From jeff at bioinformatics.org Tue Feb 6 18:11:58 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] UDDI and BXXP Message-ID: <3A8084BE.F4FA7ED9@bioinformatics.org> Jarl, I think that I mentioned these before, but maybe on the Loci list. You may have seen them, but I just want to post them again if you're looking for some ideas. http://uddi.org/ http://www.bxxp.org/bxxp/ Jeff From jarl at xs4all.nl Tue Feb 6 18:22:37 2001 From: jarl at xs4all.nl (jarl van katwijk) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] UDDI and BXXP References: <3A8084BE.F4FA7ED9@bioinformatics.org> Message-ID: <3A80873D.B5714EC2@xs4all.nl> > Hela Jeff > > I think that I mentioned these before, but maybe on the Loci list. You may > have seen them, but I just want to post them again if you're looking for some > ideas. > > http://uddi.org/ > > http://www.bxxp.org/bxxp/ Thanx.. cant have enough info, if only I had the time for it all ;) Will try hard to get a better picture of what's around and what's good for us. You checked that documents pack of Fipa? It's huge, but very interesting. For me\BL that is. Maybe I'll be silent for a few days now, but I guess you know I'm wearing of my eyes. jarl From jeff at bioinformatics.org Fri Feb 9 21:10:48 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] compaq beowulf cluster? Message-ID: <3A84A328.5D044E7A@bioinformatics.org> I was speaking with Prof. James Lyons-Weiler here at UMass Lowell today. He told me that he will be meeting with someone from Compaq in a short while about "hardware needs". I'm not clear about the purpose of the meeting, but I mentioned that we (Bioinformatics.org and Piper) were hoping to get a grant to buy a Beowulf cluster. Prof. Lyons-Weiler told me that he can procure one from Compaq. I asked him about a 22-node Alpha Beowulf, valued at about $150,000. He said that would be no problem, and that he could get one by the end of the semester. He also mentioned setting up Beowulf "Piper nodes" across the 5 UMass campuses. Well, it'd be beyond great if he could pull it off, and maybe he can. He's a new prof. with a lot of drive, and I don't think he was pulling my leg. But, like everything else, we will believe it when we see it, right? 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 xs4all.nl Sat Feb 10 04:26:17 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] compaq beowulf cluster? References: <3A84A328.5D044E7A@bioinformatics.org> Message-ID: <3A850939.36044B5B@xs4all.nl> > Prof. Lyons-Weiler told me that he can procure one from Compaq. I asked him > about a 22-node Alpha Beowulf, valued at about $150,000. He said that would > be no problem, and that he could get one by the end of the semester. He also > mentioned setting up Beowulf "Piper nodes" across the 5 UMass campuses. > > Well, it'd be beyond great if he could pull it off, and maybe he can. He's a > new prof. with a lot of drive, and I don't think he was pulling my leg. But, > like everything else, we will believe it when we see it, right? Good news Jeff, this would surely be great. Do you have any idear about the term it is about to take? jarl From jeff at bioinformatics.org Sat Feb 10 12:56:54 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] compaq beowulf cluster? References: <3A84A328.5D044E7A@bioinformatics.org> <3A850939.36044B5B@xs4all.nl> Message-ID: <3A8580E6.F9C6AAD5@bioinformatics.org> Jarl van Katwijk wrote: > > > Good news Jeff, this would surely be great. Do you have any idear about > the term it is about to take? Hi Jarl. I'm not sure what you mean by "the term it is about to take". Do you mean how long it will take? Prof. Lyons-Weiler said we could have it by May. But, I'm going to be "cautiously optimistic" about the whole thing. Say, what do you think about Khoros? Have you seen it before? 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 gvd at penguin.pharmacy.ualberta.ca Sat Feb 10 16:44:58 2001 From: gvd at penguin.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] Re: [directors] compaq beowulf cluster? In-Reply-To: <3A84A328.5D044E7A@bioinformatics.org> Message-ID: On Sat, 10 Feb 2001, J.W. Bizzaro wrote: > I was speaking with Prof. James Lyons-Weiler here at UMass Lowell today. He > told me that he will be meeting with someone from Compaq in a short while > about "hardware needs". I'm not clear about the purpose of the meeting, but I > mentioned that we (Bioinformatics.org and Piper) were hoping to get a grant to > buy a Beowulf cluster. > > Prof. Lyons-Weiler told me that he can procure one from Compaq. I asked him > about a 22-node Alpha Beowulf, valued at about $150,000. He said that would > be no problem, and that he could get one by the end of the semester. He also > mentioned setting up Beowulf "Piper nodes" across the 5 UMass campuses. > > Well, it'd be beyond great if he could pull it off, and maybe he can. He's a > new prof. with a lot of drive, and I don't think he was pulling my leg. But, > like everything else, we will believe it when we see it, right? That is really, really positive news! An investment like this in Piper/TOL would go a long way towards establishing our credibility in the open source bioinformatics community, if you catch my drift ;-) Its also very encouraging to hear others speak so confidently about our worthiness. BTW, nice work, Jeff! 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 -- -- From jarl at xs4all.nl Sun Feb 11 06:39:12 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] compaq beowulf cluster? References: <3A84A328.5D044E7A@bioinformatics.org> <3A850939.36044B5B@xs4all.nl> <3A8580E6.F9C6AAD5@bioinformatics.org> Message-ID: <3A8679E0.7FA0218@xs4all.nl> Yes, 'how long will it take', sorry, I translated a dutch way of saying too directly into english :) May would be very soon, good news! But even when this wont get a go, this mean more and more people are taking the piper project seriously. Khoros I didn't saw yet, and I didn't had time to read their specs. No time for the Fipa specs either, had something bad for dinner and was sick for 2 days. Did do some coding, but could find the concentration to read :( > Hi Jarl. I'm not sure what you mean by "the term it is about to take". Do > you mean how long it will take? Prof. Lyons-Weiler said we could have it by > May. But, I'm going to be "cautiously optimistic" about the whole thing. > > Say, what do you think about Khoros? Have you seen it before? From jeff at bioinformatics.org Sun Feb 11 13:24:14 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] Re: compaq beowulf cluster? References: <3A84A328.5D044E7A@bioinformatics.org> <3A850939.36044B5B@xs4all.nl> <3A8580E6.F9C6AAD5@bioinformatics.org> <3A8679E0.7FA0218@xs4all.nl> Message-ID: <3A86D8CE.2D1DC05D@bioinformatics.org> Jarl van Katwijk wrote: > > Yes, 'how long will it take', sorry, I translated a dutch way of saying > too directly into english :) > > May would be very soon, good news! > > But even when this wont get a go, this mean more and more people are > taking the piper project seriously. Nobody here should be holding their breath waiting for this :-) But it has been my plan all-along to get a Beowulf cluster for Piper. Whether we get one for free or through a grant, has yet to be seen, but we will get one! The cluster will meet two goals. My plan has been to make Piper available (on some big iron) as a service of Bioinformatics.org, not only to be useful to scientists but also to develop and improve the organization. In addition, this cluster will be a "big Piper node" on the Internet, and it will go a long way toward making Piper usable. I hope you feel better soon, Jarl :-) 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 Sun Feb 11 18:38:36 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] Compaq.com - CustomSystems & Solutions - High Performance Solutions Linux Platforms Linux Platforms Message-ID: <3A87227C.9FD03F80@bioinformatics.org> This is probably a good place to start looking: http://www.compaq.com/solutions/customsystems/hps/linux.html Am I window shopping? Jeff From jeff at bioinformatics.org Mon Feb 12 12:11:36 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] list of p2p apps Message-ID: <3A881948.D2FD66D9@bioinformatics.org> Jarl, This site has a big list of P2P apps on the left sidebar, for reference: http://www.peertal.com/ Jeff From jeff at bioinformatics.org Fri Feb 16 15:11:45 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] [Fwd: Call for Papers: NETTAB Workshop] Message-ID: <3A8D8981.F646F521@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: unknown sender Subject: [Biopython-announce] Call for Papers: NETTAB Workshop Date: Fri, 16 Feb 2001 13:50:34 +0100 Size: 5172 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/20010216/b8f981eb/attachment.mht From jarl at xs4all.nl Fri Feb 16 19:13:22 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] BL classes Message-ID: <3A8DC222.FD4BF217@xs4all.nl> Hi, Just a small post, it might clarify more of the BL. The inheritance structure of the BL of Piper looks like this: data <-- data that nodes transport | node <-- node layer, the core of the system | | relation | <-- Handles relations between node, also the conflicts | | | legacy <- legacy code, OS\hardware specific stuff | | resource <- Handles resources (ram, hd space, etc.) | area <-- all above this (data->resource) is private, but accessible | through wrappers | engine <- few public functions for the admin layer | | | admin <- external interfaces to engine, may be GUI or scripts | plugin <- nodes in BL are implemented by plugins | | | | | visual <- plugins of type visual, cq output nodes | | | filter <- plugins of type filter, cq internal nodes | sensor <- plugins of type sensor, cq input nodes Maybe somebody has some feedback about it. It looks like the right structure so far, the BL core already runs based on this. I'm now doing the DL and PL code. (Both BL plugins) jarl From jeff at bioinformatics.org Sat Feb 17 03:21:57 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] SourceForge: Project Info - Piper Message-ID: <3A8E34A5.AE2971ED@bioinformatics.org> http://sourceforge.net/projects/piper/ Jeff From valj01 at gel.usherb.ca Sun Feb 18 23:06:07 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] SourceForge: Project Info - Piper References: <3A8E34A5.AE2971ED@bioinformatics.org> Message-ID: <3A909BAF.C0F53357@gel.usherb.ca> > http://sourceforge.net/projects/piper/ I think you're presenting only one view of Piper... if you ask me: "Piper is a visual environment that simplifies development of signal processing/multimedia applications." Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jeff at bioinformatics.org Mon Feb 19 01:52:47 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] SourceForge: Project Info - Piper References: <3A8E34A5.AE2971ED@bioinformatics.org> <3A909BAF.C0F53357@gel.usherb.ca> Message-ID: <3A90C2BE.6D72648A@bioinformatics.org> Jean-Marc Valin wrote: > > > http://sourceforge.net/projects/piper/ > > I think you're presenting only one view of Piper... if you ask me: "Piper is a > visual environment that simplifies development of signal processing/multimedia > applications." ? :-) I should have explained. That SourceForge project is *NOT* ours. Someone else is using the name Piper. I wrote to him but haven't heard back. Anyway, it seems the project hasn't gone anywhere in 6 months. 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 Feb 19 06:50:09 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] SourceForge: Project Info - Piper References: <3A8E34A5.AE2971ED@bioinformatics.org> <3A909BAF.C0F53357@gel.usherb.ca> Message-ID: <3A910871.A9D4CF6D@xs4all.nl> > > I think you're presenting only one view of Piper... if you ask me: "Piper is a > visual environment that simplifies development of signal processing/multimedia > applications." There's only one way JM: take up the keyboard and write some for the Piper Developer's Manual ;) jarl From valj01 at gel.usherb.ca Mon Feb 19 08:24:26 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] SourceForge: Project Info - Piper References: <3A8E34A5.AE2971ED@bioinformatics.org> <3A909BAF.C0F53357@gel.usherb.ca> <3A90C2BE.6D72648A@bioinformatics.org> Message-ID: <3A911E8A.F9A6F190@gel.usherb.ca> "J.W. Bizzaro" a ?crit : > > Jean-Marc Valin wrote: > > > > > http://sourceforge.net/projects/piper/ > > > > I think you're presenting only one view of Piper... if you ask me: "Piper is a > > visual environment that simplifies development of signal processing/multimedia > > applications." > > ? :-) I should have explained. That SourceForge project is *NOT* ours. > Someone else is using the name Piper. I wrote to him but haven't heard back. > Anyway, it seems the project hasn't gone anywhere in 6 months. Oops... sorry :-) It just sounded a lot like the BL security stuff that will go into Piper. Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jeff at bioinformatics.org Thu Feb 22 16:07:39 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] [Fwd: WAX] Message-ID: <3A957F9B.C1AF7161@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: Bradley Marshall Subject: Re: WAX Date: Thu, 22 Feb 2001 10:53:35 -0800 (PST) Size: 2187 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/20010222/a6b26112/attachment.mht From jeff at bioinformatics.org Sun Feb 25 23:46:24 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:43 2006 Subject: [Pipet Devel] dl2bl file not written Message-ID: <3A99DFA0.495E1198@bioinformatics.org> Jarl, I'm getting an error that indicates the DL2BL IOR file is not being written: ------------------------------------------------------------------------ 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... Message: Piper BL 0.4.0pre10 wrote IOR file /home/jeff/piper_info/ior/bl2pl.ior ior file: /home/jeff/piper_info/ior/dl2bl.ior Wrote IOR file /home/jeff/piper_info/ior/uil2dl.ior Getting document... Connecting with the bl... IOR file for Brokering Layer not found. Connection with BL not established. Loading crash info... Aborted ------------------------------------------------------------------------ It should be written by the BL, right? I'm a bit confused, since I upgraded to GLIBC 2.2, and I'm not sure if that is causing this problem somehow. 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 xs4all.nl Mon Feb 26 04:56:23 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> Message-ID: <3A9A2847.8DFBAE12@xs4all.nl> Hi Jeff, > I'm getting an error that indicates the DL2BL IOR file is not being written: > ------------------------------------------------------------------------ > 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... > Message: Piper BL 0.4.0pre10 > wrote IOR file /home/jeff/piper_info/ior/bl2pl.ior > ior file: /home/jeff/piper_info/ior/dl2bl.ior > Wrote IOR file /home/jeff/piper_info/ior/uil2dl.ior > Getting document... > Connecting with the bl... > IOR file for Brokering Layer not found. > Connection with BL not established. > Loading crash info... > Aborted > ------------------------------------------------------------------------ > > It should be written by the BL, right? Yes. Does it exsist at all in ~/piper_info/ior/ ? > > I'm a bit confused, since I upgraded to GLIBC 2.2, and I'm not sure if that is > causing this problem somehow. Did it work before? just a short reply, have to run now, jarl From jeff at bioinformatics.org Mon Feb 26 03:18:48 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] dl2bl file not written References: <3A99DFA0.495E1198@bioinformatics.org> <3A9A2847.8DFBAE12@xs4all.nl> Message-ID: <3A9A1168.864178C9@bioinformatics.org> Jarl van Katwijk wrote: > > > It should be written by the BL, right? > Yes. Does it exsist at all in ~/piper_info/ior/ ? No, it doesn't exist. The DL raises the error. But, I checked both DL and BL code, and it seems that the BL is the one to write the file. Does the BL write a message to stdout when it writes the file? Can it write an error message when it can't? > > I'm a bit confused, since I upgraded to GLIBC 2.2, and I'm not sure if that is > > causing this problem somehow. > Did it work before? It did work *SOMETIME* before, but I didn't check just prior to upgrading to glibc 2.2. A lot of Linux programs are now requiring glibc 2.2, so that's why I need to upgrade. I'd like to know if upgrading to gcc 2.96. I'm getting some errors compiling Overflow now....oy! Perhaps glibc 2.2 and gcc 2.95 don't work together? 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 Mon Feb 26 09:30:59 2001 From: jmvalin at locusdialogue.com (Jean-Marc Valin) 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> Message-ID: <3A9A68A3.79E12CA0@locusdialogue.com> > I'd like to know if upgrading to gcc 2.96. I'm getting some errors compiling > Overflow now....oy! Perhaps glibc 2.2 and gcc 2.95 don't work together? What errors are you getting? -- with which compiler? Overflow is known to compile with 2.95.x. I *may* work with 2.96, but I cannot guarantee it will. Note that if you're using the version from CVS, I've been doing important modifications recently, so that may be the cause of your errors (try 0.3.0 until I stabilize everything and make a release). Jean-Marc From jeff at bioinformatics.org Mon Feb 26 11:11:38 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) 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> Message-ID: <3A9A803A.55492964@bioinformatics.org> Jean-Marc Valin wrote: > > What errors are you getting? -------------------------------------------------------------- Making all in data-flow make[1]: Entering directory `/usr/src/Overflow/Overflow/data-flow' Making all in src make[2]: Entering directory `/usr/src/Overflow/Overflow/data-flow/src' /bin/sh ../../libtool --mode=compile c++ -DLINUX=1 -DPROTOTYPES=1 -DHAVE_LIBM=1 -DHAVE_LIBDL=1 -DHAVE_LIBPTHREAD=1 -DHAVE_PTHREAD_CANCEL=1 -I. -I. -I../../data-flow/include -I/usr/include/gnome-xml -g -O2 -c Node.cc c++ -DLINUX=1 -DPROTOTYPES=1 -DHAVE_LIBM=1 -DHAVE_LIBDL=1 -DHAVE_LIBPTHREAD=1 -DHAVE_PTHREAD_CANCEL=1 -I. -I. -I../../data-flow/include -I/usr/include/gnome-xml -g -O2 -Wp,-MD,.deps/Node.pp -c Node.cc -fPIC -DPIC -o Node.lo In file included from /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/iostream.h:31, from /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/stl_alloc.h:45, from /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/alloc.h:21, from /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/std/bastring.h:39, from /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/string:6, from ../../data-flow/include/Node.h:21, from Node.cc:17: /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/streambuf.h: In method `struct streampos streambuf::pubseekoff(long long int, ios::seek_dir, int = 3)': /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/streambuf.h:362: conversion from `__off64_t' to non-scalar type `streampos' requested /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/streambuf.h: In method `struct streampos streambuf::pubseekpos(_G_fpos64_t, int = 3)': /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/streambuf.h:364: `struct streampos' used where a `long long int' was expected make[2]: *** [Node.lo] Error 1 make[2]: Leaving directory `/usr/src/Overflow/Overflow/data-flow/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/usr/src/Overflow/Overflow/data-flow' make: *** [all-recursive] Error 1 Making install in data-flow make[1]: Entering directory `/usr/src/Overflow/Overflow/data-flow' Making install in src make[2]: Entering directory `/usr/src/Overflow/Overflow/data-flow/src' /bin/sh ../../libtool --mode=compile c++ -DLINUX=1 -DPROTOTYPES=1 -DHAVE_LIBM=1 -DHAVE_LIBDL=1 -DHAVE_LIBPTHREAD=1 -DHAVE_PTHREAD_CANCEL=1 -I. -I. -I../../data-flow/include -I/usr/include/gnome-xml -g -O2 -c Node.cc c++ -DLINUX=1 -DPROTOTYPES=1 -DHAVE_LIBM=1 -DHAVE_LIBDL=1 -DHAVE_LIBPTHREAD=1 -DHAVE_PTHREAD_CANCEL=1 -I. -I. -I../../data-flow/include -I/usr/include/gnome-xml -g -O2 -Wp,-MD,.deps/Node.pp -c Node.cc -fPIC -DPIC -o Node.lo In file included from /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/iostream.h:31, from /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/stl_alloc.h:45, from /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/alloc.h:21, from /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/std/bastring.h:39, from /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/string:6, from ../../data-flow/include/Node.h:21, from Node.cc:17: /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/streambuf.h: In method `struct streampos streambuf::pubseekoff(long long int, ios::seek_dir, int = 3)': /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/streambuf.h:362: conversion from `__off64_t' to non-scalar type `streampos' requested /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/streambuf.h: In method `struct streampos streambuf::pubseekpos(_G_fpos64_t, int = 3)': /usr/lib/gcc-lib/i386-redhat-linux/2.95.2/../../../../include/g++-3/streambuf.h:364: `struct streampos' used where a `long long int' was expected make[2]: *** [Node.lo] Error 1 make[2]: Leaving directory `/usr/src/Overflow/Overflow/data-flow/src' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/usr/src/Overflow/Overflow/data-flow' make: *** [install-recursive] Error 1 -------------------------------------------------------------- Am I imagining things, or are these errors coming from the g++ headers and not Overflow? Note that the g++-3 libraries come from libstdc++-2.95.2. I didn't upgrade that yet. > -- with which compiler? Overflow is known > to compile with 2.95.x. It's the 2.95.x compiler that I've been using all along. > it will. Note that if you're using the version from CVS, I've been doing > important modifications recently, so that may be the cause of your > errors (try 0.3.0 until I stabilize everything and make a release). Okay, I'll stick with that for a while then. In the meantime, I'll *TRY* things with the 2.96 compiler. 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 jmvalin at locusdialogue.com Mon Feb 26 11:21:19 2001 From: jmvalin at locusdialogue.com (Jean-Marc Valin) 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> Message-ID: <3A9A827F.C6D02C89@locusdialogue.com> > Am I imagining things, or are these errors coming from the g++ headers and not > Overflow? > > Note that the g++-3 libraries come from libstdc++-2.95.2. I didn't upgrade > that yet. I'm not totally sure, but I'd guess the problem comes from the fact that the g++ headers don't like your new glibc headers... Remember that most people will tell you "not to upgrade glibc unless you really know what you're doing", as it may have lots of unexpected effects. > It's the 2.95.x compiler that I've been using all along. Good. > Okay, I'll stick with that for a while then. > > In the meantime, I'll *TRY* things with the 2.96 compiler. Keep me informed of problems with g++ 2.96, so I can improve 2.96 support. Jean-Marc From jarl at xs4all.nl Wed Feb 28 07:17:58 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> Message-ID: <3A9CEC76.7160B749@xs4all.nl> Hi Jeff, I just had a look at the current cvs code of Piper, and I got the same error you have about the DL-BL connection. After I done some it worked again. This is what I did: 1. rm ~/piper_info/BL_status_save 2. rm ~/piper_info/pids/* 3. Export the VFLOW path 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. jarl From chapmanb at arches.uga.edu Wed Feb 28 05:39:03 2001 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Fri Feb 10 19:20:44 2006 Subject: [Pipet Devel] dl2bl file not written In-Reply-To: <3A9CEC76.7160B749@xs4all.nl> 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> Message-ID: <15004.54599.870902.94467@taxus.athen1.ga.home.com> Hi Jarl! > 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. Brad From jeff at bioinformatics.org Wed Feb 28 06:27:23 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) 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> Message-ID: <3A9CE09B.EF08663C@bioinformatics.org> 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? 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. 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 --