From: Steven Truong (midair77_at_[hidden])
Date: 2007-05-18 19:38:44
Hi, all. Once again, I am ver y frustrated with what I have run into so far.
My system is CentOS 4.4 x86_64, ifort 9.1.043, torque, maui.
I configured openmpi 1.2.1 with this command.
./configure --prefix=/usr/local/openmpi-1.2.1
--with-tm=/usr/local/pbs --enable-static
Now I just tried to run a test command like in the FAQ and it did not work.
[struong_at_neptune 4cpu4npar10nsim]$ mpirun --mca btl tcp,self -np 1
--host node07 hostname
bash: orted: command not found
[neptune.myhost.com:01403] [0,0,0] ORTE_ERROR_LOG: Timeout in file
base/pls_base_orted_cmds.c at line 275
[neptune.myhost.com:01403] [0,0,0] ORTE_ERROR_LOG: Timeout in file
pls_rsh_module.c at line 1165
[neptune.myhost.com:01403] [0,0,0] ORTE_ERROR_LOG: Timeout in file
errmgr_hnp.c at line 90
[neptune.myhost.com:01403] ERROR: A daemon on node node07 failed to
start as expected.
[neptune.myhost.com:01403] ERROR: There may be more information available from
[neptune.myhost.com:01403] ERROR: the remote shell (see above).
[neptune.myhost.com:01403] ERROR: The daemon exited unexpectedly with
status 127.
[neptune.myhost.com:01403] [0,0,0] ORTE_ERROR_LOG: Timeout in file
base/pls_base_orted_cmds.c at line 188
[neptune.myhost.com:01403] [0,0,0] ORTE_ERROR_LOG: Timeout in file
pls_rsh_module.c at line 1197
--------------------------------------------------------------------------
mpirun was unable to cleanly terminate the daemons for this job.
Returned value Timeout instead of ORTE_SUCCESS.
Here is my environment:
[struong_at_neptune 4cpu4npar10nsim]$ printenv
HOSTNAME=neptune.myhost.com
TERM=xterm
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=::ffff:192.168.0.185 37304 22
INSTALL_DIR=/usr/local/rrdtool-1.2.12
SSH_TTY=/dev/pts/1
USER=struong
LS_COLORS=no=00:fi=00:di=00;34:ln=00;36:pi=40;33:so=00;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=00;32:*.cmd=00;32:*.exe=00;32:*.com=00;32:*.btm=00;32:*.bat=00;32:*.sh=00;32:*.csh=00;32:*.tar=00;31:*.tgz=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.zip=00;31:*.z=00;31:*.Z=00;31:*.gz=00;31:*.bz2=00;31:*.bz=00;31:*.tz=00;31:*.rpm=00;31:*.cpio=00;31:*.jpg=00;35:*.gif=00;35:*.bmp=00;35:*.xbm=00;35:*.xpm=00;35:*.png=00;35:*.tif=00;35:
RSHCOMMAND=/usr/bin/ssh
KDEDIR=/usr
MAIL=/var/spool/mail/struong
PATH=/usr/local/NWChem/ecce-v4.0.1/apps/scripts:/opt/intel/fce/9.1.043/bin:/usr/local/openmpi-1.2.1/bin:/opt/c3-4:/opt/bin:/usr/local/torque/bin:/usr/local/torque/sbin:/usr/local/maui/bin:/usr/local/maui/sbin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/usr/local/rrdtool-1.2.12/bin:/home/struong/bin
F90=/opt/intel/fce/9.1.043/bin/ifort
INPUTRC=/etc/inputrc
PWD=/home/struong/Set3Bench/GAM/4cpu4npar10nsim
LANG=en_US.UTF-8
F77=/opt/intel/fce/9.1.043/bin/ifort
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
SHLVL=1
HOME=/home/struong
PBS_DEFAULT=neptune
FC=/opt/intel/fce/9.1.043/bin/ifort
ECCE_HOME=/usr/local/NWChem/ecce-v4.0.1/apps
BASH_ENV=/home/struong/.bashrc
LOGNAME=struong
BUILD_DIR=/tmp/rrdbuil
SSH_CONNECTION=::ffff:192.168.0.185 37304 ::ffff:192.168.0.182 22
LESSOPEN=|/usr/bin/lesspipe.sh %s
G_BROKEN_FILENAMES=1
_=/usr/bin/printenv
OLDPWD=/home/struong
And I have not modified any MCA parameters anywhere.
It appeared that something are not right with pls (Process launch
subsystem) and related components like ssh but I set up so that i can
ssh without password to all the nodes. And could somebody tell me why
orted is not found?
[struong_at_neptune 4cpu4npar10nsim]$ ssh node07
Last login: Fri May 18 15:23:37 2007 from neptune.myhost.com
[struong_at_node07 ~]$ which orted
/usr/local/openmpi-1.2.1/bin/orted
[root_at_node07 ~]# cat /etc/ld.so.conf
include ld.so.conf.d/*.conf
/usr/ofed/lib64
/usr/local/lib
/opt/intel/fce/9.1.043/lib
/opt/intel_mkl/8.1/lib/em64t
/opt/mpich/lib
/usr/local/pbs/lib
/usr/local/maui/lib
/opt/acml3.6.0/ifort64/lib
/opt/acml3.6.0/ifort64_mp/lib
/usr/local/openmpi-1.2.1/lib
[struong_at_neptune 4cpu4npar10nsim]$ ompi_info
Open MPI: 1.2.1
Open MPI SVN revision: r14481
Open RTE: 1.2.1
Open RTE SVN revision: r14481
OPAL: 1.2.1
OPAL SVN revision: r14481
Prefix: /usr/local/openmpi-1.2.1
Configured architecture: x86_64-unknown-linux-gnu
Configured by: root
Configured on: Thu May 17 18:22:20 PDT 2007
Configure host: neptune.myhost.com
Built by: root
Built on: Thu May 17 18:33:47 PDT 2007
Built host: neptune.myhost.com
C bindings: yes
C++ bindings: yes
Fortran77 bindings: yes (all)
Fortran90 bindings: yes
Fortran90 bindings size: small
C compiler: gcc
C compiler absolute: /usr/bin/gcc
C++ compiler: g++
C++ compiler absolute: /usr/bin/g++
Fortran77 compiler: /opt/intel/fce/9.1.043/bin/ifort
Fortran77 compiler abs: /opt/intel/fce/9.1.043/bin/ifort
Fortran90 compiler: /opt/intel/fce/9.1.043/bin/ifort
Fortran90 compiler abs: /opt/intel/fce/9.1.043/bin/ifort
C profiling: yes
C++ profiling: yes
Fortran77 profiling: yes
Fortran90 profiling: yes
C++ exceptions: no
Thread support: posix (mpi: no, progress: no)
Internal debug support: no
MPI parameter check: runtime
Memory profiling support: no
Memory debugging support: no
libltdl support: yes
Heterogeneous support: yes
mpirun default --prefix: no
MCA backtrace: execinfo (MCA v1.0, API v1.0, Component v1.2.1)
MCA memory: ptmalloc2 (MCA v1.0, API v1.0, Component v1.2.1)
MCA paffinity: linux (MCA v1.0, API v1.0, Component v1.2.1)
MCA maffinity: first_use (MCA v1.0, API v1.0, Component v1.2.1)
MCA maffinity: libnuma (MCA v1.0, API v1.0, Component v1.2.1)
MCA timer: linux (MCA v1.0, API v1.0, Component v1.2.1)
MCA installdirs: env (MCA v1.0, API v1.0, Component v1.2.1)
MCA installdirs: config (MCA v1.0, API v1.0, Component v1.2.1)
MCA allocator: basic (MCA v1.0, API v1.0, Component v1.0)
MCA allocator: bucket (MCA v1.0, API v1.0, Component v1.0)
MCA coll: basic (MCA v1.0, API v1.0, Component v1.2.1)
MCA coll: self (MCA v1.0, API v1.0, Component v1.2.1)
MCA coll: sm (MCA v1.0, API v1.0, Component v1.2.1)
MCA coll: tuned (MCA v1.0, API v1.0, Component v1.2.1)
MCA io: romio (MCA v1.0, API v1.0, Component v1.2.1)
MCA mpool: rdma (MCA v1.0, API v1.0, Component v1.2.1)
MCA mpool: sm (MCA v1.0, API v1.0, Component v1.2.1)
MCA pml: cm (MCA v1.0, API v1.0, Component v1.2.1)
MCA pml: ob1 (MCA v1.0, API v1.0, Component v1.2.1)
MCA bml: r2 (MCA v1.0, API v1.0, Component v1.2.1)
MCA rcache: vma (MCA v1.0, API v1.0, Component v1.2.1)
MCA btl: self (MCA v1.0, API v1.0.1, Component v1.2.1)
MCA btl: sm (MCA v1.0, API v1.0.1, Component v1.2.1)
MCA btl: tcp (MCA v1.0, API v1.0.1, Component v1.0)
MCA topo: unity (MCA v1.0, API v1.0, Component v1.2.1)
MCA osc: pt2pt (MCA v1.0, API v1.0, Component v1.2.1)
MCA errmgr: hnp (MCA v1.0, API v1.3, Component v1.2.1)
MCA errmgr: orted (MCA v1.0, API v1.3, Component v1.2.1)
MCA errmgr: proxy (MCA v1.0, API v1.3, Component v1.2.1)
MCA gpr: null (MCA v1.0, API v1.0, Component v1.2.1)
MCA gpr: proxy (MCA v1.0, API v1.0, Component v1.2.1)
MCA gpr: replica (MCA v1.0, API v1.0, Component v1.2.1)
MCA iof: proxy (MCA v1.0, API v1.0, Component v1.2.1)
MCA iof: svc (MCA v1.0, API v1.0, Component v1.2.1)
MCA ns: proxy (MCA v1.0, API v2.0, Component v1.2.1)
MCA ns: replica (MCA v1.0, API v2.0, Component v1.2.1)
MCA oob: tcp (MCA v1.0, API v1.0, Component v1.0)
MCA ras: dash_host (MCA v1.0, API v1.3, Component v1.2.1)
MCA ras: localhost (MCA v1.0, API v1.3, Component v1.2.1)
MCA ras: gridengine (MCA v1.0, API v1.3, Component v1.2.1)
MCA ras: slurm (MCA v1.0, API v1.3, Component v1.2.1)
MCA ras: tm (MCA v1.0, API v1.3, Component v1.2.1)
MCA rds: hostfile (MCA v1.0, API v1.3, Component v1.2.1)
MCA rds: proxy (MCA v1.0, API v1.3, Component v1.2.1)
MCA rds: resfile (MCA v1.0, API v1.3, Component v1.2.1)
MCA rmaps: round_robin (MCA v1.0, API v1.3, Component v1.2.1)
MCA rmgr: proxy (MCA v1.0, API v2.0, Component v1.2.1)
MCA rmgr: urm (MCA v1.0, API v2.0, Component v1.2.1)
MCA rml: oob (MCA v1.0, API v1.0, Component v1.2.1)
MCA pls: proxy (MCA v1.0, API v1.3, Component v1.2.1)
MCA pls: gridengine (MCA v1.0, API v1.3, Component v1.2.1)
MCA pls: rsh (MCA v1.0, API v1.3, Component v1.2.1)
MCA pls: slurm (MCA v1.0, API v1.3, Component v1.2.1)
MCA pls: tm (MCA v1.0, API v1.3, Component v1.2.1)
MCA sds: env (MCA v1.0, API v1.0, Component v1.2.1)
MCA sds: seed (MCA v1.0, API v1.0, Component v1.2.1)
MCA sds: singleton (MCA v1.0, API v1.0, Component v1.2.1)
MCA sds: pipe (MCA v1.0, API v1.0, Component v1.2.1)
MCA sds: slurm (MCA v1.0, API v1.0, Component v1.2.1)
[struong_at_neptune 4cpu4npar10nsim]$ ompi_info --param pls all
MCA pls: parameter "pls_base_reuse_daemons" (current value:
"0")
If nonzero, reuse daemons to launch dynamically
spawned processes. If zero, do not reuse daemons
(default)
MCA pls: parameter "pls" (current value: <none>)
Default selection set of components for the pls
framework (<none> means "use all components that can
be found")
MCA pls: parameter "pls_base_verbose" (current value: "0")
Verbosity level for the pls framework (0 = no
verbosity)
MCA pls: parameter "pls_proxy_priority" (current value: "0")
MCA pls: parameter "pls_gridengine_debug" (current value: "0")
Enable debugging of gridengine pls component
MCA pls: parameter "pls_gridengine_verbose" (current value:
"0")
Enable verbose output of the gridengine qrsh -inherit
command
MCA pls: parameter "pls_gridengine_priority" (current value:
"100")
Priority of the gridengine pls component
MCA pls: parameter "pls_gridengine_orted" (current value:
"orted")
The command name that the gridengine pls component
will invoke for the ORTE daemon
MCA pls: parameter "pls_rsh_debug" (current value: "0")
Whether or not to enable debugging output for the rsh
pls component (0 or 1)
MCA pls: parameter "pls_rsh_num_concurrent" (current value:
"128")
How many pls_rsh_agent instances to invoke
concurrently (must be > 0)
MCA pls: parameter "pls_rsh_force_rsh" (current value: "0")
Force the launcher to always use rsh, even for local
daemons
MCA pls: parameter "pls_rsh_orted" (current value: "orted")
The command name that the rsh pls component will
invoke for the ORTE daemon
MCA pls: parameter "pls_rsh_priority" (current value: "10")
Priority of the rsh pls component
MCA pls: parameter "pls_rsh_delay" (current value: "1")
Delay (in seconds) between invocations of the remote
agent, but only used when the "debug" MCA
parameter is true, or the top-level MCA
debugging is enabled
(otherwise this value is ignored)
MCA pls: parameter "pls_rsh_reap" (current value: "1")
If set to 1, wait for all the processes to complete
before exiting. Otherwise, quit immediately --
without waiting for confirmation that all other
processes in the job have completed.
MCA pls: parameter "pls_rsh_assume_same_shell" (current value:
"1")
If set to 1, assume that the shell on the remote node
is the same as the shell on the local node.
Otherwise, probe for what the remote shell.
MCA pls: parameter "pls_rsh_agent" (current value: "ssh :
rsh")
The command used to launch executables on
remote nodes (typically either "ssh" or
"rsh")
MCA pls: parameter "pls_slurm_debug" (current value: "0")
Enable debugging of slurm pls
MCA pls: parameter "pls_slurm_priority" (current value: "75")
Default selection priority
MCA pls: parameter "pls_slurm_orted" (current value: "orted")
Command to use to start proxy orted
MCA pls: parameter "pls_slurm_args" (current value: <none>)
Custom arguments to srun
MCA pls: parameter "pls_tm_debug" (current value: "0")
Enable debugging of the TM pls
MCA pls: parameter "pls_tm_verbose" (current value: "0")
Enable verbose output of the TM pls
MCA pls: parameter "pls_tm_priority" (current value: "75")
Default selection priority
MCA pls: parameter "pls_tm_orted" (current value: "orted")
Command to use to start proxy orted
MCA pls: parameter "pls_tm_want_path_check" (current value:
"1")
Whether the launching process should check for the
pls_tm_orted executable in the PATH before launching
(the TM API does not give an idication of failure;
this is a somewhat-lame workaround; non-zero values
enable this check)
Thank you.