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The Ridgefield, Conn. laboratory of Boehringer Ingelheim Pharmaceuticals is using the cluster supercomputer to help predict the suitability of certain molecules in potential drugs. This process is ideal for a Linux cluster supercomputer because the same compute process is completed for hundreds of thousands of molecules. Computational chemists and biologists at Boehringer Ingelheim Pharmaceuticals are also using the cluster to run applications to find the best combinations of molecules and protein binding sites for drug development.
?With a 120-processor cluster, managing every aspect of the system can be quite overwhelming,? said Dave Craska, lead systems engineer for Boehringer Ingelheim Pharmaceuticals, Inc. ?The ClusterWorX software from Linux NetworX helps alleviate the complexities of cluster management, especially when upgrading and propagating new releases of software.?
Before switching to a Linux NetworX cluster, scientists at Boehringer Ingelheim Pharmaceuticals were running the same applications on a variety of systems, but results were slowed because of the limited number of available CPUs. After deploying the Linux NetworX cluster, information was processed quickly and efficiently, saving Boehringer Ingelheim Pharmaceuticals time and money.
The massive amount of data computation inherent in drug design typically requires the power of a supercomputer class system. Cluster technology is a method of linking multiple computers, or compute nodes, together to form a powerful, unified system. Linux NetworX clusters can match the performance of traditional supercomputers for a fraction of the cost.
?The bioinformatics industry is experiencing an enormous demand for cost-effective, reliable supercomputing solutions and many pharmaceutical companies are turning to Linux clusters to meet that need,? said Clark Roundy, vice president of marketing at Linux NetworX. ?Companies such as Boehringer Ingelheim Pharmaceuticals demand quick, accurate results and Linux NetworX provides the management tools to ensure our customers focus on their core competencies instead of system management.?
Boehringer Ingelheim Pharmaceuticals? Evolocity system includes 120 Pentium III 866 MHz processors, 50 GB of memory, an Intel 10/100 NIC connection and ClusterWorX cluster management software. To ensure optimum cluster operation, Boehringer Ingelheim Pharmaceuticals also signed a service and support contract with Linux NetworX.
About Boehringer Ingelheim Pharmaceuticals
Boehringer Ingelheim Pharmaceuticals, Inc., based in Ridgefield, CT, is the largest U.S. subsidiary of Boehringer Ingelheim Corporation (Ridgefield, CT) and a member of the Boehringer Ingelheim group of companies. The Boehringer Ingelheim group of companies, with headquarters in Ingelheim (Germany) is one of the 20 leading pharmaceutical firms in the world and reported revenues of almost US $5.8 billion in 2000. Boehringer Ingelheim, which has some 140 affiliated companies worldwide, focuses on human pharmaceuticals and animal health. The human pharmaceuticals business, which accounts for 95% of sales, is comprised of prescription medicines, consumer health care products and chemicals and biopharmaceuticals for industrial customers . Research and development, production, and distribution facilities are located around the globe. In 2000, Boehringer Ingelheim spent almost US $914 million on R&D, equivalent to 15.6% of net sales.
For more information on Boehringer Ingelheim, please see the international Internet website www.boehringer-ingelheim.com
About Linux NetworX
Linux NetworX (www.linuxnetworx.com) brings its powerful and easy-to-manage cluster technology to those demanding high performance and high availability systems. Linux NetworX provides solutions for organizations involved in oil and gas exploration, aeronautical and chemical modeling, biotechnology research, graphics rendering and visual effects, Web serving, ISPs, ASPs, and other technological research fields. Through its innovative Evolocity hardware, ICE™ cluster management tools and professional service and support, Linux NetworX provides end-to-end clustering solutions. To date, the company has built some of the largest cluster systems in the world, and boasts numerous Fortune 500 customers.
CONTACT:
Brad Rutledge
Linux NetworX
801-562-1010 ext. 218
brutledge@linuxnetworx.com
The Ejen program is a text generation system (“text” means, including, but not limited to, source code in any kind of programming language). It makes use of Java/XML/XSLT technologies and is implemented for now as an Ant task. This implementation allows the setup of a complete generation, compilation and deployment sequence, by maintaining only one “build” file that indicates the order in which each of these actions must be achieved.
Generally speaking, Ejen should be understood as a system that organizes a data flow, whose initial source is an XML file containing a (minimal) set of data (required by the generation process). The data flow grows by the fusion with other XML files and by going through XSL “filters”, until it is sufficiently detailed. It finally goes through XSL “templates” to produce the resulting text files.
A salient feature of this system is that it allows the use of almost any kind of text file as input, without the need of developing lengthy and complex Java extensions. The use of the JavaCC compiler compiler, when corresponding grammars (“Chomsky grammars”) are provided, allows the transformation of those files into DOM tree representations. Resulting DOM trees may then be used in the generation process, as well as other native XML files.
Ejen is not therefore by itself a code generator. It is rather a system based on Java/XML/XSLT technologies that makes the actual creation of code generators easier and faster.
A complete EJB 1.1 generation process (with test JSP files) has been written for the JBoss-[Jetty or Tomcat] server (using the HSQLDB database). This demonstration produces the entire set of Java source and XML files required by an Entity Beans (of “bean managed” type) deployment : the primary key classes, the home and remote interfaces, the complete implementation of the beans and the ejb-jar.xml deployment descriptor file. Basic JSP files, for testing purposes, are also generated in order to manage the EJB from an internet browser : database column creation/modification/destruction is managed this way, just as basic finding methods.
This demonstration has the following special feature : home and remote interfaces are deduced from a syntactical analysis of the generated bean. This feature allows the use of the generator not only to create the first EJB implementation, but also to synchronize (update) the dependent interfaces from a manual bean modification (for example, after the addition of a new and specific “findBy” method). As this system is open and flexible, this feature could be also used in order to synchronize other dependent classes (like client classes that encapsulate EJB calls).
Ejen (code generation system).
Copyright © 2001, 2002 François Wolff (ejen@noos.fr).
Ejen is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
Ejen is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
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The Net Squad recognizes the value of the open source community and has
used open source technologies in providing cost effective, high
performance solutions to clients. In an effort to further adoption of
MySQL and the MM.MySQL driver for enterprise applications, The Net Squad
is committed to providing enterprise support for these technologies.
Over 3 million users worldwide use the open source MySQL database
including Yahoo!, MP3.com, Motorola and NASA. The MM.MySQL driver is
the most widely used Java JDBC driver for the MySQL database with 1,000
new downloads a day. MySQL and MM.MySQL were leaders in a recent eWEEK
database server performance benchmark test.
“The Net Squad is the only firm in the world offering enterprise support
for the MM.MySQL driver for the MySQL database,” said Alex Bratton, CEO
of The Net Squad. “That puts us in the unique position of being the
most knowledgable team around when working with Java and MySQL
technologies. Mark Matthews, the original author of the MM.MySQL
driver, is a member of The Net Squad’s extremely talented technology
team and participates in the support effort. Our customers rely on The
Net Squad to provide critical support for their development efforts.
Mark and other members of The Net Squad team also consult directly on
client projects.”
“The Net Squad provided fast, excellent, reasonably priced service for a
mission critical portion of our online application,” said Cameron
Elliott of Global DNS.
The Net Squad has extensive experience connecting Java enterprise
platforms such as WebSphere, JRun, WebLogic, JBoss and Tomcat to MySQL
and other relational databases.
“We are pleased to have The Net Squad as a MySQL AB partner. Their
expertise working with Java and the MySQL database makes them a valuable
resource in supporting MySQL users. We believe that The Net Squad’s
corporate support for MySQL and the MM.MySQL JDBC driver will help
further adoption of MySQL in enterprise applications,” said MySQL AB
founder Michael ‘Monty’ Widenius. “The MM.MySQL driver is the most used
JDBC driver for MySQL. It’s stable, well supported and has a large user
base. The MM.MySQL driver has played an important part in making MySQL
very popular in the Java community.”
Additional information about The Net Squad’s MM.MySQL support offering
is available at http://www.thenetsquad.com/services/jdbcsupport.html.
About The Net Squad
The Net Squad, based in Oak Brook Illinois, is a Technology
Capitalist(tm) leveraging the value of existing systems and
infrastructure to produce business efficiencies, reduce costs, and open
new revenue streams. The Net Squad specializes in applying technology,
imagination and know-how to real-world business issues for businesses
who need technology guidance and manpower, startups requiring technology
leadership and investors requiring technical counsel. Additional
information about The Net Squad is available at www.thenetsquad.com.
About MySQL AB
MySQL AB develops, markets and supports the MySQL database server, the
world’s most popular open source database. The MySQL database, which is
free and available to everyone, has over three million users, including
major corporations such as Yahoo!, MP3.com (Vivendi Universal),
Motorola, NASA, Silicon Graphics, HP, Xerox, Cisco and Texas
Instruments. It is available under the open-source GNU General Public
License (GPL) or a non-GPL commercial license. MySQL is headquartered in
Uppsala, Sweden, but is a true virtual company, with employees
throughout the world. More information about MySQL is available at
www.MYSQL.com.
CONTACT: Alex Bratton — CEO, The Net Squad, 630-929-6601,
bratton@thenetsquad.com
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I installed Mandrake 8.2 on two laptops. Number one was an HP Pavilion N5340, a proven Linux workhorse I have used so long and hard that its case is now held together with duct tape. Mandrake 8.2 slipped onto this machine so smoothly that I did the installation during TV commercials. My Linksys 802.11b wireless card was detected automatically, and there is a cool little utility in the 8.2 installer that automatically goes online right away and looks for updates. There weren’t any I needed, but I’m sure there will be some later for people who wait a while to get their copies of 8.2, and they will be pleasantly surprised to find this little bit of niceness in their new Mandrake installation.
Laptop number two was a brand-new (sub-$1000) Compaq Presario 700 that came with Windows XP pre-installed. I tried over and over to get Mandrake 8.2 and Windows XP to play together nicely, but finally gave up and used Partition Commander to keep them at arm’s length during the install. Then I ran into a problem: a “hang” on boot every time it got to “initialize Eth0.” Eventually it would time out, but still frustrating. It seemed this laptop, unlike others I have owned, had a built-in NIC that actually worked with Linux, and when I configured my network for (I thought) my wireless card, this one got configured, too. Once I figured out how to turn off “Start at boot” for Eth0 in the network configuration utility, life was good. I had a nice, clean boot, nice-looking default KDE desktop (which my wife immediately started changing; this computer is for her, not me), and everything else anyone could want.
The Presario’s one remaining problem is that I have not been able to get an 802.11b card going at all in Windows XP. It looks like it’s working, but no data gets passed. The “Repair this network connection” utility in XP is not simple and straightforward like the network setup in Mandrake 8.2. I thought I ought to have XP and MSIE around for Web site design verification, but this wireless problem is frustrating; Windows XP is just too geeky for a simple person like me. I’ll probably end up running MSIE in Linux through one of Codeweavers‘ products for the moment, and will stay away from Windows until they come out with a simplified version that works with the common peripherals Mandrake sets up automatically.
Once I got tired of messing with Windows and turned back to good old Linux, I added OpenOffice and a few other applications to the basic Mandrake 8.2 installations on the two laptops, restored some backed-up data, and that was that: a wireless-networked, two-computer home office ready to take on the world, connected to the Internet through an SMC Barricade combination router and wireless access point, all set up in less than two hours of working time.
I am exceedingly satisfied with Mandrake 8.2. It is clean, smooth, and friendly. All the GUI utilities I have tried so far have done their jobs admirably. I have not had to look at a command line even once, although it’s certainly there for me any time I want to go beyond the GUI.
The bad part: None of this does Mandrake any good
The sad thing about all this is that even though I am a satisfied Mandrake “customer” I am not really a Mandrake customer this time around. I would have been happy to buy 8.2 CDs from Mandrake, either directly or through a local retail outlet, but they weren’t available when the “download edition” went onto the various Mandrake download mirrors. As I write this, Mandrakesoft is taking “pre-orders” for various version of v8.2 ranging in price from $55 (plus shipping, but without manuals or support) up to a package that includes the 8.2 ProSuite now and the 9.0 and 9.1 ProSuite versions when they eventually ship. And I see no mention of a $30-level “consumer” version, which Mandrake has generally offered in the past.
But why wait? If you (or a friend) don’t have a fast connection and CD burner handy, you can order Mandrake 8.2 “download edition” CDs right now from a whole bunch of places. I got mine from Linux Download or CDs, a one-man show in West Virginia. Why in the world does C.W., Linux Download or CD‘s owner, have Mandrake 8.2 CDs available for sale before MandrakeSoft itself? I mean, C.W. is a great guy, but shouldn’t MandrakeSoft have their own CDs available the moment they put a new release out for download, or at least have deals in place with C.W and others like him in various countries to put out “official download edition” CDs on a royalty basis as soon as the download version is on the mirrors? I’ll bet C.W. would love to work with MandrakeSoft, and so would many others.
I don’t feel guilty about getting “outside” CDs because I paid $60 to become a member of the Mandrake Linux Users Club, a way to support Mandrake that doesn’t really offer a lot in return. It says, right in the first paragraph on the MandrakeClub home page, “…your membership in Mandrake Club is, above all, a sign of your appreciation for the various services that are provided by MandrakeSoft free of charge for everyone.”
Aren’t I nice? If you downloaded Mandrake 8.2 for free and are using it, but you aren’t a member of the Mandrake Club, you should thank me for helping support your free software. I will not go into the silliness of a supposedly for profit company begging customers for money; Jack Bryar has already covered that.
There is nothing wrong with charging for GPL software. There is nothing wrong with making it easier for people to pay you to get your Linux distribution than to get it for free. A Mandrake Club that offered something like better/faster download servers or something else useful to dues-paying members would be fine, except please call it “Mandrake Premium,” and remove the charity appeal from the signup process.
There’s already an excellent software update utility built into the Mandrake Software Manager. Why in the world doesn’t it offer to connect me to Mandrake Premium for a nominal fee the first time I start it up? Where is the icon on the desktop offering Mandrake Premium? C’mon, MandrakeSoft, it’s okay to do this. It’s a perfectly legitimate business tactic. Those who don’t want to pay for the service don’t have to sign up for it. They can continue to hunt for Mandrake software on random mirrors, looking for one that’s not overloaded. Those of us who have a few bucks in our pockets — and work too many hours per day to have time to play server roulette — will happily pay. Five bucks per month is not a lot as long as we get something solid in return. Heck, give us $10 per month subscriptions that give us serious value and most of us will probably still bite, especially if you allow us to sign up for a minimum of three months ($30) instead of the current Mandrake Club requirement of an entire year ($60) all at once, which is a little steep for college students and others on tight budgets.
As a long-time Mandrake Linux user I would like to see MandrakeSoft start making smart business moves that would ensure the company’s survival. But if not, so it goes. ELX, Lycoris, Xandros, and others are all advancing rapidly. One day, probably within the next few months, at least one of them is going to have a distribution that is as polished, all-encompassing, and user-friendly as Mandrake, but backed by a saner business plan. When that day comes, I will seriously consider moving away from Mandrake. I’m sure many other loyal Mandrake users will, too.
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