From sivaraminguva at yahoo.com Wed Dec 20 05:32:19 2000 From: sivaraminguva at yahoo.com (sivaram inguva) Date: Fri Feb 10 19:19:33 2006 Subject: [Pipet Devel] (no subject) Message-ID: <20001220103219.11571.qmail@web618.mail.yahoo.com> please add me to the list __________________________________________________ Do You Yahoo!? Yahoo! Shopping - Thousands of Stores. Millions of Products. http://shopping.yahoo.com/ From jeff at bioinformatics.org Fri Dec 22 11:52:47 2000 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:19:34 2006 Subject: [Pipet Devel] ABOUT THIS LIST Message-ID: <3A4386DF.B64B2E44@bioinformatics.org> Locians, You are probably aware that the SOFTWARE DEVELOPMENT aspect of the Loci project has become the "Piper project". The program known as "Loci" has in fact become the "Build-Time Subsystem" of Piper. Some nine months ago we merged with two other projects, the Generalized Messaging System (GMS) and Overflow, and these form the "Run-Time Subsystem" of Piper. GMS and Overflow actually make up the missing components of the orginally planned Loci. I was considering keeping the name "Loci" and using it as the name of a test case of Piper, using a bioinformatics subject. One difference still exists between the goals of Loci and Piper: Loci was intended to be a bioinformatics tool, while Piper is general purpose. And many people were on this list because of the interesting discussions about bioinformatics, not because they cared about the program itself. As for this mailing list, I want to keep it. As I mention above, there may yet be a "Loci project". But, I understand that a lot of time has passed, and the discussions just aren't here anymore. You may also be interested in the software itself (Piper) and not the bioinformatics. In any case, if you'd like to unsubscribe from this list, please visit the subscription page for Loci: http://bioinformatics.org/mailman/listinfo/pipet-devel (you will need the password you got when you subscribed) If you would like to subscribe to the Piper list, please visit the subscription page for Piper: http://bioinformatics.org/mailman/listinfo/pipet-devel And, if you would like get some bionformatics news from the source of the original Loci project discussions, please join Bioinformatics.org and subscribe to BI.O News. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at yournews.nl Tue Dec 5 06:39:36 2000 From: jarl at yournews.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:39 2006 Subject: [Pipet Devel] [Fwd: ] Message-ID: <3A2CD3F8.C86B6884@yournews.nl> -------------- next part -------------- An embedded message was scrubbed... From: David Taniar Subject: no subject Date: Tue, 5 Dec 2000 15:17:59 +1100 (EST) Size: 11728 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/20001205/e38f45cd/attachment.mht From jeff at bioinformatics.org Tue Dec 5 19:03:38 2000 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:39 2006 Subject: [Pipet Devel] [Fwd: ] References: <3A2CD3F8.C86B6884@yournews.nl> Message-ID: <3A2D825A.8090E56B@bioinformatics.org> > C A L L F O R P A P E R S > ============================= > ___ __ __ __ > | | | | | | / | || Third International Symposium on > | | | | |--| | || DISTRIBUTED OBJECTS AND APPLICATIONS > _|_| |__| | | |__|| Rome, Italy, September 18-20, 2001 Man, I wish I could make that, but it's at the start of the fall semester. Jarl, that's probably a quick drive for you ;-) Do you want to submit a paper on Piper? Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jpetrone at cnri.reston.va.us Tue Dec 5 19:56:14 2000 From: jpetrone at cnri.reston.va.us (Jason Petrone) Date: Fri Feb 10 19:20:39 2006 Subject: [Pipet Devel] piper autoconf problems Message-ID: <20001205195614.C15491@cnri.reston.va.us> I'm trying to build piper from the most recent CVS snapshot, however I am having a few problems. In bl I am missing the macro AM_ACLOCAL_INCLUDE I am also getting the errors: ----------------------------------- /usr/local/bin/autoheader: /tmp/ah3FpmeH/traces.sh: line 10: unexpected EOF while looking for matching `'' /usr/local/bin/autoheader: /tmp/ah3FpmeH/traces.sh: line 12: syntax error: unexpected end of file automake: Makefile.am: required file `./AUTHORS' not found Running autoconf ... configure.in:40: /usr/bin/m4: Bad regular expression `[\([`""]\)]': Unmatched ) or \) configure.in:40: [[error: [[[backquotes and double quotes should not be backslashed in: [[configure: error: [Couldn't find the python config makefile. Maybe you are missing the development portion of the python installation]]]]]]] ]configure.in:40: /usr/bin/m4: Non-numeric argument to built-in `m4exit' ----------------------------------- I am using automake 1.4, autoconf 2.13, and have pyautomake installed. Any advice would be greatly appreciated. -jason From jeff at bioinformatics.org Tue Dec 5 19:59:40 2000 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:39 2006 Subject: [Pipet Devel] node pallet UI Message-ID: <3A2D8F7C.F3486159@bioinformatics.org> (LET ME KNOW IF SOMEONE WANTS TO PROGRAM THIS FOR US.) Pipers, One of the features for Pied/Piper (actually going back to the days of Loci and TULIP) that I have been tossing around for a while is a node pallet. Iconic/graphical programming environments typically have a window frame that is, in effect, a pallet of icons (nodes) that can be added to the program. I have considered adding this directly to the Pied/Piper UI, but I think it would clash with my "window in a window in a window" paradigm for Pied/Piper, and perhaps it would make Pied/Piper much bigger than it should be. So, I think we should make a separate UI. And that's cool, cuz that's what the DL is designed for. The node pallet should have search features and a clear indication of where the node is located. The best example of this is Napster and Gnutella. It would primarily be a clist (columned list) widget with a list of nodes. There should also be a way to eliminate or condense a list redundant nodes. Here is a rough sketch of what I am thinking about: +----------------------------------------------------------------------+ | NAME | LOCATION | CONNECTION SPEED | +----------------------------------------------------------------------+ | (+) * My Node | +----------------------------------------------------------------------+ | (+) * Your Node | +----------------------------------------------------------------------+ | (+) * Their Node | +----------------------------------------------------------------------+ Click on the (+) of "Your Node"... +----------------------------------------------------------------------+ | NAME | LOCATION | CONNECTION SPEED | +----------------------------------------------------------------------+ | (+) * My Node | +----------------------------------------------------------------------+ | (-) * Your Node | +----------------------------------------------------------------------+ | * Your Node | some.domain.com | T1 | +----------------------------------------------------------------------+ | * Your Node | some.other.domain.com | 56K | +----------------------------------------------------------------------+ | (+) * Their Node | +----------------------------------------------------------------------+ Lets say that the * represents and icon. Then, the user can drag and drop the icon onto some windowlet in Pied/Piper or some other UI compatible with the DnD protocols. DO WE HAVE ANY TAKERS? This would be done in GNOME/GTK. It doesn't have to be in Python, but I would prefer it. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From chapmanb at arches.uga.edu Tue Dec 5 22:41:56 2000 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] piper autoconf problems In-Reply-To: <20001205195614.C15491@cnri.reston.va.us> References: <20001205195614.C15491@cnri.reston.va.us> Message-ID: <14893.46468.347187.554542@taxus.athen1.ga.home.com> Hi Jason! [building from the CVS snapshot] > In bl I am missing the macro AM_ACLOCAL_INCLUDE You can just edit the configure.in in the subdirectory bl to remove this AM_ACLOCAL_INCLUDE line. I got rid of this a little while back (after the snapshot, unfortunately!) because it is a pain -- sometimes it seems to be AM_ACLOCAL_INCLUDE, sometimes it's AC_ACLOCAL_INCLUDE. Anyways, it isn't really needed, so you get rid of this line and this will hopefully make everything happy. > I am also getting the errors: > configure.in:40: [[error: [[[backquotes and double quotes should not be backslashed in: [[configure: error: [Couldn't find the python config makefile. Maybe you are > missing the development portion of the python installation]]]]]]] > ]configure.in:40: /usr/bin/m4: Non-numeric argument to built-in `m4exit' Hmmm, I've never really seen this, but it seems like the problem might be indicated in this last message. I think many linux systems come with python pre-installed, but do not include the headers and things, which you'll need to compile piper since it builds C++ extensions to python. You can check for the headers in some place like /usr/local/include/python2.0/ or /usr/include/python1.5 or something, depending on your version and the install prefix. If you don't have them I believe there is a python-dev rpm for linux systems that you'll need to install. If you do have them, then I'm kind of stumped why configure is complaining so much... Let me know if this helps. Brad From jarl at yournews.nl Wed Dec 6 03:23:14 2000 From: jarl at yournews.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] [Fwd: ] References: <3A2CD3F8.C86B6884@yournews.nl> <3A2D825A.8090E56B@bioinformatics.org> Message-ID: <3A2DF772.FD6EA7E5@yournews.nl> > > C A L L F O R P A P E R S > > ============================= > > ___ __ __ __ > > | | | | | | / | || Third International Symposium on > > | | | | |--| | || DISTRIBUTED OBJECTS AND APPLICATIONS > > _|_| |__| | | |__|| Rome, Italy, September 18-20, 2001 > > Man, I wish I could make that, but it's at the start of the fall semester. > Jarl, that's probably a quick drive for you ;-) Do you want to submit a paper > on Piper? I'm thinking about doing that, but I'm not sure. Maybe you can help me out writing it, because I dont have much experience presenting paper. bye, jarl From Alexandre.Fayolle at logilab.fr Wed Dec 6 03:33:11 2000 From: Alexandre.Fayolle at logilab.fr (Alexandre Fayolle) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] node pallet UI In-Reply-To: <3A2D8F7C.F3486159@bioinformatics.org> Message-ID: On Wed, 6 Dec 2000, J.W. Bizzaro wrote: > would primarily be a clist (columned list) widget with a list of nodes. There If you're thinking of GTK+ widgets, what you describe is rather a CTree. > Lets say that the * represents and icon. Then, the user can drag and drop the > icon onto some windowlet in Pied/Piper or some other UI compatible with the > DnD protocols. > > DO WE HAVE ANY TAKERS? This would be done in GNOME/GTK. It doesn't have to > be in Python, but I would prefer it. In case someone wants to tackle this (I personnaly do not have enough spare time), he may want to check the Narval gui which has a similar dialog (CTree, drag and drop) as a base for the Piper implementation. It is written in pyGtk. I can provide some help with code comprehension if required (ask me directly or on the piper ML). Alexandre Fayolle -- http://www.logilab.com Narval is the first software agent available as free software (GPL). LOGILAB, Paris (France). From valj01 at gel.usherb.ca Thu Dec 7 22:20:16 2000 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] Overflow 0.3.0 released Message-ID: <3A305370.6EB962AE@gel.usherb.ca> Hello everybody, I just released version 0.3.0 of Overflow (aka Open Mind Speech). There has been lots of (architectural) changes recently, but things are now stabilizing again. There has been lots of changes since version 0.2 and you are all encouraged to upgrade. One of the most noticeable changes is that it should now compile with egcs 1.1.2. Jean-Marc RELEASE NOTES: This new release includes a number of bug fixes, as well as optimizations that reduce the global overhead of using the system (vs. using plain C/C++). Overflow should now be more portable and ANSI C++ compilant. Last but not least, an important architectural change occured for all frame-based operations. -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jpetrone at cnri.reston.va.us Fri Dec 8 15:30:28 2000 From: jpetrone at cnri.reston.va.us (Jason Petrone) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] piper autoconf problems In-Reply-To: <14893.46468.347187.554542@taxus.athen1.ga.home.com>; from chapmanb@arches.uga.edu on Tue, Dec 05, 2000 at 10:41:56PM -0500 References: <20001205195614.C15491@cnri.reston.va.us> <14893.46468.347187.554542@taxus.athen1.ga.home.com> Message-ID: <20001208153028.A13311@cnri.reston.va.us> On Tue, Dec 05, 2000 at 10:41:56PM -0500, Brad Chapman wrote: > > I am also getting the errors: > > configure.in:40: [[error: [[[backquotes and double quotes should not be backslashed in: [[configure: error: [Couldn't find the python config makefile. Maybe you are > > missing the development portion of the python installation]]]]]]] > > ]configure.in:40: /usr/bin/m4: Non-numeric argument to built-in `m4exit' > > Hmmm, I've never really seen this, but it seems like the problem might > be indicated in this last message. I think many linux systems come > with python pre-installed, but do not include the headers and things, > which you'll need to compile piper since it builds C++ extensions to > python. > > Let me know if this helps. I have the python headers... The problem was that I was using autoconf-2.14. I switched back to 2.13 and it worked fine. Might want to put a note about that in the build instructions? -jason From jeff at bioinformatics.org Fri Dec 8 16:57:31 2000 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] piper autoconf problems References: <20001205195614.C15491@cnri.reston.va.us> <14893.46468.347187.554542@taxus.athen1.ga.home.com> <20001208153028.A13311@cnri.reston.va.us> Message-ID: <3A31594B.7C5EAAE9@bioinformatics.org> Jason Petrone wrote: > > The problem was that I was using autoconf-2.14. I switched back to 2.13 and > it worked fine. Hmmm. Brad, what do we need to get it to work with 2.14? > Might want to put a note about that in the build instructions? Will do. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jeff at bioinformatics.org Fri Dec 8 17:18:46 2000 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] node pallet UI References: Message-ID: <3A315E46.FA051113@bioinformatics.org> Alexandre Fayolle wrote: > > If you're thinking of GTK+ widgets, what you describe is rather a CTree. Right :-) > In case someone wants to tackle this (I personnaly do not have enough > spare time), he may want to check the Narval gui which has a similar > dialog (CTree, drag and drop) as a base for the Piper implementation. It > is written in pyGtk. I can provide some help with code comprehension if > required (ask me directly or on the piper ML). Thanks, that's good to know. The other UI's for Piper are in pyGtk too. BTW, the Narval GUI is GPL'd? Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at casema.net Fri Dec 8 21:57:52 2000 From: jarl at casema.net (jarl van katwijk) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] piper autoconf problems References: <20001205195614.C15491@cnri.reston.va.us> <14893.46468.347187.554542@taxus.athen1.ga.home.com> <20001208153028.A13311@cnri.reston.va.us> <3A31594B.7C5EAAE9@bioinformatics.org> Message-ID: <3A319FB0.10603@casema.net> > > >> The problem was that I was using autoconf-2.14. I switched back to 2.13 and >> it worked fine. > > Hmmm. Brad, what do we need to get it to work with 2.14? 2.13 still is the latest official release : /> I'll check again, but why does the configure.in file need autoconf 2.14 />/ when 2.13 is the most recent on ftp.gnu.org? / Well, as I said, it's an unreleased CVS snapshot being used. I forget the exact reasons for choosing that over the released version. All the necessary tools are available from ftp.swox.com for anyone who needs or wants them. See the GMP doc/configuration file too. jarl From jeff at bioinformatics.org Mon Dec 11 03:50:50 2000 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] automagic piper and overflow snapshots Message-ID: <3A34956A.9512A4E1@bioinformatics.org> I set up a script to automatically generate tarball snapshots of the Piper and Overflow modules in CVS (note that Overflow's CVS is at SourceForge.net while Piper's is at Bioinformatics.org). They are both generated by 3:30 AM EST (Is that 08:30 GMT?) and can be found here: ftp://bioinformatics.org/pub/piper/CVS Note that you will need automake/autoconf (read INSTALL) to build these. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From chapmanb at arches.uga.edu Fri Dec 15 16:11:16 2000 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] Re: Booting and shutting down piper In-Reply-To: <3A3A4673.BFB41895@bioinformatics.org> References: <3A35FD84.3030009@yournews.nl> <3A37120A.9B37AF7D@bioinformatics.org> <3A37550A.6000508@yournews.nl> <3A39FD42.8A01A941@bioinformatics.org> <3A39FFD4.84D44BE6@yournews.nl> <3A3A0465.4E1CF250@bioinformatics.org> <3A3A0F68.2052827E@yournews.nl> <3A3A14B5.4CBA924B@bioinformatics.org> <3A3A193E.A6940371@yournews.nl> <3A3A3DC2.2BC602B@bioinformatics.org> <3A3A40DE.276E9F33@yournews.nl> <3A3A4673.BFB41895@bioinformatics.org> Message-ID: <14906.35060.773203.260273@taxus.athen1.ga.home.com> [moving this to the list, since I'm confused by the threading of the message -- then I also don't have to worry about forwarding to everyone; apologies to list people, since this will seem disjoint] Hey guys; Holy crap -- I got back home to get the unexpected surprise of having 100 messages about Booting and Shutting down Piper. I think I sort of followed what is going on, but not really -- too many messages :-). Anyways, here is how things work right now with the UI and DL with a shutdown. The UI is easy to shut down -- it is shut down by the user. Right? This is what the 'quit' menu item is for :-). Anyways, this then shuts itself down, so that is taken care of. The DL keeps track of UIs (remember, it can have multiple user interfaces) using a ping function defined in the UIL2DL idl file: interface UilClient { readonly attribute string username; readonly attribute string password; void ping(); }; The client (UI) implements the ping function (which only needs to return when called), and the server (the DL) calls it every 20 seconds or so. If the ping fails to return (with a CORBA_COMM error) then the DL removes the connection with this UI and cleans up after it. When the DL has no UIs left (when they either shut down normally or fail this ping() test) then the DL then shuts itself down. I know that the ping function is not that fancy (the C++ book by Henning and Vinoski has a much nicer "evictor" pattern that it describes) but it is simple and seems to work okay so far. I borrowed this idea from the Berlin project, which uses something similar (at least they did when I was browsing their code). Anyways, in my opinion this works well, and should be extended to the BL and PL. I think it is better then storing PIDs and then calling kill for a couple of reasons: 1. Just as easy to implement (very important :-). 2. Works when the different layers are not on the same machine. 3. Handles more complicated client/server interactions then just one-to-one. Of course, you guys are coding it, so feel free to do whatever you want. This is just my opinion (which you did ask for :-). Let me know if this doesn't make any sense, or if you need me to answer other questions -- I got a little lost in the flood of e-mails and am waaaay behind on my e-mail in general. Also, if you need to talk to me right away ever I'm always trying to watch ICQ if I at my computer working, so feel free to drop me a line and bug me to answer a question right away :-). Brad From jarl at casema.net Sun Dec 17 20:07:11 2000 From: jarl at casema.net (jarl van katwijk) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] Re: Booting and shutting down piper References: <3A35FD84.3030009@yournews.nl> <3A37120A.9B37AF7D@bioinformatics.org> <3A37550A.6000508@yournews.nl> <3A39FD42.8A01A941@bioinformatics.org> <3A39FFD4.84D44BE6@yournews.nl> <3A3A0465.4E1CF250@bioinformatics.org> <3A3A0F68.2052827E@yournews.nl> <3A3A14B5.4CBA924B@bioinformatics.org> <3A3A193E.A6940371@yournews.nl> <3A3A3DC2.2BC602B@bioinformatics.org> <3A3A40DE.276E9F33@yournews.nl> <3A3A4673.BFB41895@bioinformatics.org> <14906.35060.773203.260273@taxus.athen1.ga.home.com> Message-ID: <3A3D633F.8040905@casema.net> > Holy crap -- I got back home to get the unexpected surprise of > having 100 messages about Booting and Shutting down Piper. I think I > sort of followed what is going on, but not really -- too many messages > :-). Past week I've been finishing the last TODO's and as a result the current cvs version more and more looks like something useble. This is what's done : - connected all layers to eath other, the UIL-DL-BL-PL chain. - implemented a bootup and shutdown procedure. I agree with your commented about this procedure being far for ideal, the current stuff is just for testing, and to have something in place. An issue to remind when we descuss todo's for later milestones. > I know that the ping function is not that fancy (the C++ book by > Henning and Vinoski has a much nicer "evictor" pattern that it > describes) but it is simple and seems to work okay so far. I borrowed > this idea from the Berlin project, which uses something similar (at > least they did when I was browsing their code). Cvs code has the DL do a 'killall BL', very ugly and need to be replaced by corba ping() and shutdown() functions. The BL->PL procedure does already has those corba features. I'll try to expand the DL sources.. dont know if I can handle that much Python. The pid files are used for 'killing when all else fails'. Like you said, this wont work on a distributed setup and needs enhancements :) Also, pid files are used to detect crashes during a restart. > Let me know if this doesn't make any sense, or if you need me to > answer other questions -- I got a little lost in the flood of > e-mails and am waaaay behind on my e-mail in general. Also, if > you need to talk to me right away ever I'm always trying to watch ICQ > if I at my computer working, so feel free to drop me a line and bug me > to answer a question right away :-). Brad: Have a look at current cvs. Up- and downloading between the UIL and PL is all working. But there're also much warnings and errors I cant understand. During commiting of a nodes network to the PL many of them scroll by. Jarl From valj01 at gel.usherb.ca Sun Dec 17 20:56:41 2000 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] Re: Booting and shutting down piper References: <3A35FD84.3030009@yournews.nl> <3A37120A.9B37AF7D@bioinformatics.org> <3A37550A.6000508@yournews.nl> <3A39FD42.8A01A941@bioinformatics.org> <3A39FFD4.84D44BE6@yournews.nl> <3A3A0465.4E1CF250@bioinformatics.org> <3A3A0F68.2052827E@yournews.nl> <3A3A14B5.4CBA924B@bioinformatics.org> <3A3A193E.A6940371@yournews.nl> <3A3A3DC2.2BC602B@bioinformatics.org> <3A3A40DE.276E9F33@yournews.nl> <3A3A4673.BFB41895@bioinformatics.org> <14906.35060.773203.260273@taxus.athen1.ga.home.com> Message-ID: <3A3D6ED9.1BF6F6B6@gel.usherb.ca> > Hey guys; > Holy crap -- I got back home to get the unexpected surprise of > having 100 messages about Booting and Shutting down Piper. I think I > sort of followed what is going on, but not really -- too many messages > :-). Same for me, I just got back from one week at the beach in Martinique, which is why you didn't hear from me (wow, no e-mail reading for a full week!). I didn't quite follow the whole discussion (not very familiar with this part of Piper), can anyone summerize for me what's going on/tell me where I should get involved in this discussion? Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jarl at yournews.nl Mon Dec 18 07:50:49 2000 From: jarl at yournews.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] After the pilot Message-ID: <3A3E0829.5000903@yournews.nl> Hi All, I added a page to the Piper Wiki where we can exhaust the idears and TODO's for after the pilot. So everything you would like to add to Piper or feel is missing and is outside the very basic scope of the pilot, put it on http://www.bioinformatics.org/piperwiki/moin.cgi/AfterThePilot bye, jarl From jeff at bioinformatics.org Tue Dec 19 08:58:36 2000 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] pipet-devel mailing list Message-ID: <3A3F698C.5980EA46@bioinformatics.org> Pipers, We created a mailing list specifically and exclusively for the actual Piper developers. This is to keep the traffic down on the piper-general (pipet-devel) list. At this point in the development of the project, there is a need for separate user/lurker and developer lists, because not everyone on piper-general wants to get 50 messages in one day about some bug we're trying to fix :-) But note that, just because the pipet-devel list is only for developers, it DOESN't mean that development is closed and private. In fact, the archives are public, and there is no restriction on posting. If at some point you are ready to contribute code to Piper, you will be added to pipet-devel :-) Here's hoping the list will be large someday. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jeff at bioinformatics.org Tue Dec 19 09:23:49 2000 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] Re: Booting and shutting down piper References: <3A35FD84.3030009@yournews.nl> <3A37120A.9B37AF7D@bioinformatics.org> <3A37550A.6000508@yournews.nl> <3A39FD42.8A01A941@bioinformatics.org> <3A39FFD4.84D44BE6@yournews.nl> <3A3A0465.4E1CF250@bioinformatics.org> <3A3A0F68.2052827E@yournews.nl> <3A3A14B5.4CBA924B@bioinformatics.org> <3A3A193E.A6940371@yournews.nl> <3A3A3DC2.2BC602B@bioinformatics.org> <3A3A40DE.276E9F33@yournews.nl> <3A3A4673.BFB41895@bioinformatics.org> <14906.35060.773203.260273@taxus.athen1.ga.home.com> <3A3D6ED9.1BF6F6B6@gel.usherb.ca> Message-ID: <3A3F6F75.D87CB1B5@bioinformatics.org> Jean-Marc Valin wrote: > > Same for me, I just got back from one week at the beach in Martinique, which is > why you didn't hear from me (wow, no e-mail reading for a full week!). I didn't > quite follow the whole discussion (not very familiar with this part of Piper), > can anyone summerize for me what's going on/tell me where I should get involved > in this discussion? I'll try to explain....... Jarl has been looking to implement a system-wide (covering all the layers of Piper) shutdown and recovery mechanism. The approach Jarl and I have settled on for the time being (it's not the best, but it will work for the pilot), is to put the PID's of each Piper process in the user's $HOME/piper_info/pids directory, then from UIL->DL->BL->PL (top to bottom) send a "kill " (not "kill -9") to the next lower layer. This will allow each layer to begin its own shutdown, and that should be that (unless a layer can't die). The other benefit of storing the PID's is to determine what is running, or what has crashed, should things be re-started. I was a bit confused about what Jarl wanted me to do in the UIL and DL, because I knew that Brad had already developed a shutdown/crash recovery mechanism. Brad explained his mechanism in a recent message and suggested that Jarl use the same approach for the other layers (all layers). My question at this point is for Jarl: Do you understand what Brad is proposing for the whole system (that which is implemented in the UIL and DL)? What do you think? Jarl also brought up a problem with sending network information (an XML "document") from the UIL to the PL. He has been getting errors from the PL. Jarl, can you send copies of those errors to this list so that Brad and Jean-Marc can see them? Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at planetX.bastards.nl Tue Dec 19 09:31:39 2000 From: jarl at planetX.bastards.nl (jarl) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] Re: Booting and shutting down piper In-Reply-To: <3A3F6F75.D87CB1B5@bioinformatics.org>; from jeff@bioinformatics.org on Tue, Dec 19, 2000 at 02:23:49PM +0000 References: <3A3A0465.4E1CF250@bioinformatics.org> <3A3A0F68.2052827E@yournews.nl> <3A3A14B5.4CBA924B@bioinformatics.org> <3A3A193E.A6940371@yournews.nl> <3A3A3DC2.2BC602B@bioinformatics.org> <3A3A40DE.276E9F33@yournews.nl> <3A3A4673.BFB41895@bioinformatics.org> <14906.35060.773203.260273@taxus.athen1.ga.home.com> <3A3D6ED9.1BF6F6B6@gel.usherb.ca> <3A3F6F75.D87CB1B5@bioinformatics.org> Message-ID: <20001219153139.A30413@planetx.bastards.nl> > > The approach Jarl and I have settled on for the time being (it's not the best, > but it will work for the pilot), is to put the PID's of each Piper process in > the user's $HOME/piper_info/pids directory, then from UIL->DL->BL->PL (top to > bottom) send a "kill " (not "kill -9") to the next lower layer. This > will allow each layer to begin its own shutdown, and that should be that > (unless a layer can't die). > > The other benefit of storing the PID's is to determine what is running, or > what has crashed, should things be re-started. > > I was a bit confused about what Jarl wanted me to do in the UIL and DL, > because I knew that Brad had already developed a shutdown/crash recovery > mechanism. Brad explained his mechanism in a recent message and suggested > that Jarl use the same approach for the other layers (all layers). > > My question at this point is for Jarl: Do you understand what Brad is > proposing for the whole system (that which is implemented in the UIL and DL)? > What do you think? I understand and I agree. The meganism between the BL and PL already IS like Brad proposed, and in my reply on Brads email I asked him to point me out where I should work on in the Python code to add such a meganism to the DL->BL communications. Also I must add that this corbatized pinging is not enough, you cant tell if a layer is crashed or termintated correctly. > > Jarl also brought up a problem with sending network information (an XML > "document") from the UIL to the PL. He has been getting errors from the PL. > Jarl, can you send copies of those errors to this list so that Brad and > Jean-Marc can see them? > I could, but I would like to see JeanMarc and Brad give it a try themselfs, because I dont really know what is an error and what is not. bye, jarl From jeff at bioinformatics.org Tue Dec 19 10:08:18 2000 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] Re: Booting and shutting down piper References: <3A3A0465.4E1CF250@bioinformatics.org> <3A3A0F68.2052827E@yournews.nl> <3A3A14B5.4CBA924B@bioinformatics.org> <3A3A193E.A6940371@yournews.nl> <3A3A3DC2.2BC602B@bioinformatics.org> <3A3A40DE.276E9F33@yournews.nl> <3A3A4673.BFB41895@bioinformatics.org> <14906.35060.773203.260273@taxus.athen1.ga.home.com> <3A3D6ED9.1BF6F6B6@gel.usherb.ca> <3A3F6F75.D87CB1B5@bioinformatics.org> <20001219153139.A30413@planetx.bastards.nl> Message-ID: <3A3F79E2.1CA768BE@bioinformatics.org> jarl wrote: > > > My question at this point is for Jarl: Do you understand what Brad is > > proposing for the whole system (that which is implemented in the UIL and DL)? > > What do you think? > I understand and I agree. The meganism between the BL and PL already IS > like Brad proposed, and in my reply on Brads email I asked him to point > me out where I should work on in the Python code to add such a meganism > to the DL->BL communications. Okay, I didn't see that message before. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein --