Understanding memory usage from top and htop

Actually from htop and top utilities, you can find how the memory is used and buffered.

When you run top, you will notice that a lot of memory are being used even though there may not be much applications currently running. The reasons for this huge usage is that the kernel allocates memory that isn't in active use by processes to things like filesystem caches to improve performance. If there is demand on the memory by another application or data, the kernel will free up the memory.

If you run top,  you will notice buffers and cached. "Buffers" represent how much portion of RAM is dedicated to cache disk block. "Cached" is similar like "Buffers", only this time it caches pages from file reading.

However if you run htop, the memory used is smaller. Both utilities are not wrong, it is a different representation of the memory usage

For more information, you may want to read an excellent article on Using Top More Efficiently 

Using ImageMagick to edit image at command line

ImageMagick is one of the oldest but still widely used graphics editing software. One of the strength of ImageMagick is the ability to do batch processing like shrinking the size of the images etc.

There are very good examples on the ImageMagick tutorial itself.

1. Example (http://www.imagemagick.org/​Usage/)
2. Stream (http://www.imagemagick.org/script/​stream.​php)
3. Animate (Animate: http://www.imagemagick.org/script/animate.​php)
4. Command-line-Options (http://www.imagemagick.org/script/command-line-options.php ) 
5. Image Format (http://www.imagemagick.org/script/formats.php ) 
6. API (http://www.imagemagick.org/script/api.php)
7. ImageMagick Studio (http://www.imagemagick.org/MagickStudio/scripts/MagickStudio.cgi)

To install ImageMagick, just type

# yum install ImageMagick

To view the image, just type

$ display

Click Top left-hand corner to launch the ImageMagick

OpenFOAM - Open Source CFD

OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.

ImageJ - Image Processing and Analysis in Java

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux.

It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

It can calculate area and pixel value statistics of user-defined selections. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering.

NAMD and VMD

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PL0OR.

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.