'TIFFTAG_GEODOUBLEPARAMS' was not declared in this scope
geotiff.cpp:3422: error: 'TIFFTAG_GEOASCIIPARAMS' was not declared in this scope
geotiff.cpp:3425: error: 'GTIFNew' was not declared in this scope
geotiff.cpp:3428: error: 'GTIFSetFromOGISDefn' cannot be used as a function
geotiff.cpp:3434: error: 'GTRasterTypeGeoKey' was not declared in this scope
geotiff.cpp:3434: error: 'TYPE_SHORT' was not declared in this scope
geotiff.cpp:3435: error: 'RasterPixelIsPoint' was not declared in this scope
geotiff.cpp:3435: error: 'GTIFKeySet' was not declared in this scope
geotiff.cpp:3438: error: 'GTIFWriteKeys' was not declared in this scope
geotiff.cpp:3439: error: 'GTIFFree' was not declared in this scope
geotiff.cpp: In static member function 'static GDALDataset* GTiffDataset::OpenDir(GDALOpenInfo*)':
geotiff.cpp:4285: error: 'XTIFFClose' was not declared in this scope
geotiff.cpp: In member function 'CPLErr GTiffDataset::OpenOffset(TIFF*, GTiffDataset**, toff_t, int, GDALAccess, int)':
geotiff.cpp:4640: error: 'TIFFTAG_GEOPIXELSCALE' was not declared in this scope
geotiff.cpp:4647: error: 'TIFFTAG_GEOTIEPOINTS' was not declared in this scope
geotiff.cpp:4659: error: 'TIFFTAG_GEOTRANSMATRIX' was not declared in this scope
geotiff.cpp:4700: error: 'TIFFTAG_GEOTIEPOINTS' was not declared in this scope
geotiff.cpp:4724: error: 'GTIF' was not declared in this scope
geotiff.cpp:4724: error: 'hGTIF' was not declared in this scope
geotiff.cpp:4725: error: 'GTIFDefn' was not declared in this scope
geotiff.cpp:4725: error: expected `;' before 'sGTIFDefn'
geotiff.cpp:4730: error: 'GTIFNew' was not declared in this scope
geotiff.cpp:4739: error: 'sGTIFDefn' was not declared in this scope
geotiff.cpp:4739: error: 'GTIFGetDefn' was not declared in this scope
geotiff.cpp:4741: error: 'GTIFGetOGISDefn' cannot be used as a function
geotiff.cpp:4748: error: 'GTRasterTypeGeoKey' was not declared in this scope
geotiff.cpp:4749: error: 'GTIFKeyGet' was not declared in this scope
geotiff.cpp:4751: error: 'RasterPixelIsPoint' was not declared in this scope
geotiff.cpp:4757: error: 'GTIFFree' was not declared in this scope
geotiff.cpp: In static member function 'static TIFF* GTiffDataset::CreateLL(const char*, int, int, int, GDALDataType, char**)':
geotiff.cpp:5707: error: 'XTIFFClose' was not declared in this scope
geotiff.cpp: In static member function 'static GDALDataset* GTiffDataset::CreateCopy(const char*, GDALDataset*, int, char**, int (*)(double, const char*, void*), void*)':
geotiff.cpp:6217: error: 'TIFFTAG_GEOPIXELSCALE' was not declared in this scope
geotiff.cpp:6226: error: 'TIFFTAG_GEOTIEPOINTS' was not declared in this scope
geotiff.cpp:6242: error: 'TIFFTAG_GEOTRANSMATRIX' was not declared in this scope
geotiff.cpp:6279: error: 'TIFFTAG_GEOTIEPOINTS' was not declared in this scope
geotiff.cpp:6301: error: 'GTIF' was not declared in this scope
geotiff.cpp:6301: error: 'psGTIF' was not declared in this scope
geotiff.cpp:6303: error: 'GTIFNew' was not declared in this scope
geotiff.cpp:6304: error: 'GTIFSetFromOGISDefn' cannot be used as a function
geotiff.cpp:6310: error: 'GTRasterTypeGeoKey' was not declared in this scope
geotiff.cpp:6310: error: 'TYPE_SHORT' was not declared in this scope
geotiff.cpp:6311: error: 'RasterPixelIsPoint' was not declared in this scope
geotiff.cpp:6311: error: 'GTIFKeySet' was not declared in this scope
geotiff.cpp:6314: error: 'GTIFWriteKeys' was not declared in this scope
geotiff.cpp:6315: error: 'GTIFFree' was not declared in this scope
geotiff.cpp:6325: error: 'XTIFFClose' was not declared in this scope
make[2]: *** [../o/geotiff.lo] Error 1
make[2]: Leaving directory `/home/andreh/workspace/project-ossim_dev/gdal/frmts/gtiff'
make[1]: *** [gtiff-install-obj] Error 2
make[1]: Leaving directory `/home/andreh/workspace/project-ossim_dev/gdal/frmts'
make: *** [frmts-target] Error 2

And this is how to get rid of it:

# open the GDALmake.opt file with an editor
gedit GDALmake.opt

# locate the CPPFLAGS line and add the include path at the end "-I/usr/include/geotiff"
CPPFLAGS    =  -I$(GDAL_ROOT)/port -I/usr/lib/include -I -I/include -I/usr/include/geotiff

5. One can now run make and make install:

make
sudo make install

Grep and punctuation marks

I've often tried to use grep to filter search results for locate and several times I've had to search for a string with locate:

locate svn

This search would obviously include all the '.svn' folders too. Trying to get rid with them with

locate svn | grep -v '.svn'

does not work, since grep uses basic regular expressions, and the period mark will simply match any character.

To explicitly indicate the usage of a punctuation mark, one has to put it in brackets. The statement will now look something like:

locate svn | grep -v '[.]svn'

I just scanned through the grep man pages, and everything is explained pretty clearly there. I'd recommend reading the bit on regular expressions.

PHP: move_uploaded_file, Permission denied

If you ever receive the failed to open stream: Permission denied error in Linux on the move_uploaded_file function, try changing the upload folder's permissions through the chmod command:

chmod 0777 upload_dir

Get JBoss Seam going on Gentoo Linux with Tomcat

I've been given a web app to do for an open source driven organization. I like the ideology behind open source, but I must say that the complexities involved in just getting started, must be the single biggest hurdle in the adoption of OSS.

Most Java and Linux fanboys might rupture a vain for me saying this, but to get any sort of Java web app going is massive pain in butt. To get Asp.Net going, one merely install visual studio and off you go. You don't even need IIS these days. To get a Java web app (dev environment) going you have to install a web server, an application server, a java framework, an IDE, IDE plugins to support the java framework and perhaps additional frameworks / tools which will allow you to work in a "code-behind" fashion. Then you have to decide on a web frameworks and the choices are endless: Spring MVC, Struts, Seam, JSF, Tapestry, Wicket, Hibernate, Stripes, etc. You can Google until you're blue in the face, but every single framework claims to be the best and all have their own following of groupies. To be honest, it is a big geeky mess!

Unfortunately I don't have the luxury of cleaning up this steaming pile of rubbish, so I'll have to get my hands dirty and figure out what the best solution is through trial and error (very scientific).

My client already has Tomcat running, so luckily I don't have to bother about figuring out which application server is the best. A further requirement is that the web framework should be quite lightweight. It seems as if JBoss' Seam framework isn't too much of a brute, so I'll go with that and probably get burned half-way in.

Even though I detest overcomplicated systems, I've grown quite fond of Gentoo. Once you've mastered this beast, it is quite pleasant to work with. (Perhaps I'll have the same feelings towards Java web apps once I've finished here, but for now it's not looking good.) So I'll run through the steps of getting Seam going on Gentoo.

To start off with, we'll need JDK (or JRE). Login as root, emerge sun-jdk (in my case version 1.6.0.07) and logout. After that we need to get Tomcat.

Note: You can try to get Tomcat going through portage, but you'll end up pulling your hair out, because Seam uses the naming-factory-dbcp.jar, which is not included in the build for some bizarre reason.

cd ~
mkdir applications
cd applications
wget http://apache.mirrors.hoobly.com/tomcat/tomcat-6/v6.0.18/bin/apache-tomcat-6.0.18.tar.gz
tar -xf apache-tomcat-6.0.18.tar.gz

Now let's set the environmental variables needed:

nano ~/.bashrc

and add these lines:

export JRE_HOME=/opt/sun-jdk-1.6.0.07
export TOMCAT_HOME=/home/yourname/applications/apache-tomcat-6.0.18
export CATALINA_HOME=$TOMCAT_HOME
export CATALINA_BASE=$TOMCAT_HOME

Note: You might want to emerge the tomcat-native package, since it will add the Apache Tomcat Native library. I'm not sure if Seam needs this, but I noticed Tomcat having a bit of a fit when it couldn't find it. The message in the $TOMCAT_HOME/logs/catalina.out was "INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path"

One can also configure an admin user, but this is not necessarily required. Edit the tomcat-users.xml file like this:

nano $TOMCAT_HOME/conf/tomcat-users.xml

<tomcat-users>
<role rolename="manager">
<user username="root" password="irock" roles="manager">
</user>

One can now start Tomcat:

cd $TOMCAT_HOME/bin
./startup.sh

You should now be able to access Tomcat on http://localhost:8080

Tomcat will display $TOMCAT_HOME/webapps/ROOT/index.html

So we can now follow Seam's Tomcat guide, which I had to modify a bit:

1. Go into the jboss-seam/examples/jpa directory
2. Copy the lib/hsqldb.jar into $TOMCAT_HOME/lib
3. Run ant tomcat6 to build the application
4. Stop Tomcat $TOMCAT_HOME/bin/shutdown.sh
5. Remove previous any exiting deployments: rm -r $TOMCAT_HOME/webapps/jboss-seam-jpa
6. Copy war file: cp dist-tomcat6/jboss-seam-jpa.war $TOMCAT_HOME/webapps
7. Start Tomcat $TOMCAT_HOME/bin/starup.sh
8. Access the app at http://localhost:8080/jboss-seam-jpa

And Bob's you're uncle!

Linux: shutdown: you must be root to do that!

In order to use the console commands shutdown, poweroff, halt or reboot, one has to be a super user. One might see messages such as:

shutdown: you must be root to do that!
poweroff: must be superuser.
reboot: must be superuser.
halt: must be superuser.

In some cases the user can simply be added to the wheel group. This should give the user enough privileges to shut the machine down. A more reliable approach is to make use of Sudo, which was specifically designed to allow ordinary users to execute certain super-user-only commands.

The following section will explain how to setup sudo to allow other users to the machine down through the command line under the Gentoo distro.

Install Sudo
Login as su:

su -

Emerge Sudo:

emerge app-admin/sudo

Configure Sudo
Run visudo:

visudo

Enter the following:

# Runas alias specification
YourUserName  ALL=(root) NOPASSWD: /sbin/reboot
YourUserName  ALL=(root) NOPASSWD: /sbin/halt
YourUserName  ALL=(root) NOPASSWD: /sbin/poweroff
YourUserName  ALL=(root) NOPASSWD: /sbin/shutdown

Replace YourUserName with the user name which requires shutdown privileges.

See this guide on how to create a group which allows all its users to shut the machine down.