Adrian, Can you try mpirun --mca btl_vader_copy_mechanism none ...
Please double check the MCA parameter name, I am AFK IIRC, the default copy mechanism used by vader directly accesses the remote process address space, and this requires some permission (ptrace?) that might be dropped by podman. Note Open MPI might not detect both MPI tasks run on the same node because of podman. If you use UCX, then btl/vader is not used at all (pml/ucx is used instead) Cheers, Gilles Sent from my iPod > On Jul 12, 2019, at 18:33, Adrian Reber via users <users@lists.open-mpi.org> > wrote: > > So upstream Podman was really fast and merged a PR which makes my > wrapper unnecessary: > > Add support for --env-host : https://github.com/containers/libpod/pull/3557 > > As commented in the PR I can now start mpirun with Podman without a > wrapper: > > $ mpirun --hostfile ~/hosts --mca orte_tmpdir_base /tmp/podman-mpirun podman > run --env-host --security-opt label=disable -v > /tmp/podman-mpirun:/tmp/podman-mpirun --userns=keep-id --net=host mpi-test > /home/mpi/ring > Rank 0 has cleared MPI_Init > Rank 1 has cleared MPI_Init > Rank 0 has completed ring > Rank 0 has completed MPI_Barrier > Rank 1 has completed ring > Rank 1 has completed MPI_Barrier > > This is example was using TCP and on an InfiniBand based system I have > to map the InfiniBand devices into the container. > > $ mpirun --mca btl ^openib --hostfile ~/hosts --mca orte_tmpdir_base > /tmp/podman-mpirun podman run --env-host -v > /tmp/podman-mpirun:/tmp/podman-mpirun --security-opt label=disable > --userns=keep-id --device /dev/infiniband/uverbs0 --device > /dev/infiniband/umad0 --device /dev/infiniband/rdma_cm --net=host mpi-test > /home/mpi/ring > Rank 0 has cleared MPI_Init > Rank 1 has cleared MPI_Init > Rank 0 has completed ring > Rank 0 has completed MPI_Barrier > Rank 1 has completed ring > Rank 1 has completed MPI_Barrier > > This is all running without root and only using Podman's rootless > support. > > Running multiple processes on one system, however, still gives me an > error. If I disable vader I guess that Open MPI is using TCP for > localhost communication and that works. But with vader it fails. > > The first error message I get is a segfault: > > [test1:00001] *** Process received signal *** > [test1:00001] Signal: Segmentation fault (11) > [test1:00001] Signal code: Address not mapped (1) > [test1:00001] Failing at address: 0x7fb7b1552010 > [test1:00001] [ 0] /lib64/libpthread.so.0(+0x12d80)[0x7f6299456d80] > [test1:00001] [ 1] > /usr/lib64/openmpi/lib/openmpi/mca_btl_vader.so(mca_btl_vader_send+0x3db)[0x7f628b33ab0b] > [test1:00001] [ 2] > /usr/lib64/openmpi/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_request_start_rdma+0x1fb)[0x7f62901d24bb] > [test1:00001] [ 3] > /usr/lib64/openmpi/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_send+0xfd6)[0x7f62901be086] > [test1:00001] [ 4] > /usr/lib64/openmpi/lib/libmpi.so.40(PMPI_Send+0x1bd)[0x7f62996f862d] > [test1:00001] [ 5] /home/mpi/ring[0x400b76] > [test1:00001] [ 6] /lib64/libc.so.6(__libc_start_main+0xf3)[0x7f62990a3813] > [test1:00001] [ 7] /home/mpi/ring[0x4008be] > [test1:00001] *** End of error message *** > > Guessing that vader uses shared memory this is expected to fail, with > all the namespace isolations in place. Maybe not with a segfault, but > each container has its own shared memory. So next step was to use the > host's ipc and pid namespace and mount /dev/shm: > > '-v /dev/shm:/dev/shm --ipc=host --pid=host' > > Which does not segfault, but still does not look correct: > > Rank 0 has cleared MPI_Init > Rank 1 has cleared MPI_Init > Rank 2 has cleared MPI_Init > [test1:17722] Read -1, expected 80000, errno = 1 > [test1:17722] Read -1, expected 80000, errno = 1 > [test1:17722] Read -1, expected 80000, errno = 1 > [test1:17722] Read -1, expected 80000, errno = 1 > [test1:17722] Read -1, expected 80000, errno = 1 > [test1:17722] Read -1, expected 80000, errno = 1 > [test1:17722] Read -1, expected 80000, errno = 1 > [test1:17722] Read -1, expected 80000, errno = 1 > [test1:17722] Read -1, expected 80000, errno = 1 > [test1:17722] Read -1, expected 80000, errno = 1 > [test1:17722] Read -1, expected 80000, errno = 1 > Rank 0 has completed ring > Rank 2 has completed ring > Rank 0 has completed MPI_Barrier > Rank 1 has completed ring > Rank 2 has completed MPI_Barrier > Rank 1 has completed MPI_Barrier > > This is using the Open MPI ring.c example with SIZE increased from 20 to > 20000. > > Any recommendations what vader needs to communicate correctly? > > Adrian > >> On Thu, Jul 11, 2019 at 12:07:35PM +0200, Adrian Reber via users wrote: >> Gilles, >> >> thanks for pointing out the environment variables. I quickly created a >> wrapper which tells Podman to re-export all OMPI_ and PMIX_ variables >> (grep "\(PMIX\|OMPI\)"). Now it works: >> >> $ mpirun --hostfile ~/hosts ./wrapper -v /tmp:/tmp --userns=keep-id >> --net=host mpi-test /home/mpi/hello >> >> Hello, world (2 procs total) >> --> Process # 0 of 2 is alive. ->test1 >> --> Process # 1 of 2 is alive. ->test2 >> >> I need to tell Podman to mount /tmp from the host into the container, as >> I am running rootless I also need to tell Podman to use the same user ID >> in the container as outside (so that the Open MPI files in /tmp) can be >> shared and I am also running without a network namespace. >> >> So this is now with the full Podman provided isolation except the >> network namespace. Thanks for you help! >> >> Adrian >> >>> On Thu, Jul 11, 2019 at 04:47:21PM +0900, Gilles Gouaillardet via users >>> wrote: >>> Adrian, >>> >>> >>> the MPI application relies on some environment variables (they typically >>> start with OMPI_ and PMIX_). >>> >>> The MPI application internally uses a PMIx client that must be able to >>> contact a PMIx server >>> >>> (that is included in mpirun and the orted daemon(s) spawned on the remote >>> hosts). >>> >>> located on the same host. >>> >>> >>> If podman provides some isolation between the app inside the container (e.g. >>> /home/mpi/hello) >>> >>> and the outside world (e.g. mpirun/orted), that won't be an easy ride. >>> >>> >>> Cheers, >>> >>> >>> Gilles >>> >>> >>>> On 7/11/2019 4:35 PM, Adrian Reber via users wrote: >>>> I did a quick test to see if I can use Podman in combination with Open >>>> MPI: >>>> >>>> [test@test1 ~]$ mpirun --hostfile ~/hosts podman run >>>> quay.io/adrianreber/mpi-test /home/mpi/hello >>>> >>>> Hello, world (1 procs total) >>>> --> Process # 0 of 1 is alive. ->789b8fb622ef >>>> >>>> Hello, world (1 procs total) >>>> --> Process # 0 of 1 is alive. ->749eb4e1c01a >>>> >>>> The test program (hello) is taken from >>>> https://raw.githubusercontent.com/openhpc/ohpc/obs/OpenHPC_1.3.8_Factory/tests/mpi/hello.c >>>> >>>> >>>> The problem with this is that each process thinks it is process 0 of 1 >>>> instead of >>>> >>>> Hello, world (2 procs total) >>>> --> Process # 1 of 2 is alive. ->test1 >>>> --> Process # 0 of 2 is alive. ->test2 >>>> >>>> My questions is how is the rank determined? What resources do I need to >>>> have >>>> in my container to correctly determine the rank. >>>> >>>> This is Podman 1.4.2 and Open MPI 4.0.1. >>>> >>>> Adrian >>>> _______________________________________________ >>>> 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 > > Adrian > > -- > Adrian Reber <adr...@lisas.de> http://lisas.de/~adrian/ > The data on your hard drive is out of balance. > _______________________________________________ > 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
