A segmentation fault occurred when attempting to reproduce certain PGEMM test samples from the CA3D paper using example_AB.exe. Currently, I am unable to ascertain whether this error is associated with a specific environment.
I tried my best to restore the compilation information from the binary file as follows,
Submitting jobs to run on the slurm cluster via sbatch scripts(see below). Error occurred when executing example_AB.exe with the following parameters,
The same error occurred when M=N=6000, K=1200000. But for M=N=K=50,000 and M=N=100,000,K=5,000, it worked fine.
By the way, while testing with M=N=K=32768 using the same sbatch script, unfortunately, the job did not complete within 15 minutes. Regrettably, I had to forcefully cancel the job as it incurs charges, and consequently, I couldn't obtain any useful log information.
The method of reproducing errors as described in the Execution section.
Core was generated by `$USER/CA3DMM/examples/example_AB.exe 1200000 6000 6000 0 0 1 1 0'.
Program terminated with signal 11, Segmentation fault.
#0 0x000000000041e2e4 in __intel_avx_rep_memcpy ()
(gdb) backtrace
#0 0x000000000041e2e4 in __intel_avx_rep_memcpy ()
#1 0x00001469ca7de08f in mca_btl_self_get ()
from /opt/app/openmpi/4.0.4/intel/2020/lib/openmpi/mca_btl_self.so
#2 0x00001469ca1aa174 in mca_pml_ob1_recv_request_get_frag ()
from /opt/app/openmpi/4.0.4/intel/2020/lib/openmpi/mca_pml_ob1.so
#3 0x00001469ca1a9c5f in mca_pml_ob1_recv_request_progress_rget ()
from /opt/app/openmpi/4.0.4/intel/2020/lib/openmpi/mca_pml_ob1.so
#4 0x00001469ca19e4aa in mca_pml_ob1_recv_frag_match_proc ()
from /opt/app/openmpi/4.0.4/intel/2020/lib/openmpi/mca_pml_ob1.so
#5 0x00001469ca1a08f9 in mca_pml_ob1_recv_frag_callback_rget ()
from /opt/app/openmpi/4.0.4/intel/2020/lib/openmpi/mca_pml_ob1.so
#6 0x00001469ca7dda30 in mca_btl_self_send ()
from /opt/app/openmpi/4.0.4/intel/2020/lib/openmpi/mca_btl_self.so
#7 0x00001469ca1acf81 in mca_pml_ob1_send_request_start_rdma ()
from /opt/app/openmpi/4.0.4/intel/2020/lib/openmpi/mca_pml_ob1.so
#8 0x00001469ca19aa81 in mca_pml_ob1_isend ()
from /opt/app/openmpi/4.0.4/intel/2020/lib/openmpi/mca_pml_ob1.so
#9 0x00001469c935a3a0 in mca_coll_basic_neighbor_alltoallv ()
from /opt/app/openmpi/4.0.4/intel/2020/lib/openmpi/mca_coll_basic.so
#10 0x00001469d7f82b1d in PMPI_Neighbor_alltoallv ()
from /opt/app/openmpi/4.0.4/intel/2020/lib/libmpi.so.40
#11 0x000000000040ad2c in mat_redist_engine_exec (engine=0x1462ced84e50, src_blk=0x1462f844aa50,
src_ld=-129717664, dst_blk=0xd693a30, dst_ld=6769816) at mat_redist.c:357
#12 0x0000000000406397 in ca3dmm_engine_exec (engine=0x1462ced84e50, src_A=0x1462f844aa50,
ldA=-129717664, src_B=0xd693a30, ldB=6769816, dst_C=0x41e2e0 <__intel_avx_rep_memcpy+672>,
ldC=1200000) at ca3dmm.c:988
#13 0x0000000000404e3e in main (argc=375, argv=0x0) at example_AB.c:169
(gdb) frame 11
#11 0x000000000040ad2c in mat_redist_engine_exec (engine=0x1462ced84e50, src_blk=0x1462f844aa50,
src_ld=-129717664, dst_blk=0xd693a30, dst_ld=6769816) at mat_redist.c:357
357 MPI_Neighbor_alltoallv(
(gdb) l
352 int *recv_displs = engine->recv_displs;
353 void *recvbuf_h = engine->recvbuf_h;
354 void *recvbuf_d = engine->recvbuf_d;
355 if (dev_type == DEV_TYPE_HOST)
356 {
357 MPI_Neighbor_alltoallv(
358 sendbuf_h, send_sizes, send_displs, engine->dtype,
359 recvbuf_h, recv_sizes, recv_displs, engine->dtype, engine->graph_comm
360 );
361 }
(gdb) p sendbuf_h
$1 = 0x1462ced84e50 <Address 0x1462ced84e50 out of bounds>
(gdb) p recvbuf_h
$2 = (void *) 0x1462c16f1410
Replaced some sensitive information, such as the home directory with username.
More detailed information about the dependencies used that may be useful.
$ ompi_info
Package: Open MPI hpctest@n6 Distribution
Open MPI: 4.0.4
Open MPI repo revision: v4.0.4
Open MPI release date: Jun 10, 2020
Open RTE: 4.0.4
Open RTE repo revision: v4.0.4
Open RTE release date: Jun 10, 2020
OPAL: 4.0.4
OPAL repo revision: v4.0.4
OPAL release date: Jun 10, 2020
MPI API: 3.1.0
Ident string: 4.0.4
Prefix: /opt/app/openmpi/4.0.4/intel/2020
Configured architecture: x86_64-unknown-linux-gnu
Configure host: n6
Configured by: hpctest
Configured on: Sat Aug 29 10:04:41 CST 2020
Configure host: n6
Configure command line: '--prefix=/opt/app/openmpi/4.0.4/intel/2020'
Built by: hpctest
Built on: Sat Aug 29 10:23:49 CST 2020
Built host: n6
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 ifort 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: icc
C compiler absolute: /opt/intel/compilers_and_libraries_2020.1.217/linux/bin/intel64/icc
C compiler family name: INTEL
C compiler version: 1910.20200306
C++ compiler: g++
C++ compiler absolute: /usr/bin/g++
Fort compiler: ifort
Fort compiler abs: /opt/intel/compilers_and_libraries_2020.1.217/linux/bin/intel64/ifort
Fort ignore TKR: yes (!DEC$ 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: basic (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA allocator: bucket (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA backtrace: execinfo (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA btl: self (MCA v2.1.0, API v3.1.0, Component v4.0.4)
MCA btl: vader (MCA v2.1.0, API v3.1.0, Component v4.0.4)
MCA btl: tcp (MCA v2.1.0, API v3.1.0, Component v4.0.4)
MCA compress: bzip (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA compress: gzip (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA crs: none (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA dl: dlopen (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA event: libevent2022 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA hwloc: hwloc201 (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA if: linux_ipv6 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA if: posix_ipv4 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA installdirs: env (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA installdirs: config (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA memory: patcher (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA mpool: hugepage (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA patcher: overwrite (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA pmix: flux (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA pmix: isolated (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA pmix: pmix3x (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA pstat: linux (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA rcache: grdma (MCA v2.1.0, API v3.3.0, Component v4.0.4)
MCA reachable: weighted (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA shmem: mmap (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA shmem: sysv (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA shmem: posix (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA timer: linux (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA errmgr: default_tool (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA errmgr: default_app (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA errmgr: default_hnp (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA errmgr: default_orted (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: env (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA ess: singleton (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: hnp (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA ess: tool (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA ess: pmi (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA ess: slurm (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA filem: raw (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA grpcomm: direct (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA iof: hnp (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA iof: orted (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA iof: tool (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA odls: pspawn (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA odls: default (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA oob: tcp (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA plm: slurm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA plm: rsh (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA plm: isolated (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA ras: simulator (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA ras: slurm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA regx: naive (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA regx: reverse (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA regx: fwd (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA rmaps: rank_file (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: mindist (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA rmaps: resilient (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: ppr (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA rmaps: round_robin (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: seq (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA rml: oob (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA routed: radix (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA routed: direct (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA routed: binomial (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA rtc: hwloc (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA schizo: flux (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA schizo: ompi (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA schizo: orte (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA schizo: singularity (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: slurm (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA state: tool (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA state: orted (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA state: novm (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA state: hnp (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA state: app (MCA v2.1.0, API v1.0.0, Component v4.0.4)
MCA bml: r2 (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA coll: sm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA coll: monitoring (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: self (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA coll: basic (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA coll: libnbc (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA coll: tuned (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA coll: sync (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA coll: inter (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA fbtl: posix (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA fcoll: dynamic_gen2 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: dynamic (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA fcoll: individual (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: vulcan (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA fcoll: two_phase (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fs: ufs (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA io: romio321 (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA io: ompio (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA osc: monitoring (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA osc: pt2pt (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA osc: rdma (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA osc: sm (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA pml: v (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA pml: ob1 (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA pml: monitoring (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pml: cm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA rte: orte (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA sharedfp: sm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA sharedfp: lockedfile (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA sharedfp: individual (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA topo: basic (MCA v2.1.0, API v2.2.0, Component v4.0.4)
MCA topo: treematch (MCA v2.1.0, API v2.2.0, Component
v4.0.4)
MCA vprotocol: pessimist (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
Brief
A segmentation fault occurred when attempting to reproduce certain PGEMM test samples from the CA3D paper using
example_AB.exe. Currently, I am unable to ascertain whether this error is associated with a specific environment.Compilation and Execution
Compilation
Compile according to README.md, that is, by using the command
make -f icc-mkl-anympi.make -jI tried my best to restore the compilation information from the binary file as follows,
Execution
Submitting jobs to run on the slurm cluster via sbatch scripts(see below). Error occurred when executing
example_AB.exewith the following parameters,The same error occurred when M=N=6000, K=1200000. But for M=N=K=50,000 and M=N=100,000,K=5,000, it worked fine.
SBATCH Script
By the way, while testing with M=N=K=32768 using the same sbatch script, unfortunately, the job did not complete within 15 minutes. Regrettably, I had to forcefully cancel the job as it incurs charges, and consequently, I couldn't obtain any useful log information.
GDB Core Dumps
The method of reproducing errors as described in the Execution section.
It shows that a segment fault occurs when
mat_redist_engine_execcallsMPI_Neighbor_alltoallvfor redistributing matrices A and B. Enteringmat_redist_engine_execto viewMPI_Neighbor_alltoallv's parametersendbuf_hshows "Address 0x1462ced84e50 out of bounds"Check Dynamic Library
Replaced some sensitive information, such as the home directory with username.
My environment
More detailed information about the dependencies used that may be useful.