openmpi - initialization failed


 
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Old 09-08-2012
openmpi - initialization failed

Hi everybody,

my problem is the following:
I'm trying to run an openmpi program on a cluster (atlasz.elte.hu, it's in hungarian, but you can try google translate),
but I always got this error:

Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(394)...........: Initialization failed
MPID_Init(121)..................:
MPIDI_Populate_vc_node_ids(1219):
MPID_Get_max_node_id(798).......: PMI_KVS_Commit returned -1

I am doing it according to the manual, for example, here is my script:

#!/bin/bash

mpirun.openmpi /users/jkobori/boxfit/out/boxfit boxfitsettings.txt

which I am runnig with the sbatch -p hpc2009 -N 4 -B 2:4:1 s.sh line.
This is the way it should be done, but it doesn't work for me.
Can You help me out?

If any additional info is needed, please, tell me.

Regards,
Joe
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HSCAN(1)							   Version 2.5.2							  HSCAN(1)

NAME
hscan - Scan clusters via RAPI and save node/instance data SYNOPSIS
hscan [-p] [--no-headers] [-d path ] cluster... hscan --version DESCRIPTION
hscan is a tool for scanning clusters via RAPI and saving their data in the input format used by hbal(1) and hspace(1). It will also show a one-line score for each cluster scanned or, if desired, the cluster state as show by the -p option to the other tools. For each cluster, one file named cluster.data will be generated holding the node and instance data. This file can then be used in hbal(1) or hspace(1) via the -t option. In case the cluster name contains slashes (as it can happen when the cluster is a fully-specified URL), these will be replaced with underscores. The one-line output for each cluster will show the following: Name The name of the cluster (or the IP address that was given, etc.) Nodes The number of nodes in the cluster Inst The number of instances in the cluster BNode The number of nodes failing N+1 BInst The number of instances living on N+1-failed nodes t_mem Total memory in the cluster f_mem Free memory in the cluster t_disk Total disk in the cluster f_disk Free disk space in the cluster Score The score of the cluster, as would be reported by hbal(1) if run on the generated data files. In case of errors while collecting data, all fields after the name of the cluster are replaced with the error display. Note: this output format is not yet final so it should not be used for scripting yet. OPTIONS
The options that can be passed to the program are as follows: -p, --print-nodes Prints the node status for each cluster after the cluster's one-line status display, in a format designed to allow the user to understand the node's most important parameters. For details, see the man page for htools(1). -d path Save the node and instance data for each cluster under path, instead of the current directory. -V, --version Just show the program version and exit. EXIT STATUS
The exist status of the command will be zero, unless for some reason loading the input data failed fatally (e.g. wrong node or instance data). BUGS
The program does not check its input data for consistency, and aborts with cryptic errors messages in this case. EXAMPLE
$ hscan cluster1 Name Nodes Inst BNode BInst t_mem f_mem t_disk f_disk Score cluster1 2 2 0 0 1008 652 255 253 0.24404762 $ ls -l cluster1.data -rw-r--r-- 1 root root 364 2009-03-23 07:26 cluster1.data REPORTING BUGS
Report bugs to project website (http://code.google.com/p/ganeti/) or contact the developers using the Ganeti mailing list (ganeti@google- groups.com). SEE ALSO
Ganeti overview and specifications: ganeti(7) (general overview), ganeti-os-interface(7) (guest OS definitions). Ganeti commands: gnt-cluster(8) (cluster-wide commands), gnt-job(8) (job-related commands), gnt-node(8) (node-related commands), gnt- instance(8) (instance commands), gnt-os(8) (guest OS commands), gnt-group(8) (node group commands), gnt-backup(8) (instance import/export commands), gnt-debug(8) (debug commands). Ganeti daemons: ganeti-watcher(8) (automatic instance restarter), ganeti-cleaner(8) (job queue cleaner), ganeti-noded(8) (node daemon), ganeti-masterd(8) (master daemon), ganeti-rapi(8) (remote API daemon). Ganeti htools: htools(1) (generic binary), hbal(1) (cluster balancer), hspace(1) (capacity calculation), hail(1) (IAllocator plugin), hscan(1) (data gatherer from remote clusters). COPYRIGHT
Copyright (C) 2006, 2007, 2008, 2009, 2010, 2011 Google Inc. Permission is granted to copy, distribute and/or modify under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. Ganeti HSCAN(1)