[MITgcm-support] eeset_parms.f and permissions error

Matthew Mazloff mmazloff at ucsd.edu
Thu Jul 3 14:49:58 EDT 2014


Hello

If you want to run 32 x32 your SIZE.h

     &           sNx =   4,
     &           sNy =   4,
     &           OLx =   4,
     &           OLy =   4,
     &           nSx =   1,
     &           nSy =   1,
     &           nPx =   8,
     &           nPy =   8,
     &           Nx  = sNx*nSx*nPx,
     &           Ny  = sNy*nSy*nPy,
     &           Nr  =  15)

you previously had
&           nSx =   6,
so you were trying to run with 6 threads

Matt

ps> 4x4 tiles is too small for all practical purposes


On Jul 3, 2014, at 11:03 AM, Anthony Coletti <ajcolett at geo.umass.edu> wrote:

> Hi all,
> 
> Just a follow-up…It still keeps trying to access this directory.  Does anyone know why this may be?  I changed my .bash_profile (Jody’s suggestion) and this didn’t seem to help.  (see email prior to this email)
> 
> If all else fails, I may have to email the engineers that run the supercomputer.  I’ll keep working on the problem to see if I can figure this one out.
> 
> Anthony
> 
> 
> Anthony J. Coletti
> Climate System Research Center
> Department of Geosciences
> Morrill Building
> 611 N. Pleasant Street
> 233 Morrill Science Center
> University of Massachusetts-Amherst
> paleoclimate.org
> Email: ajcolett at geo.umass.edu
> http://blogs.umass.edu/ajcolett/
> http://necsc.umass.edu/people/anthony-coletti
> 
> “For me, I am driven by two main philosophies: know more today about the world than I knew yesterday and lessen the  suffering of others. You'd be surprised how far that gets you.” ― Neil deGrasse Tyson
> 
> 
> 
> 
> On Jul 3, 2014, at 12:33 PM, Anthony Coletti <ajcolett at geo.umass.edu> wrote:
> 
>> Hi Jody,
>> 
>> Thank you very much for your suggestion!
>> 
>> I think I fixed that part of the issue.  I made a /tmp/ directory in my home directory and set 
>> 
>> export TMPDIR=~/tmp/
>> 
>> Once I try to run, I get this error:
>> 
>> STOP ABNORMAL END: S/R INI_THREADING_ENVIRONMENT
>> 
>> I’m assuming it has something to do with MPI.  My  SIZE.h file looks like this:
>> 
>> &           sNx =   4,
>>      &           sNy =   4,
>>      &           OLx =   4,
>>      &           OLy =   4,
>>      &           nSx =   6,
>>      &           nSy =   1,
>>      &           nPx =   8,
>>      &           nPy =   8,
>>      &           Nx  = sNx*nSx*nPx,
>>      &           Ny  = sNy*nSy*nPy,
>>      &           Nr  =  15)
>>  I am running a 32x32x15 grid.  Any suggestions on fixing this error or making my SIZE.h file more efficient?
>> 
>> Thank you!
>> 
>> Best,
>> Anthony
>> 
>> Anthony J. Coletti
>> Climate System Research Center
>> Department of Geosciences
>> Morrill Building
>> 611 N. Pleasant Street
>> 233 Morrill Science Center
>> University of Massachusetts-Amherst
>> paleoclimate.org
>> Email: ajcolett at geo.umass.edu
>> http://blogs.umass.edu/ajcolett/
>> http://necsc.umass.edu/people/anthony-coletti
>> 
>> “For me, I am driven by two main philosophies: know more today about the world than I knew yesterday and lessen the  suffering of others. You'd be surprised how far that gets you.” ― Neil deGrasse Tyson
>> 
>> 
>> 
>> 
>> On Jul 3, 2014, at 11:01 AM, Klymak Jody <jklymak at uvic.ca> wrote:
>> 
>>> Try setenv TMPDIR boo.  Where boo is somewhere you have write permission for.  Cheers.  Jody
>>> 
>>> Sent from my iPhone
>>> 
>>> On Jul 3, 2014, at 6:21, Anthony Coletti <ajcolett at geo.umass.edu> wrote:
>>> 
>>>> Hi all,
>>>> 
>>>> I successfully compiled (with MPI) the MITgcm on NICS’s new System, Darter.  Build and make operations go smoothly however when I submit the job to run and it initiates, it crashes ~ 6 seconds later with this strange error I have never seen before.
>>>> 
>>>> Fortran runtime error: At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Permission denied trying to open file '/tmp/gfortrantmp7pxkF4'Fortran runtime error: Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmp059FE4'
>>>> Permission denied trying to open file '/tmp/gfortrantmp77RFE4'
>>>> 
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmpSdSFE4'
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmpjePkF4'
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Fortran runtime error: Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmpwTYXca'Permission denied trying to open file '/tmp/gfortrantmpuafVca'
>>>> 
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmpAgnUca'
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'ȑ?')
>>>> Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmpBRmUca'At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmp3kDSBN'
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = '??{')
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmpGzrSBN'
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmpSV9RBN'
>>>> Fortran runtime error: At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Permission denied trying to open file '/tmp/gfortrantmpM17PBN'Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmp9eDSBN'At line 1798 of file eeset_parms.f (unit
>>>>  = 11, file = 'H??')
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Fortran runtime error: Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmpdSAdKY'Permission denied trying to open file '/tmp/gfortrantmpvXchKY'At line 1798 of f
>>>> ile eeset_parms.f (unit = 11, file = 'H??')
>>>> 
>>>> Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmpdJVgKY'
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmpLxVgKY'
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmp0MteKY'
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmp61EUca'Fortran runtime error: 
>>>> Permission denied trying to open file '/tmp/gfortrantmpnurVca'
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> Fortran runtime error: Fortran runtime error: Permission denied trying to open file '/tmp/gfortrantmp7whYca'Permission denied trying to open file '/tmp/gfortrantmphozYca'
>>>> 
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> At line 1798 of file eeset_parms.f (unit = 11, file = 'H??')
>>>> 
>>>> Does anyone have any input on what could be causing this error?  Is it a system problem rather than a GCM problem?  Any and all help will be appreciated!
>>>> 
>>>> Thanks,
>>>> Anthony
>>>> 
>>>> Anthony J. Coletti
>>>> Climate System Research Center
>>>> Department of Geosciences
>>>> Morrill Building
>>>> 611 N. Pleasant Street
>>>> 233 Morrill Science Center
>>>> University of Massachusetts-Amherst
>>>> paleoclimate.org
>>>> Email: ajcolett at geo.umass.edu
>>>> http://blogs.umass.edu/ajcolett/
>>>> http://necsc.umass.edu/people/anthony-coletti
>>>> 
>>>> “For me, I am driven by two main philosophies: know more today about the world than I knew yesterday and lessen the  suffering of others. You'd be surprised how far that gets you.” ― Neil deGrasse Tyson
>>>> 
>>>> 
>>>> 
>>>> 
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