Submitting awk script into cluster short.q


 
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Old 11-06-2012
Submitting awk script into cluster short.q

Hello,

I want to submit my awk script into cluster queue as my job takes about forty minutes to finish so I can not run it on the main node.
My awk script is like the following and I have three files. so, I write :

qsub -q short.q Myscript.awk file1 file2 file3

It submits the work into cluster but it gives an error after some seconds.
Code:
BEGIN{
OFS=ORS=""
}
{
..........
  nsnp++
  if((2*nind+4) != NF){........}
  for(i=1;i<=nind;i++){
   if(ID_num[i] in POP){
      pos_deb=2*(i-1)+5
     {...........}
      }
 }
 if(nsnp%1000==0){print nsnp"\n"}
}
}

Thank you very much for yout help

Last edited by Neo; 11-06-2012 at 01:05 PM..
 
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scha_cluster_get(1HA)					       Sun Cluster Commands					     scha_cluster_get(1HA)

NAME
scha_cluster_get - access cluster information SYNOPSIS
scha_cluster_get -O optag [args] DESCRIPTION
The scha_cluster_get command accesses and generates information about a cluster. You can access information about the cluster, nodes, zones, host names, resource groups, resource types, and states. The command is intended for use in shell script implementations of callback methods for resource types. These callback methods for resource types represent services that are controlled by the cluster's Resource Group Manager (RGM). This command provides the same information as the scha_resource_get() function. This command sends output to the standard output (stdout) in formatted strings on separate lines, as described in the scha_cmds(1HA) man page. You can store the output in shell variables. You can also parse the output with shell commands such as the awk command. OPTIONS
The following options are supported: -O optag The optag argument indicates the information to be accessed. Depending on the optag, an additional argument may be needed to indicate the cluster node or zone for which information is to be retrieved. Note - optag options, such as NODENAME_LOCAL and NODENAME_NODEID, are not case sensitive. You can use any combination of uppercase and lowercase letters when you specify optag options. The following optag values are supported: ALL_NODEIDS Generates on successive lines the numeric node identifiers of all nodes in the cluster. ALL_NODENAMES Generates on successive lines the names of all nodes in the cluster. ALL_NONGLOBAL_ZONES Generates on successive lines the nodename:zonename string of all the non-global zones on all nodes in the cluster. ALL_NONGLOBAL_ZONES_NODEID Generates on successive lines the nodename:zonename string of all non-global zones on the cluster node whose numeric node identifier is given as the argument. ALL_PRIVATELINK_HOSTNAMES Generates on successive lines the host names by which all cluster nodes are addressed on the cluster interconnect. ALL_RESOURCEGROUPS Generates on successive lines the names of all the resource groups that are being managed in the cluster. ALL_RESOURCETYPES Generates on successive lines the names of all the resource types that are registered in the cluster. ALL_ZONES Generates on successive lines the nodename:zonename string of all zones, including the global zone, on all nodes in the cluster. ALL_ZONES_NODEID Generates on successive lines the nodename:zonename string of all zones, including the global zone, on the cluster node whose numeric node identifier is given as the argument. CLUSTERNAME Generates the name of the cluster. NODEID_LOCAL Generates the numeric node identifier for the node where the command is executed. NODEID_NODENAME Generates the numeric node identifier of the node indicated by the name. Requires an additional unflagged argument that is the name of a cluster node. NODENAME_LOCAL Generates the name of the cluster node where the command is executed. NODENAME_NODEID Generates the name of the cluster node indicated by the numeric identifier. Requires an additional unflagged argu- ment that is a numeric cluster node identifier. NODESTATE_LOCAL Generates UP or DOWN depending on the state of the node where the command is executed. NODESTATE_NODE Generates UP or DOWN depending on the state of the named node. Requires an additional unflagged argument that is the name of a cluster node. PRIVATELINK_HOSTNAME_LOCAL Generates the host name by which the node on which the command is run is addressed over the cluster interconnect. PRIVATELINK_HOSTNAME_NODE Generates the host name by which the named node is addressed on the cluster interconnect. Requires an additional unflagged argument that is the name of a cluster node. SYSLOG_FACILITY Generates the number of the syslog(3C) facility that the RGM uses for log messages. The value is 24, which corre- sponds to the daemon facility. You can use this value as the facility level in the logger(1) command to log mes- sages in the cluster log. ZONE_LOCAL Generates the name of the zone from which the command is issued. The format of the zone name that is returned is nodename:zonename. EXAMPLES
Example 1 Using the scha_cluster Command in a Shell Script The following shell script uses the scha_cluster command to print whether each cluster node is up or down: #!/bin/sh nodenames=`scha_cluster_get -O All_Nodenames` for node in $nodenames do state=`scha_cluster_get -O NodeState_Node $node` printf "State of node: %sexit: %dvalue: %s0 "$node" $? "$state" done EXIT STATUS
The following exit status codes are returned: 0 Successful completion. nonzero An error occurred. Error codes are described in scha_calls(3HA). ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWscdev | +-----------------------------+-----------------------------+ |Interface Stability |Stable | +-----------------------------+-----------------------------+ SEE ALSO
awk(1), logger(1), sh(1), scha_cmds(1HA), syslog(3C), scha_calls(3HA), scha_cluster_get(3HA), attributes(5) Sun Cluster 3.2 6 Sep 2006 scha_cluster_get(1HA)