Dear Sir,
I’m running a cluster with OpenMPI.
$mpirun --mca mpi_show_mpi_alloc_mem_leaks 8 --mca
mpi_show_handle_leaks 1 $HOME/test/cpi
I got the error message as job failed:
Process 15 on node2
Process 6 on node1
Process 14 on node2
… … …
Process 0 on node1
Process 10 on node2
[node2][[9340,1],13][btl_openib_component.c:3002:poll_device] error
polling HP C
Q with -2 errno says Success
[node2][[9340,1],9][btl_openib_component.c:3002:poll_device] error
polling HP CQ
with -2 errno says Success
[node2][[9340,1],10][btl_openib_component.c:3002:poll_device] error
polling HP C
Q with -2 errno says Success
[node2][[9340,1],11][btl_openib_component.c:3002:poll_device] error
polling HP C
Q with -2 errno says Success
[node2][[9340,1],8][btl_openib_component.c:3002:poll_device] error
polling HP CQ
with -2 errno says Success
[node2][[9340,1],15][btl_openib_component.c:3002:poll_device] [node2]
[[9340,1],1
2][btl_openib_component.c:3002:poll_device] error polling HP CQ with
-2 errno sa
ys Success
error polling HP CQ with -2 errno says Success
[node2][[9340,1],14][btl_openib_component.c:3002:poll_device] error
polling HP C
Q with -2 errno says Success
mpirun: killing job...
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 28438 on node node1
exited on signal
0 (Unknown signal 0).
--------------------------------------------------------------------------
mpirun: clean termination accomplished
and got the message as job success
Process 1 on node1
Process 2 on node1
… … …
Process 13 on node2
Process 14 on node2
--------------------------------------------------------------------------
The following memory locations were allocated via MPI_ALLOC_MEM but
not freed via MPI_FREE_MEM before invoking MPI_FINALIZE:
Process ID: [[13692,1],12]
Hostname: node2
PID: 30183
(null)
--------------------------------------------------------------------------
[node1:32276] 15 more processes have sent help message help-mpool-
base.txt / all
mem leaks
[node1:32276] Set MCA parameter "orte_base_help_aggregate" to 0 to
see all help
/ error messages
It occurred periodic, ie. twice success, then twice failed, twice
success, then twice failed … . I download the OFED-1.4.1-rc3 from
The OpenFabrics Alliance and installed on Dell PowerEdge M600 Blade
Server. The infiniband Mezzanine Cards is Mellanox ConnectX QDR &
DDR. And infiniband switch module is Mellanox M2401G. OS is CentOS
5.3, kernel 2.6.18-128.1.6.el5, with PGI V7.2-5 compiler. It’s
running OpenSM subnet manager.
Best Regards,
Gloria Jan
Wavelink Technology Inc.
The output of the "ompi_info --all" command as:
Package: Open MPI root@vortex Distribution
Open MPI: 1.3.1
Open MPI SVN revision: r20826
Open MPI release date: Mar 18, 2009
Open RTE: 1.3.1
Open RTE SVN revision: r20826
Open RTE release date: Mar 18, 2009
OPAL: 1.3.1
OPAL SVN revision: r20826
OPAL release date: Mar 18, 2009
Ident string: 1.3.1
MCA backtrace: execinfo (MCA v2.0, API v2.0, Component
v1.3.1)
MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component
v1.3.1)
MCA paffinity: linux (MCA v2.0, API v2.0, Component v1.3.1)
MCA carto: auto_detect (MCA v2.0, API v2.0, Component
v1.3.1)
MCA carto: file (MCA v2.0, API v2.0, Component v1.3.1)
MCA maffinity: first_use (MCA v2.0, API v2.0, Component
v1.3.1)
MCA timer: linux (MCA v2.0, API v2.0, Component v1.3.1)
MCA installdirs: env (MCA v2.0, API v2.0, Component v1.3.1)
MCA installdirs: config (MCA v2.0, API v2.0, Component
v1.3.1)
MCA dpm: orte (MCA v2.0, API v2.0, Component v1.3.1)
MCA pubsub: orte (MCA v2.0, API v2.0, Component v1.3.1)
MCA allocator: basic (MCA v2.0, API v2.0, Component v1.3.1)
MCA allocator: bucket (MCA v2.0, API v2.0, Component
v1.3.1)
MCA coll: basic (MCA v2.0, API v2.0, Component v1.3.1)
MCA coll: hierarch (MCA v2.0, API v2.0, Component
v1.3.1)
MCA coll: inter (MCA v2.0, API v2.0, Component v1.3.1)
MCA coll: self (MCA v2.0, API v2.0, Component v1.3.1)
MCA coll: sm (MCA v2.0, API v2.0, Component v1.3.1)
MCA coll: sync (MCA v2.0, API v2.0, Component v1.3.1)
MCA coll: tuned (MCA v2.0, API v2.0, Component v1.3.1)
MCA io: romio (MCA v2.0, API v2.0, Component v1.3.1)
MCA mpool: fake (MCA v2.0, API v2.0, Component v1.3.1)
MCA mpool: rdma (MCA v2.0, API v2.0, Component v1.3.1)
MCA mpool: sm (MCA v2.0, API v2.0, Component v1.3.1)
MCA pml: cm (MCA v2.0, API v2.0, Component v1.3.1)
MCA pml: ob1 (MCA v2.0, API v2.0, Component v1.3.1)
MCA pml: v (MCA v2.0, API v2.0, Component v1.3.1)
MCA bml: r2 (MCA v2.0, API v2.0, Component v1.3.1)
MCA rcache: vma (MCA v2.0, API v2.0, Component v1.3.1)
MCA btl: ofud (MCA v2.0, API v2.0, Component v1.3.1)
MCA btl: openib (MCA v2.0, API v2.0, Component
v1.3.1)
MCA btl: self (MCA v2.0, API v2.0, Component v1.3.1)
MCA btl: sm (MCA v2.0, API v2.0, Component v1.3.1)
MCA btl: tcp (MCA v2.0, API v2.0, Component v1.3.1)
MCA topo: unity (MCA v2.0, API v2.0, Component v1.3.1)
MCA osc: pt2pt (MCA v2.0, API v2.0, Component v1.3.1)
MCA osc: rdma (MCA v2.0, API v2.0, Component v1.3.1)
MCA iof: hnp (MCA v2.0, API v2.0, Component v1.3.1)
MCA iof: orted (MCA v2.0, API v2.0, Component v1.3.1)
MCA iof: tool (MCA v2.0, API v2.0, Component v1.3.1)
MCA oob: tcp (MCA v2.0, API v2.0, Component v1.3.1)
MCA odls: default (MCA v2.0, API v2.0, Component
v1.3.1)
MCA ras: slurm (MCA v2.0, API v2.0, Component v1.3.1)
MCA ras: tm (MCA v2.0, API v2.0, Component v1.3.1)
MCA rmaps: rank_file (MCA v2.0, API v2.0, Component
v1.3.1)
MCA rmaps: round_robin (MCA v2.0, API v2.0, Component
v1.3.1)
MCA rmaps: seq (MCA v2.0, API v2.0, Component v1.3.1)
MCA rml: oob (MCA v2.0, API v2.0, Component v1.3.1)
MCA routed: binomial (MCA v2.0, API v2.0, Component
v1.3.1)
MCA routed: direct (MCA v2.0, API v2.0, Component
v1.3.1)
MCA routed: linear (MCA v2.0, API v2.0, Component
v1.3.1)
MCA plm: rsh (MCA v2.0, API v2.0, Component v1.3.1)
MCA plm: slurm (MCA v2.0, API v2.0, Component v1.3.1)
MCA plm: tm (MCA v2.0, API v2.0, Component v1.3.1)
MCA filem: rsh (MCA v2.0, API v2.0, Component v1.3.1)
MCA errmgr: default (MCA v2.0, API v2.0, Component
v1.3.1)
MCA ess: env (MCA v2.0, API v2.0, Component v1.3.1)
MCA ess: hnp (MCA v2.0, API v2.0, Component v1.3.1)
MCA ess: singleton (MCA v2.0, API v2.0, Component
v1.3.1)
MCA ess: slurm (MCA v2.0, API v2.0, Component v1.3.1)
MCA ess: tool (MCA v2.0, API v2.0, Component v1.3.1)
MCA grpcomm: bad (MCA v2.0, API v2.0, Component v1.3.1)
MCA grpcomm: basic (MCA v2.0, API v2.0, Component v1.3.1)
Prefix: /usr/mpi/pgi/openmpi-1.3.1
Exec_prefix: /usr/mpi/pgi/openmpi-1.3.1
Bindir: /usr/mpi/pgi/openmpi-1.3.1/bin
Sbindir: /usr/mpi/pgi/openmpi-1.3.1/sbin
Libdir: /usr/mpi/pgi/openmpi-1.3.1/lib64
Incdir: /usr/mpi/pgi/openmpi-1.3.1/include
Mandir: /usr/mpi/pgi/openmpi-1.3.1/share/man
Pkglibdir: /usr/mpi/pgi/openmpi-1.3.1/lib64/openmpi
Libexecdir: /usr/mpi/pgi/openmpi-1.3.1/libexec
Datarootdir: /usr/mpi/pgi/openmpi-1.3.1/share
Datadir: /usr/mpi/pgi/openmpi-1.3.1/share
Sysconfdir: /usr/mpi/pgi/openmpi-1.3.1/etc
Sharedstatedir: /usr/mpi/pgi/openmpi-1.3.1/com
Localstatedir: /var Infodir: /usr/share/
info
Pkgdatadir: /usr/mpi/pgi/openmpi-1.3.1/share/openmpi
Pkglibdir: /usr/mpi/pgi/openmpi-1.3.1/lib64/openmpi
Pkgincludedir: /usr/mpi/pgi/openmpi-1.3.1/include/openmpi
Configured architecture: x86_64-redhat-linux-gnu
Configure host: vortex
Configured by: root
Configured on: Sun Apr 12 23:23:14 CST 2009
Configure host: vortex
Built by: root
Built on: Sun Apr 12 23:28:52 CST 2009
Built host: vortex
C bindings: yes
C++ bindings: yes
Fortran77 bindings: yes (all)
Fortran90 bindings: yes
Fortran90 bindings size: small
C compiler: pgcc
C compiler absolute: /opt/pgi/linux86-64/7.2-5/bin/pgcc
C char size: 1
C bool size: 1
C short size: 2
C int size: 4
C long size: 8
C float size: 4
C double size: 8
C pointer size: 8
C char align: 1
C bool align: 1
C int align: 4
C float align: 4
C double align: 8
C++ compiler: pgCC
C++ compiler absolute: /opt/pgi/linux86-64/7.2-5/bin/pgCC
Fortran77 compiler: pgf77
Fortran77 compiler abs: /opt/pgi/linux86-64/7.2-5/bin/pgf77
Fortran90 compiler: pgf90
Fortran90 compiler abs: /opt/pgi/linux86-64/7.2-5/bin/pgf90
Fort integer size: 4
Fort logical size: 4
Fort logical value true: -1
Fort have integer1: yes
Fort have integer2: yes
Fort have integer4: yes
Fort have integer8: yes
Fort have integer16: no
Fort have real4: yes
Fort have real8: yes
Fort have real16: no
Fort have complex8: yes
Fort have complex16: yes
Fort have complex32: no
Fort integer1 size: 1
Fort integer2 size: 2
Fort integer4 size: 4
Fort integer8 size: 8
Fort integer16 size: -1
Fort real size: 4
Fort real4 size: 4
Fort real8 size: 8
Fort real16 size: -1
Fort dbl prec size: 4
Fort cplx size: 4
Fort dbl cplx size: 4
Fort cplx8 size: 8
Fort cplx16 size: 16
Fort cplx32 size: -1
Fort integer align: 4
Fort integer1 align: 1
Fort integer2 align: 2
Fort integer4 align: 4
Fort integer8 align: 8
Fort integer16 align: -1
Fort real align: 4
Fort real4 align: 4
Fort real8 align: 8
Fort real16 align: -1
Fort dbl prec align: 4
Fort cplx align: 4
Fort dbl cplx align: 4
Fort cplx8 align: 4
Fort cplx16 align: 8
Fort cplx32 align: -1
C profiling: yes
C++ profiling: yes Thread support: posix (mpi:
no, progress: no)
Sparse Groups: no
Build CFLAGS: -O -DNDEBUG
Build CXXFLAGS: -O -DNDEBUG
Build FFLAGS:
Build FCFLAGS: -O2
Build LDFLAGS: -export-dynamic
Build LIBS: -lnsl -lutil -lpthread
Wrapper extra CFLAGS:
Wrapper extra CXXFLAGS: -fpic
Wrapper extra FFLAGS:
Wrapper extra FCFLAGS:
Wrapper extra LDFLAGS:
Wrapper extra LIBS: -ldl -Wl,--export-dynamic -lnsl -lutil
-lpthread -ldl
Internal debug support: no
MPI parameter check: runtime
Memory profiling support: no
Memory debugging support: no
libltdl support: yes
Heterogeneous support: no
mpirun default --prefix: yes
MPI I/O support: yes
MPI_WTIME support: gettimeofday
Symbol visibility support: no
FT Checkpoint support: no (checkpoint thread: no)
MCA mca: parameter "mca_param_files" (current
value: "/home/alpha/.openmpi/mca-params.conf:/usr/mpi/pgi/open
mpi-1.3.1/etc/openmpi-mca-params.conf", data source: default value)
Path for MCA configuration files
containing default parameter values
MCA mca: parameter
"mca_base_param_file_prefix" (current value: <none>, data source:
default value)
Aggregate MCA parameter file sets
MCA mca: parameter
"mca_base_param_file_path" (current value: "/usr/mpi/pgi/
openmpi-1.3.1/share/openmpi/amca
-param-sets:/home/alpha", data source: default value)
Aggregate MCA parameter Search path
MCA mca: parameter
"mca_base_param_file_path_force" (current value: <none>, data
source: default value)
Forced Aggregate MCA parameter Search path
MCA mca: parameter "mca_component_path" (current
value: "/usr/mpi/pgi/openmpi-1.3.1/lib64/openmpi:/home/alph
a/.openmpi/components", data source: default value)
Path where to look for Open MPI and ORTE
components
MCA mca: parameter "mca_verbose" (current value:
<none>, data source: default value)
Top-level verbosity parameter
MCA mca: parameter
"mca_component_show_load_errors" (current value: "1", data source:
default value)
Whether to show errors for components that
failed to load or not
MCA mca: parameter
"mca_component_disable_dlopen" (current value: "0", data source:
default value)
Whether to attempt to disable opening
dynamic components or not
MCA mpi: parameter "mpi_param_check" (current
value: "1", data source: default value)
Whether you want MPI API parameters
checked at run-time or not. Possible values are 0 (no checking
) and 1 (perform checking at run-time)
MCA mpi: parameter "mpi_yield_when_idle" (current
value: "-1", data source: default value)
Yield the processor when waiting for MPI
communication (for MPI processes, will default to 1 when o
versubscribing nodes)
MCA mpi: parameter "mpi_event_tick_rate" (current
value: "-1", data source: default value)
How often to progress TCP communications
(0 = never, otherwise specified in microseconds)
MCA mpi: parameter "mpi_show_handle_leaks" (current
value: "1", data source: environment)
Whether MPI_FINALIZE shows all MPI handles
that were not freed or not
MCA mpi: parameter "mpi_no_free_handles" (current
value: "0", data source: environment)
Whether to actually free MPI objects when
their handles are freed
MCA mpi: parameter
"mpi_show_mpi_alloc_mem_leaks" (current value: "8", data source:
environment)
If >0, MPI_FINALIZE will show up to this
many instances of memory allocated by MPI_ALLOC_MEM that w
as not freed by MPI_FREE_MEM
MCA mpi: parameter "mpi_show_mca_params" (current
value: <none>, data source: default value)
Whether to show all MCA parameter values
during MPI_INIT or not (good for reproducability of MPI jo
bs for debug purposes). Accepted values are all, default, file, api,
and enviro - or a comma delimited combination of them
MCA mpi: parameter
"mpi_show_mca_params_file" (current value: <none>, data source:
default value)
If mpi_show_mca_params is true, setting
this string to a valid filename tells Open MPI to dump all
the MCA parameter values into a file suitable for reading via the
mca_param_files parameter (good for reproducability of MPI
jobs)
MCA mpi: parameter
"mpi_keep_peer_hostnames" (current value: "1", data source: default
value)
If nonzero, save the string hostnames of
all MPI peer processes (mostly for error / debugging outpu
t messages). This can add quite a bit of memory usage to each MPI
process.
MCA mpi: parameter "mpi_abort_delay" (current
value: "0", data source: default value)
If nonzero, print out an identifying
message when MPI_ABORT is invoked (hostname, PID of the proces
s that called MPI_ABORT) and delay for that many seconds before
exiting (a negative delay value means to never abort). This
allows attaching of a debugger before quitting the job.
MCA mpi: parameter "mpi_abort_print_stack" (current
value: "0", data source: default value)
If nonzero, print out a stack trace when
MPI_ABORT is invoked
MCA mpi: parameter "mpi_preconnect_mpi" (current
value: "0", data source: default value, synonyms: mpi_preco
nnect_all)
Whether to force MPI processes to fully
wire-up the MPI connections between MPI processes during MP
I_INIT (vs. making connections lazily -- upon the first MPI traffic
between each process peer pair)
MCA mpi: parameter "mpi_preconnect_all" (current
value: "0", data source: default value, deprecated, synonym
of: mpi_preconnect_mpi)
Whether to force MPI processes to fully
wire-up the MPI connections between MPI processes during MP
I_INIT (vs. making connections lazily -- upon the first MPI traffic
between each process peer pair)
MCA mpi: parameter "mpi_leave_pinned" (current
value: "0", data source: environment)
Whether to use the "leave pinned" protocol
or not. Enabling this setting can help bandwidth perfor
mance when repeatedly sending and receiving large messages with the
same buffers over RDMA-based networks (0 = do not use "le
ave pinned" protocol, 1 = use "leave pinned" protocol, -1 = allow
network to choose at runtime).
MCA mpi: parameter
"mpi_leave_pinned_pipeline" (current value: "0", data source:
default value)
Whether to use the "leave pinned pipeline"
protocol or not.
MCA mpi: parameter "mpi_paffinity_alone" (current
value: "0", data source: default value)
If nonzero, assume that this job is the
only (set of) process(es) running on each node and bind pro
cesses to processors, starting with processor ID 0
MCA mpi: parameter "mpi_warn_on_fork" (current
value: "1", data source: default value)
If nonzero, issue a warning if program
forks under conditions that could cause system errors
MCA mpi: information
"mpi_have_sparse_group_storage" (value: "0", data source: default
value)
Whether this Open MPI installation
supports storing of data in MPI groups in "sparse" formats (good
for extremely large process count MPI jobs that create many
communicators/groups)
MCA mpi: parameter
"mpi_use_sparse_group_storage" (current value: "0", data source:
default value)
Whether to use "sparse" storage formats
for MPI groups (only relevant if mpi_have_sparse_group_storage is 1)
MCA orte: parameter
"orte_base_help_aggregate" (current value: "1", data source: default
value)
If orte_base_help_aggregate is true,
duplicate help messages will be aggregated rather than display
ed individually. This can be helpful for parallel jobs that
experience multiple identical failures; rather than print out th
e same help/failure message N times, display it once with a count of
how many processes sent the same message.
MCA orte: parameter "orte_tmpdir_base" (current
value: <none>, data source: default value)
Base of the session directory tree
MCA orte: parameter "orte_no_session_dirs" (current
value: <none>, data source: default value)
Prohibited locations for session
directories (multiple locations separated by ',', default=NULL)
MCA orte: parameter "orte_debug" (current value:
"0", data source: default value)
Top-level ORTE debug switch (default
verbosity: 1)
MCA orte: parameter "orte_debug_verbose" (current
value: "-1", data source: default value)
Verbosity level for ORTE debug messages
(default: 1)
MCA orte: parameter "orte_debug_daemons" (current
value: "0", data source: default value)
Whether to debug the ORTE daemons or not
MCA orte: parameter
"orte_debug_daemons_file" (current value: "0", data source: default
value)
Whether want stdout/stderr of daemons to
go to a file or not
MCA orte: parameter
"orte_leave_session_attached" (current value: "0", data source:
default value)
Whether applications and/or daemons should
leave their sessions attached so that any output can be
received - this allows X forwarding without all the attendant
debugging output
MCA orte: parameter "orte_do_not_launch" (current
value: "0", data source: default value)
Perform all necessary operations to
prepare to launch the application, but do not actually launch it
MCA orte: parameter "orte_daemon_spin" (current
value: "0", data source: default value)
Have any orteds spin until we can connect
a debugger to them
MCA orte: parameter "orte_daemon_fail" (current
value: "-1", data source: default value)
Have the specified orted fail after init
for debugging purposes
MCA orte: parameter
"orte_daemon_fail_delay" (current value: "0", data source: default
value)
Have the specified orted fail after
specified number of seconds (default: 0 => no delay)
MCA orte: parameter "orte_heartbeat_rate" (current
value: "0", data source: default value)
Seconds between checks for daemon state-of-
health (default: 0 => do not check)
MCA orte: parameter "orte_startup_timeout" (current
value: "0", data source: default value)
Milliseconds/daemon to wait for startup
before declaring failed_to_start (default: 0 => do not chec
Fortran77 profiling: yes
Fortran90 profiling: yes
C++ exceptions: nok)
MCA orte: parameter "orte_timing" (current value:
"0", data source: default value)
Request that critical timing loops be
measured
MCA orte: parameter
"orte_base_user_debugger" (current value: "totalview @mpirun@ -a
@mpirun_args@ : ddt -n @
np@ -start @executable@ @executable_argv@ @single_app@ : fxp
@mpirun@ -a @mpirun_args@", data source: default value)
Sequence of user-level debuggers to search
for in orterun
MCA orte: parameter "orte_abort_timeout" (current
value: "1", data source: default value)
Max time to wait [in secs] before aborting
an ORTE operation (default: 1sec)
MCA orte: parameter "orte_timeout_step" (current
value: "1000", data source: default value)
Time to wait [in usecs/proc] before
aborting an ORTE operation (default: 1000 usec/proc)
MCA orte: parameter "orte_default_hostfile" (current
value: <none>, data source: default value)
Name of the default hostfile (relative or
absolute path)
MCA orte: parameter
"orte_keep_fqdn_hostnames" (current value: "0", data source: default
value)
Whether or not to keep FQDN hostnames
[default: no]
MCA orte: parameter "orte_contiguous_nodes" (current
value: "2147483647", data source: default value)
Number of nodes after which contiguous
nodename encoding will automatically be used [default: INT_MAX]
MCA orte: parameter "orte_tag_output" (current
value: "0", data source: default value)
Tag all output with [job,rank] (default:
false)
MCA orte: parameter "orte_xml_output" (current
value: "0", data source: default value)
Display all output in XML format (default:
false)
MCA orte: parameter "orte_timestamp_output" (current
value: "0", data source: default value)
Timestamp all application process output
(default: false)
MCA orte: parameter "orte_output_filename" (current
value: <none>, data source: default value)
Redirect output from application processes
into filename.rank [default: NULL]
MCA orte: parameter
"orte_show_resolved_nodenames" (current value: "0", data source:
default value)
Display any node names that are resolved
to a different name (default: false)
MCA orte: parameter "orte_hetero_apps" (current
value: "0", data source: default value)
Indicates that multiple app_contexts are
being provided that are a mix of 32/64 bit binaries (default: false)
MCA orte: parameter "orte_launch_agent" (current
value: "orted", data source: default value)
Command used to start processes on remote
nodes (default: orted)
MCA orte: parameter
"orte_allocation_required" (current value: "0", data source: default
value)
Whether or not an allocation by a resource
manager is required [default: no]
MCA orte: parameter "orte_xterm" (current value:
<none>, data source: default value)
Create a new xterm window and display
output from the specified ranks there [default: none]
MCA orte: parameter
"orte_forward_job_control" (current value: "0", data source: default
value)
Forward SIGTSTP (after converting to
SIGSTOP) and SIGCONT signals to the application procs [default: no]
MCA opal: parameter "opal_signal" (current value:
"6,7,8,11", data source: default value)
If a signal is received, display the stack
trace frame
MCA opal: parameter
"opal_set_max_sys_limits" (current value: "0", data source: default
value)
Set to non-zero to automatically set any
system-imposed limits to the maximum allowed
MCA opal: parameter "opal_event_include" (current
value: "poll", data source: default value)
... ... ...
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