[GE users] SunGrid Engine & BLAST

Joe Landman landman at scalableinformatics.com
Fri Jan 14 15:39:38 GMT 2005


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Hi Hrishi:

  Use lsof, the output is much cleaner and more sensible:

[root at minicc root]# lsof -i:22

COMMAND   PID USER   FD   TYPE   DEVICE SIZE NODE NAME

sshd     6675 root    3u  IPv4     5685       TCP *:ssh (LISTEN)

sshd    11367 root    4u  IPv4 32963612       TCP minicc.scalableinformatics.com:ssh->crunch.scalableinformatics.com:47061 (ESTABLISHED)


Port 22 is the sshd daemon.  Use "lsof -i:PortNumber" or  "lsof -i | 
grep pattern" for a particular service.

Joe

Hrishikesh Deshmukh wrote:

>Here is what i get, now looking at the output it means that
>535,536,537 are not in use and i can use for sge_commd,qmaster and
>execd!!! Am i right in inferring this.
>
> netstat -an | grep 28
>tcp4       0      0  129.174.206.93.28      129.174.206.93.49329   ESTABLISHED
>tcp4       0      0  129.174.206.93.49329   129.174.206.93.28      ESTABLISHED
>tcp4       0      0  129.174.206.93.28      129.174.206.93.49213   ESTABLISHED
>tcp4       0      0  129.174.206.93.49213   129.174.206.93.28      ESTABLISHED
>tcp4       0      0  *.28                   *.*                    LISTEN
>udp4       0      0  *.3283                 *.*                    
> 11003f0 stream      0      0        0  1100428        0        0
>/var/tmp/SCDynamicStoreNotifyFileDescriptor-19203
> 1100428 stream      0      0        0  11003f0        0        0
> 1100b28 dgram       0      0        0  1100c78  1100c78        0
> 1100c78 dgram       0      0        0  1100b28  1100b28        0
>emac21:/usr/local/sge/default/common sgeadmin$ netstat -an | grep 535
>udp4       0      0  *.5353                 *.*                    
>emac21:/usr/local/sge/default/common sgeadmin$ netstat -an | grep 536
>emac21:/usr/local/sge/default/common sgeadmin$ netstat -an | grep 537
>
>Hrishi
>
>On Fri, 14 Jan 2005 10:20:54 -0500 (EST), Paul Mitchell
><pmitchel at email.unc.edu> wrote:
>  
>
>>On Fri, 14 Jan 2005, Hrishikesh Deshmukh wrote:
>>
>>    
>>
>>>Here is what i get for the commands you suggested to run
>>>   starting sge_qmaster
>>>starting program: /usr/local/sge/bin/darwin/sge_commd
>>>using service "sge_commd"
>>>bound to port 28
>>>Reading in complexes:
>>>        Complex "host".
>>>        Complex "queue".
>>>Reading in execution hosts.
>>>Reading in administrative hosts.
>>>Reading in submit hosts.
>>>Reading in parallel environments:
>>>        PE "make".
>>>Reading in scheduler configuration
>>>   starting sge_schedd
>>>      
>>>
>>>netstat -an | grep $COMMD_PORT
>>>Usage: grep [OPTION]... PATTERN [FILE]...
>>>Try `grep --help' for more information.
>>>      
>>>
>>You're getting an error message from grep, probably because it cannot
>>resolve the $COMMD_PORT.  Why not try:
>>
>>        netstat -an | grep 28
>>
>>or
>>        netstat -an | grep 535
>>
>>etc.
>>
>>    
>>
>>>I have to keep setting SGE_ROOT, how do i set it permanently.
>>>I had done as suggested in the installation manual
>>>SGE_ROOT=/usr/local/sge;export SGE_ROOT;echo $SGE_ROOT
>>>Do i need to do anything more.
>>>      
>>>
>>I got tried of resetting it so I put the following lines in /etc/profile:
>>
>># The next two lines set up the gridengine environment
>>export SGE_ROOT=/usr/local/sge
>>. $SGE_ROOT/default/common/settings.sh
>>$ echo $SGE_ROOT
>>/usr/local/sge
>>
>>I also placed the following line in my .kshrc file:
>>
>>export SGE_ROOT=/usr/local/sge
>>
>>Paul Mitchell
>>
>>==============================================================================
>>        Paul Mitchell
>>        email: pmitchel at email.unc.edu
>>        phone: (919) 962-9778
>>        office: I have an office, room 14, Phillips Hall
>>==============================================================================
>>
>>
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>>
>>    
>>
>
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>  
>


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