[Beowulf] How to debug error with Open MPI 3 / Mellanox / Red Hat?
Prentice Bisbal
pbisbal at pppl.gov
Tue Apr 30 14:42:47 PDT 2019
One more thing:
https://github.com/intel/psm
Prentice
On 4/30/19 5:41 PM, Prentice Bisbal wrote:
>
> I agree with Gus that you should be asking this question on the
> OpenMPI mailing list where there's more expertise specific to
> OpenMPI. Based on your error message
>
>> mca_base_component_repository_open: unable to open
>> mca_btl_usnic: libpsm_infinipath.so.1: cannot open shared object file:
>> No such file or directory (ignored)
>
> It looks like it's not a problem with IB libraries in general, but
> that you are missing the PSM libraries. PSM is an additional library
> used by QLogic cards, so installing Mellanox OFED will not help you
> out here. In fact, it will probably just make things worse. Since
> Intel bought QLogic a while back, I think you need to install the
> Intel PSM RPMs.
>
> If you are not using QLogic cards in your cluster, you will need to
> rebuild OpenMPI without PSM support.
>
> Did you build this software on one system and install it on a shared
> filesystem, or copy it to the other nodes after the build? If so, the
> build system probably has the proper libraries installed. The
> configuration command-line for this build doesn't explicitly mention PSM:
>
>> Configure command line: '--prefix=/usr/lib64/openmpi3'
>> '--mandir=/usr/share/man/openmpi3-x86_64'
>> '--includedir=/usr/include/openmpi3-x86_64'
>> '--sysconfdir=/etc/openmpi3-x86_64'
>> '--disable-silent-rules'
>> '--enable-builtin-atomics'
>> '--enable-mpi-cxx' '--with-sge'
>> '--with-valgrind'
>> '--enable-memchecker' '--with-hwloc=/usr'
>> 'CC=gcc'
>> 'CXX=g++' 'LDFLAGS=-Wl,-z,relro ' 'CFLAGS=
>> -O2 -g
>> -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions
>> -fstack-protector-strong
>> --param=ssp-buffer-size=4
>> -grecord-gcc-switches -m64 -mtune=generic'
>> 'CXXFLAGS= -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector-strong
>> --param=ssp-buffer-size=4
>> -grecord-gcc-switches -m64 -mtune=generic'
>> 'FC=gfortran' 'FCFLAGS= -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector-strong
>> --param=ssp-buffer-size=4
>> -grecord-gcc-switches -m64 -mtune=generic'
>
> When something is included that isn't explicitly stated on the
> configuration line, that usually means the configure script looked for
> the supporting libraries, found them, and so decided to include the
> support for that feature.
>
>
> Prentice
> On 4/30/19 2:28 PM, Gus Correa wrote:
>> HI Faraz
>>
>> My impression is that you're missing the IB libraries, and that Open MPI
>> was not built with IB support.
>> This is very likely to be the case if you're using the Open MPI
>> packages from CentOS (openmpi3.x86_64, openmpi3-devel.x86_64)
>> which probably only have TCP/IP support built in (the common
>> denominator network of most computers).
>> Building Open MPI from source is not difficult, and a must if you
>> have IB cards.
>>
>> Notwithstanding the MPI expertise of the Beowulf mailing list
>> subscribers,
>> if you post your message in the Open MPI mailing list, you'll get
>> specific and detailed help in no time,
>> and minimize the suffering.
>>
>> My two cents,
>> Gus Correa
>>
>> On Tue, Apr 30, 2019 at 12:28 PM Faraz Hussain <info at feacluster.com
>> <mailto:info at feacluster.com>> wrote:
>>
>> Thanks, here is the output below:
>>
>> [hussaif1 at lustwzb34 ~]$ ompi_info
>> [lustwzb34:10457] mca_base_component_repository_open: unable to open
>> mca_btl_usnic: libpsm_infinipath.so.1: cannot open shared object
>> file:
>> No such file or directory (ignored)
>> [lustwzb34:10457] mca_base_component_repository_open: unable to open
>> mca_mtl_ofi: libpsm_infinipath.so.1: cannot open shared object file:
>> No such file or directory (ignored)
>> [lustwzb34:10457] mca_base_component_repository_open: unable to open
>> mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file:
>> No such file or directory (ignored)
>> Package: Open MPI
>> mockbuild at x86-041.build.eng.bos.redhat.com
>> <mailto:mockbuild at x86-041.build.eng.bos.redhat.com>
>> Distribution
>> Open MPI: 3.0.2
>> Open MPI repo revision: v3.0.2
>> Open MPI release date: Jun 01, 2018
>> Open RTE: 3.0.2
>> Open RTE repo revision: v3.0.2
>> Open RTE release date: Jun 01, 2018
>> OPAL: 3.0.2
>> OPAL repo revision: v3.0.2
>> OPAL release date: Jun 01, 2018
>> MPI API: 3.1.0
>> Ident string: 3.0.2
>> Prefix: /usr/lib64/openmpi3
>> Configured architecture: x86_64-unknown-linux-gnu
>> Configure host: x86-041.build.eng.bos.redhat.com
>> <http://x86-041.build.eng.bos.redhat.com>
>> Configured by: mockbuild
>> Configured on: Wed Jun 13 14:18:03 EDT 2018
>> Configure host: x86-041.build.eng.bos.redhat.com
>> <http://x86-041.build.eng.bos.redhat.com>
>> Configure command line: '--prefix=/usr/lib64/openmpi3'
>> '--mandir=/usr/share/man/openmpi3-x86_64'
>> '--includedir=/usr/include/openmpi3-x86_64'
>> '--sysconfdir=/etc/openmpi3-x86_64'
>> '--disable-silent-rules'
>> '--enable-builtin-atomics'
>> '--enable-mpi-cxx' '--with-sge'
>> '--with-valgrind'
>> '--enable-memchecker'
>> '--with-hwloc=/usr' 'CC=gcc'
>> 'CXX=g++' 'LDFLAGS=-Wl,-z,relro '
>> 'CFLAGS= -O2 -g
>> -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions
>> -fstack-protector-strong
>> --param=ssp-buffer-size=4
>> -grecord-gcc-switches -m64
>> -mtune=generic'
>> 'CXXFLAGS= -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector-strong
>> --param=ssp-buffer-size=4
>> -grecord-gcc-switches -m64
>> -mtune=generic'
>> 'FC=gfortran' 'FCFLAGS= -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector-strong
>> --param=ssp-buffer-size=4
>> -grecord-gcc-switches -m64
>> -mtune=generic'
>> Built by: mockbuild
>> Built on: Wed Jun 13 14:25:02 EDT 2018
>> Built host: x86-041.build.eng.bos.redhat.com
>> <http://x86-041.build.eng.bos.redhat.com>
>> C bindings: yes
>> C++ bindings: yes
>> Fort mpif.h: yes (all)
>> Fort use mpi: yes (limited: overloading)
>> Fort use mpi size: deprecated-ompi-info-value
>> Fort use mpi_f08: no
>> Fort mpi_f08 compliance: The mpi_f08 module was not built
>> Fort mpi_f08 subarrays: no
>> Java bindings: no
>> Wrapper compiler rpath: runpath
>> C compiler: gcc
>> C compiler absolute: /usr/bin/gcc
>> C compiler family name: GNU
>> C compiler version: 4.8.5
>> C++ compiler: g++
>> C++ compiler absolute: /usr/bin/g++
>> Fort compiler: gfortran
>> Fort compiler abs: /usr/bin/gfortran
>> Fort ignore TKR: no
>> Fort 08 assumed shape: no
>> Fort optional args: no
>> Fort INTERFACE: yes
>> Fort ISO_FORTRAN_ENV: yes
>> Fort STORAGE_SIZE: no
>> Fort BIND(C) (all): no
>> Fort ISO_C_BINDING: yes
>> Fort SUBROUTINE BIND(C): no
>> Fort TYPE,BIND(C): no
>> Fort T,BIND(C,name="a"): no
>> Fort PRIVATE: no
>> Fort PROTECTED: no
>> Fort ABSTRACT: no
>> Fort ASYNCHRONOUS: no
>> Fort PROCEDURE: no
>> Fort USE...ONLY: no
>> Fort C_FUNLOC: no
>> Fort f08 using wrappers: no
>> Fort MPI_SIZEOF: no
>> C profiling: yes
>> C++ profiling: yes
>> Fort mpif.h profiling: yes
>> Fort use mpi profiling: yes
>> Fort use mpi_f08 prof: no
>> C++ exceptions: no
>> Thread support: posix (MPI_THREAD_MULTIPLE: yes, OPAL
>> support: yes,
>> OMPI progress: no, ORTE progress: yes,
>> Event lib:
>> yes)
>> Sparse Groups: no
>> Internal debug support: no
>> MPI interface warnings: yes
>> MPI parameter check: runtime
>> Memory profiling support: no
>> Memory debugging support: no
>> dl support: yes
>> Heterogeneous support: no
>> mpirun default --prefix: no
>> MPI I/O support: yes
>> MPI_WTIME support: native
>> Symbol vis. support: yes
>> Host topology support: yes
>> MPI extensions: affinity, cuda
>> FT Checkpoint support: no (checkpoint thread: no)
>> C/R Enabled Debugging: no
>> MPI_MAX_PROCESSOR_NAME: 256
>> MPI_MAX_ERROR_STRING: 256
>> MPI_MAX_OBJECT_NAME: 64
>> MPI_MAX_INFO_KEY: 36
>> MPI_MAX_INFO_VAL: 256
>> MPI_MAX_PORT_NAME: 1024
>> MPI_MAX_DATAREP_STRING: 128
>> MCA allocator: basic (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA allocator: bucket (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA backtrace: execinfo (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA btl: openib (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA btl: self (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA btl: tcp (MCA v2.1.0, API v3.0.0, Component
>> v3.0.2)
>> MCA btl: vader (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA compress: bzip (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA compress: gzip (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA crs: none (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA dl: dlopen (MCA v2.1.0, API v1.0.0,
>> Component v3.0.2)
>> MCA event: libevent2022 (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA hwloc: external (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA if: linux_ipv6 (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA if: posix_ipv4 (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA installdirs: env (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA installdirs: config (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA memchecker: valgrind (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA memory: patcher (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA mpool: hugepage (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA patcher: overwrite (MCA v2.1.0, API v1.0.0,
>> Component
>> v3.0.2)
>> MCA pmix: pmix2x (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA pmix: flux (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA pmix: isolated (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA pstat: linux (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA rcache: grdma (MCA v2.1.0, API v3.3.0,
>> Component v3.0.2)
>> MCA shmem: mmap (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA shmem: posix (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA shmem: sysv (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA timer: linux (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA dfs: app (MCA v2.1.0, API v1.0.0, Component
>> v3.0.2)
>> MCA dfs: orted (MCA v2.1.0, API v1.0.0,
>> Component v3.0.2)
>> MCA dfs: test (MCA v2.1.0, API v1.0.0,
>> Component v3.0.2)
>> MCA errmgr: default_app (MCA v2.1.0, API v3.0.0,
>> Component
>> v3.0.2)
>> MCA errmgr: default_hnp (MCA v2.1.0, API v3.0.0,
>> Component
>> v3.0.2)
>> MCA errmgr: default_orted (MCA v2.1.0, API v3.0.0,
>> Component
>> v3.0.2)
>> MCA errmgr: default_tool (MCA v2.1.0, API v3.0.0,
>> Component
>> v3.0.2)
>> MCA errmgr: dvm (MCA v2.1.0, API v3.0.0, Component
>> v3.0.2)
>> MCA ess: env (MCA v2.1.0, API v3.0.0, Component
>> v3.0.2)
>> MCA ess: hnp (MCA v2.1.0, API v3.0.0, Component
>> v3.0.2)
>> MCA ess: pmi (MCA v2.1.0, API v3.0.0, Component
>> v3.0.2)
>> MCA ess: singleton (MCA v2.1.0, API v3.0.0,
>> Component
>> v3.0.2)
>> MCA ess: slurm (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA ess: tool (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA filem: raw (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA grpcomm: direct (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA iof: tool (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA iof: orted (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA iof: hnp (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA notifier: syslog (MCA v2.1.0, API v1.0.0,
>> Component v3.0.2)
>> MCA odls: default (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA oob: tcp (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA oob: ud (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA plm: isolated (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA plm: rsh (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA plm: slurm (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA ras: gridengine (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA ras: simulator (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA ras: slurm (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA rmaps: mindist (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA rmaps: ppr (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA rmaps: rank_file (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA rmaps: resilient (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA rmaps: round_robin (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA rmaps: seq (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA rml: oob (MCA v2.1.0, API v3.0.0, Component
>> v3.0.2)
>> MCA routed: binomial (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA routed: debruijn (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA routed: direct (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA routed: radix (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA rtc: hwloc (MCA v2.1.0, API v1.0.0,
>> Component v3.0.2)
>> MCA schizo: flux (MCA v2.1.0, API v1.0.0,
>> Component v3.0.2)
>> MCA schizo: ompi (MCA v2.1.0, API v1.0.0,
>> Component v3.0.2)
>> MCA schizo: orte (MCA v2.1.0, API v1.0.0,
>> Component v3.0.2)
>> MCA schizo: slurm (MCA v2.1.0, API v1.0.0,
>> Component v3.0.2)
>> MCA state: app (MCA v2.1.0, API v1.0.0, Component
>> v3.0.2)
>> MCA state: dvm (MCA v2.1.0, API v1.0.0, Component
>> v3.0.2)
>> MCA state: hnp (MCA v2.1.0, API v1.0.0, Component
>> v3.0.2)
>> MCA state: novm (MCA v2.1.0, API v1.0.0,
>> Component v3.0.2)
>> MCA state: orted (MCA v2.1.0, API v1.0.0,
>> Component v3.0.2)
>> MCA state: tool (MCA v2.1.0, API v1.0.0,
>> Component v3.0.2)
>> MCA bml: r2 (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA coll: basic (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA coll: inter (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA coll: libnbc (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA coll: self (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA coll: sm (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA coll: sync (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA coll: tuned (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA fbtl: posix (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA fcoll: dynamic (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA fcoll: dynamic_gen2 (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA fcoll: individual (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA fcoll: static (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA fcoll: two_phase (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA fs: ufs (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA io: ompio (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA io: romio314 (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA mtl: psm2 (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA osc: pt2pt (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA osc: rdma (MCA v2.1.0, API v3.0.0,
>> Component v3.0.2)
>> MCA osc: sm (MCA v2.1.0, API v3.0.0, Component
>> v3.0.2)
>> MCA pml: v (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA pml: cm (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA pml: monitoring (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA pml: ob1 (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA rte: orte (MCA v2.1.0, API v2.0.0,
>> Component v3.0.2)
>> MCA sharedfp: individual (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA sharedfp: lockedfile (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>> MCA sharedfp: sm (MCA v2.1.0, API v2.0.0, Component
>> v3.0.2)
>> MCA topo: treematch (MCA v2.1.0, API v2.2.0,
>> Component
>> v3.0.2)
>> MCA topo: basic (MCA v2.1.0, API v2.2.0,
>> Component v3.0.2)
>> MCA vprotocol: pessimist (MCA v2.1.0, API v2.0.0,
>> Component
>> v3.0.2)
>>
>>
>> Quoting John Hearns <hearnsj at googlemail.com
>> <mailto:hearnsj at googlemail.com>>:
>>
>> > Hello Faraz. Please start by running this command ompi_info
>> >
>> > On Tue, 30 Apr 2019 at 15:15, Faraz Hussain
>> <info at feacluster.com <mailto:info at feacluster.com>> wrote:
>> >
>> >> I installed RedHat 7.5 on two machines with the following
>> Mellanox cards:
>> >>
>> >> 87:00.0 Network controller: Mellanox Technologies MT27520 Family
>> >> [ConnectX-3 Pro
>> >>
>> >> I followed the steps outlined here to verify RDMA is working:
>> >>
>> >>
>> >>
>> https://community.mellanox.com/s/article/howto-enable-perftest-package-for-upstream-kernel
>> >>
>> >> However, I cannot seem to get Open MPI 3.0.2 to work. When I
>> run it, I
>> >> get this error:
>> >>
>> >>
>> --------------------------------------------------------------------------
>> >>
>> >> No OpenFabrics connection schemes reported that they were able
>> to be
>> >>
>> >> used on a specific port. As such, the openib BTL (OpenFabrics
>> >>
>> >> support) will be disabled for this port.
>> >>
>> >>
>> >> Local host: lustwzb34
>> >>
>> >> Local device: mlx4_0
>> >>
>> >> Local port: 1
>> >>
>> >> CPCs attempted: rdmacm, udcm
>> >>
>> >>
>> --------------------------------------------------------------------------
>> >>
>> >> Then it just hangs till I press control C.
>> >>
>> >> I understand this may be an issue with RedHat, Open MPI or
>> Mellanox.
>> >> Any ideas to debug which place it could be?
>> >>
>> >> Thanks!
>> >>
>> >> _______________________________________________
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>> >>
>>
>>
>>
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