[GE users] gamess info

lukacm at pdx.edu lukacm at pdx.edu
Tue Aug 22 19:53:26 BST 2006


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Well,

as i mentioned (at least i hope), i can run gamess using the rungms script and
ssh. It does not work using rsh because the cluster is not rsh enabled. This is
different for SGE having its own subsytem.


When i run gamess in SGE, either ssh or rsh i get similar errors:

in one case (ssh) i get only error messages as shown below (in hte previous
mail). When run with rsh, i get errors directly from the gamess program such
as:

connect to address 10.5.255.240: connect to address 10.5.255.248: Connection
refused
Connection refused
connect to address 10.5.255.240: Connection refused
trying normal rsh (/usr/bin/rsh)
connect to address 10.5.255.248: Connection refused
trying normal rsh (/usr/bin/rsh)
compute-0-14.local: Connection refused
compute-0-6.local: Connection refused
 ddikick.x: Timed out while waiting for DDI processes to check in.
 ddikick.x: Fatal error detected.
 The error is most likely to be in the application, so check for
 input errors, disk space, memory needs, application bugs, etc.
 ddikick.x will now clean up all processes, and exit...
compute-0-12.local: Connection refused
compute-0-6: Connection refused
compute-0-14: Connection refused
compute-0-13: Connection refused

This type of errors i get also when running rungms with rsh.
I have to check but it seems to me that the rsh-wrapper is not being used
properly with gamess. I mean  have all other software succesfully set up woth
SGE.

martin



Quoting Reuti <reuti at staff.uni-marburg.de>:

> Am 22.08.2006 um 19:06 schrieb lukacm at pdx.edu:
>
> > Hello,
> >
> > i made all the modifications, including the gamess running under rsh
> > (fortunately it does not require recompiling the source code),
> > however the
> > result is the same. In the output file for every job i see also this:
>
> Did you got the same error message "connection refused" with rsh and
> the rsh-wrapper? Is there a firewall on the machines?
>
> -- Reuti
>
>
> >
> > Warning: no access to tty (Bad file descriptor).
> > Thus no job control in this shell.
> >
> >
> > I had smilar messages for other applications, but i was wondering
> > if it can be
> > here the source of the problems?
> >
> > thank you
> >
> > martin
> >
> >
> >
> > Quoting Reuti <reuti at staff.uni-marburg.de>:
> >
> >> Am 22.08.2006 um 18:17 schrieb lukacm at pdx.edu:
> >>
> >>> ssh is used and tested.
> >>
> >> But this way you won't get a Tight Integration. It would be better,
> >> to stay with GAMESS with a plain rsh, setup a Tight Integration, i.e.
> >> the rsh will be caught and replaced by the SGE's own qrsh method.
> >>
> >> -- Reuti
> >>
> >>
> >>> martin
> >>>
> >>> Quoting Reuti <reuti at staff.uni-marburg.de>:
> >>>
> >>>>
> >>>> Am 21.08.2006 um 22:02 schrieb lukacm at pdx.edu:
> >>>>
> >>>>> As i said it worked with rungms. When i run the subgms, it works ,
> >>>>> it submit the
> >>>>> file but then i get these errors in the gamess error log:
> >>>>>
> >>>>> error: executing task of job 3799 failed:
> >>>>> error: commlib error: access denied (client IP resolved to host
> >>>>> name "". This is
> >>>>> not identical to clients host name "")
> >>>>> error: executing task of job 3799 failed: failed sending task to
> >>>>> execd at compute-0-6: can't find connection
> >>>>> error: commlib error: access denied (client IP resolved to host
> >>>>> name "". This is
> >>>>> not identical to clients host name "")
> >>>>> error: executing task of job 3799 failed: failed sending task to
> >>>>> execd at compute-0-2: can't find connection
> >>>>> error: commlib error: access denied (client IP resolved to host
> >>>>> name "". This is
> >>>>> not identical to clients host name "")
> >>>>> error: executing task of job 3799 failed: failed sending task to
> >>>>> execd at compute-0-11: can't find connection
> >>>>> IRCDATA: Undefined variable.
> >>>>> compute-0-12.local: Connection refused
> >>>>> compute-0-6: Connection refused
> >>>>> compute-0-2: Connection refused
> >>>>> compute-0-11: Connection refused
> >>>>
> >>>> Did you compile GAMESS to use ssh or rsh? - Reuti
> >>>>
> >>>>
> >>>>> It looks like the main host, the first one that should be running
> >>>>> the master job
> >>>>> is not started up. Similar errors appear if i run gamess, for
> >>>>> multiple machines,
> >>>>>  when the master node is not the first on in the hostlist
> >>>>> settings.
> >>>>> For example
> >>>>> if i run something like:
> >>>>>
> >>>>> /home/visible/apps/gamess/ddikick.x /home/visible/apps/gamess/
> >>>>> gamess.01.x exam20
> >>>>> -ddi 2 2 compute-0-0:cpus=1 compute-0-1:cpus=1 -scr /home/lukacm/
> >>>>> scr/
> >>>>>
> >>>>> from main node called rocks.research.pdx.edu, the result is the
> >>>>> same. However it
> >>>>> works if i run something like :
> >>>>>
> >>>>> ssh compute-0-0 /home/visible/apps/gamess/ddikick.x
> >>>>> /home/visible/apps/gamess/gamess.01.x exam20 -ddi 2 2
> >>>>> compute-0-0:cpus=1
> >>>>> compute-0-1:cpus=1 -scr /home/lukacm/scr/
> >>>>>
> >>>>> I attached an example of the generated script from subgms, for a
> >>>>> given job. I
> >>>>> did not made any modifications to subgms_export.
> >>>>>
> >>>>> The environment is set up according to the specifications and bot
> >>>>> startgames.sh
> >>>>> and stopgamess.sh are correctly installed.
> >>>>>
> >>>>>
> >>>>> thank you
> >>>>>
> >>>>> martin
> >>>>>
> >>>>>
> >>>>> Quoting Reuti <reuti at staff.uni-marburg.de>:
> >>>>>
> >>>>>> Sure, it worked for me.
> >>>>>>
> >>>>>> Hi Martin,
> >>>>>>
> >>>>>> what problems did you encounter? What did you set up in
> >>>>>> detail? For
> >>>>>> me the rungms script was a little bit to convoluted, and so I
> >>>>>> tried
> >>>>>> to shrink it as much as possible.
> >>>>>>
> >>>>>> -- Reuti
> >>>>>>
> >>>>>>
> >>>>>> Am 21.08.2006 um 21:13 schrieb lukacm at pdx.edu:
> >>>>>>
> >>>>>>> Hello,
> >>>>>>>
> >>>>>>> i followed the proceedure describe in the mailing lists about
> >>>>>>> how
> >>>>>>> to integrate
> >>>>>>> the gamess into SGE, however i could not make it run. I was
> >>>>>>> wondering if there
> >>>>>>> is someone who had it succesfully run or who would be using the
> >>>>>>> rungms script
> >>>>>>> with SGE.
> >>>>>>>
> >>>>>>> the rungms script is working and i can get a parallel
> >>>>>>> execution of
> >>>>>>> the program
> >>>>>>> however i was not able to run gamess using the method
> >>>>>>> provided at:
> >>>>>>> http://gridengine.sunsource.net/servlets/ReadMsg?
> >>>>>>> list=users&msgNo=8769
> >>>>>>>
> >>>>>>> thank you
> >>>>>>>
> >>>>>>> martin
> >>>>>>>
> >>>>>>> ----------------------------------------------------------------
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