[MITgcm-support] problem running MITgcm/verification//tutorial_global_oce_latlon/

Wed Oct 9 13:47:49 EDT 2013

Hi Jonny,

make[1]: mpif77: Command not found
make[1]: *** [bulkf_ave.o] Error 127
make[1]: Leaving directory `/nfs01/n02/n02/ggjhtw/MITgcm/verification/global_ocean.cs32x15/build'
make: *** [fwd_exe_target] Error 2
failed

No, compilation is definitely the problem! The Makefile cannot find the compiler mpif77 presumably because the path is not set correctly...

Cheers,   Jody

On Oct 9, 2013, at  10:00 AM, Jonny Williams <Jonny.Williams at bristol.ac.uk> wrote:

> Thanks Jody
> 
> I am already using genmake2 through the following call...
> 
> ~/MITgcm/tools/genmake2 -ieee -mods ../code -of ./linux_amd64_pgf90_mpi_hect3 -mpi
> 
> It seems that it's not the compilation which is the issue, rather the running of the executable file once it's been created...
> 
> Thanks again
> 
> Jonny
> 
> 
> On 9 October 2013 17:32, Jody Klymak <jklymak at uvic.ca> wrote:
> 
> Hi Jonny,
> 
> You need to run genmake2  See Sec 3.5 of the manual.  You also need to figure out where your mpi-compatible executables are kept.  The manual claims genmake2 will magically find these executables, but I am skeptical that works for most people...
> 
> If you are having trouble finding these executables and libraries, your sys admin should be able to help make a genmake2 option file for you (if someone hasn't already)
> 
> Cheers,   Jody
> 
> 
> On Oct 9, 2013, at  9:24 AM, Jonny Williams <Jonny.Williams at bristol.ac.uk> wrote:
> 
>> I would guess that the key error in this is...
>> 
>> make[1]: mpif77: Command not found
>> make[1]: *** [bulkf_ave.o] Error 127
>> make[1]: Leaving directory `/nfs01/n02/n02/ggjhtw/MITgcm/verification/global_ocean.cs32x15/build'
>> make: *** [fwd_exe_target] Error 2
>> failed
>> 
>> ?
>> 
>> 
>> 
>> 
>> 
>> On 9 October 2013 15:38, Menemenlis, Dimitris (3248) <Dimitris.Menemenlis at jpl.nasa.gov> wrote:
>> Looks like you are missing other parameter files too.
>> 
>> In verification try: ./testreport -mpi -t global_ovean.cs32x15
>> 
>> Dimitris Menemenlis
>> 818-625-6498
>> 
>> On Oct 9, 2013, at 7:32 AM, "Jonny Williams" <Jonny.Williams at bristol.ac.uk> wrote:
>> 
>>> I have now found a file which I think is along the lines of what I need (eedata). Its contents is as follows...
>>> 
>>> START
>>> 
>>> # Example "eedata" file
>>> # Lines beginning "#" are comments
>>> # nTx - No. threads per process in X
>>> # nTy - No. threads per process in Y
>>>  &EEPARMS
>>>  nTx=1,nTy=1
>>>  /
>>> # Note: Some systems use & as the
>>> # namelist terminator. Other systems
>>> # use a / character (as shown here).
>>> 
>>> END
>>> 
>>> I am now getting a different error, which is as follows...
>>> 
>>> START
>>> 
>>> Warning: ieee_inexact is signaling
>>> Warning: ieee_inexact is signaling
>>> ABNORMAL END: S/R OPEN_COPY_DATA_FILE
>>> ABNORMAL END: S/R OPEN_COPY_DATA_FILE
>>> [NID 02345] 2013-10-09 14:27:15 Apid 5947911: initiated application termination
>>> 
>>> END
>>> 
>>> Thanks again
>>> 
>>> Jonny
>>> 
>>> 
>>> On 9 October 2013 15:01, Menemenlis, Dimitris (3248) <Dimitris.Menemenlis at jpl.nasa.gov> wrote:
>>> Do you have a file called "eedata" in your run directory?
>>> 
>>> Dimitris Menemenlis
>>> 818-625-6498
>>> 
>>> On Oct 9, 2013, at 6:57 AM, "Jonny Williams" <Jonny.Williams at bristol.ac.uk> wrote:
>>> 
>>>> Hi there
>>>> 
>>>> I am trying to run the MITgcm/verification//tutorial_global_oce_latlon/ example which was pre-loaded when I downloaded the MITgcm code using CVS a couple of days ago. 
>>>> 
>>>> I plan to run parallelised codes in the future and so I am using the SIZE.h file which was originally called SIZE.h_mpi in the default installation.
>>>> 
>>>> The code compiled successfully as far as I can tell.
>>>> 
>>>> When I attempt to run the script I get the following error message in a file called testing1.e1726317 (my job is called testing1)...
>>>> 
>>>> START 
>>>> 
>>>> gPGFIO-F-209/formatted read/unit=13/'OLD' specified for file which does not exist.
>>>>  In source file eeset_parms.f, at line number 1778
>>>> [NID 02545] 2013-10-09 13:28:18 Apid 5947459: initiated application termination
>>>> 
>>>> END
>>>> 
>>>> The offending line (line 1778 of eeset_parms.f) reads as follows...
>>>> 
>>>> START
>>>> 
>>>> READ(eeDataUnit,FMT='(A)',END=1001) RECORD
>>>> 
>>>> END 
>>>> 
>>>> Is anyone able to shed any light on this?
>>>> 
>>>> For your information I am running on the HECToR supercomputer cluster in the UK using scripts which were given to me by a collaborator who is already successfully using the MITgcm model on the same machine.
>>>> 
>>>> Many thanks!
>>>> 
>>>> Jonny Williams
>>>> 
>>>> 
>>>> -- 
>>>> Dr Jonny Williams
>>>> School of Geographical Sciences
>>>> University of Bristol
>>>> University Road
>>>> BS8 1SS
>>>> 
>>>> +44 (0)117 3318352
>>>> jonny.williams at bristol.ac.uk
>>>> bit.ly/jonnywilliams
>>>> _______________________________________________
>>>> MITgcm-support mailing list
>>>> MITgcm-support at mitgcm.org
>>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>> 
>>> _______________________________________________
>>> MITgcm-support mailing list
>>> MITgcm-support at mitgcm.org
>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> Dr Jonny Williams
>>> School of Geographical Sciences
>>> University of Bristol
>>> University Road
>>> BS8 1SS
>>> 
>>> +44 (0)117 3318352
>>> jonny.williams at bristol.ac.uk
>>> bit.ly/jonnywilliams
>>> _______________________________________________
>>> MITgcm-support mailing list
>>> MITgcm-support at mitgcm.org
>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>> 
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>> 
>> 
>> 
>> 
>> -- 
>> Dr Jonny Williams
>> School of Geographical Sciences
>> University of Bristol
>> University Road
>> BS8 1SS
>> 
>> +44 (0)117 3318352
>> jonny.williams at bristol.ac.uk
>> bit.ly/jonnywilliams
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
> 
> --
> Jody Klymak    
> http://web.uvic.ca/~jklymak/
> 
> 
> 
> 
> 
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support
> 
> 
> 
> 
> -- 
> Dr Jonny Williams
> School of Geographical Sciences
> University of Bristol
> University Road
> BS8 1SS
> 
> +44 (0)117 3318352
> jonny.williams at bristol.ac.uk
> bit.ly/jonnywilliams
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support

--
Jody Klymak    
http://web.uvic.ca/~jklymak/

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