I hate odin :-( FWIW: it all works fine today, no matter how I configure it. No earthly idea what happened.
Ignore these droids.... On Oct 30, 2012, at 7:28 AM, Edgar Gabriel <gabr...@cs.uh.edu> wrote: > ok, so a couple of things. > > I still think it is the same issue that I observed 1-2 days ago. Could > you try to remove the fs/lustre component from your compilation, e.g. by > adding an .ompi_ignore file into that directory, and see whether this > fixes the issue? > > I tried on my machine (no lustre, no ib) compilations with > --disable-mpi-io *or* --disable-io-romio, and both worked correctly and > I could run things. Note, that the flags are truly different meanwhile, > since the second flag is now equivalent to --enable-mca-no-build=io:romio > The first flag disables the io, fcoll, fs and sharedfp frameworks. > (prior to ompio they had basically the same effect). > > In your particular case this means, that you disabled romio, but the > entire ompio stack is still compiled, and error must come from that > portion. If my suspecion is correct, it is still liblustre > messing around with the malloc hooks, and that causes the stack frame to > be completely broken. I thought I fixed that since we did not have the > issue on trunk, but we did observe that in the 1.7 branch 1-2 days back > as well, and I was looking into that. > > That being said, there is another malloc-hooks issue that makes me a bit > nervous. The compilation of the otf stuff produced a ton of warnings on > my machine with gcc4.6.2 also with respect to the _malloc_hooks and > _realloc_hooks. Not sure whether this contributed to the problem as > well, just thought I bring it up since we seem to have a corrupted stack > frame problem. > > Thanks > Edgar > > > On 10/30/2012 8:29 AM, Edgar Gabriel wrote: >> ok, I'll look into this. I noticed a problem with static builds on >> lustre file systems recently, and I was wandering whether its the same >> issue or not. But I'll check what's going on. >> >> THanks >> Edgar >> >> On 10/30/2012 7:22 AM, Ralph Castain wrote: >>> No to Lustre, and I didn't build static >>> >>> I'm not sure what, if any, parallel file system might be present. In the >>> case that works, I just built with no configure args other than prefix. >>> ompi_info shows both romio and mpio built, but nothing more about what >>> support they built internally. >>> >>> >>> On Oct 30, 2012, at 4:14 AM, Edgar Gabriel <gabr...@cs.uh.edu> wrote: >>> >>>> Ralph, >>>> >>>> just out curiosity: is there a lustre file system on the machine and is >>>> this a static build ? >>>> >>>> Thanks >>>> Edgar >>>> >>>> On 10/29/2012 9:17 PM, Ralph Castain wrote: >>>>> Hmmm...I added that directory and tried this on odin (which is an >>>>> IB-based machine). Any MPI proc segfaults: >>>>> >>>>> Core was generated by `./hello'. >>>>> Program terminated with signal 11, Segmentation fault. >>>>> w#0 _sysio_p_validate (pno=0x0, intnt=0x0, path=0x0) at src/inode.c:574 >>>>> 574 src/inode.c: No such file or directory. >>>>> in src/inode.c >>>>> (gdb) where >>>>> #0 _sysio_p_validate (pno=0x0, intnt=0x0, path=0x0) at src/inode.c:574 >>>>> #1 0x00002aaaabd3f3e9 in _sysio_path_walk (parent=0x0, >>>>> nd=0x7fffffffd8e0) at src/namei.c:216 >>>>> #2 0x00002aaaabd3faad in _sysio_namei (parent=0x0, path=<value optimized >>>>> out>, flags=0, intnt=0x7fffffffd950, pnop=0x7fffffffd970) at >>>>> src/namei.c:505 >>>>> #3 0x00002aaaabd3fd98 in open (path=0x2aaaac24280f >>>>> "/sys/devices/system/node", flags=<value optimized out>) at src/open.c:179 >>>>> #4 0x00002aaaabd43d5b in opendir (name=0x2aaaac24280f >>>>> "/sys/devices/system/node") at src/stddir.c:60 >>>>> #5 0x00002aaaac241825 in numa_max_node () from /usr/lib64/libnuma.so.1 >>>>> #6 0x00002aaaac241d13 in numa_init () from /usr/lib64/libnuma.so.1 >>>>> #7 0x00002aaaaaab845b in call_init () from /lib64/ld-linux-x86-64.so.2 >>>>> #8 0x00002aaaaaab8565 in _dl_init_internal () from >>>>> /lib64/ld-linux-x86-64.so.2 >>>>> #9 0x00002aaaaaaabaaa in _dl_start_user () from >>>>> /lib64/ld-linux-x86-64.so.2 >>>>> #10 0x0000000000000001 in ?? () >>>>> #11 0x00007fffffffe03c in ?? () >>>>> #12 0x0000000000000000 in ?? () >>>>> >>>>> I got the same thing whether I excluded openib or not. I then ran on my >>>>> Linux cluster, which doesn't have IB at all - and it ran fine. Also runs >>>>> clean on the Mac. However, in both those cases, I had left IO romio >>>>> enabled. >>>>> >>>>> Now on odin, I always disable-io-romio. So I tried deliberately enabling >>>>> it, and everything works. So this appears to be something that the IO >>>>> work has broken. >>>>> >>>>> Edgar: can you please fix --disable-io-romio? >>>>> >>>>> Thanks >>>>> Ralph >>>>> >>>>> >>>>> >>>>> >>>>> On Oct 29, 2012, at 11:55 AM, Edgar Gabriel <gabr...@cs.uh.edu> wrote: >>>>> >>>>>> I'm sorry to add one more thing to the list, but beyond this file, it >>>>>> looks like also the entire ompi/mca/common/verbs/ directory is also >>>>>> missing in the 1.7 branch, but is required to compile the bcoll >>>>>> framework. It is there in the trunk, but missing in the 1.7 branch... >>>>>> >>>>>> Thanks >>>>>> Edgar >>>>>> >>>>>> >>>>>> On 10/26/2012 5:31 PM, Ralph Castain wrote: >>>>>>> Okay, I'll fix for tonights tarball. >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> On Oct 26, 2012, at 3:28 PM, "Shamis, Pavel" <sham...@ornl.gov> wrote: >>>>>>> >>>>>>>> There is a bug in makefile. The file existing in svn, but it is not >>>>>>>> listed in the Makefile.am. As a result, it wasn't pulled to the >>>>>>>> tarball. >>>>>>>> >>>>>>>> Pavel (Pasha) Shamis >>>>>>>> --- >>>>>>>> Computer Science Research Group >>>>>>>> Computer Science and Math Division >>>>>>>> Oak Ridge National Laboratory >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Oct 26, 2012, at 2:33 PM, Edgar Gabriel wrote: >>>>>>>> >>>>>>>> we have trouble compiling the 1.7 series on a machine in Dresden. >>>>>>>> Specifically, we receive an error message when compiling the >>>>>>>> bcol/iboffload component (other infiniband components compile fine). >>>>>>>> >>>>>>>> Any idea/suggestions what we might be doing wrong or what to look for? >>>>>>>> >>>>>>>> make[2]: Entering directory >>>>>>>> `/home/h2/gabriel/openmpi-1.7rc4/ompi/mca/bcol/iboffload' >>>>>>>> CC bcol_iboffload_module.lo >>>>>>>> CC bcol_iboffload_mca.lo >>>>>>>> CC bcol_iboffload_endpoint.lo >>>>>>>> CC bcol_iboffload_frag.lo >>>>>>>> In file included from bcol_iboffload_frag.c:16:0: >>>>>>>> bcol_iboffload.h:46:36: fatal error: bcol_iboffload_qp_info.h: No such >>>>>>>> file or directory >>>>>>>> compilation terminated. >>>>>>>> make[2]: *** [bcol_iboffload_frag.lo] Error 1 >>>>>>>> make[2]: *** Waiting for unfinished jobs.... >>>>>>>> In file included from bcol_iboffload_mca.c:18:0: >>>>>>>> bcol_iboffload.h:46:36: fatal error: bcol_iboffload_qp_info.h: No such >>>>>>>> file or directory >>>>>>>> compilation terminated. >>>>>>>> make[2]: *** [bcol_iboffload_mca.lo] Error 1 >>>>>>>> In file included from bcol_iboffload_endpoint.c:23:0: >>>>>>>> bcol_iboffload.h:46:36: fatal error: bcol_iboffload_qp_info.h: No such >>>>>>>> file or directory >>>>>>>> compilation terminated. >>>>>>>> make[2]: *** [bcol_iboffload_endpoint.lo] Error 1 >>>>>>>> In file included from bcol_iboffload_module.c:39:0: >>>>>>>> bcol_iboffload.h:46:36: fatal error: bcol_iboffload_qp_info.h: No such >>>>>>>> file or directory >>>>>>>> compilation terminated. >>>>>>>> make[2]: *** [bcol_iboffload_module.lo] Error 1 >>>>>>>> make[2]: Leaving directory >>>>>>>> `/home/h2/gabriel/openmpi-1.7rc4/ompi/mca/bcol/iboffload' >>>>>>>> make[1]: *** [all-recursive] Error 1 >>>>>>>> make[1]: Leaving directory `/home/h2/gabriel/openmpi-1.7rc4/ompi' >>>>>>>> make: *** [all-recursive] Error 1 >>>>>>>> >>>>>>>> Thanks >>>>>>>> Edgar >>>>>>>> >>>>>>>> -- >>>>>>>> Edgar Gabriel >>>>>>>> Associate Professor >>>>>>>> Parallel Software Technologies Lab http://pstl.cs.uh.edu >>>>>>>> Department of Computer Science University of Houston >>>>>>>> Philip G. Hoffman Hall, Room 524 Houston, TX-77204, USA >>>>>>>> Tel: +1 (713) 743-3857 Fax: +1 (713) 743-3335 >>>>>>>> >>>>>>>> <signature.asc>_______________________________________________ >>>>>>>> devel mailing list >>>>>>>> de...@open-mpi.org<mailto:de...@open-mpi.org> >>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/devel >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> devel mailing list >>>>>>>> de...@open-mpi.org >>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/devel >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> devel mailing list >>>>>>> de...@open-mpi.org >>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/devel >>>>>>> >>>>>> >>>>>> -- >>>>>> Edgar Gabriel >>>>>> Associate Professor >>>>>> Parallel Software Technologies Lab http://pstl.cs.uh.edu >>>>>> Department of Computer Science University of Houston >>>>>> Philip G. Hoffman Hall, Room 524 Houston, TX-77204, USA >>>>>> Tel: +1 (713) 743-3857 Fax: +1 (713) 743-3335 >>>>>> >>>>>> _______________________________________________ >>>>>> devel mailing list >>>>>> de...@open-mpi.org >>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/devel >>>>> >>>>> >>>>> _______________________________________________ >>>>> devel mailing list >>>>> de...@open-mpi.org >>>>> http://www.open-mpi.org/mailman/listinfo.cgi/devel >>>>> >>>> >>>> -- >>>> Edgar Gabriel >>>> Associate Professor >>>> Parallel Software Technologies Lab http://pstl.cs.uh.edu >>>> Department of Computer Science University of Houston >>>> Philip G. Hoffman Hall, Room 524 Houston, TX-77204, USA >>>> Tel: +1 (713) 743-3857 Fax: +1 (713) 743-3335 >>>> >>>> _______________________________________________ >>>> devel mailing list >>>> de...@open-mpi.org >>>> http://www.open-mpi.org/mailman/listinfo.cgi/devel >>> >>> >>> _______________________________________________ >>> devel mailing list >>> de...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/devel >>> >> >> >> >> _______________________________________________ >> devel mailing list >> de...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/devel >> > > -- > Edgar Gabriel > Associate Professor > Parallel Software Technologies Lab http://pstl.cs.uh.edu > Department of Computer Science University of Houston > Philip G. Hoffman Hall, Room 524 Houston, TX-77204, USA > Tel: +1 (713) 743-3857 Fax: +1 (713) 743-3335 > > _______________________________________________ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel
