Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
On Thu, Dec 15, 2011 at 07:45:47PM -0500, Adam C Powell IV wrote: Found the problem. PETSc built on November 16 with mpi-defaults 0.6 which depended on LAM on non-openmpi arches. Now mpi-defaults 1.0.1 released 12/4 depends on MPICH2, so we have a mix of architectures installed. And mpi-defaults just went into testing today... Crap! It may be that other PETSc dependencies need rebuilding too... and there are a lot of them! Let's see: suitesparse, spooles, hypre, scotch, blacs-mpi, scalapack, mumps, all have to be rebuilt with MPICH2! What was built when: * suitesparse: April 15 2010 * spooles: May 11 2010 * hypre: August 15 2010 * scotch: April 6 2011 * blacs-mpi: August 29 2011 * scalapack: September 18 2011 * mumps: March 31 2011 None was built recently, all need to be rebuilt. mpi-defaults should not be in testing until at least these are rebuilt, probably others. Note: HDF5 is not a problem for PETSc because PETSc only links to it on OpenMPI platforms. I forgot why that is, maybe it's worth a try building PETSc against HDF5-mpich2? Maybe later... Okay, cloning this bug to a bunch of packages, see above. I've been an uploader to all except blacs-mpi and scalapack, and many of them could use some maintenance, this is a good excuse to spend time on them. :-) Adam, Is this bug still relevant? All the blocking bugs have been fixed, except 651452, which is about illuminator, which is not in testing. Cheers, Ivo -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#650804: Bug#652313: Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
On Fri, 2011-12-23 at 20:50 +0100, Muammar El Khatib wrote: Hi Adam, On Fri, Dec 23, 2011 at 14:41, Adam C Powell IV hazel...@debian.org wrote: Hi Muammar, On Fri, 2011-12-23 at 11:59 +0100, Muammar El Khatib wrote: On Thu, Dec 22, 2011 at 23:28, Adam C Powell IV hazel...@debian.org wrote: tags 652313 patch thanks On Wed, 2011-12-21 at 13:23 -0500, Adam C Powell IV wrote: retitle 652313 Needs mpich2 targets in debian/rules block 652313 by 652312 thanks I have read the thread of this report. I'll proceed to upload blacs-mpi today, so that it gets built with the mpi-defaults = 1.0 as pointed out herein, and then proceed with scalapack. Tell me if I can go ahead, or if you have already taken any action and thus I don't interfere with it. I'm not doing anything. If you upload blacs-mpi, the upload should close 652312 and 650804 with out any changes. OK, I'll do it in some minutes. I am building it, for a next upload I'll change from format 1.0 to 3.0. Excellent, thanks, it is now built everywhere, and uploaded and installed on all platforms except PPC. Let me know when you fix and upload ScaLAPACK, and after that builds and installs I'll re-upload the fixed MUMPS. -Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ signature.asc Description: This is a digitally signed message part
Bug#650804: Bug#652313: Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Hi, On Thu, Dec 22, 2011 at 23:28, Adam C Powell IV hazel...@debian.org wrote: tags 652313 patch thanks On Wed, 2011-12-21 at 13:23 -0500, Adam C Powell IV wrote: retitle 652313 Needs mpich2 targets in debian/rules block 652313 by 652312 thanks Hi Julien, On Mon, 2011-12-19 at 21:03 +0100, Julien Cristau wrote: On Mon, Dec 19, 2011 at 08:43:12 -0500, Adam C Powell IV wrote: On Sat, 2011-12-17 at 17:32 +0100, Julien Cristau wrote: On Fri, Dec 16, 2011 at 08:00:15 -0500, Adam C Powell IV wrote: I think blacs-mpi, scalapack and suitesparse make sense for no-change rebuilds. But I've been procrastinating maintenance on the rest (just took care of spooles last night, working on hypre now) so this will motivate me to finish up hypre, scotch and mumps -- I'll take care of those three. What are the archs where those rebuilds are needed? Cheers, Julien armel, armhf, mips, mipsel, s390, s390x, sparc. Can't do that for blacs-mpi, it's broken: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=650804 The bug is in the lam implementation, which does not include an f90 wrapper. When the rebuild happens, it will use mpich2 which does have an f90 wrapper so it should work. So please schedule this build. I've just confirmed that blacs-mpi builds with libmpich2-dev installed, and does not build with lam4-dev installed with the same failure mode as on the buildds. Simply rescheduling a build of blacs-mpi with the new mpi-defaults depending on mpich2 instead of lam should therefore close bug #650804. Please schedule this build on armel, mips, mipsel, s390, s390x and sparc. (armhf apparently has openmpi.) Scheduled rebuilds for scalapack. Unfortunately scalapack depends on blacs-mpi, so blacs-mpi needs to go first. Looking at the log of the scheduled build, scalapack failed because it doesn't have an mpich2 target, so that will need just a bit of work, please do not schedule a second build of scalapack. I'm attaching a patch which fixes #652313. But blacs-mpi needs to be built before uploading with this fix. I have read the thread of this report. I'll proceed to upload blacs-mpi today, so that it gets built with the mpi-defaults = 1.0 as pointed out herein, and then proceed with scalapack. Tell me if I can go ahead, or if you have already taken any action and thus I don't interfere with it. Regards, -- Muammar El Khatib. Linux user: 403107. GPG Key = 127029F1 http://muammar.me | http://proyectociencia.org ,''`. : :' : `. `' `- -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#650804: Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
tags 652313 patch thanks On Wed, 2011-12-21 at 13:23 -0500, Adam C Powell IV wrote: retitle 652313 Needs mpich2 targets in debian/rules block 652313 by 652312 thanks Hi Julien, On Mon, 2011-12-19 at 21:03 +0100, Julien Cristau wrote: On Mon, Dec 19, 2011 at 08:43:12 -0500, Adam C Powell IV wrote: On Sat, 2011-12-17 at 17:32 +0100, Julien Cristau wrote: On Fri, Dec 16, 2011 at 08:00:15 -0500, Adam C Powell IV wrote: I think blacs-mpi, scalapack and suitesparse make sense for no-change rebuilds. But I've been procrastinating maintenance on the rest (just took care of spooles last night, working on hypre now) so this will motivate me to finish up hypre, scotch and mumps -- I'll take care of those three. What are the archs where those rebuilds are needed? Cheers, Julien armel, armhf, mips, mipsel, s390, s390x, sparc. Can't do that for blacs-mpi, it's broken: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=650804 The bug is in the lam implementation, which does not include an f90 wrapper. When the rebuild happens, it will use mpich2 which does have an f90 wrapper so it should work. So please schedule this build. I've just confirmed that blacs-mpi builds with libmpich2-dev installed, and does not build with lam4-dev installed with the same failure mode as on the buildds. Simply rescheduling a build of blacs-mpi with the new mpi-defaults depending on mpich2 instead of lam should therefore close bug #650804. Please schedule this build on armel, mips, mipsel, s390, s390x and sparc. (armhf apparently has openmpi.) Scheduled rebuilds for scalapack. Unfortunately scalapack depends on blacs-mpi, so blacs-mpi needs to go first. Looking at the log of the scheduled build, scalapack failed because it doesn't have an mpich2 target, so that will need just a bit of work, please do not schedule a second build of scalapack. I'm attaching a patch which fixes #652313. But blacs-mpi needs to be built before uploading with this fix. Also, I thoughtlessly uploaded mumps earlier today, which depends on scalapack and blacs-mpi. :-( Oh it's failing everywhere, and I think I know why, will fix and re-upload after the new scalapack goes in. Thanks, Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ diff -ur scalapack-1.8.0.orig/debian/changelog scalapack-1.8.0/debian/changelog --- scalapack-1.8.0.orig/debian/changelog 2011-09-18 11:09:36.0 -0400 +++ scalapack-1.8.0/debian/changelog 2011-12-22 16:58:13.0 -0500 @@ -1,3 +1,11 @@ +scalapack (1.8.0-8) unstable; urgency=low + + [ Adam C. Powell, IV ] + * Non-maintainer upload. + * Works with mpich2 as mpi default. + + -- Muammar El Khatib muam...@debian.org Thu, 22 Dec 2011 16:58:01 -0500 + scalapack (1.8.0-7) unstable; urgency=low * Test command execution failure caused due to incompatible file location in diff -ur scalapack-1.8.0.orig/debian/patches/01_SLmake.inc.patch scalapack-1.8.0/debian/patches/01_SLmake.inc.patch --- scalapack-1.8.0.orig/debian/patches/01_SLmake.inc.patch 2011-09-18 10:28:24.0 -0400 +++ scalapack-1.8.0/debian/patches/01_SLmake.inc.patch 2011-12-22 16:04:43.0 -0500 @@ -1,7 +1,7 @@ Index: scalapack-1.8.0/SLmake.inc === scalapack-1.8.0.orig/SLmake.inc 2007-04-07 06:37:26.0 +0200 -+++ scalapack-1.8.0/SLmake.inc 2011-09-18 15:49:24.971359670 +0200 +--- scalapack-1.8.0.orig/SLmake.inc scalapack-1.8.0/SLmake.inc @@ -33,15 +33,30 @@ # # MPI setup; tailor to your system if using MPIBLACS @@ -35,7 +35,7 @@ BLACSFINIT= -lblacsF77init-lam BLACSCINIT= -lblacsCinit-lam BLACSLIB = -lblacs-lam -@@ -56,7 +71,7 @@ +@@ -56,13 +71,28 @@ BLACSCINIT= /usr/lib/libblacsCinit-mpich.a BLACSLIB = /usr/lib/libblacs-mpich.a else @@ -44,7 +44,28 @@ BLACSFINIT= -lblacsF77init-mpich BLACSCINIT= -lblacsCinit-mpich BLACSLIB = -lblacs-mpich -@@ -96,10 +111,10 @@ + endif + TESTINGdir= $(home)/TESTING + endif ++ifeq ($(MPI),mpich2) ++USEMPI= -DUsingMpiBlacs ++ifeq ($(BUILD),static) ++SMPLIB= -L/usr/lib/mpich2/lib/ -lmpich ++BLACSFINIT= /usr/lib/libblacsF77init-mpich2.a ++BLACSCINIT= /usr/lib/libblacsCinit-mpich2.a ++BLACSLIB = /usr/lib/libblacs-mpich2.a ++else ++SMPLIB= -L/usr/lib/mpich2/lib/ -lmpich ++BLACSFINIT= -lblacsF77init-mpich2 ++BLACSCINIT= -lblacsCinit-mpich2 ++BLACSLIB = -lblacs-mpich2 ++endif ++TESTINGdir= $(home)/TESTING ++endif + ifeq ($(MPI),pvm) + USEMPI= + ifeq ($(BUILD),static) +@@ -96,10 +126,10 @@ # # The fortran and C compilers, loaders, and their flags # @@ -57,7 +78,7 @@ F77FLAGS = -Wall -O6 -funroll-all-loops -ffast-math $(NOOPT) CCFLAGS = -Wall $(FPIC) -O6 -funroll-all-loops -ffast-math
Processed: Re: Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Processing commands for cont...@bugs.debian.org: tags 652313 patch Bug #652313 [src:scalapack] Needs mpich2 targets in debian/rules Ignoring request to alter tags of bug #652313 to the same tags previously set thanks Stopping processing here. Please contact me if you need assistance. -- 652313: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=652313 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#652313: Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
retitle 652313 Needs mpich2 targets in debian/rules block 652313 by 652312 thanks Hi Julien, On Mon, 2011-12-19 at 21:03 +0100, Julien Cristau wrote: On Mon, Dec 19, 2011 at 08:43:12 -0500, Adam C Powell IV wrote: On Sat, 2011-12-17 at 17:32 +0100, Julien Cristau wrote: On Fri, Dec 16, 2011 at 08:00:15 -0500, Adam C Powell IV wrote: I think blacs-mpi, scalapack and suitesparse make sense for no-change rebuilds. But I've been procrastinating maintenance on the rest (just took care of spooles last night, working on hypre now) so this will motivate me to finish up hypre, scotch and mumps -- I'll take care of those three. What are the archs where those rebuilds are needed? Cheers, Julien armel, armhf, mips, mipsel, s390, s390x, sparc. Can't do that for blacs-mpi, it's broken: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=650804 The bug is in the lam implementation, which does not include an f90 wrapper. When the rebuild happens, it will use mpich2 which does have an f90 wrapper so it should work. So please schedule this build. Scheduled rebuilds for scalapack. Unfortunately scalapack depends on blacs-mpi, so blacs-mpi needs to go first. Looking at the log of the scheduled build, scalapack failed because it doesn't have an mpich2 target, so that will need just a bit of work, please do not schedule a second build of scalapack. suitesparse doesn't seem to have any lam dependencies? D'oh! You're right. My mistake, closing that bug now. Thanks, Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ signature.asc Description: This is a digitally signed message part
Processed: Re: Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Processing commands for cont...@bugs.debian.org: retitle 652313 Needs mpich2 targets in debian/rules Bug #652313 [src:scalapack] Rebuild with mpi-defaults = 1.0 Changed Bug title to 'Needs mpich2 targets in debian/rules' from 'Rebuild with mpi-defaults = 1.0' block 652313 by 652312 Bug #652313 [src:scalapack] Needs mpich2 targets in debian/rules Was blocked by: 652307 Added blocking bug(s) of 652313: 652312 thanks Stopping processing here. Please contact me if you need assistance. -- 652313: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=652313 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
On Sat, 2011-12-17 at 17:32 +0100, Julien Cristau wrote: On Fri, Dec 16, 2011 at 08:00:15 -0500, Adam C Powell IV wrote: I think blacs-mpi, scalapack and suitesparse make sense for no-change rebuilds. But I've been procrastinating maintenance on the rest (just took care of spooles last night, working on hypre now) so this will motivate me to finish up hypre, scotch and mumps -- I'll take care of those three. What are the archs where those rebuilds are needed? Cheers, Julien armel, armhf, mips, mipsel, s390, s390x, sparc. Thanks! Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ signature.asc Description: This is a digitally signed message part
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
On Mon, Dec 19, 2011 at 08:43:12 -0500, Adam C Powell IV wrote: On Sat, 2011-12-17 at 17:32 +0100, Julien Cristau wrote: On Fri, Dec 16, 2011 at 08:00:15 -0500, Adam C Powell IV wrote: I think blacs-mpi, scalapack and suitesparse make sense for no-change rebuilds. But I've been procrastinating maintenance on the rest (just took care of spooles last night, working on hypre now) so this will motivate me to finish up hypre, scotch and mumps -- I'll take care of those three. What are the archs where those rebuilds are needed? Cheers, Julien armel, armhf, mips, mipsel, s390, s390x, sparc. Can't do that for blacs-mpi, it's broken: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=650804 Scheduled rebuilds for scalapack. suitesparse doesn't seem to have any lam dependencies? Cheers, Julien -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
On Fri, Dec 16, 2011 at 08:00:15 -0500, Adam C Powell IV wrote: I think blacs-mpi, scalapack and suitesparse make sense for no-change rebuilds. But I've been procrastinating maintenance on the rest (just took care of spooles last night, working on hypre now) so this will motivate me to finish up hypre, scotch and mumps -- I'll take care of those three. What are the archs where those rebuilds are needed? Cheers, Julien -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Hi, On Thu, Dec 15, 2011 at 19:45:47 -0500, Adam C Powell IV wrote: Found the problem. PETSc built on November 16 with mpi-defaults 0.6 which depended on LAM on non-openmpi arches. Now mpi-defaults 1.0.1 released 12/4 depends on MPICH2, so we have a mix of architectures installed. And mpi-defaults just went into testing today... Crap! It may be that other PETSc dependencies need rebuilding too... and there are a lot of them! Let's see: suitesparse, spooles, hypre, scotch, blacs-mpi, scalapack, mumps, all have to be rebuilt with MPICH2! What was built when: * suitesparse: April 15 2010 * spooles: May 11 2010 * hypre: August 15 2010 * scotch: April 6 2011 * blacs-mpi: August 29 2011 * scalapack: September 18 2011 * mumps: March 31 2011 None was built recently, all need to be rebuilt. mpi-defaults should not be in testing until at least these are rebuilt, probably others. Note: HDF5 is not a problem for PETSc because PETSc only links to it on OpenMPI platforms. I forgot why that is, maybe it's worth a try building PETSc against HDF5-mpich2? Maybe later... Okay, cloning this bug to a bunch of packages, see above. I've been an uploader to all except blacs-mpi and scalapack, and many of them could use some maintenance, this is a good excuse to spend time on them. :-) If any of those can be fixed with a no-change rebuild on the buildds, rather than a source upload, let debian-release know, and we'll schedule them. Thanks, Julien -- Julien Cristau julien.cris...@logilab.fr Logilab http://www.logilab.fr/ Informatique scientifique gestion de connaissances -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
On Fri, 2011-12-16 at 09:57 +0100, Julien Cristau wrote: Hi, On Thu, Dec 15, 2011 at 19:45:47 -0500, Adam C Powell IV wrote: Found the problem. PETSc built on November 16 with mpi-defaults 0.6 which depended on LAM on non-openmpi arches. Now mpi-defaults 1.0.1 released 12/4 depends on MPICH2, so we have a mix of architectures installed. And mpi-defaults just went into testing today... Crap! It may be that other PETSc dependencies need rebuilding too... and there are a lot of them! Let's see: suitesparse, spooles, hypre, scotch, blacs-mpi, scalapack, mumps, all have to be rebuilt with MPICH2! What was built when: * suitesparse: April 15 2010 * spooles: May 11 2010 * hypre: August 15 2010 * scotch: April 6 2011 * blacs-mpi: August 29 2011 * scalapack: September 18 2011 * mumps: March 31 2011 None was built recently, all need to be rebuilt. mpi-defaults should not be in testing until at least these are rebuilt, probably others. Note: HDF5 is not a problem for PETSc because PETSc only links to it on OpenMPI platforms. I forgot why that is, maybe it's worth a try building PETSc against HDF5-mpich2? Maybe later... Okay, cloning this bug to a bunch of packages, see above. I've been an uploader to all except blacs-mpi and scalapack, and many of them could use some maintenance, this is a good excuse to spend time on them. :-) If any of those can be fixed with a no-change rebuild on the buildds, rather than a source upload, let debian-release know, and we'll schedule them. Thanks Julien. I think blacs-mpi, scalapack and suitesparse make sense for no-change rebuilds. But I've been procrastinating maintenance on the rest (just took care of spooles last night, working on hypre now) so this will motivate me to finish up hypre, scotch and mumps -- I'll take care of those three. -Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ signature.asc Description: This is a digitally signed message part
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
reopen 651452 found 651452 0.11.0-12 thanks Hi! * Adam C Powell IV hazel...@debian.org [111214 15:33]: Better to rip out the -llam and replace LLAM in the patch with -lmpi. I'll test then upload -12 with this change and let's see how it builds. That didn't work, too: It fails to build on armel, sparc due to that precise error (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte'). BTW: The build-depends in the sid chroot on smetana.debian.org, the sparc porter box, are still available. And the machine builds the package quite fast. Furthermore it's unbuildable on mips, mipsel and s390 as configure doesn't find the PETSc libraries, which looks like the error I described in mail #27 of this bug. Please don't zero-day NMU! Of course. Just for the record: When I did a zero-day NMU it was a bug of an RC bug without any maintainer reaction for more than 7 days. So the 0-day NMU was covered by the developers reference. Now that you are working on the issue, I can't. Best Regards, Alexander -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Processed: Re: Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Processing commands for cont...@bugs.debian.org:
reopen 651452
Bug #651452 {Done: hazel...@debian.org (Adam C. Powell, IV)}
[src:illuminator] illuminator: FTBFS on archs where petsc uses liblam
(tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
'reopen' may be inappropriate when a bug has been closed with a version;
you may need to use 'found' to remove fixed versions.
found 651452 0.11.0-12
Bug #651452 [src:illuminator] illuminator: FTBFS on archs where petsc uses
liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Bug Marked as found in versions illuminator/0.11.0-12.
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Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
On Thu, 2011-12-15 at 09:55 +0100, Alexander Reichle-Schmehl wrote: reopen 651452 found 651452 0.11.0-12 thanks Hi! * Adam C Powell IV hazel...@debian.org [111214 15:33]: Better to rip out the -llam and replace LLAM in the patch with -lmpi. I'll test then upload -12 with this change and let's see how it builds. That didn't work, too: It fails to build on armel, sparc due to that precise error (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte'). BTW: The build-depends in the sid chroot on smetana.debian.org, the sparc porter box, are still available. And the machine builds the package quite fast. Okay. I don't believe this is an illuminator error. The issue is that LAM should not be anywhere on the system, nothing should be linked with it, nothing should use its headers, nothing should try to link with it. The lam_mpi_byte symbol is probably a #define in the LAM headers, which shouldn't even be installed. libmpich2-dev has been the mpi-default-dev package on non-openmpi platforms for nearly seven months, so everything should have been rebuilt against it. So where is the LAM contamination coming from? I'll log into smetana and see what I can figure out. Furthermore it's unbuildable on mips, mipsel and s390 as configure doesn't find the PETSc libraries, which looks like the error I described in mail #27 of this bug. The PETSc libraries are installed, and the test is from petsc.m4 . But we don't know what the linking error is that causes it to fail, could be the same kind of error as the one in the tsview link. Please don't zero-day NMU! Of course. Just for the record: When I did a zero-day NMU it was a bug of an RC bug without any maintainer reaction for more than 7 days. So the 0-day NMU was covered by the developers reference. Now that you are working on the issue, I can't. Understood. The problem is on my end. I'm afraid since I subscribed to debian-science-maintainers there's been too much traffic on that list for me to read, and bug emails which used to come to my address and go into my bugs folder go into that folder instead. So I had no idea any of this was happening until I scanned d-s-m 8 days later... Thanks, Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ signature.asc Description: This is a digitally signed message part
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
clone 651452 -1 reassign -1 src:petsc retitle -1 Rebuild with mpi-defaults = 1.0 found -1 3.1.dfsg-11.1 block 651452 by -1 clone 651452 -2 reassign -2 src:suitesparse retitle -2 Rebuild with mpi-defaults = 1.0 found -2 3.4.0-2 block -1 by -2 clone 651452 -3 reassign -3 src:spooles retitle -3 Rebuild with mpi-defaults = 1.0 found -3 2.2-8 block -1 by -3 clone 651452 -4 reassign -4 src:hypre retitle -4 Rebuild with mpi-defaults = 1.0 found -4 2.4.0b-7 block -1 by -4 clone 651452 -5 reassign -5 src:scotch retitle -5 Rebuild with mpi-defaults = 1.0 found -5 5.1.11.dfsg-7 block -1 by -5 clone 651452 -6 reassign -6 src:blacs-mpi retitle -6 Rebuild with mpi-defaults = 1.0 found -6 1.1-30.1 block -1 by -6 clone 651452 -7 reassign -7 src:scalapack retitle -7 Rebuild with mpi-defaults = 1.0 found -7 1.8.0-7 block -1 by -7 clone 651452 -8 reassign -8 src:mumps retitle -8 Rebuild with mpi-defaults = 1.0 found -8 4.9.2.dfsg-7 block -1 by -8 clone 651452 -9 reassign -9 src:mpi-defaults retitle -9 Get this out of testing until its rdepends have rebuilt found -9 1.0.1 block -9 by 651452 block -9 by -1 block -9 by -2 block -9 by -3 block -9 by -4 block -9 by -5 block -9 by -6 block -9 by -7 block -9 by -8 thanks On Thu, 2011-12-15 at 14:36 -0500, Adam C Powell IV wrote: On Thu, 2011-12-15 at 09:55 +0100, Alexander Reichle-Schmehl wrote: reopen 651452 found 651452 0.11.0-12 thanks Hi! * Adam C Powell IV hazel...@debian.org [111214 15:33]: Better to rip out the -llam and replace LLAM in the patch with -lmpi. I'll test then upload -12 with this change and let's see how it builds. That didn't work, too: It fails to build on armel, sparc due to that precise error (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte'). BTW: The build-depends in the sid chroot on smetana.debian.org, the sparc porter box, are still available. And the machine builds the package quite fast. Okay. I don't believe this is an illuminator error. The issue is that LAM should not be anywhere on the system, nothing should be linked with it, nothing should use its headers, nothing should try to link with it. The lam_mpi_byte symbol is probably a #define in the LAM headers, which shouldn't even be installed. libmpich2-dev has been the mpi-default-dev package on non-openmpi platforms for nearly seven months, so everything should have been rebuilt against it. So where is the LAM contamination coming from? Found the problem. PETSc built on November 16 with mpi-defaults 0.6 which depended on LAM on non-openmpi arches. Now mpi-defaults 1.0.1 released 12/4 depends on MPICH2, so we have a mix of architectures installed. And mpi-defaults just went into testing today... Crap! It may be that other PETSc dependencies need rebuilding too... and there are a lot of them! Let's see: suitesparse, spooles, hypre, scotch, blacs-mpi, scalapack, mumps, all have to be rebuilt with MPICH2! What was built when: * suitesparse: April 15 2010 * spooles: May 11 2010 * hypre: August 15 2010 * scotch: April 6 2011 * blacs-mpi: August 29 2011 * scalapack: September 18 2011 * mumps: March 31 2011 None was built recently, all need to be rebuilt. mpi-defaults should not be in testing until at least these are rebuilt, probably others. Note: HDF5 is not a problem for PETSc because PETSc only links to it on OpenMPI platforms. I forgot why that is, maybe it's worth a try building PETSc against HDF5-mpich2? Maybe later... Okay, cloning this bug to a bunch of packages, see above. I've been an uploader to all except blacs-mpi and scalapack, and many of them could use some maintenance, this is a good excuse to spend time on them. :-) -Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ signature.asc Description: This is a digitally signed message part
Processed: Re: Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Processing commands for cont...@bugs.debian.org: clone 651452 -1 Bug#651452: illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Bug 651452 cloned as bug 652307. reassign -1 src:petsc Bug #652307 [src:illuminator] illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Bug reassigned from package 'src:illuminator' to 'src:petsc'. Bug No longer marked as found in versions illuminator/0.11.0-8.2, illuminator/0.11.0-8.1, and illuminator/0.11.0-12. retitle -1 Rebuild with mpi-defaults = 1.0 Bug #652307 [src:petsc] illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Changed Bug title to 'Rebuild with mpi-defaults = 1.0' from 'illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')' found -1 3.1.dfsg-11.1 Bug #652307 [src:petsc] Rebuild with mpi-defaults = 1.0 Bug Marked as found in versions petsc/3.1.dfsg-11.1. block 651452 by -1 Bug #651452 [src:illuminator] illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Was not blocked by any bugs. Added blocking bug(s) of 651452: 652307 clone 651452 -2 Bug#651452: illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Bug 651452 cloned as bug 652308. reassign -2 src:suitesparse Bug #652308 [src:illuminator] illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Bug reassigned from package 'src:illuminator' to 'src:suitesparse'. Bug No longer marked as found in versions illuminator/0.11.0-8.2, illuminator/0.11.0-8.1, and illuminator/0.11.0-12. retitle -2 Rebuild with mpi-defaults = 1.0 Bug #652308 [src:suitesparse] illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Changed Bug title to 'Rebuild with mpi-defaults = 1.0' from 'illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')' found -2 3.4.0-2 Bug #652308 [src:suitesparse] Rebuild with mpi-defaults = 1.0 The source suitesparse and version do not appear to match any binary packages Bug Marked as found in versions suitesparse/3.4.0-2. block -1 by -2 Bug #652307 [src:petsc] Rebuild with mpi-defaults = 1.0 Was not blocked by any bugs. Added blocking bug(s) of 652307: 652308 clone 651452 -3 Bug#651452: illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Bug 651452 cloned as bug 652309. reassign -3 src:spooles Bug #652309 [src:illuminator] illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Bug reassigned from package 'src:illuminator' to 'src:spooles'. Bug No longer marked as found in versions illuminator/0.11.0-8.2, illuminator/0.11.0-8.1, and illuminator/0.11.0-12. retitle -3 Rebuild with mpi-defaults = 1.0 Bug #652309 [src:spooles] illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Changed Bug title to 'Rebuild with mpi-defaults = 1.0' from 'illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')' found -3 2.2-8 Bug #652309 [src:spooles] Rebuild with mpi-defaults = 1.0 Bug Marked as found in versions spooles/2.2-8. block -1 by -3 Bug #652307 [src:petsc] Rebuild with mpi-defaults = 1.0 Was blocked by: 652308 Added blocking bug(s) of 652307: 652309 clone 651452 -4 Bug#651452: illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Bug 651452 cloned as bug 652310. reassign -4 src:hypre Bug #652310 [src:illuminator] illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Bug reassigned from package 'src:illuminator' to 'src:hypre'. Bug No longer marked as found in versions illuminator/0.11.0-8.2, illuminator/0.11.0-8.1, and illuminator/0.11.0-12. retitle -4 Rebuild with mpi-defaults = 1.0 Bug #652310 [src:hypre] illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Changed Bug title to 'Rebuild with mpi-defaults = 1.0' from 'illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')' found -4 2.4.0b-7 Bug #652310 [src:hypre] Rebuild with mpi-defaults = 1.0 Bug Marked as found in versions hypre/2.4.0b-7. block -1 by -4 Bug #652307 [src:petsc] Rebuild with mpi-defaults = 1.0 Was blocked by: 652309 652308 Added blocking bug(s) of 652307: 652310 clone 651452 -5 Bug#651452: illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o:
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
reopen 651452 retitle 651452 illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') found 651452 0.11.0-8.2 clone 651452 -1 retitle -1 illuminat: Build-Conflicts on libmpich2-dev to strict thanks Hi! * Alexander Reichle-Schmehl alexan...@schmehl.info [111212 13:45]: The problem seems to be, that petsc is linked to liblam on sparc, and therefore the additional linkerflad -llam is needed on that arch. I have no idea, why this issue han't shown up on armel, mips, mipsel or s390, the other arches on which petsc uses lam. My patch adds the missing flag on sparc. And here we are again, this time on armel. I have no idea, why 0.11.0-8.1 was build successfull on armel, as it seems to be the very same isssue according to the build logs: https://buildd.debian.org/status/logs.php?pkg=illuminatorarch=armel The trivial workarround would be to extend the host arch query in debian/rules similimar to the following: DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH) ifeq ($(DEB_HOST_ARCH), sparc) LLAM=-llam else ifeq ($(DEB_HOST_ARCH), armel) LLAM=-llam else LLAM= endif endif Note that I didn't test it, and as I have shown nicely in my NMU that isn't very reliable. So it might be better to check the lib itself, e.g. with objdump -x /usr/lib/libpetsc.so|grep -i liblam.so|grep NEEDED That shows the exptected line on sparc on armel, while it doesn't on amd64, but I didn't to further checks. + * Add libmpich2-dev to build-conflicts to prevent FTBFS as described in +http://bugs.debian.org/651452#22 and #27) Sorry, but that seems to have been a really bad idea, as not the build-depends on armhf, mips, mipsel, s390 and s390x can't be fullfilled at all. I'm not sure if it would be better to drop that complelty (as that seems to be a problem not showing up on the buildds) or make that a arch-specific build-conflict (which would be cleaner solution, but the list would need to be maintained). I clone this bug, as this is a different issue. Best Regards, Alexander -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Processed: Re: Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Processing commands for cont...@bugs.debian.org:
reopen 651452
Bug #651452 {Done: Alexander Reichle-Schmehl toli...@debian.org}
[src:illuminator] illuminator: FTBFS on sparc (tsview-tsview.o: undefined
reference to symbol 'lam_mpi_byte')
'reopen' may be inappropriate when a bug has been closed with a version;
you may need to use 'found' to remove fixed versions.
retitle 651452 illuminator: FTBFS on archs where petsc uses liblam
(tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Bug #651452 [src:illuminator] illuminator: FTBFS on sparc (tsview-tsview.o:
undefined reference to symbol 'lam_mpi_byte')
Changed Bug title to 'illuminator: FTBFS on archs where petsc uses liblam
(tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')' from
'illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol
'lam_mpi_byte')'
found 651452 0.11.0-8.2
Bug #651452 [src:illuminator] illuminator: FTBFS on archs where petsc uses
liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Bug Marked as found in versions illuminator/0.11.0-8.2.
clone 651452 -1
Bug#651452: illuminator: FTBFS on archs where petsc uses liblam
(tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Bug 651452 cloned as bug 652025.
retitle -1 illuminat: Build-Conflicts on libmpich2-dev to strict
Bug #652025 [src:illuminator] illuminator: FTBFS on archs where petsc uses
liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Changed Bug title to 'illuminat: Build-Conflicts on libmpich2-dev to strict'
from 'illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o:
undefined reference to symbol 'lam_mpi_byte')'
thanks
Stopping processing here.
Please contact me if you need assistance.
--
652025: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=652025
651452: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=651452
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Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Hi Alexander, On Wed, 2011-12-14 at 10:09 +0100, Alexander Reichle-Schmehl wrote: reopen 651452 retitle 651452 illuminator: FTBFS on archs where petsc uses liblam (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') found 651452 0.11.0-8.2 clone 651452 -1 retitle -1 illuminat: Build-Conflicts on libmpich2-dev to strict That's not going to work: illuminator Build-Depends on mpi-default-dev, which depends on libmpich2-dev on several arches. Better to rip out the -llam and replace LLAM in the patch with -lmpi. I'll test then upload -12 with this change and let's see how it builds. Please don't zero-day NMU! -Adam -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ signature.asc Description: This is a digitally signed message part
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
tags 651452 + patch tags 651452 + pending thanks Hi! * Alexander Reichle-Schmehl alexan...@schmehl.info [111209 14:41]: However I get now the same FTBFS as originally reported. I guess we call that progress... I think I solved the problem, however I only found a kind of grude workarround, not a real solution. The problem seems to be, that petsc is linked to liblam on sparc, and therefore the additional linkerflad -llam is needed on that arch. I have no idea, why this issue han't shown up on armel, mips, mipsel or s390, the other arches on which petsc uses lam. My patch adds the missing flag on sparc. A nicer fix would be to some detect automatically, if -llam is needed or not based upon... uh... Don't know what. That being said, I uploaded the fix to delayed/4. Please tell me, if I should delay it longer. As you can see I also added libmpich2-dev to the build-conflicts. That's to prevent FTBFS issues as seen while trying to fix the issue in the porter chroots (see bug log for details). Best Regards, Alexander diff -Nru illuminator-0.11.0/debian/changelog illuminator-0.11.0/debian/changelog --- illuminator-0.11.0/debian/changelog 2011-12-04 16:20:54.0 +0100 +++ illuminator-0.11.0/debian/changelog 2011-12-12 13:11:42.0 +0100 @@ -1,3 +1,15 @@ +illuminator (0.11.0-8.2) unstable; urgency=medium + + * Non-maintainer upload. + * Add -llam to tsclients linker flags to fix FTBFS on sparc (Closes: #651452) +* Add Architecture query to debian/rules +* Change patches/include-all-libs.patch to include LLAM + * Urgency set to medium due to rc bug fix + * Add libmpich2-dev to build-conflicts to prevent FTBFS as described in +http://bugs.debian.org/651452#22 and #27) + + -- Alexander Reichle-Schmehl toli...@debian.org Mon, 12 Dec 2011 12:10:27 + + illuminator (0.11.0-8.1) unstable; urgency=medium * Non-maintainer upload. diff -Nru illuminator-0.11.0/debian/control illuminator-0.11.0/debian/control --- illuminator-0.11.0/debian/control 2011-12-04 14:51:46.0 +0100 +++ illuminator-0.11.0/debian/control 2011-12-12 13:10:23.0 +0100 @@ -6,7 +6,7 @@ Standards-Version: 3.9.1 Build-Depends: debhelper (= 5.0), quilt, libpetsc3.1-dev, geomview, pkg-config, libglib2.0-dev, libxml2-dev, libimlib2-dev, libreadline-dev, libglade2-dev, libgnomeui-dev, libncurses-dev Build-Depends-Indep: cxref, texlive-latex-extra, texlive-latex-recommended, hevea, lmodern -Build-Conflicts: cpml-ev5, cpml-ev6 +Build-Conflicts: cpml-ev5, cpml-ev6, libmpich2-dev Build-Conflicts-Indep: latex2html Vcs-Git: git://git.debian.org/git/debian-science/packages/illuminator.git Vcs-Browser: http://git.debian.org/?p=debian-science/packages/illuminator.git diff -Nru illuminator-0.11.0/debian/patches/include-all-libs.patch illuminator-0.11.0/debian/patches/include-all-libs.patch --- illuminator-0.11.0/debian/patches/include-all-libs.patch 2010-11-30 16:32:21.0 +0100 +++ illuminator-0.11.0/debian/patches/include-all-libs.patch 2011-12-12 12:31:15.0 +0100 @@ -9,7 +9,7 @@ # A little timestep visualizer tsview_SOURCES = tsview.c -tsview_LDADD = libluminate/libluminate.la -lncurses -lhistory -lreadline -+tsview_LDADD = libluminate/libluminate.la -lpetsc -lncurses -lhistory -lreadline ++tsview_LDADD = libluminate/libluminate.la $(LLAM) -lpetsc -lncurses -lhistory -lreadline tsview_CFLAGS = $(PETSC_INCLUDE) $(GTK_CFLAGS) $(GEOMVIEW_CFLAGS) # -DDEBUG # Next-generation timestep visualizer @@ -37,7 +37,7 @@ # A little timestep visualizer tsview_SOURCES = tsview.c -tsview_LDADD = libluminate/libluminate.la -lncurses -lhistory -lreadline -+tsview_LDADD = libluminate/libluminate.la -lpetsc -lncurses -lhistory -lreadline ++tsview_LDADD = libluminate/libluminate.la $(LLAM) -lpetsc -lncurses -lhistory -lreadline tsview_CFLAGS = $(PETSC_INCLUDE) $(GTK_CFLAGS) $(GEOMVIEW_CFLAGS) # -DDEBUG # Next-generation timestep visualizer diff -Nru illuminator-0.11.0/debian/rules illuminator-0.11.0/debian/rules --- illuminator-0.11.0/debian/rules 2010-11-30 16:26:54.0 +0100 +++ illuminator-0.11.0/debian/rules 2011-12-12 12:57:10.0 +0100 @@ -4,6 +4,15 @@ package=illuminator +DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH) + +ifeq ($(DEB_HOST_ARCH), sparc) + LLAM=-llam +else + LLAM= +endif + + patch: dh_testdir if [ ! -e illuminator.m4.backup ]; then \ @@ -23,7 +32,7 @@ build: stamp-configure dh_testdir - $(MAKE) + LLAM=$(LLAM) $(MAKE) touch $@ clean:
Processed: Re: Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Processing commands for cont...@bugs.debian.org: tags 651452 + patch Bug #651452 [src:illuminator] illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Added tag(s) patch. tags 651452 + pending Bug #651452 [src:illuminator] illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte') Added tag(s) pending. thanks Stopping processing here. Please contact me if you need assistance. -- 651452: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=651452 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Hi! Am 12.12.2011 13:45, schrieb Alexander Reichle-Schmehl: That being said, I uploaded the fix to delayed/4. Please tell me, if I should delay it longer. Ups. I haven't, but did a direct upload. Sorry, forget the -e 4 when dput-ing it :( Best regards, Alexander -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
X-Debbugs-Cc: Alexander Reichle-Schmehl alexan...@schmehl.info, Julien Cristau jcris...@debian.org Dear Alexander and Julien, Please accept my apologies for uploading just now without incorporating yoru recent changes. I had not seen your NMU uploads because they came via the BTS system to debian-science-maintainers, a very high traffic list which I'm unfortunately not able to read as frequently as I'd like. Your messages came during a particularly busy couple of weeks, and just now when I tried to catch up by preparing the illuminator upload, I did so before reading through the last two weeks of d-s-m traffic. I'll prepare a new -10 upload by the end of the day incorporating your recent changes. Regards, Adam On Mon, 2011-12-12 at 13:45 +0100, Alexander Reichle-Schmehl wrote: tags 651452 + patch tags 651452 + pending thanks Hi! * Alexander Reichle-Schmehl alexan...@schmehl.info [111209 14:41]: However I get now the same FTBFS as originally reported. I guess we call that progress... I think I solved the problem, however I only found a kind of grude workarround, not a real solution. The problem seems to be, that petsc is linked to liblam on sparc, and therefore the additional linkerflad -llam is needed on that arch. I have no idea, why this issue han't shown up on armel, mips, mipsel or s390, the other arches on which petsc uses lam. My patch adds the missing flag on sparc. A nicer fix would be to some detect automatically, if -llam is needed or not based upon... uh... Don't know what. That being said, I uploaded the fix to delayed/4. Please tell me, if I should delay it longer. As you can see I also added libmpich2-dev to the build-conflicts. That's to prevent FTBFS issues as seen while trying to fix the issue in the porter chroots (see bug log for details). Best Regards, Alexander -- debian-science-maintainers mailing list debian-science-maintain...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ signature.asc Description: This is a digitally signed message part
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Hi! Am 08.12.2011 20:00, schrieb Julien Cristau: See https://buildd.debian.org/status/fetch.php?pkg=illuminatorarch=sparcver=0.11.0-8.1stamp=1323062646 /usr/lib/lam/bin/mpicc -g -O2 -o .libs/tsview tsview-tsview.o libluminate/.libs/libluminate.so -lpetsc -lncurses -lhistory -lreadline /usr/bin/ld: tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte' /usr/bin/ld: note: 'lam_mpi_byte' is defined in DSO /usr/lib/liblam.so.4 so try adding it to the linker command line /usr/lib/liblam.so.4: could not read symbols: Invalid operation collect2: ld returned 1 exit status make[3]: *** [tsview] Error 1 Just a small update: I got the b-d installed smetana.debian.org. However, I fail to reproduce this bug: When I try to build the package, it FTBFS even sooner: checking for dgemv_ in -lblas... (cached) yes checking for dgetrf_ in -llapack... (cached) yes checking for sqrt in -lcpml... (cached) no checking for PetscPrintf in -lpetsc... no configure: error: PETSc libraries not found make: *** [stamp-configure] Error 1 dpkg-buildpackage: error: debian/rules build gave error exit status 2 However, we do have: $ dpkg -l|grep petsc ii libpetsc3.13.1.dfsg-11.1 Shared libraries for version 3.1 of PETSc ii libpetsc3.1-de 3.1.dfsg-11.1 Static libraries, shared links, header files Strangely that's the very same version I used in the FTBFS on the buildd (and on my amd64 machine). Best regards, Alexander -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Hi! Am 09.12.2011 12:57, schrieb Alexander Reichle-Schmehl: Just a small update: I got the b-d installed smetana.debian.org. However, I fail to reproduce this bug: When I try to build the package, it FTBFS even sooner: checking for dgemv_ in -lblas... (cached) yes checking for dgetrf_ in -llapack... (cached) yes checking for sqrt in -lcpml... (cached) no checking for PetscPrintf in -lpetsc... no configure: error: PETSc libraries not found make: *** [stamp-configure] Error 1 dpkg-buildpackage: error: debian/rules build gave error exit status 2 Thanks to the help of ukleinek and KiBi I solved that one: On the sparc chroot libmpich2-dev was installed, which made that test fail. Not sure if that's a bug in libpetsc3.1-dev. However I get now the same FTBFS as originally reported. I guess we call that progress... Best regards, Alexander -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#651452: illuminator: FTBFS on sparc (tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte')
Source: illuminator Version: 0.11.0-8.1 Severity: serious Justification: fails to build from source (but built successfully in the past) X-Debbugs-Cc: Alexander Reichle-Schmehl toli...@debian.org See https://buildd.debian.org/status/fetch.php?pkg=illuminatorarch=sparcver=0.11.0-8.1stamp=1323062646 /usr/lib/lam/bin/mpicc -g -O2 -o .libs/tsview tsview-tsview.o libluminate/.libs/libluminate.so -lpetsc -lncurses -lhistory -lreadline /usr/bin/ld: tsview-tsview.o: undefined reference to symbol 'lam_mpi_byte' /usr/bin/ld: note: 'lam_mpi_byte' is defined in DSO /usr/lib/liblam.so.4 so try adding it to the linker command line /usr/lib/liblam.so.4: could not read symbols: Invalid operation collect2: ld returned 1 exit status make[3]: *** [tsview] Error 1 Cheers, Julien -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
