I manage a cluster that is very heterogeneous. Some nodes have
InfiniBand, while others have 10 Gb/s Ethernet. We recently upgraded to
CentOS 7, and built a new software stack for CentOS 7. We are using
OpenMPI 4.0.3, and we are using Slurm 19.05.5 as our job scheduler.
We just noticed that when jobs are sent to the nodes with IB, the
segfault immediately, with the segfault appearing to come from
libibverbs.so. This is what I see in the stderr output for one of these
failed jobs:
srun: error: greene021: tasks 0-3: Segmentation fault
And here is what I see in the log messages of the compute node where
that segfault happened:
Jul 23 15:19:41 greene021 kernel: mpihello[7911]: segfault at
7f0635f38910 ip 00007f0635f49405 sp 00007ffe354485a0 error 4
Jul 23 15:19:41 greene021 kernel: mpihello[7912]: segfault at
7f23d51ea910 ip 00007f23d51fb405 sp 00007ffef250a9a0 error 4
Jul 23 15:19:41 greene021 kernel: in
libibverbs.so.1.5.22.4[7f23d51ec000+18000]
Jul 23 15:19:41 greene021 kernel:
Jul 23 15:19:41 greene021 kernel: mpihello[7909]: segfault at
7ff504ba5910 ip 00007ff504bb6405 sp 00007ffff917ccb0 error 4
Jul 23 15:19:41 greene021 kernel: in
libibverbs.so.1.5.22.4[7ff504ba7000+18000]
Jul 23 15:19:41 greene021 kernel:
Jul 23 15:19:41 greene021 kernel: mpihello[7910]: segfault at
7fa58abc5910 ip 00007fa58abd6405 sp 00007ffdde50c0d0 error 4
Jul 23 15:19:41 greene021 kernel: in
libibverbs.so.1.5.22.4[7fa58abc7000+18000]
Jul 23 15:19:41 greene021 kernel:
Jul 23 15:19:41 greene021 kernel: in
libibverbs.so.1.5.22.4[7f0635f3a000+18000]
Jul 23 15:19:41 greene021 kernel
Any idea what is going on here, or how to debug further? I've been using
OpenMPI for years, and it usually just works.
I normally start my job with srun like this:
srun ./mpihello
But even if I try to take IB out of the equation by starting the job
like this:
mpirun -mca btl ^openib ./mpihello
I still get a segfault issue, although the message to stderr is now a
little different:
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 8502 on node greene021
exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
The segfaults happens immediately. It seems to happen as soon as
MPI_Init() is called. The program I'm running is very simple MPI "Hello
world!" program.
The output of ompi_info is below my signature, in case that helps.
Prentice
$ ompi_info
Package: Open MPI u...@host.example.com Distribution
Open MPI: 4.0.3
Open MPI repo revision: v4.0.3
Open MPI release date: Mar 03, 2020
Open RTE: 4.0.3
Open RTE repo revision: v4.0.3
Open RTE release date: Mar 03, 2020
OPAL: 4.0.3
OPAL repo revision: v4.0.3
OPAL release date: Mar 03, 2020
MPI API: 3.1.0
Ident string: 4.0.3
Prefix: /usr/pppl/gcc/9.3-pkgs/openmpi-4.0.3
Configured architecture: x86_64-unknown-linux-gnu
Configure host: dawson027.pppl.gov
Configured by: lglant
Configured on: Mon Jun 1 12:37:07 EDT 2020
Configure host: dawson027.pppl.gov
Configure command line: '--prefix=/usr/pppl/gcc/9.3-pkgs/openmpi-4.0.3'
'--with-ucx' '--with-verbs' '--with-libfabric'
'--with-libevent=/usr'
'--with-libevent-libdir=/usr/lib64'
'--with-pmix=/usr/pppl/pmix/3.1.5' '--with-pmi'
Built by: lglant
Built on: Mon Jun 1 13:05:40 EDT 2020
Built host: dawson027.pppl.gov
C bindings: yes
C++ bindings: no
Fort mpif.h: yes (all)
Fort use mpi: yes (full: ignore TKR)
Fort use mpi size: deprecated-ompi-info-value
Fort use mpi_f08: yes
Fort mpi_f08 compliance: The mpi_f08 module is available, but due to
limitations in the gfortran compiler and/or Open
MPI, does not support the following: array
subsections, direct passthru (where possible) to
underlying Open MPI's C functionality
Fort mpi_f08 subarrays: no
Java bindings: no
Wrapper compiler rpath: runpath
C compiler: gcc
C compiler absolute: /usr/pppl/gcc/9.3.0/bin/gcc
C compiler family name: GNU
C compiler version: 9.3.0
C++ compiler: g++
C++ compiler absolute: /usr/pppl/gcc/9.3.0/bin/g++
Fort compiler: gfortran
Fort compiler abs: /usr/pppl/gcc/9.3.0/bin/gfortran
Fort ignore TKR: yes (!GCC$ ATTRIBUTES NO_ARG_CHECK ::)
Fort 08 assumed shape: yes
Fort optional args: yes
Fort INTERFACE: yes
Fort ISO_FORTRAN_ENV: yes
Fort STORAGE_SIZE: yes
Fort BIND(C) (all): yes
Fort ISO_C_BINDING: yes
Fort SUBROUTINE BIND(C): yes
Fort TYPE,BIND(C): yes
Fort T,BIND(C,name="a"): yes
Fort PRIVATE: yes
Fort PROTECTED: yes
Fort ABSTRACT: yes
Fort ASYNCHRONOUS: yes
Fort PROCEDURE: yes
Fort USE...ONLY: yes
Fort C_FUNLOC: yes
Fort f08 using wrappers: yes
Fort MPI_SIZEOF: yes
C profiling: yes
C++ profiling: no
Fort mpif.h profiling: yes
Fort use mpi profiling: yes
Fort use mpi_f08 prof: yes
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_WTIME support: native
Symbol vis. support: yes
Host topology support: yes
IPv6 support: no
MPI1 compatibility: no
MPI extensions: affinity, cuda, pcollreq
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: bucket (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA allocator: basic (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA backtrace: execinfo (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA btl: self (MCA v2.1.0, API v3.1.0, Component v4.0.3)
MCA btl: uct (MCA v2.1.0, API v3.1.0, Component v4.0.3)
MCA btl: tcp (MCA v2.1.0, API v3.1.0, Component v4.0.3)
MCA btl: usnic (MCA v2.1.0, API v3.1.0, Component v4.0.3)
MCA btl: vader (MCA v2.1.0, API v3.1.0, Component v4.0.3)
MCA btl: openib (MCA v2.1.0, API v3.1.0, Component v4.0.3)
MCA compress: gzip (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA compress: bzip (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA crs: none (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA dl: dlopen (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA event: external (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA hwloc: hwloc201 (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA if: linux_ipv6 (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA if: posix_ipv4 (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA installdirs: env (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA installdirs: config (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA memory: patcher (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA mpool: hugepage (MCA v2.1.0, API v3.0.0, Component
v4.0.3)
MCA patcher: overwrite (MCA v2.1.0, API v1.0.0, Component
v4.0.3)
MCA pmix: flux (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA pmix: isolated (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA pmix: s2 (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA pmix: ext3x (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA pmix: s1 (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA pmix: pmix3x (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA pstat: linux (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA rcache: grdma (MCA v2.1.0, API v3.3.0, Component v4.0.3)
MCA reachable: weighted (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA shmem: posix (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA shmem: mmap (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA shmem: sysv (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA timer: linux (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA errmgr: default_app (MCA v2.1.0, API v3.0.0, Component
v4.0.3)
MCA errmgr: default_orted (MCA v2.1.0, API v3.0.0, Component
v4.0.3)
MCA errmgr: default_tool (MCA v2.1.0, API v3.0.0, Component
v4.0.3)
MCA errmgr: default_hnp (MCA v2.1.0, API v3.0.0, Component
v4.0.3)
MCA ess: env (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA ess: hnp (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA ess: pmi (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA ess: slurm (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA ess: singleton (MCA v2.1.0, API v3.0.0, Component
v4.0.3)
MCA ess: tool (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA filem: raw (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA grpcomm: direct (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA iof: tool (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA iof: hnp (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA iof: orted (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA odls: pspawn (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA odls: default (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA oob: tcp (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA plm: slurm (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA plm: rsh (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA plm: isolated (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA ras: slurm (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA ras: simulator (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA regx: fwd (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA regx: naive (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA regx: reverse (MCA v2.1.0, API v1.0.0, Component
v4.0.3)
MCA rmaps: rank_file (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA rmaps: ppr (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA rmaps: resilient (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA rmaps: round_robin (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA rmaps: mindist (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA rmaps: seq (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA rml: oob (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA routed: direct (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA routed: binomial (MCA v2.1.0, API v3.0.0, Component
v4.0.3)
MCA routed: radix (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA rtc: hwloc (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA schizo: slurm (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA schizo: orte (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA schizo: ompi (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA schizo: flux (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA state: orted (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA state: novm (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA state: hnp (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA state: app (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA state: tool (MCA v2.1.0, API v1.0.0, Component v4.0.3)
MCA bml: r2 (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA coll: self (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA coll: sm (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA coll: inter (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA coll: libnbc (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA coll: sync (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA coll: monitoring (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA coll: basic (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA coll: tuned (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA fbtl: posix (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA fcoll: dynamic (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA fcoll: two_phase (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA fcoll: dynamic_gen2 (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA fcoll: vulcan (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA fcoll: individual (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA fs: ufs (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA io: romio321 (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA io: ompio (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA mtl: ofi (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA mtl: psm (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA osc: ucx (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA osc: pt2pt (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA osc: monitoring (MCA v2.1.0, API v3.0.0, Component
v4.0.3)
MCA osc: sm (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA osc: rdma (MCA v2.1.0, API v3.0.0, Component v4.0.3)
MCA pml: v (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA pml: ob1 (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA pml: ucx (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA pml: cm (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA pml: monitoring (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA rte: orte (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA sharedfp: individual (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA sharedfp: sm (MCA v2.1.0, API v2.0.0, Component v4.0.3)
MCA sharedfp: lockedfile (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
MCA topo: treematch (MCA v2.1.0, API v2.2.0, Component
v4.0.3)
MCA topo: basic (MCA v2.1.0, API v2.2.0, Component v4.0.3)
MCA vprotocol: pessimist (MCA v2.1.0, API v2.0.0, Component
v4.0.3)
