The version that “lstopo --version” reports is the same (1.8) on all nodes, but we may indeed be hitting the second issue. We can try to compile a new version of openmpi, but how do we ensure that the external programs (e.g. SLURM) are using the same hwloc version as the one embedded in openmpi? Is it enough to just compile hwloc 1.9 separately as well and link against that? Also, if this is an issue, should we file a bug against hwloc or openmpi on Ubuntu for mismatching versions?
> On 09 Dec 2014, at 00:50, Ralph Castain <r...@open-mpi.org> wrote: > > Hmmm…they probably linked that to the external, system hwloc version, so it > sounds like one or more of your nodes has a different hwloc rpm on it. > > I couldn’t leaf thru your output well enough to see all the lstopo versions, > but you might check to ensure they are the same. > > Looking at the code base, you may also hit a problem here. OMPI 1.6 series > was based on hwloc 1.3 - the output you sent indicated you have hwloc 1.8, > which is quite a big change. OMPI 1.8 series is based on hwloc 1.9, so at > least that is closer (though probably still a mismatch). > > Frankly, I’d just download and install an OMPI tarball myself and avoid these > headaches. This mismatch in required versions is why we embed hwloc as it is > a critical library for OMPI, and we had to ensure that the version matched > our internal requirements. > > >> On Dec 8, 2014, at 8:50 AM, Pim Schellart <p.schell...@gmail.com> wrote: >> >> It is the default openmpi that comes with Ubuntu 14.04. >> >>> On 08 Dec 2014, at 17:17, Ralph Castain <r...@open-mpi.org> wrote: >>> >>> Pim: is this an OMPI you built, or one you were given somehow? If you built >>> it, how did you configure it? >>> >>>> On Dec 8, 2014, at 8:12 AM, Brice Goglin <brice.gog...@inria.fr> wrote: >>>> >>>> It likely depends on how SLURM allocates the cpuset/cgroup inside the >>>> nodes. The XML warning is related to these restrictions inside the node. >>>> Anyway, my feeling is that there's a old OMPI or a old hwloc somewhere. >>>> >>>> How do we check after install whether OMPI uses the embedded or the >>>> system-wide hwloc? >>>> >>>> Brice >>>> >>>> >>>> >>>> >>>> Le 08/12/2014 17:07, Pim Schellart a écrit : >>>>> Dear Ralph, >>>>> >>>>> the nodes are called coma## and as you can see in the logs the nodes of >>>>> the broken example are the same as the nodes of the working one, so that >>>>> doesn’t seem to be the cause. Unless (very likely) I’m missing something. >>>>> Anything else I can check? >>>>> >>>>> Regards, >>>>> >>>>> Pim >>>>> >>>>>> On 08 Dec 2014, at 17:03, Ralph Castain <r...@open-mpi.org> wrote: >>>>>> >>>>>> As Brice said, OMPI has its own embedded version of hwloc that we use, >>>>>> so there is no Slurm interaction to be considered. The most likely cause >>>>>> is that one or more of your nodes is picking up a different version of >>>>>> OMPI. So things “work” if you happen to get nodes where all the versions >>>>>> match, and “fail” when you get a combination that includes a different >>>>>> version. >>>>>> >>>>>> Is there some way you can narrow down your search to find the node(s) >>>>>> that are picking up the different version? >>>>>> >>>>>> >>>>>>> On Dec 8, 2014, at 7:48 AM, Pim Schellart <p.schell...@gmail.com> wrote: >>>>>>> >>>>>>> Dear Brice, >>>>>>> >>>>>>> I am not sure why this is happening since all code seems to be using >>>>>>> the same hwloc library version (1.8) but it does :) An MPI program is >>>>>>> started through SLURM on two nodes with four CPU cores total (divided >>>>>>> over the nodes) using the following script: >>>>>>> >>>>>>> #! /bin/bash >>>>>>> #SBATCH -N 2 -n 4 >>>>>>> /usr/bin/mpiexec /usr/bin/lstopo --version >>>>>>> /usr/bin/mpiexec /usr/bin/lstopo --of xml >>>>>>> /usr/bin/mpiexec /path/to/my_mpi_code >>>>>>> >>>>>>> When this is submitted multiple times it gives “out-of-order” warnings >>>>>>> in about 9/10 cases but works without warnings in 1/10 cases. I >>>>>>> attached the output (with xml) for both the working and `broken` case. >>>>>>> Note that the xml is of course printed (differently) multiple times for >>>>>>> each task/core. As always, any help would be appreciated. >>>>>>> >>>>>>> Regards, >>>>>>> >>>>>>> Pim Schellart >>>>>>> >>>>>>> P.S. $ mpirun --version >>>>>>> mpirun (Open MPI) 1.6.5 >>>>>>> >>>>>>> <broken.log><working.log> >>>>>>> >>>>>>>> On 07 Dec 2014, at 13:50, Brice Goglin <brice.gog...@inria.fr> wrote: >>>>>>>> >>>>>>>> Hello >>>>>>>> The github issue you're refering to was closed 18 months ago. The >>>>>>>> warning (it's not an error) is only supposed to appear if you're >>>>>>>> importing in a recent hwloc a XML that was exported from a old hwloc. I >>>>>>>> don't see how that could happen when using Open MPI since the hwloc >>>>>>>> versions on both sides is the same. >>>>>>>> Make sure you're not confusing with another error described here >>>>>>>> >>>>>>>> http://www.open-mpi.org/projects/hwloc/doc/v1.10.0/a00028.php#faq_os_error >>>>>>>> Otherwise please report the exact Open MPI and/or hwloc versions as >>>>>>>> well >>>>>>>> as the XML lstopo output on the nodes that raise the warning (lstopo >>>>>>>> foo.xml). Send these to hwloc mailing lists such as >>>>>>>> hwloc-us...@open-mpi.org or hwloc-de...@open-mpi.org >>>>>>>> Thanks >>>>>>>> Brice >>>>>>>> >>>>>>>> >>>>>>>> Le 07/12/2014 13:29, Pim Schellart a écrit : >>>>>>>>> Dear OpenMPI developers, >>>>>>>>> >>>>>>>>> this might be a bit off topic but when using the SLURM scheduler >>>>>>>>> (with cpuset support) on Ubuntu 14.04 (openmpi 1.6) hwloc sometimes >>>>>>>>> gives a "out-of-order topology discovery” error. According to issue >>>>>>>>> #103 on github (https://github.com/open-mpi/hwloc/issues/103) this >>>>>>>>> error was discussed before and it was possible to sort it out in >>>>>>>>> “insert_object_by_parent”, is this still considered? If not, what >>>>>>>>> (top level) hwloc API call should we look for in the SLURM sources to >>>>>>>>> start debugging? Any help will be most welcome. >>>>>>>>> >>>>>>>>> Kind regards, >>>>>>>>> >>>>>>>>> Pim Schellart >>>>>>>>> _______________________________________________ >>>>>>>>> devel mailing list >>>>>>>>> de...@open-mpi.org >>>>>>>>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel >>>>>>>>> Link to this post: >>>>>>>>> http://www.open-mpi.org/community/lists/devel/2014/12/16441.php >>>>>>> _______________________________________________ >>>>>>> devel mailing list >>>>>>> de...@open-mpi.org >>>>>>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel >>>>>>> Link to this post: >>>>>>> http://www.open-mpi.org/community/lists/devel/2014/12/16447.php >>>>>> _______________________________________________ >>>>>> devel mailing list >>>>>> de...@open-mpi.org >>>>>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel >>>>>> Link to this post: >>>>>> http://www.open-mpi.org/community/lists/devel/2014/12/16448.php >>>>> _______________________________________________ >>>>> devel mailing list >>>>> de...@open-mpi.org >>>>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel >>>>> Link to this post: >>>>> http://www.open-mpi.org/community/lists/devel/2014/12/16449.php >>>> >>>> _______________________________________________ >>>> devel mailing list >>>> de...@open-mpi.org >>>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel >>>> Link to this post: >>>> http://www.open-mpi.org/community/lists/devel/2014/12/16450.php >>> >>> _______________________________________________ >>> devel mailing list >>> de...@open-mpi.org >>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel >>> Link to this post: >>> http://www.open-mpi.org/community/lists/devel/2014/12/16451.php >> >> _______________________________________________ >> devel mailing list >> de...@open-mpi.org >> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel >> Link to this post: >> http://www.open-mpi.org/community/lists/devel/2014/12/16452.php > > _______________________________________________ > devel mailing list > de...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel > Link to this post: > http://www.open-mpi.org/community/lists/devel/2014/12/16453.php
