[Bug 234837] Re: Binutils corrupts Open MPI
Copied to hardy-updates. ** Changed in: openmpi (Ubuntu Hardy) Status: Fix Committed = Fix Released -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
Thanks to all that tested. We have 4 positives and no negatives, I'm therefore asking archive to publish this to hardy-updates. ** Changed in: openmpi (Ubuntu Hardy) Status: Confirmed = Fix Committed ** Tags added: verification-done ** Tags removed: verification-needed -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
The fix worked for me too. -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
accepted into hardy-proposed, please test ** Tags added: verification-needed -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
Nice! I had the same problems as reported in bug #224706 and now they are gone. Johannes -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
I can confirm that this indeed fixed the problems that I have been having (and that I reported in #224706). ilmar -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
The fix works fine for me. Thanks! Olaf -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
I reported the bug marked as a duplicate of this (https://bugs.launchpad.net/ubuntu/+source/openmpi/+bug/224706), and have had problems with using Python on top of openmpi. We have been building our own packages for openmpi based on Debian. A fix for Hardy would be highly appreciated, so that we no longer have to make people using our software add third-party repositories. Bottom line, I would be happy to test and confirm this. In fact, there are several people here who would like to test such a fix. ilmar -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
This bug was fixed in the package openmpi - 1.2.6-2ubuntu1 --- openmpi (1.2.6-2ubuntu1) intrepid; urgency=low * debian/rules: unexport LDFLAGS fix SIGSEGV when initialising mpi (LP: #234837). * Modify Maintainer value to match the DebianMaintainerField specification. -- Cesare Tirabassi [EMAIL PROTECTED] Sun, 15 Jun 2008 21:39:00 +0200 ** Changed in: openmpi (Ubuntu Intrepid) Status: Incomplete = Fix Released -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
motu-sru is subscribed to give clearance for uploading the fix to hardy- proposed: 1. The openmpi package is currently broken in Hardy, since it requires compilation without the -Wl,-Bsymbolic linker option. Any user attempt to initialise the library either directly or through 3rd party applications fails with a SIGSEGV. 2. The bug has been fixed in the release version by disabling dpkg-buildpackage LDFLAGS default. 3. A minimal patch applicable to the stable version of the package is attached. 4. TEST CASE: A simple test case is defined here. It will be appreciated if users which are using the library through other applications can also confirm the fix, or otherwise. 4.1 In Hardy, install the r-cran-rmpi package with your preferred package manager. This should drag in all required dependencies, including openmpi. 4.2 Try the following simple command in a terminal: echo 'library(Rmpi); cat(Still alive\n)' | R --slave This should fail with a SIGSEGV (Address/Memory not mapped) signal. 4.3 Enable the hardy-proposed repository. For instance, you can do this by adding the following line to /etc/apt/sources.list: deb http://archive.ubuntu.com/ubuntu/ hardy-proposed universe Update your local cache and upgrade. This should upgrade at least the following packages: openmpi-bin, libopenmpi1, openmpi-common 4.4 Re-run the command from step 4.2 in a terminal. Initialisation should be successfull and you should see the message Still alive on the screen. 4.5 Disable the hardy-proposed repository. 5. There is obviously a potential for regression. I believe this is mitigated by the fact that in Debian (and Ubuntu before the dpkg- buildpackage change) this has not shown any ill effect. WARNING: Any user willing to help with testing is more than welcome. Please be aware that there might be some time before the updated packages will be available in your mirror. The sru needs to be approved and the package manually copied by an archive admin, this may take from 1 to several days to be processed. ** Attachment added: Patch for hardy-proposed http://launchpadlibrarian.net/15345656/openmpi_1.2.5-1ubuntu1.1.diff ** Changed in: openmpi (Ubuntu Hardy) Importance: Undecided = Medium Status: New = Confirmed -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
Where is LDFLAGS defined in the first place? We built the package from source without the patch, and this worked. Also, should InfiniBand be disabled as Dirk suggested? ilmar -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
I know, but I find it annoying to having to edit /etc/openmpi/openmpi- mca-params.conf, and since it is disabled in openmpi i newer versions it could as well be removed. ilmar -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
ACK from motu-sru. -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
Re: [Bug 234837] Re: Binutils corrupts Open MPI
On Mon, Jun 16, 2008 at 01:31:53PM -, ilmarw wrote: I know, but I find it annoying to having to edit /etc/openmpi/openmpi- mca-params.conf, and since it is disabled in openmpi i newer versions it could as well be removed. Our (as in Debian Open MPI maintainers in discussion with upstream) consensus was that it is still preferable to have the 'meep' rather than to disable IB for those who actually have the hardware. Luckily that is all somewhat moot now as the code will behave better going forward and deal with this autoMAGICally. Dirk -- Three out of two people have difficulties with fractions. -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
Disabling IB was only about the MEEP! You don't have IB hardware! warning. Andreas -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
** Also affects: openmpi (Ubuntu) Importance: Undecided Status: New ** Changed in: binutils (Ubuntu) Status: New = Invalid ** Changed in: binutils (Ubuntu Hardy) Status: New = Invalid -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
Re: [Bug 234837] Re: Binutils corrupts Open MPI
On Sun, Jun 15, 2008 at 07:30:25PM -, Cesare Tirabassi wrote: ** Also affects: openmpi (Ubuntu) Importance: Undecided Status: New ** Changed in: binutils (Ubuntu) Status: New = Invalid ** Changed in: binutils (Ubuntu Hardy) Status: New = Invalid Care to explain? As my bug report stated, the _only_ change was the Gutsy/Hardy upgrade as I compiled the _same sources_. This is no Open MPI bug. This is a toolchain bug that happens to break Open MPI. Dirk -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a direct subscriber of the bug. -- Three out of two people have difficulties with fractions. -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
I can add that the problem has been introduced somewhere within the hardy development time. We have a machine that has been installed around february/march with a then-current hardy. This includes a working OpenMPI package. The update to the released hardy broke openMPI. Yours, Steffen (Whose bugs 210273 and 224706 have been marked a duplicate of this). So if this bug is invalid I'd like to know if someone is working on any of the other two. Yours, Steffen -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
On 15 June 2008 at 19:53, Steffen Neumann wrote: | I can add that the problem has been introduced somewhere | within the hardy development time. We have a machine | that has been installed around february/march with a then-current hardy. | This includes a working OpenMPI package. The update to the released hardy | broke openMPI. Yes, exactly what I observerd too. | Yours, | Steffen | | (Whose bugs 210273 and 224706 have been marked a duplicate of this). | So if this bug is invalid I'd like to know if someone is working on any of | the other two. I am as stunned by this as Steffen and am eagerly awaiting an explanation. Dirk who happens to co-maintain Open MPI in Debian and suspects that Open MPI is not at fault here but rather how the package was built for Hardy / whatever changed for the compilers / linkers / ... in hardy as _the same source package built on Gutsy_ works for me. | Yours, | Steffen | | -- | Binutils corrupts Open MPI | https://bugs.launchpad.net/bugs/234837 | You received this bug notification because you are a direct subscriber | of the bug. -- Three out of two people have difficulties with fractions. -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
I still have not received any answer to my emails (Friday 13 June @12:22:46 CEST and Sunday 15 June @21:25:20 CEST). In summary, this is apparently caused by compiling openmpi with -Wl,-Bsymbolic-functions (default from latest dpkg-buildpackage). This could possibly be due to any of the three libopenmpi1 different interrelated libraries sharing symbols? Can you and/or Manuel comment on this before we release a fix? ** Changed in: openmpi (Ubuntu Intrepid) Status: New = Incomplete -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
Cesare, Thanks for your mail! On 15 June 2008 at 20:53, Cesare Tirabassi wrote: | I still have not received any answer to my emails (Friday 13 June @12:22:46 CEST and Sunday 15 June @21:25:20 CEST). I replied to your email from Friday on Friday right when I got, ie before leaving for work: From: Dirk Eddelbuettel [EMAIL PROTECTED] To: Cesare Tirabassi [EMAIL PROTECTED] Subject: Re: SUSPECT: Re: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron Date: Fri, 13 Jun 2008 07:27:37 -0500 and exim4 had no issues as far as I can see 2008-06-13 07:27:37 1K78NV-00078e-Jd = [EMAIL PROTECTED] U=edd P=local S=1869 [EMAIL PROTECTED] 2008-06-13 07:27:39 1K78NV-00078e-Jd = [EMAIL PROTECTED] R=smarthost T=remote_smtp_smarthost H=smtp.g.comcast.net [76.96.30.117] X=TLS1.0:RSA_AES_256_CBC_SHA1:32 DN=C=US,ST=Pennsylvania,L=Philadelphia,O=Comcast Cable Communications Management LLC,OU=Business Center,CN=smtp.comcast.net 2008-06-13 07:27:39 1K78NV-00078e-Jd Completed Did you get that or not? Today I only received (automated) Launchpad messages from you but no direct mail. I did send you one given that I had not heard from you. Looks like there may be email troubles at your end? Just to be sure, I added both you email addresses as CC. | In summary, this is apparently caused by compiling openmpi with -Wl ,-Bsymbolic-functions (default from latest dpkg-buildpackage). If it is dpkg-buildpackages, it would 'hit' us too as we're building in unstable. So I think it may be something else. Could it be that Ubuntu has a different GCC default in stripping symbols or something? The first person I talked to about this was doko but is always so overwhelmed that he told me to please file a bug report which I did. Which promptly got ignored by everybody. | This could possibly be due to any of the three libopenmpi1 different interrelated libraries sharing symbols? That was my immediate gut reaction as well. But that is a design choice Open MPI made upstream, and we (as in Debian's Open MPI maintainer) do not fight it. *If* you guys changed build options, I'd start by reverting to what we do. But if you guys changed nothing, well then I am at a loss. | Can you and/or Manuel comment on this before we release a fix? [ CCing Manuel who you forgot to CC. ] Sure. Let's hash this out for a moment to get it right. Manuel may want to comment as I may well have overlooked or forgotten something. Dirk | ** Changed in: openmpi (Ubuntu Intrepid) |Status: New = Incomplete | | -- | Binutils corrupts Open MPI | https://bugs.launchpad.net/bugs/234837 | You received this bug notification because you are a direct subscriber | of the bug. -- Three out of two people have difficulties with fractions. -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
Well, by looking at your buildd build log your default LDFLAGS is while we do use -Wl,-Bsymbolic. I guess you never received my emails as I was explaining that in details. Anyhow, compiling unexporting LDFLAGS in debian/rules works as expected: [EMAIL PROTECTED]:/root/debian# echo 'library(Rmpi); cat(Still alive\n)' | R --slave [norsetto:13561] mca: base: components_open: component timer / linux open function failed [norsetto:13561] mca: base: component_find: unable to open osc pt2pt: file not found (ignored) libibverbs: Fatal: couldn't read uverbs ABI version. -- [0,0,0]: OpenIB on host norsetto was unable to find any HCAs. Another transport will be used instead, although this may result in lower performance. -- Still alive The above is with the patched and rebuilt 1.2.5-1. You seem to confirm that upstream decided to share symbols between libraries, it is therefore a design choice and not a bug; I'm therefore happy to release this fix for intrepid right now. For hardy we need an sru, for which we need cooperation from you and possibly others since we need at least 3 persons to test and confirm this works (and doesn't break anything else) before we can make it official. I'll work on this first thing tomorrow morning. -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 234837] Re: Binutils corrupts Open MPI
Just back in from a long run... On 15 June 2008 at 22:49, Cesare Tirabassi wrote: | Well, by looking at your buildd build log your default LDFLAGS is | while we do use -Wl,-Bsymbolic. That'll do to break the package, I suppose! | I guess you never received my emails as | I was explaining that in details. That email lossage is a side issue we should take up on the side. Any idea why I am not getting yours / your not getting mine? | Anyhow, compiling unexporting LDFLAGS | in debian/rules works as expected: | | [EMAIL PROTECTED]:/root/debian# echo 'library(Rmpi); cat(Still alive\n)' | | R --slave | [norsetto:13561] mca: base: components_open: component timer / linux open | function failed | [norsetto:13561] mca: base: component_find: unable to open osc pt2pt: file not | found (ignored) | libibverbs: Fatal: couldn't read uverbs ABI version. | -- | [0,0,0]: OpenIB on host norsetto was unable to find any HCAs. | Another transport will be used instead, although this may result in | lower performance. | -- | Still alive Perfect. And if you uncomment the line saying btl = ^openib in /etc/openmpi/openmpi-mca-params.conf as in # Disable the use of InfiniBand # btl = ^openib btl = ^openib you will suppress the noise telling you that you have no IB hardware... This has now been improved upstream, by the way. | The above is with the patched and rebuilt 1.2.5-1. Yes, look good! Thanks for that! | You seem to confirm that upstream decided to share symbols between | libraries, it is therefore a design choice and not a bug; I'm therefore | happy to release this fix for intrepid right now. For hardy we need an | sru, for which we need cooperation from you and possibly others since we | need at least 3 persons to test and confirm this works (and doesn't | break anything else) before we can make it official. Let me know how I can help. As I said, same code / same everything but built on Gutsy (ie without -Wl,-Bsymbolic) works. | I'll work on this first thing tomorrow morning. Much appreciated. This seems to have bitten a few people, and is too obscure for most to figure out by themselves. Dirk | -- | Binutils corrupts Open MPI | https://bugs.launchpad.net/bugs/234837 | You received this bug notification because you are a direct subscriber | of the bug. -- Three out of two people have difficulties with fractions. -- Binutils corrupts Open MPI https://bugs.launchpad.net/bugs/234837 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
