mpiblast 1.4.0 pio
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mpiBLAST 1.4.0-pio
mpiBLAST is an MPI based parallel implementation of NCBI BLAST. more>>
mpiBLAST is an MPI based parallel implementation of NCBI BLAST. The project consists of a pair of programs that replace formatdb and blastall with versions that execute BLAST jobs in parallel on a cluster of computers with MPI installed. There are two primary advantages to using mpiBLAST versus traditional BLAST.
First, mpiBLAST splits the database across each node in the cluster. Because each nodes segment of the database is smaller it can usually reside in the buffer-cache, yielding a significant speedup due to the elimination of disk I/O. Second, it allows BLAST users to take advantage of efficient, low-cost Beowulf clusters because interprocessor communication demands are low.
mpiBLAST achieves super-linear speedup in situations where the database is too large to fit into RAM, and near linear speedup in other situations. It does not require a dedicated cluster.
<<lessFirst, mpiBLAST splits the database across each node in the cluster. Because each nodes segment of the database is smaller it can usually reside in the buffer-cache, yielding a significant speedup due to the elimination of disk I/O. Second, it allows BLAST users to take advantage of efficient, low-cost Beowulf clusters because interprocessor communication demands are low.
mpiBLAST achieves super-linear speedup in situations where the database is too large to fit into RAM, and near linear speedup in other situations. It does not require a dedicated cluster.
Download (0.33MB)
Added: 2007-06-29 License: GPL (GNU General Public License) Price:
848 downloads
Poster 1.4.0
Poster provides a developer tool for interacting with web services and other web resources. more>>
Poster provides a developer tool for interacting with web services and other web resources.
A developer tool for interacting with web services and other web resources that lets you make HTTP requests, set the entity body, and content type. This allows you to interact with web services and inspect the results.
After you install it, just go to View-Sidebar-Poster to open the tool as a sidebar. After that, try a GET or POST on your favorite web service or site.
<<lessA developer tool for interacting with web services and other web resources that lets you make HTTP requests, set the entity body, and content type. This allows you to interact with web services and inspect the results.
After you install it, just go to View-Sidebar-Poster to open the tool as a sidebar. After that, try a GET or POST on your favorite web service or site.
Download (0.016MB)
Added: 2007-04-05 License: MPL (Mozilla Public License) Price:
940 downloads
hideBad 1.4.0
hideBad is a Firefox extension that hides bad things. more>>
hideBad is a Firefox extension that hides bad things. Saves all the tabs in the current window, closes them, and replaces them with the homepage tabs. Saved tabs can later be recovered. Can clear the following at the users choice:
- History
- Recently Closed Tabs list
- Saved form info
- Saved passwords
- Download history
- Cookies
- Cache
- Searchbar
<<less- History
- Recently Closed Tabs list
- Saved form info
- Saved passwords
- Download history
- Cookies
- Cache
- Searchbar
Download (0.021MB)
Added: 2007-07-30 License: MPL (Mozilla Public License) Price:
855 downloads
OpenAFS 1.4.0
OpenAFS is a client-server distributed filesystem. more>>
AFS is a distributed filesystem product, pioneered at Carnegie Mellon University and supported and developed as a product by Transarc Corporation (now IBM Pittsburgh Labs).
It offers a client-server architecture for file sharing, providing location independence, scalability and transparent migration capabilities for data.
IBM branched the source of the AFS product, and made a copy of the source available for community development and maintenance. They called the release OpenAFS.
Enhancements:
- OpenAFS 1.4.0 adds large file support in Unix and Unix-like clients and in servers.
- Kerberos 5 integration has been improved. aklog now ships with OpenAFS 1.4.0.
- Several new operating system versions are now supported, including Solaris 10 on both SPARC and Intel.
<<lessIt offers a client-server architecture for file sharing, providing location independence, scalability and transparent migration capabilities for data.
IBM branched the source of the AFS product, and made a copy of the source available for community development and maintenance. They called the release OpenAFS.
Enhancements:
- OpenAFS 1.4.0 adds large file support in Unix and Unix-like clients and in servers.
- Kerberos 5 integration has been improved. aklog now ships with OpenAFS 1.4.0.
- Several new operating system versions are now supported, including Solaris 10 on both SPARC and Intel.
Download (55.5MB)
Added: 2005-11-02 License: IBM Public License Price:
1457 downloads
first4 1.4.0 Alpha 1
first4 is a financial software. more>>
first4 is a financial software.
Main features:
- Address management, unlimited Directories can be created
- Stock management
- Order management and Inventory
- Documents can be created (Offers, Order confirmations, Delivery notes and Invoices)
- a simple financial module
- multi user
first4 is still under development and not all modules are migrated.
For Templates, Language-Files and SQL-Initfile please visit www.linux-box.ch.
<<lessMain features:
- Address management, unlimited Directories can be created
- Stock management
- Order management and Inventory
- Documents can be created (Offers, Order confirmations, Delivery notes and Invoices)
- a simple financial module
- multi user
first4 is still under development and not all modules are migrated.
For Templates, Language-Files and SQL-Initfile please visit www.linux-box.ch.
Download (2.6MB)
Added: 2007-02-27 License: GPL (GNU General Public License) Price:
969 downloads
BibShelf 1.4.0
BibShelf is a book organizer integrating well with the GNOME desktop environment. more>>
BibShelf is a book organizer integrating well with the GNOME desktop environment.
BibShelf project helps you to keep track of your book collection. You can fill in such things as the book summary, review, rating and the ISBN.
Never forget when it was that you read a book, BibShelf lets you save the date so you do no longer need to waste your brain capacity for storing this information.
<<lessBibShelf project helps you to keep track of your book collection. You can fill in such things as the book summary, review, rating and the ISBN.
Never forget when it was that you read a book, BibShelf lets you save the date so you do no longer need to waste your brain capacity for storing this information.
Download (0.45MB)
Added: 2006-02-17 License: GPL (GNU General Public License) Price:
1344 downloads
JVOIPLIB 1.4.0
JVOIPLIB is an object-oriented Voice over IP (VoIP) library written in C++. more>>
JVOIPLIB is an object-oriented Voice over IP (VoIP) library written in C++.
It is based upon work done for my thesis at the School for Knowledge Technology (or School voor Kennistechnologie in Dutch), a cooperation between the Hasselt University and the Maastricht University.
A part of this library was developed at the Expertise Centre for Digital Media (EDM) in Diepenbeek, Belgium. The EDM is a research institute of the Hasselt University.
Main features:
- Easy VoIP session creation and destruction.
- Highly configurable sessions: sampling rate, sample interval, compression type, ... can all be selected by the user. These features can also be changed during a session.
- Openness and extensibility: the object-oriented nature of the library makes it very easy to add features; new components can easily be tested by registering them as User Defined modules.
- Support for 3D effects: for my thesis I also did some research and development about VoIP in networked virtual environments, which included adding 3D effects to sound. For this reason, Ive added this feature to the library.
<<lessIt is based upon work done for my thesis at the School for Knowledge Technology (or School voor Kennistechnologie in Dutch), a cooperation between the Hasselt University and the Maastricht University.
A part of this library was developed at the Expertise Centre for Digital Media (EDM) in Diepenbeek, Belgium. The EDM is a research institute of the Hasselt University.
Main features:
- Easy VoIP session creation and destruction.
- Highly configurable sessions: sampling rate, sample interval, compression type, ... can all be selected by the user. These features can also be changed during a session.
- Openness and extensibility: the object-oriented nature of the library makes it very easy to add features; new components can easily be tested by registering them as User Defined modules.
- Support for 3D effects: for my thesis I also did some research and development about VoIP in networked virtual environments, which included adding 3D effects to sound. For this reason, Ive added this feature to the library.
Download (0.56MB)
Added: 2005-10-18 License: LGPL (GNU Lesser General Public License) Price:
1466 downloads
Xclasses 1.4.0
Xclasses is a C layout library for the X Window System. more>>
Xclasses is a C layout library for the X Window System. All objects (called gadgets) are font sensitive, i.e. their size changes with the size of the used screen font and the size of the window.
All this is done by Xclasses itself. The user may choose any kind of font style and size.
All objects (gadgets) have the same base class (class gadget) so there are all
used the same. Gadgets are put together in groups (class group also bases on
gadget) which manage the correct size of all gadgets (and/or groups!) inside.
Why use Xclasses?
Xclasses is completely written in C++ so it is really object orientated! But C-Users may use it because most C compilers support C++ and for using Xclasses you neddnt to know much about C++.
Xclasses is easy to use, no pointer or handles to manage or remember - simply classes (for C users: like structs with functions added). If you dont want to do some special things (like writing a multiplayer arcade game or a new window manager) you dont even need to know anything about X-Windows functions and how it works - Xclasses has its own classes for all of this that put many complex X functions to some easy functions together.
Xclasses project makes easy font and context sensitiv GUIs. And you dont need much time to develop a GUI!
Installation:
To install the compiled library start "./build install".
This copies the library to /usr/local/lib/ and the includes to /usr/local/include/. A global config file for all Xclasses programs is installed in /usr/lib/X11/Xclasses/.
Each time you want to compile a Xclasses program you should execute the "setenvxc" script like this ". ./setenvxc" in ksh or bash or but its source into your profile.
Now you can compile the example programs in the example dir, enter
./build examples
in the Xclasses top directory (where you found this README).
If you got the sources and want to compile them yourself use the "build" script:
./build config will ask some config questions
./build make will make the library
or
./build all build config & make
Enhancements:
- compiler problems with GCC 3.x fixed
<<lessAll this is done by Xclasses itself. The user may choose any kind of font style and size.
All objects (gadgets) have the same base class (class gadget) so there are all
used the same. Gadgets are put together in groups (class group also bases on
gadget) which manage the correct size of all gadgets (and/or groups!) inside.
Why use Xclasses?
Xclasses is completely written in C++ so it is really object orientated! But C-Users may use it because most C compilers support C++ and for using Xclasses you neddnt to know much about C++.
Xclasses is easy to use, no pointer or handles to manage or remember - simply classes (for C users: like structs with functions added). If you dont want to do some special things (like writing a multiplayer arcade game or a new window manager) you dont even need to know anything about X-Windows functions and how it works - Xclasses has its own classes for all of this that put many complex X functions to some easy functions together.
Xclasses project makes easy font and context sensitiv GUIs. And you dont need much time to develop a GUI!
Installation:
To install the compiled library start "./build install".
This copies the library to /usr/local/lib/ and the includes to /usr/local/include/. A global config file for all Xclasses programs is installed in /usr/lib/X11/Xclasses/.
Each time you want to compile a Xclasses program you should execute the "setenvxc" script like this ". ./setenvxc" in ksh or bash or but its source into your profile.
Now you can compile the example programs in the example dir, enter
./build examples
in the Xclasses top directory (where you found this README).
If you got the sources and want to compile them yourself use the "build" script:
./build config will ask some config questions
./build make will make the library
or
./build all build config & make
Enhancements:
- compiler problems with GCC 3.x fixed
Download (0.95MB)
Added: 2006-03-22 License: LGPL (GNU Lesser General Public License) Price:
1313 downloads
MP-MPICH 1.4.0
MP-MPICH provides a Multi-platform MPI implementation. more>>
MP-MPICH provides a Multi-platform MPI implementation.
MP-MICH is a Multi-platform uniform MPI implementation, based on MPICH and SCI-MPICH, resulting in a high performance, consistent MPI across both ethernet and SCI networks in a hybrid environment. There is a single, standardized source tree for all platforms. It is compliant with the MPI-1 standard.
MP-MPICH uses one common source tree for this purpose. It has a new device for Windows NT/2000/2003 to communicate via sockets, and an adapted shared memory device for SMP systems. Additionally, MP-MPICH is a superset of SCI-MPICH, that means that it includes another new device to support direct communication via a fast SCI interconnect. With SCI-MPICH, inter-process message latencies for small messages (for processes running on separate nodes) below 4 us are achieved, and the current measured maximum inter-node (PingPong-)bandwidth is at about 310 MB/s.
In fact, the development of MP-MPICH started when the first release of SCI-MPICH was finished. This release was designed for Solaris and Linux, but since it uses our SMI library which is also available for Windows NT, we thought it would be fun to port SCI-MPICH to NT. The initial port took only 4 hours and we were up and running with SCI-MPICH for NT. The additional/modified devices which are necessary to use MPICH on NT without these extremely fast SCI boards required more time to develop.
<<lessMP-MICH is a Multi-platform uniform MPI implementation, based on MPICH and SCI-MPICH, resulting in a high performance, consistent MPI across both ethernet and SCI networks in a hybrid environment. There is a single, standardized source tree for all platforms. It is compliant with the MPI-1 standard.
MP-MPICH uses one common source tree for this purpose. It has a new device for Windows NT/2000/2003 to communicate via sockets, and an adapted shared memory device for SMP systems. Additionally, MP-MPICH is a superset of SCI-MPICH, that means that it includes another new device to support direct communication via a fast SCI interconnect. With SCI-MPICH, inter-process message latencies for small messages (for processes running on separate nodes) below 4 us are achieved, and the current measured maximum inter-node (PingPong-)bandwidth is at about 310 MB/s.
In fact, the development of MP-MPICH started when the first release of SCI-MPICH was finished. This release was designed for Solaris and Linux, but since it uses our SMI library which is also available for Windows NT, we thought it would be fun to port SCI-MPICH to NT. The initial port took only 4 hours and we were up and running with SCI-MPICH for NT. The additional/modified devices which are necessary to use MPICH on NT without these extremely fast SCI boards required more time to develop.
Download (11.8MB)
Added: 2007-03-02 License: BSD License Price:
977 downloads
EuroMath2 1.4.0
EuroMath2 project is a platform for editors editing various XML files with multiple namespaces. more>>
EuroMath2 project is a platform for editors editing various XML files with multiple namespaces. Able to contain and manage editors with WYSIWYG capability.
By default it contains:
- a basic XSL-FO editor, capable of editing XML documents transformable to XSL-FO,
- a read-only support for SVG and MathML,
- a (very incomplete) XHTML support (implemented using a stylesheet capable of transforming XHTML into the XSL-FO)
The power of EuroMath2 lies in its extendability by plugins. EuroMath2 offers well-defined XML processing engine extendable by custom plugins and/or XSLT stylesheets. Custom editors may use the default editor, that offers wizards for complex document modification operations. EuroMath comes in two favours: a standalone application, and an Eclipse plugin. For more information how to download and run EuroMath please see the download section.
Main features:
- Open-source, free software released under the MPL1.1 license
- Fully customizable transformers executing XSLT scripts or Eclipse Java plugins.
- XML element/attribute autocompletion driven by custom DTD, XML Schema, Relax, RelaxNG, Trex
- Entity support
- Fully supports documents with multiple namespaces
<<lessBy default it contains:
- a basic XSL-FO editor, capable of editing XML documents transformable to XSL-FO,
- a read-only support for SVG and MathML,
- a (very incomplete) XHTML support (implemented using a stylesheet capable of transforming XHTML into the XSL-FO)
The power of EuroMath2 lies in its extendability by plugins. EuroMath2 offers well-defined XML processing engine extendable by custom plugins and/or XSLT stylesheets. Custom editors may use the default editor, that offers wizards for complex document modification operations. EuroMath comes in two favours: a standalone application, and an Eclipse plugin. For more information how to download and run EuroMath please see the download section.
Main features:
- Open-source, free software released under the MPL1.1 license
- Fully customizable transformers executing XSLT scripts or Eclipse Java plugins.
- XML element/attribute autocompletion driven by custom DTD, XML Schema, Relax, RelaxNG, Trex
- Entity support
- Fully supports documents with multiple namespaces
Download (8.4MB)
Added: 2006-09-05 License: MPL (Mozilla Public License) Price:
1144 downloads
c-ares 1.4.0
c-ares is a C library that resolves names asynchronously. more>>
c-ares project is a C library that resolves names asynchronously.
Enhancements:
- ares_save_options, ares_destroy_options, ares_process_fd, and ares_parse_ns_reply were added.
- The transaction IDs were made "secure".
- A few parsing issues and minor bugs were fixed.
<<lessEnhancements:
- ares_save_options, ares_destroy_options, ares_process_fd, and ares_parse_ns_reply were added.
- The transaction IDs were made "secure".
- A few parsing issues and minor bugs were fixed.
Download (0.42MB)
Added: 2007-06-08 License: MIT/X Consortium License Price:
876 downloads
Oggasm 1.4.0
Oggasm is a program that makes converting your mp3 collection into oggs a all but painless process. more>>
Oggasm is a program that makes converting your mp3 collection into oggs a all but painless process.
Using oggenc and mpg321, with perl glueing it all together, oggasm is able to go through an entire collection, identify id3 tags and then convert those mp3s into oggs while keeping the id3 tags intact.
TODO:
server-client model: When oggasm is started I want it to creat a list of jobs that need to be done and then assign those jobs to various clients that could either be running on the same machine or on other machines connected via a network.
Im of two minds on how to do this. Either I learn how to use sockets and develop my own communication protocol to tell the clients what to do, or I create physical files that are grabed by the client via ftp or samba. Each one has its advantages and disadvantages and I hope to look into it more soon.
One thing that is very important is that a client machines need to be able to come and go as necessary. So oggasm might start with 2 clients, be at 5 later in the day, and then down to 1 when it all finishes.
network functionality: How this will look will rest largly on how the server-client model ends up looking. But most likely the it will involve using ftp or samba to grab files from the server machine, convert them, and then send them back to the server. After that the
client will be assigned a new job.
improvments to user interface: This will be a on going process. As I continue to get more feedback on how people felt their experience with oggasm was I can improve how it the interface looks. Recent changes with 1.3 will allow updates to the interface to be much smother than before.
more encoder/decoder options: certainly oggenc will remain the primary encoder, however other free codecs might come along someday, and it would be nice if oggasm was modular enough to beable to plug in different encoders. I would also like to support different decoders as not everyone has mpg321 (however I will NOT provide support of non-free decoders).
<<lessUsing oggenc and mpg321, with perl glueing it all together, oggasm is able to go through an entire collection, identify id3 tags and then convert those mp3s into oggs while keeping the id3 tags intact.
TODO:
server-client model: When oggasm is started I want it to creat a list of jobs that need to be done and then assign those jobs to various clients that could either be running on the same machine or on other machines connected via a network.
Im of two minds on how to do this. Either I learn how to use sockets and develop my own communication protocol to tell the clients what to do, or I create physical files that are grabed by the client via ftp or samba. Each one has its advantages and disadvantages and I hope to look into it more soon.
One thing that is very important is that a client machines need to be able to come and go as necessary. So oggasm might start with 2 clients, be at 5 later in the day, and then down to 1 when it all finishes.
network functionality: How this will look will rest largly on how the server-client model ends up looking. But most likely the it will involve using ftp or samba to grab files from the server machine, convert them, and then send them back to the server. After that the
client will be assigned a new job.
improvments to user interface: This will be a on going process. As I continue to get more feedback on how people felt their experience with oggasm was I can improve how it the interface looks. Recent changes with 1.3 will allow updates to the interface to be much smother than before.
more encoder/decoder options: certainly oggenc will remain the primary encoder, however other free codecs might come along someday, and it would be nice if oggasm was modular enough to beable to plug in different encoders. I would also like to support different decoders as not everyone has mpg321 (however I will NOT provide support of non-free decoders).
Download (0.008MB)
Added: 2005-09-20 License: GPL (GNU General Public License) Price:
1494 downloads
MoSSHe 1.4.0
MoSSHe is a simple, lightweight server monitoring package. more>>
MoSSHe (MOnitoring with SSH Environment) is a simple, lightweight (both in size and system requirements) server monitoring package designed for secure and in-depth monitoring of a handful of typical/critical internet systems. For example in a current setup I do 264 checks on 29 servers - on average 9 checks for each system. MoSSHe supports email alerts out of the box - and whatever you can script.
The web interface to status and logs reflects this approach: less than 10 systems are ideal for the "big" (showall) web display, less then 50 for the problem-centric (tactical) view. More than 100 systems should easily be possible, but I have not tested such an extended setup.
In contrast to many other NMS (Network Management Systems) it is not possible to "overload" a MoSSHe system - the minimum checkup intervals will simply extend with each added system, though. For the setup mentioned above the time needed for 264 checks on 29 servers is 100 seconds. But for your setup it may vary significantly.
Via the web interface you can view the overall status (tactical.py), server status and service history, but you cannot modify anything - which makes it quite safe for even non-admin multiuser use...
<<lessThe web interface to status and logs reflects this approach: less than 10 systems are ideal for the "big" (showall) web display, less then 50 for the problem-centric (tactical) view. More than 100 systems should easily be possible, but I have not tested such an extended setup.
In contrast to many other NMS (Network Management Systems) it is not possible to "overload" a MoSSHe system - the minimum checkup intervals will simply extend with each added system, though. For the setup mentioned above the time needed for 264 checks on 29 servers is 100 seconds. But for your setup it may vary significantly.
Via the web interface you can view the overall status (tactical.py), server status and service history, but you cannot modify anything - which makes it quite safe for even non-admin multiuser use...
Download (0.023MB)
Added: 2007-02-01 License: GPL (GNU General Public License) Price:
996 downloads
XMLPublication 0.4.1
XMLPublication project is a collection of tools to generate Web pages from desktop documents. more>>
XMLPublication project is a collection of tools to generate Web pages from desktop documents or other structured documents, such as books with paragraphs, or tabular data.
It cuts documents into Web pages, and creates customizable multi-indices.
All this is done through a repeatable process in which data is separated from presentation and user settings. It uses XML techniques, particularly XSLT and Ant.
Enhancements:
- we used
<<lessIt cuts documents into Web pages, and creates customizable multi-indices.
All this is done through a repeatable process in which data is separated from presentation and user settings. It uses XML techniques, particularly XSLT and Ant.
Enhancements:
- we used
tags, but switched to
in this version, because
as a wrapper is not valid with respect to the HTML DTD. It should pass intact through most of the HTML editors (testers wellcome !).
- I wrote a SAX filter to replace the XSLT transform that wraps paragraphs inside HTML tags; to integrate it, I used styler , a Task for Ant; it makes useful combinations of XSLT transformations and SAX filters. This should allow to treat MUCH LARGER FILES more quickly.
- test with JDK 1.4.0 , Saxon 6.5.2, and last Tidy from CVS on Linux RedHat 7.0; it should still work on Windows.
Download (1.4MB)
Added: 2006-10-04 License: GPL (GNU General Public License) Price:
1115 downloads
innotop 1.4.0
innotop project is a MySQL and InnoDB monitor that lets you view and manage whats happening inside your MySQL servers. more>>
innotop project is a MySQL and InnoDB monitor that lets you view and manage whats happening inside your MySQL servers.
Features include a top-like query list, a top-like InnoDB transaction list, and much more. This tool gives you a high level of insight into the inner workings of InnoDB.
<<lessFeatures include a top-like query list, a top-like InnoDB transaction list, and much more. This tool gives you a high level of insight into the inner workings of InnoDB.
Download (0.061MB)
Added: 2007-03-04 License: GPL (GNU General Public License) Price:
966 downloads
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