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From: Adam C P. IV <haz...@de...> - 2009-08-04 13:59:28
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Hi, The following segfault-inducing code came in from a user (details at http://bugs.debian.org/535318 ): from numpy import * from pysparse import * m = 4 n = 3 nodec=0 A = spmatrix.ll_mat(m*n, m*n) H = 3 V = 2 a = [0,0,0,] #row index b = [0,1,n] #column index val = [H+V, -H, -V] #node value w=m*n nodec=0 w=m*n bottomr=w-n for i in range(w): for j in range(w): if (nodec)<bottomr:#check necessary to make sure we don't #try puting south neighbours for the bottom row of nodes b.append(nodec+n) a.append(nodec-1)#row index, we skipped the first node val.append(-V) nodec=nodec+1 A.put(val,a,b) print A for i in range(w): for j in range(w): if (nodec-n)>=0: #check necessary to make sure we don't #try puting north neighbours for the top row of nodes b.append(nodec-n) a.append(nodec-1)#row index val.append(-V) nodec=nodec+1 A.put(val,a,b) print A Also a log of crash: In [20]: a Out[20]: [1, 3, 5] In [21]: b Out[21]: [2, 3, 5] In [22]: c Out[22]: [4, 5, 9] In [23]: A.take(c,a,b) Segmentation fault Any ideas? Bug in user's code, pysparse, or Debian packaging? Thanks, -Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ |
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From: Adam C P. IV <haz...@de...> - 2009-08-04 22:58:50
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On Tue, 2009-08-04 at 12:12 -0400, Dominique Orban wrote: > On Tue, Aug 4, 2009 at 9:37 AM, Adam C Powell IV <haz...@de...> > wrote: > Hi, > > The following segfault-inducing code came in from a user > (details at > http://bugs.debian.org/535318 ): > > from numpy import * > from pysparse import * [snip] > Segmentation fault > > Any ideas? Bug in user's code, pysparse, or Debian packaging? > Hi, > > > Thanks for the report. Lots of bugs in user's code. Still Pysparse > should not have crashed with a segfault. I have now added appropriate > argument checking. Thank you. Any idea when a new release might happen? > The user who reported the bug is also the author of the Deb package. > He says he will fix the package soon. Sorry I wasn't clear: the package author is me, the user who reported this is Oz Nahum (or Nahum Oz?). -Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ |
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From: Dominique O. <dom...@gm...> - 2009-08-04 23:14:47
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On Tue, Aug 4, 2009 at 6:44 PM, Adam C Powell IV <haz...@de...>wrote: > On Tue, 2009-08-04 at 12:12 -0400, Dominique Orban wrote: > > On Tue, Aug 4, 2009 at 9:37 AM, Adam C Powell IV <haz...@de...> > > wrote: > > Hi, > > > > The following segfault-inducing code came in from a user > > (details at > > http://bugs.debian.org/535318 ): > > > > from numpy import * > > from pysparse import * > [snip] > > Segmentation fault > > > > Any ideas? Bug in user's code, pysparse, or Debian packaging? > > Hi, > > > > > > Thanks for the report. Lots of bugs in user's code. Still Pysparse > > should not have crashed with a segfault. I have now added appropriate > > argument checking. > > Thank you. Any idea when a new release might happen? I updated the Pysparse svn repository earlier today (revision 124). Oz's code now terminates with appropriate error messages. What is best for you? Are you able to grab the svn tree to package the source into a deb or would you rather a tar.gz of the source tree? I admit I've been relying on svn so far and haven't released the source tree much. > > The user who reported the bug is also the author of the Deb package. > > He says he will fix the package soon. > > Sorry I wasn't clear: the package author is me, the user who reported > this is Oz Nahum (or Nahum Oz?). Ah I misunderstood that. Oz was trying to package Pysparse into a deb at some point, which is why I thought he was still the package author. Thank you for your help. I'll mention on the website that a deb is now available. -- Dominique |
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From: Adam C P. IV <haz...@de...> - 2009-08-04 23:48:18
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On Tue, 2009-08-04 at 19:14 -0400, Dominique Orban wrote: > On Tue, Aug 4, 2009 at 6:44 PM, Adam C Powell IV <haz...@de...> > wrote: > On Tue, 2009-08-04 at 12:12 -0400, Dominique Orban wrote: > > On Tue, Aug 4, 2009 at 9:37 AM, Adam C Powell IV > <haz...@de...> > > wrote: > > Hi, > > > > The following segfault-inducing code came in from a > user > > (details at > > http://bugs.debian.org/535318 ): > > > > from numpy import * > > from pysparse import * > > [snip] > > Segmentation fault > > > > Any ideas? Bug in user's code, pysparse, or Debian > packaging? > > Hi, > > > > > > Thanks for the report. Lots of bugs in user's code. Still > Pysparse > > should not have crashed with a segfault. I have now added > appropriate > > argument checking. > > > Thank you. Any idea when a new release might happen? > > > I updated the Pysparse svn repository earlier today (revision 124). > Oz's code now terminates with appropriate error messages. What is best > for you? Are you able to grab the svn tree to package the source into > a deb or would you rather a tar.gz of the source tree? I admit I've > been relying on svn so far and haven't released the source tree much. I'd be happy to package the SVN tree, I do that also for Elmer. But an occasional release would be nice, whenever is convenient for you. > > The user who reported the bug is also the author of the Deb > package. > > He says he will fix the package soon. > > > Sorry I wasn't clear: the package author is me, the user who > reported > this is Oz Nahum (or Nahum Oz?). > > > Ah I misunderstood that. Oz was trying to package Pysparse into a deb > at some point, which is why I thought he was still the package author. > Thank you for your help. I'll mention on the website that a deb is now > available. Great, thanks. My .deb has been in unstable for almost three years now, and released as part of Lenny (5.0). I think it's also been in Ubuntu universe since Hardy Heron (8.04), maybe even Gutsy Gibbon (7.10). -Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ |
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From: Daniel W. <dan...@gm...> - 2009-08-05 14:13:27
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Hi Adam, Hope all is well. Isn't it probably best to the deb release from an official pysparse release? The latest release is 1.0.1, which at this stage is a little old. So, maybe we should do a pysparse release and then do the deb. Dominque, Shall I go ahead and do that? The version number probably needs bumping to 1.1 as there are a lot of extra features that you've added, but a script that uses 1.0 will probably still work with 1.1. Right? On Tue, Aug 4, 2009 at 7:47 PM, Adam C Powell IV<haz...@de...> wrote: > On Tue, 2009-08-04 at 19:14 -0400, Dominique Orban wrote: >> On Tue, Aug 4, 2009 at 6:44 PM, Adam C Powell IV <haz...@de...> >> wrote: >> On Tue, 2009-08-04 at 12:12 -0400, Dominique Orban wrote: >> > On Tue, Aug 4, 2009 at 9:37 AM, Adam C Powell IV >> <haz...@de...> >> > wrote: >> > Hi, >> > >> > The following segfault-inducing code came in from a >> user >> > (details at >> > http://bugs.debian.org/535318 ): >> > >> > from numpy import * >> > from pysparse import * >> >> [snip] >> > Segmentation fault >> > >> > Any ideas? Bug in user's code, pysparse, or Debian >> packaging? >> > Hi, >> > >> > >> > Thanks for the report. Lots of bugs in user's code. Still >> Pysparse >> > should not have crashed with a segfault. I have now added >> appropriate >> > argument checking. >> >> >> Thank you. Any idea when a new release might happen? >> >> >> I updated the Pysparse svn repository earlier today (revision 124). >> Oz's code now terminates with appropriate error messages. What is best >> for you? Are you able to grab the svn tree to package the source into >> a deb or would you rather a tar.gz of the source tree? I admit I've >> been relying on svn so far and haven't released the source tree much. > > I'd be happy to package the SVN tree, I do that also for Elmer. But an > occasional release would be nice, whenever is convenient for you. > >> > The user who reported the bug is also the author of the Deb >> package. >> > He says he will fix the package soon. >> >> >> Sorry I wasn't clear: the package author is me, the user who >> reported >> this is Oz Nahum (or Nahum Oz?). >> >> >> Ah I misunderstood that. Oz was trying to package Pysparse into a deb >> at some point, which is why I thought he was still the package author. >> Thank you for your help. I'll mention on the website that a deb is now >> available. > > Great, thanks. My .deb has been in unstable for almost three years now, > and released as part of Lenny (5.0). I think it's also been in Ubuntu > universe since Hardy Heron (8.04), maybe even Gutsy Gibbon (7.10). > > -Adam > -- > GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 > > Engineering consulting with open source tools > http://www.opennovation.com/ > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Pysparse-developers mailing list > Pys...@li... > https://lists.sourceforge.net/lists/listinfo/pysparse-developers > > -- Daniel Wheeler |
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From: Dominique O. <dom...@gm...> - 2009-08-05 14:18:39
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On Wed, Aug 5, 2009 at 10:13 AM, Daniel Wheeler <dan...@gm...>wrote: > Hi Adam, Hope all is well. Isn't it probably best to the deb release > from an official pysparse release? The latest release is 1.0.1, which > at this stage is a little old. So, maybe we should do a pysparse > release and then do the deb. > > Dominque, Shall I go ahead and do that? The version number probably > needs bumping to 1.1 as there are a lot of extra features that you've > added, but a script that uses 1.0 will probably still work with 1.1. > Right? Hi Daniel, Yes, please go ahead a issue a new 1.1 release. I'm currently tied up with lots of commitments. And yes, everything is backward compatible. Thanks! -- Dominique |
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From: Adam C P. IV <haz...@de...> - 2009-08-05 18:16:26
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Hi Dan, Yes, an official release would be helpful. Using SVN is generally a temporary thing, e.g. Elmer is hoping to release 6.0 this Fall, and is a complex package, so I wanted to use SVN to iron out the bugs before release. So if there's a 1.1.0 pysparse soon, I'll go ahead and package that. Thanks, Adam On Wed, 2009-08-05 at 10:13 -0400, Daniel Wheeler wrote: > Hi Adam, Hope all is well. Isn't it probably best to the deb release > from an official pysparse release? The latest release is 1.0.1, which > at this stage is a little old. So, maybe we should do a pysparse > release and then do the deb. > > Dominque, Shall I go ahead and do that? The version number probably > needs bumping to 1.1 as there are a lot of extra features that you've > added, but a script that uses 1.0 will probably still work with 1.1. > Right? -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ |
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From: Daniel W. <dan...@gm...> - 2009-08-05 19:09:54
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On Wed, Aug 5, 2009 at 2:02 PM, Adam C Powell IV<haz...@de...> wrote: > Hi Dan, > > Yes, an official release would be helpful. Using SVN is generally a > temporary thing, e.g. Elmer is hoping to release 6.0 this Fall, and is a > complex package, so I wanted to use SVN to iron out the bugs before > release. I see. You just need to iron out dependencies and stuff like that > So if there's a 1.1.0 pysparse soon, I'll go ahead and package that. I'll do it soon and give you a heads up when it is done. This is going into the Debian repositories correct? What about Ubuntu? One other thing. Now that pysparse will be in the repositories (and also trilinos in lenny and karmic), I don't think there is anything stopping us going ahead with getting fipy in there. How should I proceed with that? -- Daniel Wheeler |
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From: Adam C P. IV <haz...@de...> - 2009-08-05 19:30:17
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On Wed, 2009-08-05 at 15:09 -0400, Daniel Wheeler wrote: > On Wed, Aug 5, 2009 at 2:02 PM, Adam C Powell IV<haz...@de...> wrote: > > Hi Dan, > > > > Yes, an official release would be helpful. Using SVN is generally a > > temporary thing, e.g. Elmer is hoping to release 6.0 this Fall, and is a > > complex package, so I wanted to use SVN to iron out the bugs before > > release. > > I see. You just need to iron out dependencies and stuff like that Yeah, that's not a problem. > > So if there's a 1.1.0 pysparse soon, I'll go ahead and package that. > > I'll do it soon and give you a heads up when it is done. This is going > into the Debian repositories correct? What about Ubuntu? Yes, into Debian. Ubuntu slurps Debian packages into their "universe" soon after release. So the Karmic universe is already well-established by now, and they'll only update packages if they are core to their release plans -- which pysparse almost certainly is not. > One other thing. Now that pysparse will be in the repositories (and > also trilinos in lenny and karmic), I don't think there is anything > stopping us going ahead with getting fipy in there. How should I > proceed with that? Indeed, that was my original motivation for packaging PySparse. :-) I'll revisit that after packaging the new PySparse release. -Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ |
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From: Daniel W. <dan...@gm...> - 2009-08-31 22:47:39
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Hi, I did a release of version 1.1 of pysparse, which involved: - bumping version number to 1.1 - creating tags/version-1_1 branch - releasing using the tags/version-1_1 branch - bumping version number to 1.2a1 (just a way to say that you don't have version 1,1 but a later revision on trunk) Future bug fixes should be done on "branches/version-1_1". "tags/version-1_1" is just a place holder to remember which revision version 1.1 was, it shouldn't be touched. There are a lot of changes from 1.0 and I don't know what all of them are.I think the main difference between 1.1 and 1,0 is the vastly superior indexing capabilities thanks to Dominque's wonderful effort to get fancy type indexing working in pysparse. Cheers On Wed, Aug 5, 2009 at 3:29 PM, Adam C Powell IV<haz...@de...> wrote: > On Wed, 2009-08-05 at 15:09 -0400, Daniel Wheeler wrote: >> On Wed, Aug 5, 2009 at 2:02 PM, Adam C Powell IV<haz...@de...> wrote: >> > Hi Dan, >> > >> > Yes, an official release would be helpful. Using SVN is generally a >> > temporary thing, e.g. Elmer is hoping to release 6.0 this Fall, and is a >> > complex package, so I wanted to use SVN to iron out the bugs before >> > release. >> >> I see. You just need to iron out dependencies and stuff like that > > Yeah, that's not a problem. > >> > So if there's a 1.1.0 pysparse soon, I'll go ahead and package that. >> >> I'll do it soon and give you a heads up when it is done. This is going >> into the Debian repositories correct? What about Ubuntu? > > Yes, into Debian. Ubuntu slurps Debian packages into their "universe" > soon after release. So the Karmic universe is already well-established > by now, and they'll only update packages if they are core to their > release plans -- which pysparse almost certainly is not. > >> One other thing. Now that pysparse will be in the repositories (and >> also trilinos in lenny and karmic), I don't think there is anything >> stopping us going ahead with getting fipy in there. How should I >> proceed with that? > > Indeed, that was my original motivation for packaging PySparse. :-) > > I'll revisit that after packaging the new PySparse release. > > -Adam > -- > GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 > > Engineering consulting with open source tools > http://www.opennovation.com/ > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Pysparse-developers mailing list > Pys...@li... > https://lists.sourceforge.net/lists/listinfo/pysparse-developers > > -- Daniel Wheeler |
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From: Adam C P. IV <haz...@de...> - 2009-08-31 23:49:37
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Thanks very much Dan! I'll package it soon. -Adam On Mon, 2009-08-31 at 18:47 -0400, Daniel Wheeler wrote: > Hi, > > I did a release of version 1.1 of pysparse, which involved: > > - bumping version number to 1.1 > - creating tags/version-1_1 branch > - releasing using the tags/version-1_1 branch > - bumping version number to 1.2a1 (just a way to say that you don't > have version 1,1 but a later revision on trunk) > > Future bug fixes should be done on "branches/version-1_1". > "tags/version-1_1" is just a place holder to remember which revision > version 1.1 was, it shouldn't be touched. > > There are a lot of changes from 1.0 and I don't know what all of them > are.I think the main difference between 1.1 and 1,0 is the vastly > superior indexing capabilities thanks to Dominque's wonderful effort > to get fancy type indexing working in pysparse. > > Cheers > > On Wed, Aug 5, 2009 at 3:29 PM, Adam C Powell IV<haz...@de...> wrote: > > On Wed, 2009-08-05 at 15:09 -0400, Daniel Wheeler wrote: > >> On Wed, Aug 5, 2009 at 2:02 PM, Adam C Powell IV<haz...@de...> wrote: > >> > Hi Dan, > >> > > >> > Yes, an official release would be helpful. Using SVN is generally a > >> > temporary thing, e.g. Elmer is hoping to release 6.0 this Fall, and is a > >> > complex package, so I wanted to use SVN to iron out the bugs before > >> > release. > >> > >> I see. You just need to iron out dependencies and stuff like that > > > > Yeah, that's not a problem. > > > >> > So if there's a 1.1.0 pysparse soon, I'll go ahead and package that. > >> > >> I'll do it soon and give you a heads up when it is done. This is going > >> into the Debian repositories correct? What about Ubuntu? > > > > Yes, into Debian. Ubuntu slurps Debian packages into their "universe" > > soon after release. So the Karmic universe is already well-established > > by now, and they'll only update packages if they are core to their > > release plans -- which pysparse almost certainly is not. > > > >> One other thing. Now that pysparse will be in the repositories (and > >> also trilinos in lenny and karmic), I don't think there is anything > >> stopping us going ahead with getting fipy in there. How should I > >> proceed with that? > > > > Indeed, that was my original motivation for packaging PySparse. :-) > > > > I'll revisit that after packaging the new PySparse release. > > > > -Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ |
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