From jarl at xs4all.nl Sat Mar 3 19:28:25 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] dl2bl file not written References: <3A99DFA0.495E1198@bioinformatics.org> <3A9A2847.8DFBAE12@xs4all.nl> <3A9A1168.864178C9@bioinformatics.org> <3A9A68A3.79E12CA0@locusdialogue.com> <3A9A803A.55492964@bioinformatics.org> <3A9CEC76.7160B749@xs4all.nl> <15004.54599.870902.94467@taxus.athen1.ga.home.com> Message-ID: <3AA18C29.D75E217F@xs4all.nl> > > Could you check > > this out, I tried to find the Python code for a delay, but couldn't find > > any. > > $ python > Python 2.1a2 (#1, Feb 3 2001, 15:37:56) > [GCC 2.95.2 19991024 (release/franzo)] on linux2 > Type "copyright", "credits" or "license" for more information. > >>> import time > >>> time.sleep(5) > > This'll delay for 5 seconds, so you can use this to build in a waiting > time if you need to. Hope this helps. > Thnx Brad, I'll have a look tomorrow. I got this email very late.. seems my fetchmail was confused. jarl From jarl at xs4all.nl Sat Mar 3 19:36:11 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] dl2bl file not written References: <3A99DFA0.495E1198@bioinformatics.org> <3A9A2847.8DFBAE12@xs4all.nl> <3A9A1168.864178C9@bioinformatics.org> <3A9A68A3.79E12CA0@locusdialogue.com> <3A9A803A.55492964@bioinformatics.org> <3A9CEC76.7160B749@xs4all.nl> <3A9CE09B.EF08663C@bioinformatics.org> Message-ID: <3AA18DFB.1B50A08A@xs4all.nl> "J.W. Bizzaro" wrote: > > Jarl van Katwijk wrote: > > > > I think the problem is that ./runpiper executes the BL too soon after > > the PL is still booting up. If you know how to build in a delay before > > the execution of the BL the problem is probably gone. Could you check > > this out, I tried to find the Python code for a delay, but couldn't find > > any. > > For a better, permanent solution, can we at some point have the PL (or each > layer) "say" that they are ready? Can we have the PL place its PID in a file > somewhere? The PL does do a pid writeout, to ~/piper_info/pids/PL.pid.{pidnr.} The exsistence of this pid file does not garantee that the PL has fully initialized. I agree this needs to be changed. I'll recode the dl,bl and pl so that they only do a pid writeout after they are ready. > > I just think that an arbitrary delay might not always work. What if the PL is > on a slower computer and requires more time than N seconds? And, on faster > computers the PL might start much quicker than N seconds. Yes, you're right. Will be fixed. I hope to have some time to do some browsing, probably there're must better meganisms around. jarl From jeff at bioinformatics.org Sun Mar 11 18:44:21 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] overflow compile problems Message-ID: <3AAC0DD5.1A8B3806@bioinformatics.org> I upgraded to gcc 2.96 and glibc 2.2, and I still get some errors compiling from the latest source: ---------------------------------------- make[3]: Entering directory `/usr/src/Overflow/Overflow/vflow/src' /bin/sh ../libtool --mode=link c++ -g -O2 -L/usr/lib -o vflow main.o Probe.o TextProbe.o PlotProbe.o canvas-background.o GUINode.o GUINetwork.o GUIDocument.o GUITerminal.o GUILink.o GUINodeParameters.o GUINetTerminal.o GUINetPopup.o GRunContext.o -rdynamic -L/usr/lib -L/usr/X11R6/lib -rdynamic -lgnomeui -lart_lgpl -lgdk_imlib -lSM -lICE -lgtk -lgdk -lgmodule -lXi -lXext -lX11 -lgnome -lgnomesupport -lesd -laudiofile -lm -ldb -lglib -ldl -L/usr/lib -lxml -lz -L/usr/lib -lgthread -lglib -lpthread ../../data-flow/src/libflow.la -lrfftw -lfftw -lpthread c++ -g -O2 -L/usr/lib -o .libs/vflow main.o Probe.o TextProbe.o PlotProbe.o canvas-background.o GUINode.o GUINetwork.o GUIDocument.o GUITerminal.o GUILink.o GUINodeParameters.o GUINetTerminal.o GUINetPopup.o GRunContext.o -rdynamic -L/usr/lib -L/usr/X11R6/lib -rdynamic -lgnomeui -lart_lgpl -lgdk_imlib -lSM -lICE -lgtk -lgdk -lgmodule -lXi -lXext -lX11 -lgnome -lgnomesupport -lesd -laudiofile -lm -ldb -lglib -ldl -L/usr/lib -lxml -lz -L/usr/lib -lgthread -lglib -lpthread ../../data-flow/src/.libs/libflow.so -lpthread -ldl -lm -lrfftw -lfftw -lpthread -Wl,--rpath -Wl,/opt/overflow/lib Probe.o: In function `_Rb_tree, __default_alloc_template >, pair, __default_alloc_template > const, pair, bool> >, _Select1st, __default_alloc_template > const, pair, bool> > >, less, __default_alloc_template > >, allocator, bool> > >::_M_copy(_Rb_tree_node, __default_alloc_template > const, pair, bool> > > *, _Rb_tree_node, __default_alloc_template > const, pair, bool> > > *)': /usr/include/NodeFactory.h(.gnu.linkonce.d.__vt_5Probe+0x34): undefined reference to `Node::setDebugMode(void)' /usr/include/NodeFactory.h(.gnu.linkonce.d.__vt_5Probe+0x40): undefined reference to `Node::resetDebugMode(void)' TextProbe.o: In function `NodeFactory::Create(basic_string, __default_alloc_template > const &, ParameterSet const &)': /usr/src/Overflow/Overflow/vflow/src/../../data-flow/include/sstream.h(.gnu.linkonce.d.__vt_9TextProbe+0x34): undefined reference to `Node::setDebugMode(void)' /usr/src/Overflow/Overflow/vflow/src/../../data-flow/include/sstream.h(.gnu.linkonce.d.__vt_9TextProbe+0x40): undefined reference to `Node::resetDebugMode(void)' PlotProbe.o: In function `NodeFactory::Create(basic_string, __default_alloc_template > const &, ParameterSet const &)': /usr/local/include/g++-3/stl_vector.h(.gnu.linkonce.d.__vt_9PlotProbe+0x34): undefined reference to `Node::setDebugMode(void)' /usr/local/include/g++-3/stl_vector.h(.gnu.linkonce.d.__vt_9PlotProbe+0x40): undefined reference to `Node::resetDebugMode(void)' collect2: ld returned 1 exit status make[3]: *** [vflow] Error 1 make[3]: Leaving directory `/usr/src/Overflow/Overflow/vflow/src' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/src/Overflow/Overflow/vflow' make[1]: *** [all-recursive-am] Error 2 make[1]: Leaving directory `/usr/src/Overflow/Overflow/vflow' make: *** [all-recursive] Error 1 --------------------------------------- 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 Sun Mar 11 19:36:25 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] bl compile error Message-ID: <3AAC1A09.94E1F8E7@bioinformatics.org> ----------------------------------- ... c++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include -I../include -I/opt/omniORB_300/include -I/usr/lib/glib/include -I/usr/X11R6/include -I/usr/lib/glib/include -D__x86__ -D__linux__ -g -O2 -c messaging_list.c messaging_list.c: In function `void *fill_clist (GtkCList *, const gchar **, const gchar **, int)': messaging_list.c:50: `strlen' undeclared (first use this function) messaging_list.c:50: (Each undeclared identifier is reported only once for each function it appears in.) gmake[4]: *** [messaging_list.o] Error 1 gmake[4]: Leaving directory `/usr/home/jeff/piper-2001/piper-20010311-install/bl/src' ... ----------------------------------- 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 Sun Mar 11 19:40:52 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] overflow compile problems References: <3AAC0DD5.1A8B3806@bioinformatics.org> Message-ID: <3AAC1B14.E521C8D@bioinformatics.org> So, where do Node::setDebugMode(void) Node::resetDebugMode(void) come from? I seem to be missing these in my libraries. 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 valj01 at gel.usherb.ca Sun Mar 11 22:32:11 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] overflow compile problems References: <3AAC0DD5.1A8B3806@bioinformatics.org> <3AAC1B14.E521C8D@bioinformatics.org> Message-ID: <3AAC433B.9574BBE4@gel.usherb.ca> > So, where do > > Node::setDebugMode(void) > Node::resetDebugMode(void) > > come from? I seem to be missing these in my libraries. Once again, you seem to have conflicts between two (or more) versions installed. Node::setDebugMode(void) was removed a while ago, so nothing's supposed to use it anymore. There shouldn't be any reference to setDebugMode in your source tree. Jean-Marc P.S. Have you checked for old Overflow includes in places like /usr/include? -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jarl at xs4all.nl Mon Mar 12 05:11:49 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] overflow compile problems References: <3AAC0DD5.1A8B3806@bioinformatics.org> Message-ID: <3AACA0E5.3DE7FFD2@xs4all.nl> > I upgraded to gcc 2.96 and glibc 2.2, and I still get some errors compiling > from the latest source: > > ---------------------------------------- [cut compile dump] jeff, are you able to compile any c++ source at all? Try samba or some KDE application. Else downgrade to gcc 2.95.2 that was compiled against libc 2.2. jarl From valj01 at gel.usherb.ca Mon Mar 12 08:41:49 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] overflow compile problems References: <3AAC0DD5.1A8B3806@bioinformatics.org> <3AACA0E5.3DE7FFD2@xs4all.nl> Message-ID: <3AACD21D.F903A256@gel.usherb.ca> > > I upgraded to gcc 2.96 and glibc 2.2, and I still get some errors compiling > > from the latest source: > > jeff, are you able to compile any c++ source at all? Try samba or some > KDE application. Else downgrade to gcc 2.95.2 that was compiled against > libc 2.2. That's a good idea in general. In this case, I strongly suspect that it's not a compiler "error", but a problem with old versions of the source laying around. Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jeff at bioinformatics.org Mon Mar 12 09:49:00 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] overflow compile problems References: <3AAC0DD5.1A8B3806@bioinformatics.org> <3AAC1B14.E521C8D@bioinformatics.org> <3AAC433B.9574BBE4@gel.usherb.ca> Message-ID: <3AACE1DC.2585337F@bioinformatics.org> Jean-Marc Valin wrote: > > Once again, you seem to have conflicts between two (or more) versions installed. > Node::setDebugMode(void) was removed a while ago, so nothing's supposed to use > it anymore. There shouldn't be any reference to setDebugMode in your source > tree. Heh. I thought that I deleted them all from /usr/include, but it appears that I didn't. Silly me. I keep the libraries in /opt/overflow/include now. Back to compiling. Thanks! 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 Mon Mar 12 10:24:47 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] bl compile error References: <3AAC1A09.94E1F8E7@bioinformatics.org> Message-ID: <3AACEA3F.EE4DAC75@bioinformatics.org> Okay, I got Overflow to compile with gcc 2.96 and glibc 2.2, woohoo! I tried building Piper against the new Overflow, but I get the same BL error. Jarl? "J.W. Bizzaro" wrote: > > ----------------------------------- > ... > c++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include -I../include > -I/opt/omniORB_300/include -I/usr/lib/glib/include -I/usr/X11R6/include > -I/usr/lib/glib/include -D__x86__ -D__linux__ -g -O2 -c messaging_list.c > messaging_list.c: In function `void *fill_clist (GtkCList *, const > gchar **, const gchar **, int)': > messaging_list.c:50: `strlen' undeclared (first use this function) > messaging_list.c:50: (Each undeclared identifier is reported only once > for each function it appears in.) > gmake[4]: *** [messaging_list.o] Error 1 > gmake[4]: Leaving directory > `/usr/home/jeff/piper-2001/piper-20010311-install/bl/src' > ... > ----------------------------------- 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 xs4all.nl Mon Mar 12 17:11:16 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] bl compile error References: <3AAC1A09.94E1F8E7@bioinformatics.org> <3AACEA3F.EE4DAC75@bioinformatics.org> Message-ID: <3AAD4984.FE60E5C3@xs4all.nl> > I tried building Piper against the new Overflow, but I get the same BL error. > Jarl? > > > > ----------------------------------- > > ... > > messaging_list.c:50: `strlen' undeclared (first use this function) > > ----------------------------------- Maybe my cvs commit will help you out. jarl From valj01 at gel.usherb.ca Mon Mar 12 21:45:34 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] overflow compile problems References: <3AAC0DD5.1A8B3806@bioinformatics.org> Message-ID: <3AAD89CE.8972F610@gel.usherb.ca> I have something to suggest regarding Overflow (PL) and Piper versions. Let's agree that the Piper CVS version be in sync with the Overflow CVS and that we try to make releases that fit together. Of course, there are pros and cons... What do you think? Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jarl at xs4all.nl Tue Mar 13 04:29:55 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] overflow compile problems References: <3AAC0DD5.1A8B3806@bioinformatics.org> <3AAD89CE.8972F610@gel.usherb.ca> Message-ID: <3AADE893.949CA6DE@xs4all.nl> Jean-Marc Valin wrote: > > I have something to suggest regarding Overflow (PL) and Piper versions. Let's > agree that the Piper CVS version be in sync with the Overflow CVS and that we > try to make releases that fit together. Of course, there are pros and cons... > What do you think? > Good thing, but it wont always be possible to update Piper code. Or are you willing to delay Overflow cvs commits\releases in order to allow syncing? jarl From jeff at bioinformatics.org Tue Mar 13 08:18:56 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] overflow compile problems References: <3AAC0DD5.1A8B3806@bioinformatics.org> <3AAD89CE.8972F610@gel.usherb.ca> Message-ID: <3AAE1E40.F36CC821@bioinformatics.org> Jean-Marc Valin wrote: > > I have something to suggest regarding Overflow (PL) and Piper versions. Let's > agree that the Piper CVS version be in sync with the Overflow CVS and that we > try to make releases that fit together. Of course, there are pros and cons... > What do you think? Are you proposing some way to automate CVS synching, or using the same version numbers, or just keeping Piper and Overflow compatible? 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 Mar 13 17:14:01 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] [Fwd: Piper Program] Message-ID: <3AAE9BA8.4B837273@bioinformatics.org> I'm going to give this guy a call tomorrow. I'm also still talking to John Kennedy from Open Channel Software about a collaboration of some sort. It may involve Bioinformatics.org directly and Piper indirectly. We'll see. I'll keep everyone informed. Jeff -------------- next part -------------- An embedded message was scrubbed... From: "Rozenman, Yury" Subject: Piper Program Date: Tue, 13 Mar 2001 16:43:02 -0500 Size: 2316 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/20010313/2a86fa21/attachment.mht From jeff at bioinformatics.org Tue Mar 13 17:52:58 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] Re: [Fwd: Piper Program] References: <20010313223229.21453.qmail@web11505.mail.yahoo.com> Message-ID: <3AAEA4CA.7B7C4385@bioinformatics.org> ming luo wrote: > > I am kind of confused about the juno thing, are they the email/ISP service? Yes, they are. > why do they do bioinformatics? "potential revenue generation and potential contribution to society." See below. > is juno part of the goverment? Nope. I just found this press release on their website. It explains quite a bit, although Piper is not meant to be a distributed *parallel* computing system. It even mentions Yuri Rozenman: http://www.juno.com/corp/news/supercomputer.html Cheers. Jeff From jmvalin at locusdialogue.com Tue Mar 13 18:23:27 2001 From: jmvalin at locusdialogue.com (Jean-Marc Valin) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] Re: [Fwd: Piper Program] References: <20010313223229.21453.qmail@web11505.mail.yahoo.com> <3AAEA4CA.7B7C4385@bioinformatics.org> Message-ID: <3AAEABEF.6D2B3DA1@locusdialogue.com> > I just found this press release on their website. It explains quite a bit, > although Piper is not meant to be a distributed *parallel* computing > system. It even mentions Yuri Rozenman: What do you mean by *parallel*? Why distribute if you don't run stuff in parallel? Or I just got a different meaning for the word? Jean-Marc From jmvalin at locusdialogue.com Tue Mar 13 18:29:41 2001 From: jmvalin at locusdialogue.com (Jean-Marc Valin) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] overflow compile problems References: <3AAC0DD5.1A8B3806@bioinformatics.org> <3AAD89CE.8972F610@gel.usherb.ca> <3AADE893.949CA6DE@xs4all.nl> Message-ID: <3AAEAD65.7F3D62F7@locusdialogue.com> > Good thing, but it wont always be possible to update Piper code. Or are > you willing to delay Overflow cvs commits\releases in order to allow > syncing? I could give a notice when I break source compatibility in the Overflow CVS? That way those you want to update Piper can do so and those who want to be able to build Piper just don't update Overflow until Piper supports the changes. Would that be enough? Jean-Marc From jeff at bioinformatics.org Tue Mar 13 18:33:29 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] Re: [Fwd: Piper Program] References: <20010313223229.21453.qmail@web11505.mail.yahoo.com> <3AAEA4CA.7B7C4385@bioinformatics.org> <3AAEABEF.6D2B3DA1@locusdialogue.com> Message-ID: <3AAEAE49.CF2A87F1@bioinformatics.org> Jean-Marc Valin wrote: > > What do you mean by *parallel*? Why distribute if you don't run stuff in > parallel? Or I just got a different meaning for the word? When I think of distributed parallel computing, I think of SETI@Home and similar projects. They automatically break up a single data set and send the pieces to identical processes. With Piper, the data and the processes can be different. I'm not saying that Piper can't do parallel processing, but it is meant to be much more flexible. For one, a user can create a sequential (serial) workflow path and not be limited to a parallel one. And I imagine Piper would be good at tying together parallel systems. Jeff From gvd at penguin.pharmacy.ualberta.ca Tue Mar 13 20:14:57 2001 From: gvd at penguin.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] Re: [Fwd: Piper Program] In-Reply-To: <3AAEA4CA.7B7C4385@bioinformatics.org> Message-ID: Hey all, I read the press release. It reminds me somewhat of what parabon is also trying to do (for profit, I believe): http://www.parabon.com Notice they have a 'folderol' clone project... Regards, g. -- -- Gary Van Domselaar Ph.D. Candidate, Associate Director, Faculty of Pharmacy, Bioinformatics.org: The Open Lab University of Alberta gary@bioinformatics.org gary@penguin.pharmacy.ualberta.ca http://bioinformatics.org/gary -- -- On Tue, 13 Mar 2001, J.W. Bizzaro wrote: > ming luo wrote: > > > > I am kind of confused about the juno thing, are they the email/ISP service? > > Yes, they are. > > > why do they do bioinformatics? > > "potential revenue generation and potential contribution to society." See > below. > > > is juno part of the goverment? > > Nope. > > I just found this press release on their website. It explains quite a bit, > although Piper is not meant to be a distributed *parallel* computing > system. It even mentions Yuri Rozenman: > > http://www.juno.com/corp/news/supercomputer.html > > Cheers. > Jeff > > _______________________________________________ > pipet-devel maillist - pipet-devel@bioinformatics.org > http://bioinformatics.org/mailman/listinfo/pipet-devel > From jeff at bioinformatics.org Tue Mar 13 20:25:46 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] Re: [Fwd: Piper Program] References: Message-ID: <3AAEC89A.1FF28E79@bioinformatics.org> Gary Van Domselaar wrote: > > I read the press release. It reminds me somewhat of what parabon is also > trying to do (for profit, I believe): > http://www.parabon.com That type of parallel computing is considered to be a form of P2P computing. O'Reilly has a whole list of projects like it: http://www.oreillynet.com/pub/t/73 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 xs4all.nl Wed Mar 14 05:58:34 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] overflow compile problems References: <3AAC0DD5.1A8B3806@bioinformatics.org> <3AAD89CE.8972F610@gel.usherb.ca> <3AADE893.949CA6DE@xs4all.nl> <3AAEAD65.7F3D62F7@locusdialogue.com> Message-ID: <3AAF4EDA.AE658B5C@xs4all.nl> > > Good thing, but it wont always be possible to update Piper code. Or are > > you willing to delay Overflow cvs commits\releases in order to allow > > syncing? > > I could give a notice when I break source compatibility in the Overflow > CVS? That way those you want to update Piper can do so and those who > want to be able to build Piper just don't update Overflow until Piper > supports the changes. Would that be enough? A little more would be nice, dont completely stick to your 'own' codebase. Like the recent update of Overflow I updated Piper so it could compile with the cvs Overflow again. Thee kinda work can be done by everybode, including you. I'm saying that in general it's a good thing that we do some more work on 'other people's' work. Currently the layers and people relation is too much 1-on-1. Dont get me wrong, I know it whould take a long time to work on code you didn't write, and that we all are very buzy. jarl From jeff at bioinformatics.org Wed Mar 14 14:49:32 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] talk with Yuri Message-ID: <3AAFCB4C.AD120446@bioinformatics.org> Greetings. I just got off the phone with Yuri, the Senior VP from Juno Online. We spent a bit of time explaining how our systems work, or will work. He had a number of questions about Piper, and from what I could gather, Piper seems to be what they need to interact with their system...recall this press release: http://www.juno.com/corp/news/supercomputer.html He said that he will call me back on Friday and that he would like to come out here to UMass to discuss this further. He indicated that Juno may want UMass involved in some research on the feasibility of the project. So, now all I have to do is get UMass to even recognize that we exist! :-P Cheers. Jeff From jeff at bioinformatics.org Thu Mar 15 15:50:59 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] [Fwd: ATP] Message-ID: <3AB12B33.321965FC@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: "John B. Kennedy" Subject: ATP Date: Thu, 15 Mar 2001 14:32:50 -0600 Size: 3357 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/20010315/2220d506/attachment.mht From jeff at bioinformatics.org Thu Mar 15 17:17:16 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] [Fwd: ATP] Message-ID: <3AB13F6C.DC4473D4@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: "J.W. Bizzaro" Subject: Re: ATP Date: Thu, 15 Mar 2001 17:16:32 -0500 Size: 3126 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/20010315/3f96b0b7/attachment.mht From jeff at bioinformatics.org Thu Mar 15 17:30:44 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] [Fwd: ATP] Message-ID: <3AB14294.2895E61@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: "J.W. Bizzaro" Subject: Re: ATP Date: Thu, 15 Mar 2001 17:30:19 -0500 Size: 1060 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/20010315/9fb0575f/attachment.mht From jarl at xs4all.nl Thu Mar 15 22:19:35 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] [Fwd: ATP] References: <3AB13F6C.DC4473D4@bioinformatics.org> Message-ID: <3AB18647.F852EF1E@xs4all.nl> "J.W. Bizzaro" wrote: > > > > ------------------------------------------------------------------------ > > Subject: Re: ATP > Date: Thu, 15 Mar 2001 17:16:32 -0500 > From: "J.W. Bizzaro" > To: "John B. Kennedy" > CC: Doug Curry > References: > > "John B. Kennedy" wrote: > > > > She said the first answer was fine, but the second did not matter. It seems > > that they want to fund only projects that have a high technical risk and a > > low business risk. They like to be the funder of projects that are too early > > for VC but the market is clearly there once built. > > I read some of what was there on the website. It does appear that they are > looking for technologies that would be revolutionary, if only they would > work. Another way to look at it, is they don't require fruit from the > labor, but, if there is fuit, it must be marketable. Jeff, Exciting news you brough up. Looks like piper could use some more resources, and as long as we keep LGPL alive all should be well. I'm curious though if there will be any concequences for Piper. Because if any funds were granted, they will be for 'the' Piper project. What about when elements will be dropped, or redesigned? Which features will we need to keep? I know this wont be possible to answer presicely but I'm sure you have a fealing about this. And skip the obvious features ;) > Because, in my > opinion, there is nothing that you cannot program a computer to do, isolated > inside of its own environment, the "computational universe", given enough > time. There are sone wiseass algoritms that dont agree, like time-exponential. Cant think of any use for them .. > > while keeping close to the open source principles > > that you and your fellow collaborators believe in. 'keeping close to open source', Is this diplomat slang for 'remaining LGPL'? From jarl at xs4all.nl Fri Mar 16 18:05:00 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:45 2006 Subject: [Pipet Devel] Piper design issue References: <3AB14294.2895E61@bioinformatics.org> Message-ID: <3AB29C1C.92783E2B@xs4all.nl> Hi Pipers, The BL sources are nearing a status where they can be commited to the Piper cvs tree. This is great for me because it clears up much about what Piper will be capable of. Once you read the code you'll understand too ;) Nah, ok, not a lot of you will read them I guess, and most of it you already knew I guess. And some day I'll add it to the PiperDesign.html anyway. But there's one issue that's big enough to discuss, the transparency of the BL for passing DL -> PL communications. For the BL's sake in theory there's no limitation of what can be passed on, I see none for the PL because a NEW pl will be used, in paralel if needed. The problem is with the UI and DL which are not capable of handling new and threaded remote input. When a DL has commited a network that is to be executed on multiple machines, it will receive PUSHED responses. Like on a plain text terminal it's possible to put text by applications. I would like to add a 'virtual tty' or 'graphical output area' to the UI and DL designs. When it's possible for nodes\networks to push their output to the UI Piper will be a much more powerfull system. I'm thinking of adding a Corba server orb to the DL that handles stuff like: - create_virtual_tty(); - display(tty,text); - display related api subset.. .... - close_virtual_tty(); etc. What do you think about this? And what about the amound of work it will take to implement? jarl From jeff at bioinformatics.org Wed Mar 21 02:55:24 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] new BL error Message-ID: <3AB85E6C.1AA32D54@bioinformatics.org> ... Making install in plugins gmake[2]: Entering directory `/usr/home/jeff/piper-2001/piper-20010321-install/bl/plugins' /bin/sh ../libtool --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include -I../include -I/opt/omniORB_300/include -g -ggdb -D__x86__ -D__linux__ -Wall -I../src -I/usr/lib/glib/include -I/usr/X11R6/include -I/usr/lib/glib/include -I/opt/overflow/include -I/usr/include/gnome-xml -g -O2 -c plugin_sensor_localhost.c rm -f .libs/plugin_sensor_localhost.lo c++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include -I../include -I/opt/omniORB_300/include -g -ggdb -D__x86__ -D__linux__ -Wall -I../src -I/usr/lib/glib/include -I/usr/X11R6/include -I/usr/lib/glib/include -I/opt/overflow/include -I/usr/include/gnome-xml -g -O2 -Wp,-MD,.deps/plugin_sensor_localhost.pp -c plugin_sensor_localhost.c -fPIC -DPIC -o .libs/plugin_sensor_localhost.lo plugin_sensor_localhost.c: In function `gint plugin_collector_localhost_init (messaging_object *)': plugin_sensor_localhost.c:388: cannot convert `gint (*) (messaging_object *)' to `void *' for argument `6' to `messaging_db_collector_register (messaging_object *, const gchar *, const gchar *, const gchar *, const gchar *, void *, void *, void *, void *)' plugin_sensor_localhost.c: In function `gint plugin_sensor_localhost_init (messaging_object *)': plugin_sensor_localhost.c:401: cannot convert `gint (*) (messaging_object *)' to `void *' for argument `5' to `messaging_db_sensor_register (messaging_object *, const gchar *, const gchar *, const gchar *, void *, void *, GtkWidget *(*) (messaging_object *, int), void *, void *, void *)' gmake[2]: *** [plugin_sensor_localhost.lo] Error 1 gmake[2]: Leaving directory `/usr/home/jeff/piper-2001/piper-20010321-install/bl/plugins' gmake[1]: *** [install-recursive] Error 1 gmake[1]: Leaving directory `/usr/home/jeff/piper-2001/piper-20010321-install/bl' make: *** [install-recursive] Error 1 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 Wed Mar 21 19:27:38 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] Piper design issue References: <3AB14294.2895E61@bioinformatics.org> <3AB29C1C.92783E2B@xs4all.nl> Message-ID: <3AB946FA.77B6A089@bioinformatics.org> Hi Jarl! Sorry for taking a while to get back to this. Jarl van Katwijk wrote: > > But there's one issue that's big enough to discuss, the transparency of > the BL for passing DL -> PL communications. For the BL's sake in theory > there's no limitation of what can be passed on, I see none for the PL > because a NEW pl will be used, in paralel if needed. What do you mean by "a new PL"? > The problem is with > the UI and DL which are not capable of handling new and threaded remote > input. > > When a DL has commited a network that is to be executed on multiple > machines, it will receive PUSHED responses. Can you give me an example of a pushed response? > Like on a plain text > terminal it's possible to put text by applications. I would like to add > a 'virtual tty' or 'graphical output area' to the UI and DL designs. > When it's possible for nodes\networks to push their output to the UI > Piper will be a much more powerfull system. [...] > What do you think about this? And what about the amound of work it will > take to implement? I was thinking about a node that would work as an interactive tty/console, perhaps running Peep or bash. Are you talking about text that the UI and DL would not "expect", text that is only for the user and not to be passed on? Couldn't we put a "text viewer" in the pipeline of whatever application to do this? 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 Wed Mar 21 19:31:54 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] new BL error References: <3AB85E6C.1AA32D54@bioinformatics.org> Message-ID: <3AB947FA.458262BD@bioinformatics.org> I've been trying to get Piper/Overflow to build under GLIBC 2.2 + GCC 2.96. Overflow compiles and installs fine, and it looks like Piper compiles, but it doesn't install. I get that error I posted. Jarl, you said that you have uncommitted code. Do you think that it will fix the error? 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 xs4all.nl Wed Mar 21 20:01:49 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] Piper design issue References: <3AB14294.2895E61@bioinformatics.org> <3AB29C1C.92783E2B@xs4all.nl> <3AB946FA.77B6A089@bioinformatics.org> Message-ID: <3AB94EFD.90B9E152@xs4all.nl> > Hi Jarl! Sorry for taking a while to get back to this. Hela Jeff, nah, dont mind, I'm slow too.. still got your BL compiling error on hold. > > But there's one issue that's big enough to discuss, the transparency of > > the BL for passing DL -> PL communications. For the BL's sake in theory > > there's no limitation of what can be passed on, I see none for the PL > > because a NEW pl will be used, in paralel if needed. > > What do you mean by "a new PL"? A new instance. same binairy, just a new copy. > > The problem is with > > the UI and DL which are not capable of handling new and threaded remote > > input. > > > > When a DL has commited a network that is to be executed on multiple > > machines, it will receive PUSHED responses. > Can you give me an example of a pushed response? Like an error message, a node has gone very wrong an want to output a message about this event. Maybe the error is just temporary, and needs to be updated, or removed. > > What do you think about this? And what about the amound of work it will > > take to implement? > > I was thinking about a node that would work as an interactive tty/console, > perhaps running Peep or bash. > > Are you talking about text that the UI and DL would not "expect", text that is > only for the user and not to be passed on? Yes. > Couldn't we put a "text viewer" in the pipeline of whatever application to do > this? The UI and DL need to be enhanced to accept messages from the BL\PL backend, rather that just commit an execution network and exspect only the end results. Maybe we could extend the bl->dl->ui communication, the code that routes the results after a network has executed. jarl From jarl at xs4all.nl Wed Mar 21 20:26:45 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] new BL error References: <3AB85E6C.1AA32D54@bioinformatics.org> <3AB947FA.458262BD@bioinformatics.org> Message-ID: <3AB954D5.524C69E6@xs4all.nl> > Jarl, you said that you have uncommitted code. Do you think that it will fix > the error? Gcc 2.96 is giving me a hard time ;-) Have a look @ the cvs commits I made and hopefully I 'fixed' most compilation errors. Changes are great there will be more. jarl From valj01 at gel.usherb.ca Wed Mar 21 20:46:49 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] new BL error References: <3AB85E6C.1AA32D54@bioinformatics.org> <3AB947FA.458262BD@bioinformatics.org> Message-ID: <3AB95989.89A636E6@gel.usherb.ca> > I've been trying to get Piper/Overflow to build under GLIBC 2.2 + GCC 2.96. > Overflow compiles and installs fine, and it looks like Piper compiles, but it > doesn't install. I get that error I posted. Overflow does *compile* with 2.96, but not everything works as it's supposed to (don't know yet whether the problem is my code or gcc 2.96) Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jeff at bioinformatics.org Thu Mar 22 04:02:15 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] new BL error References: <3AB85E6C.1AA32D54@bioinformatics.org> <3AB947FA.458262BD@bioinformatics.org> <3AB954D5.524C69E6@xs4all.nl> Message-ID: <3AB9BF97.D39F1052@bioinformatics.org> Jarl van Katwijk wrote: > > > Jarl, you said that you have uncommitted code. Do you think that it will fix > > the error? > Gcc 2.96 is giving me a hard time ;-) Have a look @ the cvs commits I > made and hopefully I 'fixed' most compilation errors. Changes are great > there will be more. I just tried the new code and still get that error :-( 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 xs4all.nl Thu Mar 22 09:31:32 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] new BL error References: <3AB85E6C.1AA32D54@bioinformatics.org> <3AB947FA.458262BD@bioinformatics.org> <3AB954D5.524C69E6@xs4all.nl> <3AB9BF97.D39F1052@bioinformatics.org> Message-ID: <3ABA0CC4.352FC433@xs4all.nl> > > > Jarl, you said that you have uncommitted code. Do you think that it will fix > > > the error? > > Gcc 2.96 is giving me a hard time ;-) Have a look @ the cvs commits I > > made and hopefully I 'fixed' most compilation errors. Changes are great > > there will be more. > > I just tried the new code and still get that error :-( You better dont use gcc beta's. I wont use it, and I cant fix these errors so it seems. I'll have a look at those errors later on, but dont exspect me to be able to fix them, I'm sorry. jarl From jeff at bioinformatics.org Thu Mar 22 16:37:36 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] new BL error Message-ID: <3ABA70A0.D5ACBAD3@bioinformatics.org> Jean-Marc Valin wrote: > > Overflow does *compile* with 2.96, but not everything works as it's supposed to > (don't know yet whether the problem is my code or gcc 2.96) Just an academic question here: Is the problem that we're having with GCC 2.96 related to C++ standards changing? Again, I'm not a C/C++ expert, but I'm a little surprised that a "minor" upgrade in GCC can break so many things. 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 Thu Mar 22 16:38:25 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] Piper design issue Message-ID: <3ABA70D1.53DD30C8@bioinformatics.org> Jarl van Katwijk wrote: > > The UI and DL need to be enhanced to accept messages from the BL\PL > backend, rather that just commit an execution network and exspect only > the end results. Maybe we could extend the bl->dl->ui communication, the > code that routes the results after a network has executed. We were also planning on a channel for "process status", right? For example, the user would need to know (1) if the process started or not, (2) if it is still running correctly, (3) how long it has been running, (4) if it encountered an error, and (5) if it finished without an error. Could you tell me if your idea for a virtual terminal is the same or not? 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 jmvalin at locusdialogue.com Thu Mar 22 16:58:48 2001 From: jmvalin at locusdialogue.com (Jean-Marc Valin) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] new BL error References: <3ABA70A0.D5ACBAD3@bioinformatics.org> Message-ID: <3ABA7598.585838D3@locusdialogue.com> > > Overflow does *compile* with 2.96, but not everything works as it's supposed to > > (don't know yet whether the problem is my code or gcc 2.96) > > Just an academic question here: Is the problem that we're having with GCC 2.96 > related to C++ standards changing? Again, I'm not a C/C++ expert, but I'm a > little surprised that a "minor" upgrade in GCC can break so many things. I'm not too sure about the problem... it may actually be related to libstdc++, but I'm not sure... BTW, there's a lot of differences between 2.95.x and 2.96 (which is *supposed* to be experimental stuff leading towards 3.0). Actually, I've even found that if I try compiling with -O0, the link fails because of internal g++ symbols, so that's at least a bug... Anyway, the result from the limited time I tried compiling/running on a RH7 box is that wierd things happen. I didn't investigate enough to tell whose fault it is. I'm waiting for gcc 3.0 to come out and make sure that it can compile Overflow correctly. Right now, I thing the only problem with gcc 3.0 is some "fludge" I use in the which is not ANSI C++ and which gcc 3.0 screws up. Jean-Marc From jmvalin at locusdialogue.com Thu Mar 22 17:01:39 2001 From: jmvalin at locusdialogue.com (Jean-Marc Valin) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] new BL error References: <3ABA70A0.D5ACBAD3@bioinformatics.org> Message-ID: <3ABA7643.E8354D41@locusdialogue.com> "J.W. Bizzaro" a ?crit : > > Jean-Marc Valin wrote: > > > > Overflow does *compile* with 2.96, but not everything works as it's supposed to > > (don't know yet whether the problem is my code or gcc 2.96) > > Just an academic question here: Is the problem that we're having with GCC 2.96 > related to C++ standards changing? Again, I'm not a C/C++ expert, but I'm a > little surprised that a "minor" upgrade in GCC can break so many things. Oh, and BTW, these a couple things that I have to refrain from doing because g++ 2.95.x won't take them. It has to do with libstdc++ v2, which doesn't quite follow the standard. When all compilers strictly follow the ANSI C++ standard, my life will be much much simpler (that is as far as Overflow is concerned). Jean-Marc From jarl at xs4all.nl Thu Mar 22 17:25:51 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] new BL error References: <3ABA70A0.D5ACBAD3@bioinformatics.org> Message-ID: <3ABA7BEF.CC984AFC@xs4all.nl> "J.W. Bizzaro" wrote: > > Jean-Marc Valin wrote: > > > > Overflow does *compile* with 2.96, but not everything works as it's supposed to > > (don't know yet whether the problem is my code or gcc 2.96) > > Just an academic question here: Is the problem that we're having with GCC 2.96 > related to C++ standards changing? Again, I'm not a C/C++ expert, but I'm a > little surprised that a "minor" upgrade in GCC can break so many things. Yes true, it's very hard to write multi compiler C++. And like Jean Marc mentioned, gcc 2.96 is related to the developement of gcc 3.00. I understand why you ask, you fear that 3.01 and so on will be a problem too. I exspect there'll be some issues with every release, but not as many as we'll face now. Is this really true, did Redhand bundle a developement gcc with RH7? They are really trying hard to have people download binairy rpm's.. jarl From jarl at xs4all.nl Thu Mar 22 17:46:48 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] Piper design issue References: <3ABA70D1.53DD30C8@bioinformatics.org> Message-ID: <3ABA80D8.4D5B7395@xs4all.nl> > We were also planning on a channel for "process status", right? For example, > the user would need to know (1) if the process started or not, (2) if it is > still running correctly, (3) how long it has been running, (4) if it > encountered an error, and (5) if it finished without an error. Could you tell > me if your idea for a virtual terminal is the same or not? Oh yes, it's another member of the family. I picture before me an set of functions that allow the 'other' layers to offer information to the other. A Piper-wide feedback system. In fact it's very simple, just should be able to: - open new incoming connection any time from a lower layer (in respect to the sequence UI->Dl->BL->PL) - accept feedback data 'chunks' over open connections - keep alive - close connection and the data chunks are sto constain all the needed data. We just add new "action id's" we we need some. struct feeback { long ID; /* piper wide unique sequence id */ long source; long destination; int action /* what is this data about? */ gchar* rawdata; /* data, depending on the action */ } We can have action id 274 be 'open virtual tty', or action 12 "report status". jarl From jmvalin at locusdialogue.com Thu Mar 22 17:50:42 2001 From: jmvalin at locusdialogue.com (Jean-Marc Valin) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] new BL error References: <3ABA70A0.D5ACBAD3@bioinformatics.org> <3ABA7BEF.CC984AFC@xs4all.nl> Message-ID: <3ABA81C2.3D6C8CBE@locusdialogue.com> > Yes true, it's very hard to write multi compiler C++. And like Jean Marc > mentioned, gcc 2.96 is related to the developement of gcc 3.00. I > understand why you ask, you fear that 3.01 and so on will be a problem > too. I exspect there'll be some issues with every release, but not as > many as we'll face now. What I've heard is that they made sure the gcc 2.95.x stays both source and binary compatible, then they started a development branch, which they called 2.96, which may break compatibility every day... towards 3.0, which should stay (source and binary) compatible for a while. You can go to http://gcc.gnu.org to have the gcc team's opinion on RH releasing a development compiler... Now, gcc changed the name of their develoment branch to 2.97 to avoid confusion with the RH 2.96 compiler. > Is this really true, did Redhand bundle a developement gcc with RH7? > They are really trying hard to have people download binairy rpm's.. They say 2.96 is better (in their opinion) than 2.95.2, so they choosed it. BTW, even binary RPM's don't work, because they're dynamically linked with libraries that have a different ABI! So if you want to use one of the Overflow rpm's I provided, you need to have the 2.95.x libstdc++. Jean-Marc From jeff at bioinformatics.org Thu Mar 22 18:14:54 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] Fw: Objects in Bio- & Chem-Informatics 2001 Call for Participation Message-ID: <3ABA876E.7A9249C2@bioinformatics.org> I won't be able to make the NETTAB conference in Italy, but the OBCI conference will be held here in Mass this year. I've been wanting to go to this for a while, and now's my chance. I will definitely present Piper or "BioPiper". Jeff -------------- next part -------------- An embedded message was scrubbed... From: unknown sender Subject: [Bio_BB]Fw: Objects in Bio- & Chem-Informatics 2001 Call for Participation Date: Thu, 22 Mar 2001 20:03:16 -0300 Size: 5140 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/20010322/8bada775/attachment.mht From jeff at bioinformatics.org Thu Mar 22 18:45:57 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] Re: gcc 2.96 References: <3ABA8537.FA9E02D@xs4all.nl> Message-ID: <3ABA8EB5.47933D52@bioinformatics.org> Jarl van Katwijk wrote: > > Hope you still got gcc 2.96 , I've done some more hacking of the BL > sources, let me know what it does. Hey, what do you know, it compiles now! Great! But, see runtime errors below. I can tell that there is an error related to libflow possibly not compiling, as Jean-Marc said (vflow and libflow compile together?). Also, I still get that "DL2BL IOR file not found." The last time I checked, it wasn't being written by the BL. Jarl, don't you get that error too? Try deleting the piper_info directory and see what happens. Cheers. Jeff -------------------------------- jeff@dexter:jeff> piper rm: cannot remove `/home/jeff/piper_info/ior/*': No such file or directory Starting processing layer... Starting brokering layer... Starting definition layer... Starting pied... PL: error while loading shared libraries: libflow-0.4.so: cannot load shared object file: No such file or directory BL: error while loading shared libraries: libflow-0.4.so: cannot load shared object file: No such file or directory Default location of the DL2BL IOR file: /home/jeff/piper_info/ior/dl2bl.ior Wrote IOR file /home/jeff/piper_info/ior/uil2dl.ior Getting document... error: net LoadFile already existed error: net SaveAs already existed error: net LP already existed error: net HP already existed error: net LPC_DECOMP already existed error: net SpectrumProbe already existed Connecting with the bl... DL2BL IOR file not found. Connection with BL not established. Loading crash info... Aborted -------------------------------- -- 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 valj01 at gel.usherb.ca Thu Mar 22 19:09:42 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] Re: gcc 2.96 References: <3ABA8537.FA9E02D@xs4all.nl> <3ABA8EB5.47933D52@bioinformatics.org> Message-ID: <3ABA9446.7319A62D@gel.usherb.ca> > error: net LoadFile already existed > error: net SaveAs already existed > error: net LP already existed > error: net HP already existed > error: net LPC_DECOMP already existed > error: net SpectrumProbe already existed How many times should I repeat... If you're doing any development involving Overflow, install it in a dir like /opt/overflow and "rm -rf /opt/overflow" before any "make install". Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jeff at bioinformatics.org Thu Mar 22 19:45:37 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] Re: gcc 2.96 References: <3ABA8537.FA9E02D@xs4all.nl> <3ABA8EB5.47933D52@bioinformatics.org> <3ABA9446.7319A62D@gel.usherb.ca> Message-ID: <3ABA9CB1.C1A3A1BD@bioinformatics.org> Jean-Marc Valin wrote: > > How many times should I repeat... If you're doing any development involving > Overflow, install it in a dir like /opt/overflow and "rm -rf /opt/overflow" > before any "make install". I don't get it. I build Overflow in /usr/src/Overflow. The directory Overflow gets installed to is /opt/overflow. When I build Piper, I point to /opt/overflow as the location of the libraries. What should I do that is different? It sounds like you're saying, "remove Overflow before you install Overflow." 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 Thu Mar 22 19:51:29 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] Re: gcc 2.96 References: <3ABA8537.FA9E02D@xs4all.nl> <3ABA8EB5.47933D52@bioinformatics.org> <3ABA9446.7319A62D@gel.usherb.ca> Message-ID: <3ABA9E11.3B32FC02@bioinformatics.org> Jean-Marc Valin wrote: > > How many times should I repeat... If you're doing any development involving > Overflow, install it in a dir like /opt/overflow and "rm -rf /opt/overflow" > before any "make install". Also, I don't see any mention of removing a directory in the README file. 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 xs4all.nl Thu Mar 22 19:51:18 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:46 2006 Subject: [Pipet Devel] Re: gcc 2.96 References: <3ABA8537.FA9E02D@xs4all.nl> <3ABA8EB5.47933D52@bioinformatics.org> Message-ID: <3ABA9E06.8ADD2F39@xs4all.nl> "J.W. Bizzaro" wrote: > > Jarl van Katwijk wrote: > > > > Hope you still got gcc 2.96 , I've done some more hacking of the BL > > sources, let me know what it does. > > Hey, what do you know, it compiles now! Great! hehe. sweet. I can code blinded mama! > But, see runtime errors below. > I can tell that there is an error related to libflow possibly not compiling, Correct, You need to fix the overflow lib and have another try. Or check the libraries ("ldd") you'll need for the BL and PL. And the ones you've got ;) ("ldconfig -p" ) > Also, I still get that "DL2BL IOR file not found." The last time I checked, > it wasn't being written by the BL. Logical, the BL isn't even being executed when you have missing libraries. > Jarl, don't you get that error too? Try > deleting the piper_info directory and see what happens. Recompiled everything and attached the logs of the runs. The submit stalled the GUI btw :( Too late to figure that out right now. > error: net LoadFile already existed Remarkable, the DL is starting some version of overflow.. bye, jarl -------------- next part -------------- rm: cannot remove `/root/piper_info/ior/*': No such file or directory wrote IOR file /root/piper_info/ior/bl2pl.ior Message: Piper BL 0.4.0pre10 Loading plugin /usr/local/lib/libplugin_sensor_DL.so... OK. Loading plugin /usr/local/lib/libplugin_sensor_PL.so... OK. Loading plugin /usr/local/lib/libplugin_sensor_localhost.so... OK. Loading plugin /usr/local/lib/libplugin_sensor_syslogd.so... OK. Loading plugin /usr/local/lib/libplugin_visual_DL.so... OK. Loading plugin /usr/local/lib/libplugin_visual_PL.so... OK. Loading plugin /usr/local/lib/libplugin_visual_devel.so... OK. Loading plugin /usr/local/lib/libplugin_visual_festival.so... OK. Loading plugin /usr/local/lib/libplugin_visual_localhost.so... OK. Loading plugin /usr/local/lib/libplugin_visual_statusbar.so... OK. Nothing to load, setting up default... activating DL plugin sensor activating PL plugin sensor pong! Default location of the DL2BL IOR file: /root/piper_info/ior/dl2bl.ior Wrote IOR file /root/piper_info/ior/uil2dl.ior Toolbox load error: /usr/local/lib/vq.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi Toolbox load error: /usr/local/lib/hmm.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi Toolbox load error: /usr/local/lib/nnet.tlb: undefined symbol: __ti7istream Toolbox load error: /usr/local/lib/image.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi Toolbox load error: /usr/local/lib/audio_blocks.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi activating Localhost plugin sensor activating Syslogd plugin sensor activating DL plugin visual activating PL plugin visual activating visual SCRATCH MO activating visual Festival MO activating visual LOCALHOST MO error: net LP already existed error: net HP already existed error: net LPC_DECOMP already existed Accepted DL 1 Released DL 1 Removed DL client Getting document... Loading crash info... no crash info Adding a Network... Document:ShowNetwork shutting down BL... Connecting with the bl... setting up a connection with a unique dl_id... got dl_id... shutting down DL... terminating DL... Removing MO 16 from MO_LLIST Removing MO 15 from MO_LLIST Removing MO 14 from MO_LLIST Removing MO 13 from MO_LLIST Removing MO 12 from MO_LLIST Removing MO 11 from MO_LLIST Removing MO 10 from MO_LLIST Removing MO 9 from MO_LLIST Removing MO 8 from MO_LLIST Removing MO 7 from MO_LLIST Removing MO 6 from MO_LLIST Removing MO 5 from MO_LLIST shutting down PL... Removing MO 4 from MO_LLIST Removing MO 3 from MO_LLIST Removing MO 2 from MO_LLIST Removing MO 1 from MO_LLIST terminating BL... terminating PL... -------------- next part -------------- Message: Piper BL 0.4.0pre10 wrote IOR file /root/piper_info/ior/bl2pl.ior Loading plugin /usr/local/lib/libplugin_sensor_DL.so... OK. Loading plugin /usr/local/lib/libplugin_sensor_PL.so... OK. Loading plugin /usr/local/lib/libplugin_sensor_localhost.so... OK. Loading plugin /usr/local/lib/libplugin_sensor_syslogd.so... OK. Loading plugin /usr/local/lib/libplugin_visual_DL.so... OK. Loading plugin /usr/local/lib/libplugin_visual_PL.so... OK. Loading plugin /usr/local/lib/libplugin_visual_devel.so... OK. Loading plugin /usr/local/lib/libplugin_visual_festival.so... OK. Loading plugin /usr/local/lib/libplugin_visual_localhost.so... OK. Loading plugin /usr/local/lib/libplugin_visual_statusbar.so... OK. Loading configuration REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. activating DL plugin sensor activating PL plugin sensor pong! activating Localhost plugin sensor activating Syslogd plugin sensor activating DL plugin visual activating PL plugin visual activating visual SCRATCH MO activating visual Festival MO activating visual LOCALHOST MO REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. Default location of the DL2BL IOR file: /root/piper_info/ior/dl2bl.ior Wrote IOR file /root/piper_info/ior/uil2dl.ior Toolbox load error: /usr/local/lib/vq.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi Toolbox load error: /usr/local/lib/hmm.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi Toolbox load error: /usr/local/lib/nnet.tlb: undefined symbol: __ti7istream Toolbox load error: /usr/local/lib/image.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi Toolbox load error: /usr/local/lib/audio_blocks.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi error: net LP already existed error: net HP already existed error: net LPC_DECOMP already existed Accepted DL 1 Released DL 1 Removed DL client Getting document... Loading crash info... no crash info Adding a Network... Document:ShowNetwork shutting down BL... Connecting with the bl... setting up a connection with a unique dl_id... got dl_id... shutting down DL... terminating DL... Removing MO 16 from MO_LLIST Removing MO 15 from MO_LLIST Removing MO 14 from MO_LLIST Removing MO 13 from MO_LLIST Removing MO 12 from MO_LLIST Removing MO 11 from MO_LLIST Removing MO 10 from MO_LLIST Removing MO 9 from MO_LLIST Removing MO 8 from MO_LLIST Removing MO 7 from MO_LLIST Removing MO 6 from MO_LLIST Removing MO 5 from MO_LLIST Removing MO 4 from MO_LLIST Removing MO 3 from MO_LLIST Removing MO 2 from MO_LLIST Removing MO 1 from MO_LLIST terminating BL... shutting down PL... terminating PL... -------------- next part -------------- Message: Piper BL 0.4.0pre10 wrote IOR file /root/piper_info/ior/bl2pl.ior Loading plugin /usr/local/lib/libplugin_sensor_DL.so... OK. Loading plugin /usr/local/lib/libplugin_sensor_PL.so... OK. Loading plugin /usr/local/lib/libplugin_sensor_localhost.so... OK. Loading plugin /usr/local/lib/libplugin_sensor_syslogd.so... OK. Loading plugin /usr/local/lib/libplugin_visual_DL.so... OK. Loading plugin /usr/local/lib/libplugin_visual_PL.so... OK. Loading plugin /usr/local/lib/libplugin_visual_devel.so... OK. Loading plugin /usr/local/lib/libplugin_visual_festival.so... OK. Loading plugin /usr/local/lib/libplugin_visual_localhost.so... OK. Loading plugin /usr/local/lib/libplugin_visual_statusbar.so... OK. Loading configuration REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. activating DL plugin sensor activating PL plugin sensor pong! activating Localhost plugin sensor activating Syslogd plugin sensor activating DL plugin visual activating PL plugin visual activating visual SCRATCH MO activating visual Festival MO activating visual LOCALHOST MO REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. REDEFINE conflict, an existing relation is redefined. Default location of the DL2BL IOR file: /root/piper_info/ior/dl2bl.ior Wrote IOR file /root/piper_info/ior/uil2dl.ior Toolbox load error: /usr/local/lib/vq.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi Toolbox load error: /usr/local/lib/hmm.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi Toolbox load error: /usr/local/lib/nnet.tlb: undefined symbol: __ti7istream Toolbox load error: /usr/local/lib/image.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi Toolbox load error: /usr/local/lib/audio_blocks.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi error: net LP already existed error: net HP already existed error: net LPC_DECOMP already existed Accepted DL 1 convert: Unable to map file. convert: Unable to map file. convert: no delegates configuration file found (delegates.mgk). convert: Unable to map file. convert: Unable to map file. convert: no delegates configuration file found (delegates.mgk). MDO 39017 is allowed to access MO pipeLine_MO Filled MDO dataDescription with MO->dataDescription DL plugin sensor passes data to pipeline Warning: MDO 17767 with datadescription DL plugin sensor is not allowed to MO Syslogd plugin collector with datadescription Syslogd plugin sensor Warning: MDO 17767 with datadescription DL plugin sensor is not allowed to MO Localhost plugin collector with datadescription localhost plugin sensor Warning: MDO 17767 with datadescription DL plugin sensor is not allowed to MO PL plugin collector with datadescription PL plugin sensor MDO 17767 with datadescription DL plugin sensor is allowed to MO DL plugin collector with datadescription DL plugin sensor MDO 17767 is allowed to access MO DL plugin collector pipeLine_MO passes data to DL plugin collector with 1 childs MDO 18547 is allowed to access MO DL plugin visual DL plugin collector passes data to DL plugin visual with 1 childs plugin_visual_DL_procedure... nothing to do yet MDO 22714 is allowed to access MO PL plugin sensor DL plugin visual passes data to PL plugin sensor with 1 childs error: net LoadFile already existed error: net SaveAs already existed error: net find_beat already existed error: net hello already existed error: net play_mp3 already existed error: net tone already existed error: net LP already existed error: net HP already existed error: net LPC_DECOMP already existed Node.cc line 214: Node Catch1 (type 5Catch) The node is not properly connected Node.cc line 223: Node ALL_NETWORK_OUTPUTS (type 9Collector) Exception caught in node initialization MDO 56401 is allowed to access MO pipeLine_MO PL plugin sensor passes data to pipeLine_MO with 4 childs MDO 17767 is allowed to access MO Syslogd plugin collector pipeLine_MO passes data to Syslogd plugin collector with 0 childs MDO 17767 is allowed to access MO Localhost plugin collector pipeLine_MO passes data to Localhost plugin collector with 0 childs MDO 17767 is allowed to access MO PL plugin collector pipeLine_MO passes data to PL plugin collector with 1 childs MDO 17767 is allowed to access MO DL plugin collector pipeLine_MO passes data to DL plugin collector with 1 childs From valj01 at gel.usherb.ca Thu Mar 22 21:15:06 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:47 2006 Subject: [Pipet Devel] Re: gcc 2.96 References: <3ABA8537.FA9E02D@xs4all.nl> <3ABA8EB5.47933D52@bioinformatics.org> <3ABA9446.7319A62D@gel.usherb.ca> <3ABA9CB1.C1A3A1BD@bioinformatics.org> Message-ID: <3ABAB1AA.29AD95ED@gel.usherb.ca> "J.W. Bizzaro" a ?crit : > > Jean-Marc Valin wrote: > > > > How many times should I repeat... If you're doing any development involving > > Overflow, install it in a dir like /opt/overflow and "rm -rf /opt/overflow" > > before any "make install". > > I don't get it. I build Overflow in /usr/src/Overflow. The directory > Overflow gets installed to is /opt/overflow. When I build Piper, I point to > /opt/overflow as the location of the libraries. What should I do that is > different? It sounds like you're saying, "remove Overflow before you install > Overflow." Actually, I just changed the doc for 0.4. You don't need to specify VFLOW_PATH for the default location. I should check that I don't load twice, but for now, you can just unset VFLOW_PATH and it'll work! > Also, I don't see any mention of removing a directory in the README file. The README is about using Overflow... now, you're installing many versions onver another without removing the files that aren't needed anymore. There's no way for Overflow which toolbox it need to load and which one it shouldn't load because is a file left by a previous version. Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jeff at bioinformatics.org Thu Mar 22 21:13:33 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:47 2006 Subject: [Pipet Devel] Re: gcc 2.96 References: <3ABA8537.FA9E02D@xs4all.nl> <3ABA8EB5.47933D52@bioinformatics.org> <3ABA9446.7319A62D@gel.usherb.ca> <3ABA9CB1.C1A3A1BD@bioinformatics.org> <3ABAB1AA.29AD95ED@gel.usherb.ca> Message-ID: <3ABAB14D.68BF6D13@bioinformatics.org> Jean-Marc Valin wrote: > > Actually, I just changed the doc for 0.4. You don't need to specify VFLOW_PATH > for the default location. I should check that I don't load twice, but for now, > you can just unset VFLOW_PATH and it'll work! Okay, I'll go try 0.4. > The README is about using Overflow... now, you're installing many versions onver > another without removing the files that aren't needed anymore. There's no way > for Overflow which toolbox it need to load and which one it shouldn't load > because is a file left by a previous version. Hmmmm, actually, I do remove /opt/overflow each time (before) I install a new version of Oveflow. I also noticed that Jarl gets the same messages (per his last e-mail). 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 valj01 at gel.usherb.ca Thu Mar 22 21:25:52 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:47 2006 Subject: [Pipet Devel] Re: gcc 2.96 References: <3ABA8537.FA9E02D@xs4all.nl> <3ABA8EB5.47933D52@bioinformatics.org> <3ABA9446.7319A62D@gel.usherb.ca> <3ABA9CB1.C1A3A1BD@bioinformatics.org> <3ABAB1AA.29AD95ED@gel.usherb.ca> <3ABAB14D.68BF6D13@bioinformatics.org> Message-ID: <3ABAB430.7C246E9B@gel.usherb.ca> "J.W. Bizzaro" a ?crit : > > Jean-Marc Valin wrote: > > > > Actually, I just changed the doc for 0.4. You don't need to specify VFLOW_PATH > > for the default location. I should check that I don't load twice, but for now, > > you can just unset VFLOW_PATH and it'll work! > > Okay, I'll go try 0.4. What I'm saying is that the pre-0.4 CVS version you have also looks automatically at the right place and specifying VFLOW_PATH make Overflow load the same thing twice... > > > The README is about using Overflow... now, you're installing many versions onver > > another without removing the files that aren't needed anymore. There's no way > > for Overflow which toolbox it need to load and which one it shouldn't load > > because is a file left by a previous version. > > Hmmmm, actually, I do remove /opt/overflow each time (before) I install a new > version of Oveflow. I also noticed that Jarl gets the same messages (per his > last e-mail). Jarl, you should unset VFLOW_PATH too! (that is, as long as you keep Overflow in the directory you specified with --prefix) Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jeff at bioinformatics.org Thu Mar 22 21:23:43 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:47 2006 Subject: [Pipet Devel] Re: gcc 2.96 References: <3ABA8537.FA9E02D@xs4all.nl> <3ABA8EB5.47933D52@bioinformatics.org> <3ABA9446.7319A62D@gel.usherb.ca> <3ABA9CB1.C1A3A1BD@bioinformatics.org> <3ABAB1AA.29AD95ED@gel.usherb.ca> <3ABAB14D.68BF6D13@bioinformatics.org> <3ABAB430.7C246E9B@gel.usherb.ca> Message-ID: <3ABAB3AF.B3DEC09F@bioinformatics.org> Jean-Marc Valin wrote: > > What I'm saying is that the pre-0.4 CVS version you have also looks > automatically at the right place and specifying VFLOW_PATH make Overflow load > the same thing twice... Right-o, I just noticed that I still have VFLOW_PATH set in my .bashrc file. I'll remove it and try again. 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 Thu Mar 22 23:25:28 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:47 2006 Subject: [Pipet Devel] Overflow install error Message-ID: <3ABAD038.367ECD62@bioinformatics.org> I know that you just told me not to use GCC 2.96, but I thought that I might give the code in CVS a try. Anyway, FYI, here is an error I caught: ------------------------- ... Making install in src make[2]: Entering directory `/usr/src/Overflow/Overflow/audio_blocks/src' /bin/sh ../libtool --mode=compile c++ -DLINUX=1 -DPROTOTYPES=1 -DHAVE_FLOAT_H=1 -DHAVE_SYS_SOUNDCARD_H=1 -DHAVE_LIBM=1 -DHAVE_LIBPTHREAD=1 -DHAVE_FFTW=1 -I. -I. -I../../data-flow/include -I../include -I/usr/include -g -O2 -c RFFT.cc c++ -DLINUX=1 -DPROTOTYPES=1 -DHAVE_FLOAT_H=1 -DHAVE_SYS_SOUNDCARD_H=1 -DHAVE_LIBM=1 -DHAVE_LIBPTHREAD=1 -DHAVE_FFTW=1 -I. -I. -I../../data-flow/include -I../include -I/usr/include -g -O2 -Wp,-MD,.deps/RFFT.pp -c RFFT.cc -fPIC -DPIC -o RFFT.lo In file included from /usr/local/include/g++-3/complex:8, from RFFT.cc:23: /usr/local/include/g++-3/std/complext.h:314: declaration of `double hypot (double, double)' throws different exceptions /usr/include/bits/mathinline.h:617: than previous declaration `double hypot (double, double) throw ()' make[2]: *** [RFFT.lo] Error 1 make[2]: Leaving directory `/usr/src/Overflow/Overflow/audio_blocks/src' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/usr/src/Overflow/Overflow/audio_blocks' make: *** [install-recursive] Error 1 --------------------------- 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 Fri Mar 23 00:15:43 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:47 2006 Subject: [Pipet Devel] Overflow install error References: <3ABAD038.367ECD62@bioinformatics.org> Message-ID: <3ABADBFF.4AB1DE79@gel.usherb.ca> > I know that you just told me not to use GCC 2.96, but I thought that I might > give the code in CVS a try. Anyway, FYI, here is an error I caught: I know, I got that one too... I finally found out what the problem is... because FFTW is in /usr/include, configure adds a -I/usr/include to the g++ command line. Now, there's a complex.h in /usr/include that seem to conflict with the complex.h in /usr/include/g++-3/. It works fine on my Mandrake box (and I have a /usr/include/complex.h). I don't know exactly who's fault it is (should the complier guaranty I can add -I/usr/include?)... I'll try (eventually) to find a workaround. In the mean time, you can either a) manually edit the Makefile to remove the -I/usr/include b) fix the FFTW autoconf macro in acinclude.m4 Good luck! Jean-Marc > Making install in src > make[2]: Entering directory `/usr/src/Overflow/Overflow/audio_blocks/src' > /bin/sh ../libtool --mode=compile c++ -DLINUX=1 -DPROTOTYPES=1 > -DHAVE_FLOAT_H=1 -DHAVE_SYS_SOUNDCARD_H=1 -DHAVE_LIBM=1 -DHAVE_LIBPTHREAD=1 > -DHAVE_FFTW=1 -I. -I. -I../../data-flow/include -I../include > -I/usr/include -g -O2 -c RFFT.cc > c++ -DLINUX=1 -DPROTOTYPES=1 -DHAVE_FLOAT_H=1 -DHAVE_SYS_SOUNDCARD_H=1 > -DHAVE_LIBM=1 -DHAVE_LIBPTHREAD=1 -DHAVE_FFTW=1 -I. -I. > -I../../data-flow/include -I../include -I/usr/include -g -O2 > -Wp,-MD,.deps/RFFT.pp -c RFFT.cc -fPIC -DPIC -o RFFT.lo > In file included from /usr/local/include/g++-3/complex:8, > from RFFT.cc:23: > /usr/local/include/g++-3/std/complext.h:314: declaration of `double hypot > (double, double)' throws > different exceptions > /usr/include/bits/mathinline.h:617: than previous declaration `double > hypot (double, double) throw ()' -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca