From jeff at bioinformatics.org Thu Aug 2 22:16:18 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:52 2006 Subject: [Pipet Devel] problem found Message-ID: <3B6A0972.CBA74B65@bioinformatics.org> I found the source of the problem I had where the DL2BL IOR wasn't being read. It turns out that it IS a timing problem. On line 71 of runpiper.py, the IOR must be getting purged (as if old) after it is created: os.system("rm ~/piper_info/ior/*") So, I commented it out, and I get the messages I should (maybe not) get. Here is the output with a pre-Copenhagen BL: ---------------------------------------------------- Starting processing layer... Starting brokering layer... Starting definition layer... Starting pied... Message: wrote IOR file /home/jeff/piper_info/ior/bl2pl.ior Piper BL 0.5.0pre1 Thu Aug 2 22:05:52 2001 | 1 | Info | Accepted DL, created area 1 Thu Aug 2 22:05:52 2001 | 2 | Debug | Engine locked (from resource::node_id_lock) Thu Aug 2 22:05:52 2001 | 3 | Debug | Engine unlocked (from resource::node_id_lock) node_new: node pipeLine_NODE got allowedFilter Thu Aug 2 22:05:52 2001 | 4 | Debug | Engine locked (from resource::data_id_lock) Thu Aug 2 22:05:52 2001 | 5 | Debug | Engine unlocked (from resource::data_id_lock) Thu Aug 2 22:05:52 2001 | 6 | Info | Registered node pipeLine_NODE to area 1 Thu Aug 2 22:05:52 2001 | 7 | Warning | Node pipeLine_NODE failed to initialise Thu Aug 2 22:05:52 2001 | 8 | Debug | Engine locked (from resource::node_id_lock) Thu Aug 2 22:05:52 2001 | 9 | Debug | Engine unlocked (from resource::node_id_lock) node_new: node visual_NODE got allowedFilter Thu Aug 2 22:05:52 2001 | 10 | Debug | Engine locked (from resource::data_id_lock) Thu Aug 2 22:05:52 2001 | 11 | Debug | Engine unlocked (from resource::data_id_lock) Thu Aug 2 22:05:52 2001 | 12 | Info | Registered node visual_NODE to area 1Thu Aug 2 22:05:52 2001 | 13 | Warning | Node visual_NODE failed to initialiseThu Aug 2 22:05:52 2001 | 14 | Debug | Engine locked (from resource::node_id_lock) Thu Aug 2 22:05:52 2001 | 15 | Debug | Engine unlocked (from resource::node_id_lock) Thu Aug 2 22:05:52 2001 | 16 | Warning | Can not initialize a node (unfinished node) with NULL function(s) node_new: node unfinished node got allowedFilter Thu Aug 2 22:05:52 2001 | 17 | Debug | Engine locked (from resource::data_id_lock) Thu Aug 2 22:05:52 2001 | 18 | Debug | Engine unlocked (from resource::data_id_lock) Thu Aug 2 22:05:52 2001 | 19 | Debug | Engine locked (from legacy::load_plugin) Thu Aug 2 22:05:52 2001 | 20 | Debug | Registered sensor_BL Thu Aug 2 22:05:52 2001 | 21 | Info | Loading plugin /usr/lib/libplugin_sensor_BL.so... Thu Aug 2 22:05:52 2001 | 22 | Debug | Engine unlocked (from legacy::load_plugin) Thu Aug 2 22:05:52 2001 | 23 | Info | Registered node BL plugin sensor to area 1 Thu Aug 2 22:05:52 2001 | 24 | Message | Node BL plugin sensor initialised Thu Aug 2 22:05:52 2001 | 25 | Debug | Engine locked (from resource::node_id_lock) Thu Aug 2 22:05:52 2001 | 26 | Debug | Engine unlocked (from resource::node_id_lock) node_new: node BL plugin sensor Collector got allowedFilter Collects and handles BL XML streams Thu Aug 2 22:05:52 2001 | 27 | Debug | Engine locked (from resource::data_id_lock) Thu Aug 2 22:05:52 2001 | 28 | Debug | Engine unlocked (from resource::data_id_lock) Thu Aug 2 22:05:52 2001 | 29 | Info | Registered node BL plugin sensor Collector to area 1 Thu Aug 2 22:05:52 2001 | 30 | Warning | Node BL plugin sensor Collector failed to initialise Thu Aug 2 22:05:52 2001 | 31 | Debug | Engine locked (from resource::node_id_lock) Thu Aug 2 22:05:52 2001 | 32 | Debug | Engine unlocked (from resource::node_id_lock) Thu Aug 2 22:05:52 2001 | 33 | Warning | Can not initialize a node (unfinished node) with NULL function(s) node_new: node unfinished node got allowedFilter Thu Aug 2 22:05:52 2001 | 34 | Debug | Engine locked (from resource::data_id_lock) Thu Aug 2 22:05:52 2001 | 35 | Debug | Engine unlocked (from resource::data_id_lock) Thu Aug 2 22:05:52 2001 | 36 | Debug | Engine locked (from legacy::load_plugin) Thu Aug 2 22:05:52 2001 | 37 | Debug | Registered sensor_DL Default location of the DL2BL IOR file: /home/jeff/piper_info/ior/dl2bl.ior Getting document... Aborted -------------------------------------- I'll have to try the latest BL. What do you think Jarl? Is it ready? This is why we need to make the layers/components runable stand-alone. I'll try to get PiedPiper to run stand-alone by looping all signals back, sort of a debug mode. It will let me work on it without some of the other components being functional. Jeff From jeff at bioinformatics.org Fri Aug 3 17:19:33 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:53 2006 Subject: [Pipet Devel] [Fwd: Zope and the PiperNet] Message-ID: <3B6B1565.97F557A9@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: Michael McLay Subject: Re: Zope and the PiperNet Date: Fri, 3 Aug 2001 03:31:33 -0400 Size: 8404 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/20010803/2521833b/attachment.mht From jeff at bioinformatics.org Fri Aug 3 17:22:14 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:53 2006 Subject: [Pipet Devel] Re: Zope and the PiperNet References: <3B688FAF.DE5E9E14@bioinformatics.org> <01080303313306.04329@fermi.eeel.nist.gov> Message-ID: <3B6B1606.27B87A2A@bioinformatics.org> Michael and Tres, The way Piper is structured, as you may have seen in our documentation, Zope may best work as backend-ware, making use of Piper as middle-ware (and frontend-ware). Programs and systems that fill this role in Piper are called "processors", since they process the data/workflow. Currently, the program Overflow, a high-speed but localized dataflow system, is our reference processor, and one of Piper's initial tasks is to distribute and interconnect Overflow instances around the Internet. But, as I said, Piper is being developed to use all sorts of programs or systems as processors. Having spoken with Jarl a bit about authentication, it seems that processors or their plugins/wrappers will have to play some role in authentication. So, it is good that Zope has its own way of doing that. One of our tasks will be to develop an authentication scheme that will work with Zope and many other processors. But, I am not the security expert here. I'll leave further discussions to Jarl. However, regarding BEEP and peer-to-peer communications, if Zope is to work on the PiperNet, the program must leave network management to Piper. So, we can use BEEP, but Zope would have to be agnostic to whatever we're using. IOW, Zope would not use BEEP directly. Again, this is Jarl's area. Regarding the GUI and how nodes and networks are represented graphically, which *IS* my area, the Piper GUI has been forged by repeatedly asking how "such and such a task" can be represented this way. We have something that we believe is very flexible. It will be interesting to see what requirements Zope may have, and it should result in an even better GUI. I'm open to ideas and look forward to working with Zope in this area. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Tue Aug 7 02:46:13 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:53 2006 Subject: [Pipet Devel] FAQ - DBDOM Message-ID: <3B6F8EB5.5272ECC0@bioinformatics.org> http://dbdom.sourceforge.net/ Jeff From jeff at bioinformatics.org Wed Aug 22 21:42:54 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:53 2006 Subject: [Pipet Devel] Mark Mitchell - GCC 3.0.1 Released Message-ID: <3B845F9E.DD75757F@bioinformatics.org> http://gcc.gnu.org/ml/gcc/2001-08/msg00973.html Jeff From jeff at bioinformatics.org Sat Aug 25 06:59:15 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:53 2006 Subject: [Pipet Devel] [Fwd: pipet-devel subscription] Message-ID: <3B878503.588150DD@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: "mail-list client" Subject: RE: pipet-devel subscription Date: Sat, 25 Aug 2001 05:38:55 +0100 Size: 1912 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/20010825/08fb862a/attachment.mht From jeff at bioinformatics.org Sat Aug 25 07:10:09 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:53 2006 Subject: [Pipet Devel] Re: pipet-devel subscription References: Message-ID: <3B878791.92DA4E4E@bioinformatics.org> mail-list client wrote: > > I'm really interested in joining the project with C++ work. > Please feel free to make any questions. Great to hear, Miguel! I just subscribed you to the pipet-devel list. We have a lot of C++ coding to do, and any help will be appreciated. Are you familiar with DOM and CORBA? We are planning on using the Xerces DOM libs: http://xml.apache.org/xerces-c/ and we are currently using omniORB: http://www.uk.research.att.com/omniORB/ We've been communicating mostly through chat since our meeting in Copenhagen. Jarl (bstard) is usually on if I'm not, and he's the infrastructure expert. irc.openprojects.net #pipernet What are your interests? Are you interested more in infrastructure or user interfaces? My area is UIs. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Wed Aug 29 02:04:03 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:53 2006 Subject: [Pipet Devel] compiling 0.0.2 Message-ID: <3B8C85D3.A6BED3A7@bioinformatics.org> I got stuck here: ------------------------------------------- Making all in interfaces gmake[5]: Entering directory `/usr/home/jeff/piper-2001/piper-0.0.2-test1/piper/dl/vflow/interfaces' c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I/usr/include/gnome-xml -I/usr/local/include/python1.5 -I/usr/local/lib/python1.5/config -fPIC -g -O2 `overflow-config libflow --cflags` -g -O2 -c mod_vflow_wrap.c /bin/sh: overflow-config: command not found ------------------------------------------- overflow-config is in the Overflow source dir, *but* the flag --with-overflow=/opt/overflow points to the *installation* dir. They're not the same on my system. Is this something that was changed recently? I was able to compile recent snapshots. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From valj01 at gel.usherb.ca Wed Aug 29 22:49:21 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:53 2006 Subject: [Pipet Devel] compiling 0.0.2 References: <3B8C85D3.A6BED3A7@bioinformatics.org> Message-ID: <3B8DA9B1.CD7361C8@gel.usherb.ca> > overflow-config is in the Overflow source dir, *but* the flag > --with-overflow=/opt/overflow points to the *installation* dir. They're not > the same on my system. > > Is this something that was changed recently? I was able to compile recent > snapshots. overflow-config just doesn't seem to be in your PATH. Check you Overflow installation, that should work. Jean-Marc