[MITgcm-support] Reading errors (Martin Losch)

Estanislao Gavilan Pascual-Ahuir dramauh at hotmail.com
Thu Aug 22 06:39:30 EDT 2019


Hi Martin ,

Before anything thank you so much for your help. I will try to answer all you questions.

what is the platform, the compiler?
The platform in linux 2.6.32-431.TH.x86_64 GNU/Linux. Red Hat Enterprise Linux Server release 6.5. I am using intel compilers wrapped them in mpi. The version of the compiler is  14.0.2
details of the configuration (content of code-directory and namelist files)
I am running a simple simulation with open boundaries. I load the packages gfd, obcs, mnc and diagnostics  using the packages.config.  The frequency of the open boundaries is stated in the data file. This is the data file
 Model parameters
# Continuous equation parameters
 &PARM01
 tRef=23.,23.,
 sRef=35.,35.,
 selectCoriMap=4,
 viscAh=4.E2,
 f0=1.E-4,
 beta=1.E-11,
 rhoNil=1000.,
 gBaro=9.81,
 rigidLid=.FALSE.,
 implicitFreeSurface=.TRUE.,
# momAdvection=.FALSE.,
 tempStepping=.FALSE.,
 saltStepping=.FALSE.,
 &

# Elliptic solver parameters
 &PARM02
 cg2dTargetResidual=1.E-7,
 cg2dMaxIters=1000,
 &

# Time stepping parameters
 &PARM03
 nIter0=0,
 nTimeSteps=100,
 deltaT=1200.0,
 pChkptFreq=31104000.0,
 chkptFreq=15552000.0,
 dumpFreq=15552000.0,
 monitorFreq=1200.,
 monitorSelect=2,
 periodicExternalForcing=.TRUE.,
 externForcingPeriod= 1200.,
 externForcingCycle = 12000000.,
 &
# Gridding parameters
 &PARM04
 usingSphericalPolarGrid=.TRUE.,
 delX=43*1.,
 delY=43*1.,
 xgOrigin=-21.,
 ygOrigin=-21.,
 delR=2*500.,
 &

# Input datasets
 &PARM05
 bathyFile='bathy_cir.bin'
 meridWindFile=,
 &

This is the data.obcs

# Open-boundaries
 &OBCS_PARM01
 OBCSfixTopo=.FALSE.,
 OB_Ieast=0,
 OB_Iwest=0,
 OB_Jnorth(16:28)=13*41,
 OB_Jsouth(16:28)=13*3,
 useOBCSprescribe = .TRUE.,
 OBNvFile = 'OBzonalV.bin',
 OBSvFile = 'OBzonalV.bin',
 OBNuFile = 'OBmeridU.bin',
 OBSuFile = 'OBmeridU.bin',
 OBCS_monitorFreq=1200.00,
 OBCS_monSelect = 1,
 &

 &OBCS_PARM02
 &
are you using latest code (some of the flags in the build-option look very outdated ?)?
Yes, it is the latest code (version MITgcm_c67k). About the flags in my build version, I did not make my own one. I used one that I found in our research group.

Kind regards,

Estanislao

________________________________
De: MITgcm-support <mitgcm-support-bounces at mitgcm.org> en nombre de mitgcm-support-request at mitgcm.org <mitgcm-support-request at mitgcm.org>
Enviado: jueves, 22 de agosto de 2019 11:57
Para: mitgcm-support at mitgcm.org <mitgcm-support at mitgcm.org>
Asunto: MITgcm-support Digest, Vol 194, Issue 10

Send MITgcm-support mailing list submissions to
        mitgcm-support at mitgcm.org

To subscribe or unsubscribe via the World Wide Web, visit
        http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support
or, via email, send a message with subject or body 'help' to
        mitgcm-support-request at mitgcm.org

You can reach the person managing the list at
        mitgcm-support-owner at mitgcm.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of MITgcm-support digest..."


Today's Topics:

   1. Reading errors (Estanislao Gavilan Pascual-Ahuir)
   2. Re: Reading errors (Martin Losch)


----------------------------------------------------------------------

Message: 1
Date: Thu, 22 Aug 2019 08:51:28 +0000
From: Estanislao Gavilan Pascual-Ahuir <dramauh at hotmail.com>
To: "mitgcm-support at mitgcm.org" <mitgcm-support at mitgcm.org>
Subject: [MITgcm-support] Reading errors
Message-ID:
        <DB8PR04MB7002D32A678367A36AD841A0A9A50 at DB8PR04MB7002.eurprd04.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

Hi Community,

 I have just started using MITgcm model. Last week I spent some time learning how to open boundary conditions. I was able to sort out everything except for this (error 1). It turns out that the model cannot find the bin file. After doing some research in the mailbox of mitgcm. I found out that is due to the compiler settings. As it was advice, I set -DWORDLENGTH=1. Now, I am having a different error (error 2).

 error 1 forrtl: severe (36): attempt to access non-existent record, unit 16, file /estanis/MITgcm/verification/tutorial_circular_polar_basin/run/obzonalv.bin
 error 2 'forrtl: severe (66): output statement overflows record'

I went again to the emailbox and I found out I need to change this.



  case nas+pgi:
     set LN         = ( '/bin/ln -s' )
     set CPP        = ( '/lib/cpp -traditional -P' )
     set DEFINES    = ( ${DEFINES} '-DALLOW_USE_MPI -DALWAYS_USE_MPI
-DWORDLENGTH=4' )
     set FC         = ( 'ifort' )
     set FFLAGS     = ( '-fp-model strict -132 -r8 -i4 -w95 -W0 -WB -convert
big_endian -assume byterecl' )
     set FOPTIM     = ( '-O0 -noalign')
     set LINK       = ( 'ifort' )
     set INCLUDES   = ( '-I/opt/sgi/mpt/1.12.0.nas/include
-I/opt/pd/netcdf/3.6.0-p1/include' )
     set LIBS       = ( '-L/opt/sgi/mpt/1.12.0.nas/lib -lmpi
-L/opt/pd/netcdf/3.6.0-p1/lib -lnetcdf' )
     breaksw

However, this solution was for a specific configuration for a cluster in Columbia (I think). My build file is a bit different:

#  tested on faulks, 20030818
#
#  Build options for the intel 8.0 fortran compiler
#  the compiler is now called ifort (not ifc) and it appears to
#  need -DWORDLENGTH=1 and not -DWORDLENGTH=4 (which is what ifc 6.0) used to have.
#  ph: use ifort compiler options -convert big_endian -assume byterecl
FC=mpif90
F90C=mpif90
CC=mpicc
DEFINES="-DWORDLENGTH=4 -DALLOW_USE_MPI -DALWAYS_USE_MPI"
#DEFINES="-DALLOW_USE_MPI -DALWAYS_USE_MPI"
LINK=mpif90
CPP="cpp  -traditional -P"
#INCLUDES='-I/usr/include/netcdf'
#INCLUDES="-I. -I$NETCDF/include -I/nuist/p/public/app/mvapich2/2.0b/intel/include"
#LIBS="-L$NETCDF/lib -lnetcdff -lnetcdf -L/nuist/p/public/app/mvapich2/2.0b/intel/lib -lmpich -lpthread"
INCLUDES="-I. -I$NETCDF/include -I/WORK/app/netcdf/4.3.2/01-CF-14/include -I/usr/local/mpi3-dynamic/include"
LIBS="-L$NETCDF/lib -lnetcdff -lnetcdf  -I/WORK/app/netcdf/4.3.2/01-CF-14/lib"
#  Note that the -mp switch is for ieee "maintain precision" and is
#  roughly equivalent to -ieee
if test "x$IEEE" = x ; then
# lz(   FOPTIM='-O3 -align' )
    FOPTIM=
#P3 FOPTIM=$FOPTIM' -tpp6 -xWKM'
#P4 FOPTIM=$FOPTIM' -tpp7 -xWKM'
    FFLAGS="-132 -r8 -i4  -g -convert big_endian -assume byterecl $INCLUDES -I/usr/local/mpi3-dynamic/include"
    FOPTIM="-O1 -align"
else
    FOPTIM="-O0 -noalign"
    FFLAGS="-132 -r8 -i4 -w95 -W0 -WB -xN -pc64 -convert big_endian -assume byterecl $INCLUDES -I/usr/local/mpi3-dynamic/include"
   #FFLAGS='-mp -132 -r8 -i4 -w95 -W0 -WB'
fi
#if test "x$IEEE" = x ; then
#    FFLAGS='-Wimplicit -Wunused -Wuninitialized  -fno-second-underscore'
#    FOPTIM='-O3 -funroll-loops'
#else
#    FFLAGS='-Wimplicit -Wunused -ffloat-store'
#    FOPTIM='-O0 '
#fi

Thanks in advance for all your help

 Kind regards,

Estanis




[https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>  Virus-free. www.avast.com<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20190822/f4f9e3d8/attachment-0001.html>

------------------------------

Message: 2
Date: Thu, 22 Aug 2019 11:57:46 +0200
From: Martin Losch <Martin.Losch at awi.de>
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] Reading errors
Message-ID: <9FF2A137-C599-44C8-B120-D9A4DAF9508B at awi.de>
Content-Type: text/plain; charset="utf-8"

Hi Estanis,

this looks like a convoluted problem. We would need more information about the problem:
what is the platform, the compiler?
details of the configuration (content of code-directory and namelist files)
are you using latest code (some of the flags in the build-option look very outdated ?)?

Your error message (attempt to access non-existent record) usually means that you are reading beyond the end of the file (i.e. not enough data in the file)

Not finding an input file usually does not have anything to do with the compiler setting, especially not the WORDLENGTH.

Martin

> On 22. Aug 2019, at 10:51, Estanislao Gavilan Pascual-Ahuir <dramauh at hotmail.com> wrote:
>
> Hi Community,
>
>  I have just started using MITgcm model. Last week I spent some time learning how to open boundary conditions. I was able to sort out everything except for this (error 1). It turns out that the model cannot find the bin file. After doing some research in the mailbox of mitgcm. I found out that is due to the compiler settings. As it was advice, I set -DWORDLENGTH=1. Now, I am having a different error (error 2).
>
>  error 1 forrtl: severe (36): attempt to access non-existent record, unit 16, file /estanis/MITgcm/verification/tutorial_circular_polar_basin/run/obzonalv.bin
>  error 2 'forrtl: severe (66): output statement overflows record'
>
> I went again to the emailbox and I found out I need to change this.
>
>
>   case nas+pgi:
>      set LN         = ( '/bin/ln -s' )
>      set CPP        = ( '/lib/cpp -traditional -P' )
>      set DEFINES    = ( ${DEFINES} '-DALLOW_USE_MPI -DALWAYS_USE_MPI
> -DWORDLENGTH=4' )
>      set FC         = ( 'ifort' )
>      set FFLAGS     = ( '-fp-model strict -132 -r8 -i4 -w95 -W0 -WB -convert
> big_endian -assume byterecl' )
>      set FOPTIM     = ( '-O0 -noalign')
>      set LINK       = ( 'ifort' )
>      set INCLUDES   = ( '-I/opt/sgi/mpt/1.12.0.nas/include
> -I/opt/pd/netcdf/3.6.0-p1/include' )
>      set LIBS       = ( '-L/opt/sgi/mpt/1.12.0.nas/lib -lmpi
> -L/opt/pd/netcdf/3.6.0-p1/lib -lnetcdf' )
>      breaksw
>
> However, this solution was for a specific configuration for a cluster in Columbia (I think). My build file is a bit different:
>
> #  tested on faulks, 20030818
> #
> #  Build options for the intel 8.0 fortran compiler
> #  the compiler is now called ifort (not ifc) and it appears to
> #  need -DWORDLENGTH=1 and not -DWORDLENGTH=4 (which is what ifc 6.0) used to have.
> #  ph: use ifort compiler options -convert big_endian -assume byterecl
> FC=mpif90
> F90C=mpif90
> CC=mpicc
> DEFINES="-DWORDLENGTH=4 -DALLOW_USE_MPI -DALWAYS_USE_MPI"
> #DEFINES="-DALLOW_USE_MPI -DALWAYS_USE_MPI"
> LINK=mpif90
> CPP="cpp  -traditional -P"
> #INCLUDES='-I/usr/include/netcdf'
> #INCLUDES="-I. -I$NETCDF/include -I/nuist/p/public/app/mvapich2/2.0b/intel/include"
> #LIBS="-L$NETCDF/lib -lnetcdff -lnetcdf -L/nuist/p/public/app/mvapich2/2.0b/intel/lib -lmpich -lpthread"
> INCLUDES="-I. -I$NETCDF/include -I/WORK/app/netcdf/4.3.2/01-CF-14/include -I/usr/local/mpi3-dynamic/include"
> LIBS="-L$NETCDF/lib -lnetcdff -lnetcdf  -I/WORK/app/netcdf/4.3.2/01-CF-14/lib"
> #  Note that the -mp switch is for ieee "maintain precision" and is
> #  roughly equivalent to -ieee
> if test "x$IEEE" = x ; then
> # lz(   FOPTIM='-O3 -align' )
>     FOPTIM=
> #P3 FOPTIM=$FOPTIM' -tpp6 -xWKM'
> #P4 FOPTIM=$FOPTIM' -tpp7 -xWKM'
>     FFLAGS="-132 -r8 -i4  -g -convert big_endian -assume byterecl $INCLUDES -I/usr/local/mpi3-dynamic/include"
>     FOPTIM="-O1 -align"
> else
>     FOPTIM="-O0 -noalign"
>     FFLAGS="-132 -r8 -i4 -w95 -W0 -WB -xN -pc64 -convert big_endian -assume byterecl $INCLUDES -I/usr/local/mpi3-dynamic/include"
>    #FFLAGS='-mp -132 -r8 -i4 -w95 -W0 -WB'
> fi
> #if test "x$IEEE" = x ; then
> #    FFLAGS='-Wimplicit -Wunused -Wuninitialized  -fno-second-underscore'
> #    FOPTIM='-O3 -funroll-loops'
> #else
> #    FFLAGS='-Wimplicit -Wunused -ffloat-store'
> #    FOPTIM='-O0 '
> #fi
>
> Thanks in advance for all your help
>
>  Kind regards,
>
> Estanis
>
>
>
>
>        Virus-free. www.avast.com<http://www.avast.com>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support



------------------------------

Subject: Digest Footer

_______________________________________________
MITgcm-support mailing list
MITgcm-support at mitgcm.org
http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support


------------------------------

End of MITgcm-support Digest, Vol 194, Issue 10
***********************************************

[https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>  Virus-free. www.avast.com<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20190822/58b5e2e3/attachment-0001.html>


More information about the MITgcm-support mailing list