[MITgcm-support] cubeSphereExchange and MPI error?
Anthony Coletti
ajcolett at geo.umass.edu
Wed Jul 9 09:05:46 EDT 2014
Thanks Jean-Michel. I'll take a look at my data file.
> On Jul 9, 2014, at 8:53 AM, Jean-Michel Campin <jmc at ocean.mit.edu> wrote:
>
> Hi Anthony,
>
> likely that there is something not right in your main parameter file "data".
>
> Cheers,
> Jean-Michel
>
>> On Tue, Jul 08, 2014 at 03:13:08PM -0400, Anthony Coletti wrote:
>> Hi Jean-Michel,
>>
>> I have realized I made the mistake of not specifying -mods=../code in my batch script. That could be why none of my packages installed - so you are correct in mentioning that. Thank you. Unfortunately another error has popped up and the model still crashes after ~6 seconds:
>>
>> ModuleCmd_Switch.c(172):ERROR:152: Module 'PrgEnv-cray' is currently not loaded
>> At line 2825 of file ini_parms.f (unit = 11, file = '/lustre/medusa/acoletti/gfortrantm
>> pLb7lfy')
>> Fortran runtime error: Cannot match namelist object name .
>> At line 2825 of file ini_parms.f (unit = 11, file = '/lustre/medusa/acoletti/gfortrantm
>> p0SUaGP')
>> Fortran runtime error: Cannot match namelist object name .
>> At line 2825 of file ini_parms.f (unit = 11, file = '/lustre/medusa/acoletti/gfortrantm
>> pjDleuD')
>> Fortran runtime error: Cannot match namelist object name .
>> At line 2825 of file ini_parms.f (unit = 11, file = '/lustre/medusa/acoletti/gfortrantm
>> p0mWCfy')
>>
>> There are 20 (or so) more lines of this error each specifying a different gfortran tmp file.
>>
>> Here is line 2825 of my ini_parms.f file. I think it is having a problem with PARM03 in the 'data' file? I am not completely familiar with fortran so I am not sure what namelist object it is referring to:
>>
>> 816 C-- Time stepping parameters
>> 2817 rCD = -1.D0
>> 2818 epsAB_CD = UNSET_RL
>> 2819 latBandClimRelax = UNSET_RL
>> 2820 deltaTtracer = 0.D0
>> 2821 forcing_In_AB = .TRUE.
>> 2822 WRITE(msgBuf,'(A)') ' INI_PARMS ; starts to read PARM03'
>> 2823 CALL PRINT_MESSAGE( msgBuf, standardMessageUnit,
>> 2824 & SQUEEZE_RIGHT, myThid )
>> 2825 READ(UNIT=iUnit,NML=PARM03) !,IOSTAT=errIO)
>> 2826 IF ( errIO .LT. 0 ) THEN
>> 2827 WRITE(msgBuf,'(A)')
>> 2828 & 'S/R INI_PARMS: Error reading model parameter file "data"'
>> 2829 CALL PRINT_ERROR( msgBuf, myThid )
>> 2830 WRITE(msgBuf,'(A)') 'S/R INI_PARMS: Problem in namelist PARM03'
>> 2831 CALL PRINT_ERROR( msgBuf, myThid )
>> 2832 STOP 'ABNORMAL END: S/R INI_PARMS'
>> 2833 ELSE
>> 2834 WRITE(msgBuf,'(A)') ' INI_PARMS ; read PARM03 : OK'
>> 2835 CALL PRINT_MESSAGE( msgBuf, standardMessageUnit,
>> 2836 & SQUEEZE_RIGHT, myThid )
>> 2837 ENDIF
>>
>> 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 8, 2014, at 8:45 AM, Anthony Coletti <ajcolett at geo.umass.edu> wrote:
>>>
>>> Hi Jean-Michel,
>>>
>>> Let’s start with the exch2 problem,
>>>
>>> So I check the PACKAGES_CONFIG.h and it seems you are right..for some reason, exch2 is undef
>>>
>>> Here is the copy of my PACKAGES_CONFIG.h file:
>>>
>>> reated by convert_cpp_cmd2defines with the following command line arguments:
>>> -bPACKAGES_CONFIG_H Disabled packages: -UALLOW_ADMTLM -UALLOW_AIM_V23 -UALLOW_ATM2D -UALLOW_ATM_COMMON -UALLOW_A
>>> TM_COMPON_INTERF -UALLOW_ATM_OCN_COUPLER -UALLOW_ATM_PHYS -UALLOW_AUTODIFF -UALLOW_BBL -UALLOW_BULK_FORCE -UALLOW
>>> _CAL -UALLOW_CD_CODE -UALLOW_CFC -UALLOW_CHEAPAML -UALLOW_CHRONOS -UALLOW_COMPON_COMMUNIC -UALLOW_COST -UALLOW_CT
>>> RL -UALLOW_DIAGNOSTICS -UALLOW_DIC -UALLOW_DOWN_SLOPE -UALLOW_EBM -UALLOW_ECCO -UALLOW_EMBED_FILES -UALLOW_EXCH2
>>> -UALLOW_EXF -UALLOW_FIZHI -UALLOW_FLT -UALLOW_FRAZIL -UALLOW_GCHEM -UALLOW_GGL90 -UALLOW_GMREDI -UALLOW_GRDCHK -U
>>> ALLOW_GRIDALT -UALLOW_ICEFRONT -UALLOW_KPP -UALLOW_LAND -UALLOW_LAYERS -UALLOW_LONGSTEP -UALLOW_MATRIX -UALLOW_MN
>>> C -UALLOW_MY82 -UALLOW_MYPACKAGE -UALLOW_OBCS -UALLOW_OCN_COMPON_INTERF -UALLOW_OFFLINE -UALLOW_OPENAD -UALLOW_OP
>>> PS -UALLOW_PP81 -UALLOW_PROFILES -UALLOW_PTRACERS -UALLOW_RBCS -UALLOW_REGRID -UALLOW_RUNCLOCK -UALLOW_SALT_PLUME
>>> -UALLOW_SBO -UALLOW_SEAICE -UALLOW_SHAP_FILT -UALLOW_SHELFICE -UALLOW_SHOWFLOPS -UALLOW_SMOOTH -UALLOW_SPHERE -U
>>> ALLOW_STREAMICE -UALLOW_THSICE -UALLOW_TIMEAVE -UALLOW_ZONAL_FILT Enabled packages: -DALLOW_DEBUG -DALLOW_GENER
>>> IC_ADVDIFF -DALLOW_MDSIO -DALLOW_MOM_COMMON -DALLOW_MOM_FLUXFORM -DALLOW_MOM_VECINV -DALLOW_MONITOR -DALLOW_RW
>>> */
>>>
>>> #ifndef PACKAGES_CONFIG_H
>>> #define PACKAGES_CONFIG_H
>>> /* Disabled packages: */
>>> #undef ALLOW_ADMTLM
>>> #undef ALLOW_AIM_V23
>>> #undef ALLOW_ATM2D
>>> #undef ALLOW_ATM_COMMON
>>> #undef ALLOW_ATM_COMPON_INTERF
>>> #undef ALLOW_ATM_OCN_COUPLER
>>> #undef ALLOW_ATM_PHYS
>>> #undef ALLOW_AUTODIFF
>>> #undef ALLOW_BBL
>>> #undef ALLOW_BULK_FORCE
>>> #undef ALLOW_CAL
>>> #undef ALLOW_CD_CODE
>>> #undef ALLOW_CFC
>>> #undef ALLOW_CHEAPAML
>>> #undef ALLOW_CHRONOS
>>> #undef ALLOW_COMPON_COMMUNIC
>>> #undef ALLOW_COST
>>> #undef ALLOW_CTRL
>>> #undef ALLOW_DIAGNOSTICS
>>> #undef ALLOW_DIC
>>> #undef ALLOW_DOWN_SLOPE
>>> #undef ALLOW_EBM
>>> #undef ALLOW_ECCO
>>> #undef ALLOW_EMBED_FILES
>>> #undef ALLOW_EXCH2
>>> #undef ALLOW_EXF
>>> #undef ALLOW_FIZHI
>>> #undef ALLOW_FLT
>>> #undef ALLOW_FRAZIL
>>> #undef ALLOW_GCHEM
>>> #undef ALLOW_GGL90
>>> #undef ALLOW_GMREDI
>>> #undef ALLOW_GRDCHK
>>> #undef ALLOW_GRIDALT
>>> #undef ALLOW_ICEFRONT
>>> #undef ALLOW_KPP
>>> #undef ALLOW_LAND
>>> #undef ALLOW_LAYERS
>>> #undef ALLOW_LONGSTEP
>>> #undef ALLOW_MATRIX
>>> #undef ALLOW_MNC
>>> #undef ALLOW_MY82
>>> #undef ALLOW_MYPACKAGE
>>> #undef ALLOW_OBCS
>>> #undef ALLOW_OCN_COMPON_INTERF
>>> #undef ALLOW_OFFLINE
>>> #undef ALLOW_OPENAD
>>> #undef ALLOW_OPPS
>>> #undef ALLOW_PP81
>>> #undef ALLOW_PROFILES
>>> #undef ALLOW_PTRACERS
>>> #undef ALLOW_RBCS
>>> #undef ALLOW_REGRID
>>> #undef ALLOW_RUNCLOCK
>>> #undef ALLOW_SALT_PLUME
>>> #undef ALLOW_SBO
>>> #undef ALLOW_SEAICE
>>> #undef ALLOW_SHAP_FILT
>>> #undef ALLOW_SHELFICE
>>> #undef ALLOW_SHOWFLOPS
>>> #undef ALLOW_SMOOTH
>>> #undef ALLOW_SPHERE
>>> #undef ALLOW_STREAMICE
>>> #undef ALLOW_THSICE
>>> #undef ALLOW_TIMEAVE
>>> #undef ALLOW_ZONAL_FILT
>>> /* */
>>> /* Enabled packages: */
>>> #define ALLOW_DEBUG
>>> #define ALLOW_GENERIC_ADVDIFF
>>> #define ALLOW_MDSIO
>>> #define ALLOW_MOM_COMMON
>>> #define ALLOW_MOM_FLUXFORM
>>> #define ALLOW_MOM_VECINV
>>> #define ALLOW_MONITOR
>>> #define ALLOW_RW
>>> #endif /* PACKAGES_CONFIG_H */
>>>
>>>
>>> I wonder why that would be considering I have the packages to install listed in my packages.config file.
>>>
>>> This is the command I use for compiling the GCM which seems correct:
>>> ../../../tools/genmake2 -optfile=../../../tools/build_options/linux_amd64_gfortran -mpi
>>>
>>>
>>> And here is some lines from genmake2:
>>>
>>> === Processing options files and arguments ===
>>> getting local config information: none found
>>> Warning: ROOTDIR was not specified ; try using a local copy of MITgcm found at "../../.."
>>> getting OPTFILE information:
>>> using OPTFILE="../../../tools/build_options/linux_amd64_gfortran"
>>> getting AD_OPTFILE information:
>>> using AD_OPTFILE="../../../tools/adjoint_options/adjoint_default"
>>> check makedepend (local: 0, system: 0, 0)
>>> Turning on MPI cpp macros
>>>
>>> === Checking system libraries ===
>>> Do we have the system() command using gfortran... yes
>>> Do we have the fdate() command using gfortran... yes
>>> Do we have the etime() command using gfortran... no
>>> Can we call simple C routines (here, "cloc()") using gfortran... yes
>>> Can we unlimit the stack size using gfortran... yes
>>> Can we register a signal handler using gfortran... yes
>>> Can we use stat() through C calls... yes
>>> Can we create NetCDF-enabled binaries... yes
>>> Can we create LAPACK-enabled binaries... no
>>> Can we call FLUSH intrinsic subroutine... yes
>>>
>>> === Setting defaults ===
>>> Adding MODS directories:
>>> Making source files in eesupp from templates
>>> Making source files in pkg/exch2 from templates
>>> Making source files in pkg/regrid from templates
>>>
>>> === Determining package settings ===
>>> getting package dependency info from ../../../pkg/pkg_depend
>>> getting package groups info from ../../../pkg/pkg_groups
>>> checking list of packages to compile:
>>> before group expansion packages are: default_pkg_list
>>> replacing "default_pkg_list" with: gfd
>>> replacing "gfd" with: mom_common mom_fluxform mom_vecinv generic_advdiff debug mdsio rw monitor
>>> after group expansion packages are: mom_common mom_fluxform mom_vecinv generic_advdiff debug mdsio rw monitor
>>> applying DISABLE settings
>>> applying ENABLE settings
>>> packages are: debug generic_advdiff mdsio mom_common mom_fluxform mom_vecinv monitor rw
>>> applying package dependency rules
>>> packages are: debug generic_advdiff mdsio mom_common mom_fluxform mom_vecinv monitor rw
>>> Adding STANDARDDIRS='eesupp model'
>>> Searching for *OPTIONS.h files in order to warn about the presence
>>> of "#define "-type statements that are no longer allowed:
>>> found CPP_EEOPTIONS="../../../eesupp/inc/CPP_EEOPTIONS.h"
>>> found CPP_OPTIONS="../../../model/inc/CPP_OPTIONS.h"
>>> Creating the list of files for the adjoint compiler.
>>>
>>> === Creating the Makefile ===
>>> setting INCLUDES
>>> Determining the list of source and include files
>>> Writing makefile: Makefile
>>> Add the source list for AD code generation
>>> Making list of "exceptions" that need ".p" files
>>> Making list of NOOPTFILES
>>> Add rules for links
>>> Adding makedepend marker
>>>
>>> FYI: I am building a simulation using the 32x6x32x15 MPI run.
>>>
>>> The makefile looks okay…it seems to be making the dependencies. I do have 2 or 3 sets of this warning:
>>>
>>> gfortran -fconvert=big-endian -fimplicit-none -mcmodel=medium -O0 -funroll-loops -c solve_tridiagonal.f
>>> cat solve_uv_tridiago.F | cpp -traditional -P -DWORDLENGTH=4 -DNML_TERMINATOR -DALLOW_USE_MPI -DALWAYS_USE_MPI -DALLOW_USE_MPI -DHAVE_SYSTEM -DHAVE_FDATE -DHAVE_CLOC -DHAVE_SETRLSTK -DHAVE_SIGREG -DHAVE_STAT -DHAVE_NETCDF -DHAVE_FLUSH -I/opt/cray/netcdf-hdf5parallel/4.3.1/GNU/48/include -I/opt/cray/mpt/6.3.0/gni/mpich2-gnu/48/include | ../../../tools/set64bitConst.sh > solve_uv_tridiago.f
>>> gfortran -fconvert=big-endian -fimplicit-none -mcmodel=medium -O0 -funroll-loops -c solve_uv_tridiago.f
>>> solve_uv_tridiago.f:1076.72:
>>>
>>> DO bj=2,nSy
>>> 1
>>> Warning: DO loop at (1) will be executed zero times
>>> solve_uv_tridiago.f:1103.24:
>>>
>>> DO bj=nSy-1,1,-1
>>> 1
>>> Warning: DO loop at (1) will be executed zero times
>>>
>>>
>>> I am not sure if that means anything.
>>>
>>>
>>> Attached is my ini_threading_environment.f (small f)
>>> <ini_threading_environment.f>
>>>
>>>
>>> Thanks for your fruitful insight!
>>> 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 7, 2014, at 11:30 PM, Jean-Michel Campin <jmc at ocean.mit.edu> wrote:
>>>>
>>>> PACKAGES_CONFIG.h
>>>
>>> _______________________________________________
>>> MITgcm-support mailing list
>>> MITgcm-support at mitgcm.org
>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
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