Dear Brice, the BIOS is the most latest. However, i wonder if this could be a hardware error, as openmpi sources claim. Is there any way to find out if this is a hardware error?
Thanks > From: users-requ...@open-mpi.org > Subject: users Digest, Vol 3074, Issue 1 > To: us...@open-mpi.org > Date: Sat, 20 Dec 2014 12:00:02 -0500 > > Send users mailing list submissions to > us...@open-mpi.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.open-mpi.org/mailman/listinfo.cgi/users > or, via email, send a message with subject or body 'help' to > users-requ...@open-mpi.org > > You can reach the person managing the list at > users-ow...@open-mpi.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of users digest..." > > > Today's Topics: > > 1. Re: Deadlock in OpenMPI 1.8.3 and PETSc 3.4.5 > (Jeff Squyres (jsquyres)) > 2. Hwloc error with Openmpi 1.8.3 on AMD 64 (Sergio Manzetti) > 3. Re: Hwloc error with Openmpi 1.8.3 on AMD 64 (Brice Goglin) > 4. best function to send data (Diego Avesani) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 19 Dec 2014 19:26:58 +0000 > From: "Jeff Squyres (jsquyres)" <jsquy...@cisco.com> > To: "Open MPI User's List" <us...@open-mpi.org> > Cc: "petsc-ma...@mcs.anl.gov" <petsc-ma...@mcs.anl.gov> > Subject: Re: [OMPI users] Deadlock in OpenMPI 1.8.3 and PETSc 3.4.5 > Message-ID: <027ab453-de85-4f08-bdd7-a676ca90e...@cisco.com> > Content-Type: text/plain; charset="us-ascii" > > On Dec 19, 2014, at 10:44 AM, George Bosilca <bosi...@icl.utk.edu> wrote: > > > Regarding your second point, while I do tend to agree that such issue is > > better addressed in the MPI Forum, the last attempt to fix this was > > certainly not a resounding success. > > Yeah, fair enough -- but it wasn't a failure, either. It could definitely be > moved forward, but it will take time/effort, which I unfortunately don't > have. I would be willing, however, to spin up someone who *does* have > time/effort available to move the proposal forward. > > > Indeed, there is a slight window of opportunity for inconsistencies in the > > recursive behavior. > > You're right; it's a small window in the threading case, but a) that's the > worst kind :-), and b) the non-threaded case is actually worse (because the > global state can change from underneath the loop). > > > But the inconsistencies were already in the code, especially in the single > > threaded case. As we never received any complaints related to this topic I > > did not deemed interesting to address them with my last commit. Moreover, > > the specific behavior needed by PETSc is available in Open MPI when > > compiled without thread support, as the only thing that "protects" the > > attributes is that global mutex. > > Mmmm. Ok, I see your point. But this is a (very) slippery slope. > > > For example, in ompi_attr_delete_all(), it gets the count of all attributes > > and then loops <count> times to delete each attribute. But each attribute > > callback can now insert or delete attributes on that entity. This can mean > > that the loop can either fail to delete an attribute (because some > > attribute callback already deleted it) or fail to delete *all* attributes > > (because some attribute callback added more). > > > > To be extremely precise the deletion part is always correct > > ...as long as the hash map is not altered from the application (e.g., by > adding or deleting another attribute during a callback). > > I understand that you mention above that you're not worried about this case. > I'm just picking here because there is quite definitely a case where the loop > is *not* correct. PETSc apparently doesn't trigger this badness, but... like > I said above, it's a (very) slippery slope. > > > as it copies the values to be deleted into a temporary array before calling > > any callbacks (and before releasing the mutex), so we only remove what was > > in the object attribute hash when the function was called. Don't > > misunderstand we have an extremely good reason to do it this way, we need > > to call the callbacks in the order in which they were created (mandated by > > the MPI standard). > > > > ompi_attr_copy_all() has similar problems -- in general, the hash that it > > is looping over can change underneath it. > > > > For the copy it is a little bit more tricky, as the calling order is not > > imposed. Our peculiar implementation of the hash table (with array) makes > > the code work, with a single (possible minor) exception when the hash table > > itself is grown between 2 calls. However, as stated before this issue was > > already present in the code in single threaded cases for years. Addressing > > it is another 2 line patch, but I leave this exercise to an interested > > reader. > > Yeah, thanks for that. :-) > > To be clear: both the copy and the delete code could be made thread safe. I > just don't think we should be encouraging users to be exercising undefined / > probably not-portable MPI code. > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > > > ------------------------------ > > Message: 2 > Date: Fri, 19 Dec 2014 20:58:46 +0100 > From: Sergio Manzetti <sergio.manze...@outlook.com> > To: "us...@open-mpi.org" <us...@open-mpi.org> > Subject: [OMPI users] Hwloc error with Openmpi 1.8.3 on AMD 64 > Message-ID: <dub126-w2190e22e21596a1b834cf4e3...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > Dear all, when trying to run NWchem with openmpi, I get this error. > > > > **************************************************************************** > * Hwloc has encountered what looks like an error from the operating system. > * > * object intersection without inclusion! > * Error occurred in topology.c line 594 > * > * Please report this error message to the hwloc user's mailing list, > * along with the output from the hwloc-gather-topology.sh script. > > Is there any rationale for solving this? > > Thanks > > > -------------- next part -------------- > HTML attachment scrubbed and removed > > ------------------------------ > > Message: 3 > Date: Fri, 19 Dec 2014 21:13:19 +0100 > From: Brice Goglin <brice.gog...@inria.fr> > To: Open MPI Users <us...@open-mpi.org> > Subject: Re: [OMPI users] Hwloc error with Openmpi 1.8.3 on AMD 64 > Message-ID: <549486df.50...@inria.fr> > Content-Type: text/plain; charset="windows-1252" > > Hello, > > The rationale is to read the message and do what it says :) > > Have a look at > www.open-mpi.org/projects/hwloc/doc/v1.10.0/a00028.php#faq_os_error > Try upgrading your BIOS and kernel. > > Otherwise install hwloc and send the output (tarball) of > hwloc-gather-topology to hwloc-users (not to OMPI users). > > thanks > Brice > > > > Le 19/12/2014 20:58, Sergio Manzetti a ?crit : > > > > > > Dear all, when trying to run NWchem with openmpi, I get this error. > > > > > > > > **************************************************************************** > > * Hwloc has encountered what looks like an error from the operating > > system. > > * > > * object intersection without inclusion! > > * Error occurred in topology.c line 594 > > * > > * Please report this error message to the hwloc user's mailing list, > > * along with the output from the hwloc-gather-topology.sh script. > > > > Is there any rationale for solving this? > > > > Thanks > > > > > > _______________________________________________ > > users mailing list > > us...@open-mpi.org > > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > > Link to this post: > > http://www.open-mpi.org/community/lists/users/2014/12/26045.php > > -------------- next part -------------- > HTML attachment scrubbed and removed > > ------------------------------ > > Message: 4 > Date: Fri, 19 Dec 2014 23:56:36 +0100 > From: Diego Avesani <diego.aves...@gmail.com> > To: Open MPI Users <us...@open-mpi.org> > Subject: [OMPI users] best function to send data > Message-ID: > <cag8o1y4b0uwydtrb+swdbra4tbk6ih5toeypga8b6vs-oty...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > dear all users, > I am new in MPI world. > I would like to know what is the best choice and meaning between different > function. > > In my program I would like that each process send a vector of data to all > the other process. What do you suggest? > Is it correct MPI_Bcast or I am missing something? > > Thanks a lot > > Diego > -------------- next part -------------- > HTML attachment scrubbed and removed > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > > ------------------------------ > > End of users Digest, Vol 3074, Issue 1 > **************************************
