[GE users] newbie problem ... help needed

templedf dan.templeton at sun.com
Fri Feb 5 13:43:55 GMT 2010


Then the problem is what Chris and I suggested.  ifort isn't in your 
default path.  You have three options:

1) Add the directory where ifort lives to your default path, e.g. in the 
.cshrc or .profile
2) Submit your job with "-V" to transfer your entire shell environment 
along with your job
3) Submit your job with "-v PATH" to transfer just your shell's PATH 
variable along with your job

Daniel

On 02/05/10 00:32, legol18 wrote:
> the one I mentioned was initially was when i used ssh from the same account on the cluster. When I try doing it through a different machine ::
> ____________________________________________
>
> /home/rajat/oldb/popl/lxpeff/pp: line 9: ifort: command not found
> ____________________________________________
>
>    
>> I tried, it gives the same error
>> _____________________________________________
>>
>> Warning: untrusted X11 forwarding setup failed: xauth key data not generated
>> Warning: No xauth data; using fake authentication data for X11 forwarding.
>> /home/rajat/oldb/popl/lxpeff/pp: line 9: ifort: command not found
>> _____________________________________________
>>
>>
>> So, what happens if instead of steps 3&  4, you log out and then run the job script directly via ssh as I described before?
>>
>> Daniel
>>
>>
>> On 02/04/10 06:38, Rajat. wrote:
>>
>>      Well, the way I am running my job is as follows::
>>      (I am a newbie with this cluster stuff so i`ll let u know about the entire process, please bear it with me )
>>
>>      1.) I remote log to the cluster via ssh from my laptop
>>      2.) Then cd to my destination directory where my program is, over there I create this file job file.
>>      3.) Once its done, I open up qmon via terminal ($ qmon&)
>>      4.) Over there I submit my job.
>>
>>      It`s then that I am getting all those errors
>>
>>      By the way, I forgot mentioning that it`s a linux cluster.
>>
>>      Regards,
>>
>>
>>      
>>> What happens if you run your job script on one of the remote nodes via
>>> ssh (i.e. ssh host1 /path/to/script.sh) ?  I assume the problem is that
>>> you're setting your path after you log in to include where ifort lives.
>>> By default Grid Engine does not transfer your shell's environment along
>>> with your job.  The PATH for the job is therefore whatever you get when
>>> you log in by default.  (There's another subtler problem that could also
>>> be the culprit, but let's try the more obvious one first.)  To get the
>>> job to inherit your environment, try using either -V or -v PATH when you
>>> submit the job.
>>>
>>> Daniel
>>>
>>> On 02/04/10 04:52, legol18 wrote:
>>>        
>>>> Hi,
>>>>
>>>> I just started using the grid engine on my cluster.
>>>> I use "g77","ifort" or "icc" for compiling my programs and they are already installed on the cluster.
>>>>
>>>> I am creating the job script inside which I am compiling the program and executing it ::
>>>>
>>>> JOB FILE :
>>>> ____________________________________________
>>>>
>>>> # /bin/csh
>>>>
>>>> cd /home/rajat/oldb/popl/lxpeff
>>>> # compile the fortran code then execute it with the ./ option
>>>> g77 test.f90 -o test
>>>> ./test
>>>> ____________________________________________
>>>>
>>>> Now, as mentioned, I have ifort installed on my cluster still the process gets terminated with the following error
>>>>
>>>> ERROR :
>>>> _____________________________________________
>>>>
>>>> opt/gridengine/default/spool/compute-0-0/job_scripts/53: line 9: ifort: command not found
>>>> /opt/gridengine/default/spool/compute-0-0/job_scripts/53: line 10: ./test: No such file or directory
>>>> _____________________________________________
>>>>
>>>> On the other hand if I try running a previously complied executable (which I compile normally on the terminal), it works fine.
>>>>
>>>> Am I missing something?
>>>>
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