My openmpi3.0.x run (called nscf run) was reading data from a routine Quantum Espresso input file edited by hand. The preliminary run (called scf run) was done with openmpi3.0.x on a similar input file also edited by hand.
Vahid > On Jan 18, 2018, at 6:39 PM, Jeff Squyres (jsquyres) <jsquy...@cisco.com> > wrote: > > FWIW: If your Open MPI 3.0.x runs are reading data that was written by MPI IO > via Open MPI 1.10.x or 1.8.x runs, that data formats may not be compatible > (and could lead to errors like you're seeing -- premature end of file, etc.). > > >> On Jan 18, 2018, at 5:34 PM, Vahid Askarpour <vh261...@dal.ca> wrote: >> >> Hi Jeff, >> >> I compiled Quantum Espresso/EPW with openmpi-3.0.x. The openmpi was compiled >> with intel14. >> >> A preliminary run for EPW using Quantum Espresso crashed with the following >> message: >> >> end of file while reading crystal k points >> >> There are 1728 k points in the input file and Quantum Espresso, by default, >> can read up to 40000 k points. >> >> This error did not occur with openmpi-1.8.1. >> >> So I will just continue to use openmpi-1.8.1 as it does not crash. >> >> Thanks, >> >> Vahid >> >>> On Jan 11, 2018, at 12:50 PM, Jeff Squyres (jsquyres) <jsquy...@cisco.com> >>> wrote: >>> >>> You are correct: 3.0.1 has not been released yet. >>> >>> However, our nightly snapshots of the 3.0.x branch are available for >>> download. These are not official releases, but they are great for getting >>> users to test what will eventually become an official release (i.e., 3.0.1) >>> to see if particular bugs have been fixed. This is one of the benefits of >>> open source. :-) >>> >>> Here's where the 3.0.1 nightly snapshots are available for download: >>> >>> https://www.open-mpi.org/nightly/v3.0.x/ >>> >>> They are organized by date. >>> >>> >>>> On Jan 11, 2018, at 11:34 AM, Vahid Askarpour <vh261...@dal.ca> wrote: >>>> >>>> Hi Jeff, >>>> >>>> I looked for the 3.0.1 version but I only found the 3.0.0 version >>>> available for download. So I thought it may take a while for the 3.0.1 to >>>> become available. Or did I miss something? >>>> >>>> Thanks, >>>> >>>> Vahid >>>> >>>>> On Jan 11, 2018, at 12:04 PM, Jeff Squyres (jsquyres) >>>>> <jsquy...@cisco.com> wrote: >>>>> >>>>> Vahid -- >>>>> >>>>> Were you able to give it a whirl? >>>>> >>>>> Thanks. >>>>> >>>>> >>>>>> On Jan 5, 2018, at 7:58 PM, Vahid Askarpour <vh261...@dal.ca> wrote: >>>>>> >>>>>> Gilles, >>>>>> >>>>>> I will try the 3.0.1rc1 version to see how it goes. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Vahid >>>>>> >>>>>>> On Jan 5, 2018, at 8:40 PM, Gilles Gouaillardet >>>>>>> <gilles.gouaillar...@gmail.com> wrote: >>>>>>> >>>>>>> Vahid, >>>>>>> >>>>>>> This looks like the description of the issue reported at >>>>>>> https://github.com/open-mpi/ompi/issues/4336 >>>>>>> The fix is currently available in 3.0.1rc1, and I will back port the >>>>>>> fix fo the v2.x branch. >>>>>>> A workaround is to use ROM-IO instead of ompio, you can achieve this >>>>>>> with >>>>>>> mpirun —mca io ^ompio ... >>>>>>> (FWIW 1.10 series use ROM-IO by default, so there is no leak out of the >>>>>>> box) >>>>>>> >>>>>>> IIRC, a possible (and ugly) workaround for the compilation issue is to >>>>>>> configure —with-ucx=/usr ... >>>>>>> That being said, you should really upgrade to a supported version of >>>>>>> Open MPI as previously suggested >>>>>>> >>>>>>> Cheers, >>>>>>> >>>>>>> Gilles >>>>>>> >>>>>>> On Saturday, January 6, 2018, Jeff Squyres (jsquyres) >>>>>>> <jsquy...@cisco.com> wrote: >>>>>>> You can still give Open MPI 2.1.1 a try. It should be source >>>>>>> compatible with EPW. Hopefully the behavior is close enough that it >>>>>>> should work. >>>>>>> >>>>>>> If not, please encourage the EPW developers to upgrade. v3.0.x is the >>>>>>> current stable series; v1.10.x is ancient. >>>>>>> >>>>>>> >>>>>>> >>>>>>>> On Jan 5, 2018, at 5:22 PM, Vahid Askarpour <vh261...@dal.ca> wrote: >>>>>>>> >>>>>>>> Thank you Jeff for your suggestion to use the v.2.1 series. >>>>>>>> >>>>>>>> I am attempting to use openmpi with EPW. On the EPW website >>>>>>>> (http://epw.org.uk/Main/DownloadAndInstall), it is stated that: >>>>>>>> >>>>>>>>> Compatibility of EPW >>>>>>>>> >>>>>>>>> EPW is tested and should work on the following compilers and >>>>>>>>> libraries: >>>>>>>>> >>>>>>>>> • gcc640 serial >>>>>>>>> • gcc640 + openmpi-1.10.7 >>>>>>>>> • intel 12 + openmpi-1.10.7 >>>>>>>>> • intel 17 + impi >>>>>>>>> • PGI 17 + mvapich2.3 >>>>>>>>> EPW is know to have the following incompatibilities with: >>>>>>>>> >>>>>>>>> • openmpi 2.0.2 (but likely on all the 2.x.x version): Works but >>>>>>>>> memory leak. If you open and close a file a lot of times with openmpi >>>>>>>>> 2.0.2, the memory increase linearly with the number of times the file >>>>>>>>> is open. >>>>>>>> >>>>>>>> So I am hoping to avoid the 2.x.x series and use the 1.10.7 version >>>>>>>> suggested by the EPW developers. However, it appears that this is not >>>>>>>> possible. >>>>>>>> >>>>>>>> Vahid >>>>>>>> >>>>>>>>> On Jan 5, 2018, at 5:06 PM, Jeff Squyres (jsquyres) >>>>>>>>> <jsquy...@cisco.com> wrote: >>>>>>>>> >>>>>>>>> I forget what the underlying issue was, but this issue just came up >>>>>>>>> and was recently fixed: >>>>>>>>> >>>>>>>>> https://github.com/open-mpi/ompi/issues/4345 >>>>>>>>> >>>>>>>>> However, the v1.10 series is fairly ancient -- the fix was not >>>>>>>>> applied to that series. The fix was applied to the v2.1.x series, >>>>>>>>> and a snapshot tarball containing the fix is available here >>>>>>>>> (generally just take the latest tarball): >>>>>>>>> >>>>>>>>> https://www.open-mpi.org/nightly/v2.x/ >>>>>>>>> >>>>>>>>> The fix is still pending for the v3.0.x and v3.1.x series (i.e., >>>>>>>>> there are pending pull requests that haven't been merged yet, so the >>>>>>>>> nightly snapshots for the v3.0.x and v3.1.x branches do not yet >>>>>>>>> contain this fix). >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> On Jan 5, 2018, at 1:34 PM, Vahid Askarpour <vh261...@dal.ca> wrote: >>>>>>>>>> >>>>>>>>>> I am attempting to install openmpi-1.10.7 on CentOS Linux (7.4.1708) >>>>>>>>>> using GCC-6.4.0. >>>>>>>>>> >>>>>>>>>> When compiling, I get the following error: >>>>>>>>>> >>>>>>>>>> make[2]: Leaving directory >>>>>>>>>> '/home/vaskarpo/bin/openmpi-1.10.7/ompi/mca/pml/ob1' >>>>>>>>>> Making all in mca/pml/ucx >>>>>>>>>> make[2]: Entering directory >>>>>>>>>> '/home/vaskarpo/bin/openmpi-1.10.7/ompi/mca/pml/ucx' >>>>>>>>>> CC pml_ucx.lo >>>>>>>>>> CC pml_ucx_request.lo >>>>>>>>>> CC pml_ucx_datatype.lo >>>>>>>>>> CC pml_ucx_component.lo >>>>>>>>>> CCLD mca_pml_ucx.la >>>>>>>>>> libtool: error: require no space between '-L' and '-lrt' >>>>>>>>>> make[2]: *** [Makefile:1725: mca_pml_ucx.la] Error 1 >>>>>>>>>> make[2]: Leaving directory >>>>>>>>>> '/home/vaskarpo/bin/openmpi-1.10.7/ompi/mca/pml/ucx' >>>>>>>>>> make[1]: *** [Makefile:3261: all-recursive] Error 1 >>>>>>>>>> make[1]: Leaving directory '/home/vaskarpo/bin/openmpi-1.10.7/ompi' >>>>>>>>>> make: *** [Makefile:1777: all-recursive] Error 1 >>>>>>>>>> >>>>>>>>>> Thank you, >>>>>>>>>> >>>>>>>>>> Vahid >>>>>>>>>> _______________________________________________ >>>>>>>>>> users mailing list >>>>>>>>>> users@lists.open-mpi.org >>>>>>>>>> https://lists.open-mpi.org/mailman/listinfo/users >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Jeff Squyres >>>>>>>>> jsquy...@cisco.com >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> users mailing list >>>>>>>>> users@lists.open-mpi.org >>>>>>>>> https://lists.open-mpi.org/mailman/listinfo/users >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> users mailing list >>>>>>>> users@lists.open-mpi.org >>>>>>>> https://lists.open-mpi.org/mailman/listinfo/users >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Jeff Squyres >>>>>>> jsquy...@cisco.com >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> users mailing list >>>>>>> users@lists.open-mpi.org >>>>>>> https://lists.open-mpi.org/mailman/listinfo/users >>>>>>> _______________________________________________ >>>>>>> users mailing list >>>>>>> users@lists.open-mpi.org >>>>>>> https://lists.open-mpi.org/mailman/listinfo/users >>>>>> >>>>>> _______________________________________________ >>>>>> users mailing list >>>>>> users@lists.open-mpi.org >>>>>> https://lists.open-mpi.org/mailman/listinfo/users >>>>> >>>>> >>>>> -- >>>>> Jeff Squyres >>>>> jsquy...@cisco.com >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> users mailing list >>>>> users@lists.open-mpi.org >>>>> https://lists.open-mpi.org/mailman/listinfo/users >>>> >>>> _______________________________________________ >>>> users mailing list >>>> users@lists.open-mpi.org >>>> https://lists.open-mpi.org/mailman/listinfo/users >>> >>> >>> -- >>> Jeff Squyres >>> jsquy...@cisco.com >>> >>> >>> >>> _______________________________________________ >>> users mailing list >>> users@lists.open-mpi.org >>> https://lists.open-mpi.org/mailman/listinfo/users >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org >> https://lists.open-mpi.org/mailman/listinfo/users > > > -- > Jeff Squyres > jsquy...@cisco.com > > > > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.org/mailman/listinfo/users _______________________________________________ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
