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Hi Michael and Martin</div>
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I figured out the problem, Michael pointed me in the correct way. I did not notice that the forcing cycle cannot be bigger than the forcing period times the number of time steps of your forcing files (ie.1200x100). I thought that if I set a big forcing cycle
the forcing files were going to keep constant once the model gets to the last time step. In this experiment, I was trying to ramp up a source-sink circulation during the first 100 time steps. Then, I wanted to keep it constant (That is why I set a huge period
cycle). It seems I will need to used restart files to do this. Thanks so much for your time and all your help. I would not be able to figure out this by myself</div>
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Kind regards,</div>
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Estanislao</div>
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<br>
Message: 1<br>
Date: Sun, 25 Aug 2019 21:04:55 -0500<br>
From: Michael Schaferkotter <schaferk@bellsouth.net><br>
To: mitgcm-support@mitgcm.org<br>
Subject: Re: [MITgcm-support] Reading errors<br>
Message-ID: <0A6D5C87-53FC-4FF9-B7E7-34CBB169C096@bellsouth.net><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
0. i misread the original post and had the idea that the simulation was 2d.<br>
that/s why there was the comment about setting delY.<br>
<br>
1. the parameters given in SIZE.h imply that you should use 43 in the MATLAB scripts as stated by another.<br>
<br>
2.<br>
> & OLx = 2,<br>
> & OLy = 2,<br>
<br>
<br>
i never found success with using these values (2), so i always set them to 3.<br>
<br>
3.<br>
> > > > OB_Jnorth(16:28)=13*41,<br>
> > > > > OB_Jsouth(16:28)=13*3,<br>
<br>
namelists are not standard and can cause problems for various reasons.<br>
<br>
so i would always explicitly list the values using only -1,0,1 (-1 on north and east)<br>
<br>
OB_Jnorth=15*0,13*-1,15*0<br>
OB_Jsouth=15*0,13*1,15*0<br>
<br>
4.<br>
i never cared for using reentrant methods and would force the boundaries with values such that the transport was corrected for incoming signals. For outgoing signals and to reduce boundary reflections, a method by Lavelle and Thacker was incorporated into the
OBCS package.<br>
<br>
5. the periodic forcing parameters must be consistent. (i never used periodic forcing)<br>
<br>
<br>
> On Aug 24, 2019, at 21:11, Estanislao Gavilan Pascual-Ahuir <dramauh@hotmail.com> wrote:<br>
> <br>
> Hi Michael,<br>
> <br>
> My SIZE.h file is this one <br>
> <br>
> INTEGER sNx<br>
> INTEGER sNy<br>
> INTEGER OLx<br>
> INTEGER OLy<br>
> INTEGER nSx<br>
> INTEGER nSy<br>
> INTEGER nPx<br>
> INTEGER nPy<br>
> INTEGER Nx<br>
> INTEGER Ny<br>
> INTEGER Nr<br>
> PARAMETER (<br>
> & sNx = 43,<br>
> & sNy = 43,<br>
> & OLx = 2,<br>
> & OLy = 2,<br>
> & nSx = 1,<br>
> & nSy = 1,<br>
> & nPx = 1,<br>
> & nPy = 1,<br>
> & Nx = sNx*nSx*nPx,<br>
> & Ny = sNy*nSy*nPy,<br>
> & Nr = 2)<br>
> C MAX_OLX :: Set to the maximum overlap region size of any array<br>
> C MAX_OLY that will be exchanged. Controls the sizing of exch<br>
> C routine buffers.<br>
> INTEGER MAX_OLX<br>
> INTEGER MAX_OLY<br>
> PARAMETER ( MAX_OLX = OLx,<br>
> & MAX_OLY = OLy )<br>
> <br>
> About the second comment. I set it just in case because I found in the example. About the OBCS, the indexes can be other than 1,0 or -1. My guess, if you have a big domain and you want to open a boundary in the last row it is easier to put -1 than 5984. For
my experiments, I have designed a circular domain and I decided to leave the two first and last rows and columns as land. I do not think this is causing the problem because if I run the model without forcing period the model works perfectly fine. He reads
only the first time step of my forcing bin file but it works. It is just when I activate the forcing period in the data namelist.
<br>
> <br>
> <br>
> Kind regards,<br>
> <br>
> Estanislao<br>
> <br>
> PS:thank you in advance for all your help. I am really stuck with this matter.<br>
> <br>
> ----------------------------------------------------------------------<br>
> <br>
> Message: 1<br>
> Date: Sat, 24 Aug 2019 09:49:09 -0500<br>
> From: Michael Schaferkotter <schaferk@bellsouth.net><br>
> To: mitgcm-support@mitgcm.org<br>
> Subject: Re: [MITgcm-support] MITgcm-support Digest, Vol 194, Issue 16<br>
> Message-ID: <ACF3B949-4FA8-403F-A0F4-FCFFEB5B7616@bellsouth.net><br>
> Content-Type: text/plain; charset="utf-8"<br>
> <br>
> 1. please post the SIZE.h file.<br>
> unless the behaviors induced by the paramters has changed, the info in thisfile will permit straightening out ofthese extents issues.<br>
> <br>
> 2. below in parm04<br>
> delY is set to 43*1 (why set it? i would not assume that there is no side effect from this, maybe there isn/t, i don/t know)<br>
> <br>
> below in OBCS_PARMO1<br>
> <br>
> > > OB_Jnorth(16:28)=13*41,<br>
> > > > > OB_Jsouth(16:28)=13*3,<br>
> <br>
> iirc, the values of these arrays are -1,0,1<br>
> it/s been a while since i setup and ran a simulation<br>
> <br>
> <br>
> Sent from Here3.<br>
> <br>
> > On Aug 24, 2019, at 09:11, Estanislao Gavilan Pascual-Ahuir <dramauh@hotmail.com> wrote:<br>
> > <br>
> > Hi Martin, <br>
> > <br>
> > I tried increasing the nx from 13 to 43 and I have the same error...This is a nightmare. Do you think I might need to make a bigger boundary?Maybe 13 is cells is too small.. Thank you so much in advance for your help.<br>
> > <br>
> > Kind regards,<br>
> > <br>
> > Estanislao<br>
> > De: MITgcm-support <mitgcm-support-bounces@mitgcm.org> en nombre de mitgcm-support-request@mitgcm.org <mitgcm-support-request@mitgcm.org><br>
> > Enviado: s?bado, 24 de agosto de 2019 8:45<br>
> > Para: mitgcm-support@mitgcm.org <mitgcm-support@mitgcm.org><br>
> > Asunto: MITgcm-support Digest, Vol 194, Issue 16<br>
> > <br>
> > Send MITgcm-support mailing list submissions to<br>
> > mitgcm-support@mitgcm.org<br>
> > <br>
> > To subscribe or unsubscribe via the World Wide Web, visit<br>
> > <a href="http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support">http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support</a><br>
> > or, via email, send a message with subject or body 'help' to<br>
> > mitgcm-support-request@mitgcm.org<br>
> > <br>
> > You can reach the person managing the list at<br>
> > mitgcm-support-owner@mitgcm.org<br>
> > <br>
> > When replying, please edit your Subject line so it is more specific<br>
> > than "Re: Contents of MITgcm-support digest..."<br>
> > <br>
> > <br>
> > Today's Topics:<br>
> > <br>
> > 1. Re: Reading errors (Martin Losch)<br>
> > <br>
> > <br>
> > ----------------------------------------------------------------------<br>
> > <br>
> > Message: 1<br>
> > Date: Sat, 24 Aug 2019 08:45:29 +0200<br>
> > From: Martin Losch <Martin.Losch@awi.de><br>
> > To: <mitgcm-support@mitgcm.org><br>
> > Subject: Re: [MITgcm-support] Reading errors<br>
> > Message-ID: <C4098FFF-029D-4EEC-AC58-566F448B660A@awi.de><br>
> > Content-Type: text/plain; charset="us-ascii"<br>
> > <br>
> > Hi, I do think, that this may be your problem, because your fields are actually too small! You use nx=13, when it should be 43. Even if only part of your Northern or Southern boundary is really "open", you need to provide the full field. Please refer to
the documentation for more details. Unfortunately, we don't have any verification experiments with exactly your configuration. Most of the time all boundaries are declared as open, even when only a few are actually "wet", e.g. the verification/dome experiment,
where the open point along the northern bounary are only a few.<br>
> > <br>
> > So, I think you can fix your problem by changing 13 to 43 in your matlab scripts.<br>
> > <br>
> > Martin<br>
> > <br>
> > > On 24. Aug 2019, at 03:07, Estanislao Gavilan Pascual-Ahuir <dramauh@hotmail.com> wrote:<br>
> > > <br>
> > > Hi Martin<br>
> > > <br>
> > > I am not sure if that is the problem because I used readbin.m to check the input files and the matrix were correct. This is the MATLAB code I used.
<br>
> > > % creat N time slabs for testing<br>
> > > ieee='b';<br>
> > > prec='real*4';<br>
> > > v0=0.0041;<br>
> > > N=100<br>
> > > vvel=ones(13,2,N); <br>
> > > uMerid=zeros(13,2,N); <br>
> > > for i=1:N<br>
> > > vZonal(:,:,i)=v0*vvel(:,:,i)*i/N;<br>
> > > end<br>
> > > fid=fopen('OBmeridU.bin','w',ieee); fwrite(fid,uMerid,prec);fclose(fid);<br>
> > > fid=fopen('OBzonalV.bin','w',ieee); fwrite(fid,vZonal,prec); fclose(fid);<br>
> > > <br>
> > > I have even tried to use your code, but the files do not change the size. They are always 11KB<br>
> > > <br>
> > > % creat N time slabs for testing<br>
> > > v0=0.0041;<br>
> > > N=100<br>
> > > vvel=ones(13,2,N); <br>
> > > uMerid=zeros(13,2,N); <br>
> > > for i=1:N<br>
> > > vZonal(:,:,i)=v0*vvel(:,:,i)*i/N;<br>
> > > end<br>
> > > fid=fopen('OBmeridU.bin','w',ieee); <br>
> > > for i=1:N<br>
> > > fwrite(fid,squeeze(uMerid(:,:,i)),prec);<br>
> > > end<br>
> > > fclose(fid);<br>
> > > fid=fopen('OBzonalV.bin','w',ieee); <br>
> > > for i=1:N<br>
> > > fwrite(fid,squeeze(vZonal(:,:,i)),prec);<br>
> > > end<br>
> > > fclose(fid);<br>
> > > <br>
> > > Kind regards,<br>
> > > <br>
> > > Estanislao<br>
> > > <br>
> > > De: MITgcm-support <mitgcm-support-bounces@mitgcm.org> en nombre de mitgcm-support-request@mitgcm.org <mitgcm-support-request@mitgcm.org><br>
> > > Enviado: viernes, 23 de agosto de 2019 18:00<br>
> > > Para: mitgcm-support@mitgcm.org <mitgcm-support@mitgcm.org><br>
> > > Asunto: MITgcm-support Digest, Vol 194, Issue 14<br>
> > > <br>
> > > Send MITgcm-support mailing list submissions to<br>
> > > mitgcm-support@mitgcm.org<br>
> > > <br>
> > > To subscribe or unsubscribe via the World Wide Web, visit<br>
> > > <a href="http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support">
http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support</a><br>
> > > or, via email, send a message with subject or body 'help' to<br>
> > > mitgcm-support-request@mitgcm.org<br>
> > > <br>
> > > You can reach the person managing the list at<br>
> > > mitgcm-support-owner@mitgcm.org<br>
> > > <br>
> > > When replying, please edit your Subject line so it is more specific<br>
> > > than "Re: Contents of MITgcm-support digest..."<br>
> > > <br>
> > > <br>
> > > Today's Topics:<br>
> > > <br>
> > > 1. Re: Reading errors (Martin Losch)<br>
> > > <br>
> > > <br>
> > > ----------------------------------------------------------------------<br>
> > > <br>
> > > Message: 1<br>
> > > Date: Fri, 23 Aug 2019 10:02:49 +0200<br>
> > > From: Martin Losch <Martin.Losch@awi.de><br>
> > > To: MITgcm Support <mitgcm-support@mitgcm.org><br>
> > > Subject: Re: [MITgcm-support] Reading errors<br>
> > > Message-ID: <1AB158B6-A07E-43EB-A3F6-6530BDE345C9@awi.de><br>
> > > Content-Type: text/plain; charset="utf-8"<br>
> > > <br>
> > > Hi Estanis,<br>
> > > <br>
> > > this most likely means that your OBzonalV.bin is ?too short?.<br>
> > > Guess from you parameters you'll need fields with dimension (nt,nz,nx) = (100,2,43). In you data file you do not specify the ?readBinaryPrec?, so that will default to ?real*4?, single precision, ?float32?, but check in your stdout, so in python this would
mean writing a file like this:<br>
> > > <br>
> > > import numpy as np<br>
> > > import sys<br>
> > > nt=100<br>
> > > nx=43<br>
> > > nz=2<br>
> > > <br>
> > > data = np.zeros((nt,nz,nx),dtype=?float32') # or some other values, but dtype is important<br>
> > > if sys.byteorder == 'little': data.byteswap(True)<br>
> > > #<br>
> > > fid = open(?OBzonalV.bin',"wb")<br>
> > > data.tofile(fid)<br>
> > > fid.close()<br>
> > > # switch back to machine format<br>
> > > if sys.byteorder == 'little': data.byteswap(True)<br>
> > > <br>
> > > With this I get a file of this size:<br>
> > > <br>
> > > >>> du -h ./OBzonalV.bin<br>
> > > 36K ./OBzonalV.bin<br>
> > > <br>
> > > >>> ls -l OBzonalV.bin<br>
> > > -rw-r--r-- 1 mlosch DMAWI\KLI04 34400 Aug 23 09:53 OBzonalV.bin<br>
> > > <br>
> > > <br>
> > > # in matlab it would be similar, but note the different order of dimensions:<br>
> > > data = zeros(nx,nz,nt);<br>
> > > accuracy = ?real*4?;<br>
> > > [fid message] = fopen(?OBzonalV.bin','w','ieee-be');<br>
> > > count = fwrite(fid,data,accuracy);<br>
> > > for k=1:nt<br>
> > > fwrite(fid,squeeze(data(:,:,k)),accuracy);<br>
> > > end<br>
> > > fclose(fid);<br>
> > > <br>
> > > <br>
> > > <br>
> > > About the NETCDF_ROOT and other INCLUDES: this file is meant to be as generic as possible, i.e. the code at the end of the build options file will look for paths in the usual places. In 95% of the cases this works. If you have a special installation,
you might want to hard-wire the paths, as you have done, then you don?t need the rest anymore. Alternatively you could set the environment varialbes NETCDF_ROOT and MPI_INC_DIR, e.g. like this<br>
> > > <br>
> > > export NETCDF_ROOT=/WORK/app/netcdf/4.3.2/01-CF-14/<br>
> > > export MPI_INC_DIR=/usr/local/mpi3-dynamic/include<br>
> > > <br>
> > > ***before*** you run genmake2, then it should work, too.<br>
> > > <br>
> > > Martin<br>
> > > <br>
> > > > On 23. Aug 2019, at 04:37, Estanislao Gavilan Pascual-Ahuir <dramauh@hotmail.com> wrote:<br>
> > > > <br>
> > > > <br>
> > > > Hi Martin and Jean-Michel<br>
> > > > I still have the error forrtl: severe (36): attempt to access non-existent record, unit 16, file /bblablabla/run/OBzonalV.bin. In addition, I saw this message after doing make depend f90mkdepend: no source file found for module this. I am no sure
if this is important.<br>
> > > > <br>
> > > > I followed your advice. I start doing a simulation in serial mode without obcs and the model ran perfectly fine. Once I opened the obcs (i.e useOBCS= TRUE), I had that error. Following the architecture of my cluster change a little bit the linux_ia64_ifort.
By the way, do I need the last set of conditions of NETCDF_ROOT and netcdf test? I was thinking to remove them.<br>
> > > > <br>
> > > > Kind regards,<br>
> > > > <br>
> > > > Estanis<br>
> > > > <br>
> > > > #!/bin/bash<br>
> > > > #<br>
> > > > # Tested on uv100.awi.de (SGI UV 100, details:<br>
> > > > # <a href="http://www.sgi.com/products/servers/uv/specs.html">
http://www.sgi.com/products/servers/uv/specs.html</a>)<br>
> > > > # a) For more speed, provided your data size does not exceed 2GB you can<br>
> > > > # remove -fPIC which carries a performance penalty of 2-6%.<br>
> > > > # b) You can replace -fPIC with '-mcmodel=medium -shared-intel' which may<br>
> > > > # perform faster than -fPIC and still support data sizes over 2GB per<br>
> > > > # process but all the libraries you link to must be compiled with<br>
> > > > # -fPIC or -mcmodel=medium<br>
> > > > # c) flags adjusted for ifort 12.1.0<br>
> > > > <br>
> > > > FC=ifort<br>
> > > > F90C=ifort<br>
> > > > CC=icc<br>
> > > > # requires that all static libraries are available:<br>
> > > > #LINK='ifort -static'<br>
> > > > LINK='ifort'<br>
> > > > # for adjoint runs the default makedepend often cannot handle enough files<br>
> > > > #MAKEDEPEND=tools_xmakedepend<br>
> > > > <br>
> > > > DEFINES='-DWORDLENGTH=4'<br>
> > > > CPP='cpp -traditional -P'<br>
> > > > F90FIXEDFORMAT='-fixed -Tf'<br>
> > > > EXTENDED_SRC_FLAG='-132'<br>
> > > > #OMPFLAG='-openmp'<br>
> > > > <br>
> > > > NOOPTFLAGS="-O0 -g -m64"<br>
> > > > NOOPTFILES=''<br>
> > > > <br>
> > > > MCMODEL='-fPIC'<br>
> > > > # for large memory requirements uncomment this line<br>
> > > > #MCMODEL='-mcmodel=medium -shared-intel'<br>
> > > > <br>
> > > > FFLAGS="$FFLAGS -W0 -WB -convert big_endian -assume byterecl $MCMODEL"<br>
> > > > #- might want to use '-r8' for fizhi pkg:<br>
> > > > #FFLAGS="$FFLAGS -r8"<br>
> > > > <br>
> > > > if test "x$IEEE" = x ; then #- with optimisation:<br>
> > > > FOPTIM='-O3 -align'<br>
> > > > # does not work when -static does not work<br>
> > > > # FOPTIM='-fast -align'<br>
> > > > # instead you can use<br>
> > > > # FOPTIM='-O3 -ipo -align'<br>
> > > > else<br>
> > > > if test "x$DEVEL" = x ; then #- no optimisation + IEEE :<br>
> > > > FOPTIM='-O0 -noalign -fp-model precise'<br>
> > > > # -fltconsistency<br>
> > > > else #- development/check options:<br>
> > > > FOPTIM='-O0 -noalign -fp-model precise'<br>
> > > > FOPTIM="$FOPTIM -g -check all -fpe0 -traceback -ftrapuv -fp-model except -warn all"<br>
> > > > fi<br>
> > > > fi<br>
> > > > <br>
> > > > F90FLAGS=$FFLAGS<br>
> > > > F90OPTIM=$FOPTIM<br>
> > > > CFLAGS="-O0 -ip $MCMODEL"<br>
> > > > <br>
> > > > INCLUDEDIRS=''<br>
> > > > INCLUDES='-I. -I$NETCDF/include -I/WORK/app/netcdf/4.3.2/01-CF-14/include -I/usr/local/mpi3-dynamic/include'<br>
> > > > LIBS='-L$NETCDF/lib -lnetcdff -lnetcdf -I/WORK/app/netcdf/4.3.2/01-CF-14/lib'<br>
> > > > <br>
> > > > if [ "x$NETCDF_ROOT" != x ] ; then<br>
> > > > INCLUDEDIRS="${NETCDF_ROOT}/include"<br>
> > > > INCLUDES="-I${NETCDF_ROOT}/include"<br>
> > > > LIBS="-L${NETCDF_ROOT}/lib"<br>
> > > > elif [ "x$NETCDF_HOME" != x ]; then<br>
> > > > INCLUDEDIRS="${NETCDF_HOME}/include"<br>
> > > > INCLUDES="-I${NETCDF_HOME}/include"<br>
> > > > LIBS="-L${NETCDF_HOME}/lib"<br>
> > > > elif [ "x$NETCDF_INC" != x -a"x$NETCDF_LIB" != x ]; then<br>
> > > > NETCDF_INC=`echo $NETCDF_INC | sed 's/-I//g'`<br>
> > > > NETCDF_LIB=`echo $NETCDF_LIB | sed 's/-L//g'`<br>
> > > > INCLUDEDIRS="${NETCDF_INC}"<br>
> > > > INCLUDES="-I${NETCDF_INC}"<br>
> > > > LIBS="-L${NETCDF_LIB}"<br>
> > > > elif [ "x$NETCDF_INCDIR" != x -a "x$NETCDF_LIBDIR" != x ]; then<br>
> > > > INCLUDEDIRS="${NETCDF_INCDIR}"<br>
> > > > INCLUDES="-I${NETCDF_INCDIR}"<br>
> > > > LIBS="-L${NETCDF_LIBDIR}"<br>
> > > > elif test -d /usr/include/netcdf-3 ; then<br>
> > > > INCLUDEDIRS='/usr/include/netcdf-3'<br>
> > > > INCLUDES='-I/usr/include/netcdf-3'<br>
> > > > LIBS='-L/usr/lib/netcdf-3 -L/usr/lib64/netcdf-3'<br>
> > > > elif test -d /usr/include/netcdf ; then<br>
> > > > INCLUDEDIRS='/usr/include/netcdf'<br>
> > > > INCLUDES='-I/usr/include/netcdf'<br>
> > > > elif test -d /usr/local/netcdf ; then<br>
> > > > INCLUDEDIRS='/usr/include/netcdf/include'<br>
> > > > INCLUDES='-I/usr/local/netcdf/include'<br>
> > > > LIBS='-L/usr/local/netcdf/lib'<br>
> > > > elif test -d /usr/local/include/netcdf.inc ; then<br>
> > > > INCLUDEDIRS='/usr/local/include'<br>
> > > > INCLUDES='-I/usr/local/include'<br>
> > > > LIBS='-L/usr/local/lib64'<br>
> > > > fi<br>
> > > > <br>
> > > > if [ -n "$MPI_INC_DIR" -a "x$MPI" = xtrue ] ; then<br>
> > > > LIBS="$LIBS -lmpi"<br>
> > > > INCLUDES="$INCLUDES -I$MPI_INC_DIR"<br>
> > > > INCLUDEDIRS="$INCLUDEDIRS $MPI_INC_DIR"<br>
> > > > #- used for parallel (MPI) DIVA<br>
> > > > MPIINCLUDEDIR="$MPI_INC_DIR"<br>
> > > > fi<br>
> > > > <br>
> > > > <br>
> > > > ----------------------------------------------------------------------<br>
> > > > <br>
> > > > Message: 1<br>
> > > > Date: Thu, 22 Aug 2019 13:10:55 +0200<br>
> > > > From: Martin Losch <Martin.Losch@awi.de><br>
> > > > To: MITgcm Support <mitgcm-support@mitgcm.org><br>
> > > > Subject: Re: [MITgcm-support] Reading errors<br>
> > > > Message-ID: <325AC4E8-1648-4C6A-BFED-7722921C733E@awi.de><br>
> > > > Content-Type: text/plain; charset="utf-8"<br>
> > > > <br>
> > > > Hi Estanis,<br>
> > > > <br>
> > > > thanks for the details. This is what I would do:<br>
> > > > <br>
> > > > - At the compile level use a standard build options file, with an intel compiler on a linux system I would start with MITgcm/tools/build_options/linux_amd64_ifort, or linux_ia64_ifort (depending on the output of uname -a, in fact, genmake2 is probably
able to pick the correct file if you don?t specify it), and since your domain is small I would first try without MPI, ie. like this:<br>
> > > > <br>
> > > > ${somepath}/tools/genmake2 -of ${somepath}/tools/build_options/linux_amd64_ifort -mods ../code<br>
> > > > make CLEAN && make depend && make<br>
> > > > <br>
> > > > - With this non-MPI configuration I would try to run the model. First with useOBCS=.FALSE. (just a few timesteps), and then with .TRUE.<br>
> > > > <br>
> > > > - once this works, you can recompile with MPI (if you really need it), like this:<br>
> > > > <br>
> > > > ${somepath}/tools/genmake2 -of ${somepath}/tools/build_options/linux_amd64_ifort -mods ../code -mpi<br>
> > > > make CLEAN && make depend && make<br>
> > > > (note that the extra flag ?-mpi" is enough)<br>
> > > > <br>
> > > > and check if you get the same. For further help, you should record the potential error messages after each step.<br>
> > > > <br>
> > > > Martin<br>
> > > > <br>
> > > > PS. Some comments about your namelist below:<br>
> > > > <br>
> > > > > On 22. Aug 2019, at 12:39, Estanislao Gavilan Pascual-Ahuir <dramauh@hotmail.com> wrote:<br>
> > > > > <br>
> > > > > Hi Martin ,<br>
> > > > > <br>
> > > > > Before anything thank you so much for your help. I will try to answer all you questions.<br>
> > > > > <br>
> > > > > what is the platform, the compiler?<br>
> > > > > 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<br>
> > > > > details of the configuration (content of code-directory and namelist files)<br>
> > > > > I am running a simple simulation with open boundaries. I load the packages gfd, obcs, mnc and diagnostics using the packagesconfig. The frequency of the open boundaries is stated in the data file. This is the data file<br>
> > > > > Model parameters<br>
> > > > > # Continuous equation parameters<br>
> > > > > &PARM01<br>
> > > > > tRef=23.,23.,<br>
> > > > > sRef=35.,35.,<br>
> > > > > selectCoriMap=4,<br>
> > > > > viscAh=4.E2,<br>
> > > > with your grid choice (sphericalPolarGrid), the coriolis parameter is computed and these values are not used.<br>
> > > > > f0=1.E-4,<br>
> > > > > beta=1.E-11,<br>
> > > > > rhoNil=1000.,<br>
> > > > > gBaro=9.81,<br>
> > > > > rigidLid=.FALSE.,<br>
> > > > > implicitFreeSurface=.TRUE.,<br>
> > > > > # momAdvection=.FALSE.,<br>
> > > > > tempStepping=.FALSE.,<br>
> > > > > saltStepping=.FALSE.,<br>
> > > > > &<br>
> > > > > <br>
> > > > > # Elliptic solver parameters<br>
> > > > > &PARM02<br>
> > > > > cg2dTargetResidual=1.E-7,<br>
> > > > > cg2dMaxIters=1000,<br>
> > > > > &<br>
> > > > > <br>
> > > > > # Time stepping parameters<br>
> > > > > &PARM03<br>
> > > > > nIter0=0,<br>
> > > > > nTimeSteps=100,<br>
> > > > > deltaT=1200.0,<br>
> > > > > pChkptFreq=31104000.0,<br>
> > > > > chkptFreq=15552000.0,<br>
> > > > > dumpFreq=15552000.0,<br>
> > > > # this will give you monitor output every timestep (which is what you want while debugging), later I would set it to something like 20-50 * deltaT<br>
> > > > > monitorFreq=1200.,<br>
> > > > > monitorSelect=2,<br>
> > > > > periodicExternalForcing=.TRUE.,<br>
> > > > # this means that you will read data each time step. Is that what you want?<br>
> > > > > externForcingPeriod= 1200.,<br>
> > > > # with your choice of externForcingPeriod, this requires that you have 1000. records in the file(s)<br>
> > > > > externForcingCycle = 12000000.,<br>
> > > > > &<br>
> > > > > # Gridding parameters<br>
> > > > > &PARM04<br>
> > > > > usingSphericalPolarGrid=.TRUE.,<br>
> > > > # alternatively you can say dxSpacing = 1., dySpacing = 1.,<br>
> > > > > delX=43*1.,<br>
> > > > > delY=43*1.,<br>
> > > > > xgOrigin=-21.,<br>
> > > > > ygOrigin=-21.,<br>
> > > > > delR=2*500.,<br>
> > > > > &<br>
> > > > > <br>
> > > > > # Input datasets<br>
> > > > > &PARM05<br>
> > > > > bathyFile='bathy_cir.bin'<br>
> > > > > meridWindFile=,<br>
> > > > > &<br>
> > > > > <br>
> > > > > This is the data.obcs<br>
> > > > > <br>
> > > > > # Open-boundaries<br>
> > > > > &OBCS_PARM01<br>
> > > > > OBCSfixTopo=.FALSE.,<br>
> > > > # if I understand the configuration correctly, you have a zonally reentrant channel with wall in the north and the south (python notation: bathy[0+2,:] = 0, and bathy[ny-1,:] = 0, except where you have the open boundaries)? you could actually save two
grid rows (have 40 instead of 43 point in j-direction and set bathy[0,:]=0, bathy[ny,:]=0)<br>
> > > > > OB_Ieast=0,<br>
> > > > > OB_Iwest=0,<br>
> > > > > OB_Jnorth(16:28)=13*41,<br>
> > > > > OB_Jsouth(16:28)=13*3,<br>
> > > > > useOBCSprescribe = .TRUE.,<br>
> > > > These files should be found, if they are in the same directory where you run your model. They should each contain (according to you dimensions and time parameters) for 100 timesteps 100 fields of dimension (nx,nz). For anything above 1000 timesteps,
they should have 1000 fields (because after the 1000ths record, the model starts from the beginning again, according to you externForcingCycle)<br>
> > > > > OBNvFile = 'OBzonalV.bin',<br>
> > > > > OBSvFile = 'OBzonalV.bin',<br>
> > > > > OBNuFile = 'OBmeridU.bin',<br>
> > > > > OBSuFile = 'OBmeridU.bin?,<br>
> > > > # same as before this will give you a lot of output. You may want to comment out this line, becasue OBCS_monitorFreq = monitorFreq by default<br>
> > > > > OBCS_monitorFreq=1200.00,<br>
> > > > > OBCS_monSelect = 1,<br>
> > > > > &<br>
> > > > > <br>
> > > > > &OBCS_PARM02<br>
> > > > > &<br>
> > > > > are you using latest code (some of the flags in the build-option look very outdated ?)?<br>
> > > > > 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.<br>
> > > > > <br>
> > > > > Kind regards,<br>
> > > > > <br>
> > > > > Estanislao<br>
> > > > > <br>
> > > > <br>
> > > > <br>
> > > > <br>
> > > > ------------------------------<br>
> > > > <br>
> > > > Message: 2<br>
> > > > Date: Thu, 22 Aug 2019 09:33:18 -0400<br>
> > > > From: Jean-Michel Campin <jmc@mit.edu><br>
> > > > To: mitgcm-support@mitgcm.org<br>
> > > > Subject: Re: [MITgcm-support] Reading errors<br>
> > > > Message-ID: <20190822133318.GA13562@ocean.mit.edu><br>
> > > > Content-Type: text/plain; charset=us-ascii<br>
> > > > <br>
> > > > Hi Estanis,<br>
> > > > <br>
> > > > Just a small adjustment: <br>
> > > > the standard optfile for intel compiler (version 11 and newer) is:<br>
> > > > linux_amd64_ifort11<br>
> > > > in MITgcm/tools/build_options<br>
> > > > The optfile "linux_amd64_ifort" is for older version (10 and older).<br>
> > > > <br>
> > > > However, if you are compiling with intel MPI (recent version of the compiler),<br>
> > > > then you need to use: linux_amd64_ifort+impi<br>
> > > > <br>
> > > > Cheers,<br>
> > > > Jean-Michel<br>
> > > > <br>
> > > > On Thu, Aug 22, 2019 at 01:10:55PM +0200, Martin Losch wrote:<br>
> > > > > Hi Estanis,<br>
> > > > > <br>
> > > > > thanks for the details. This is what I would do:<br>
> > > > > <br>
> > > > > - At the compile level use a standard build options file, with an intel compiler on a linux system I would start with MITgcm/tools/build_options/linux_amd64_ifort, or linux_ia64_ifort (depending on the output of uname -a, in fact, genmake2 is probably
able to pick the correct file if you don???t specify it), and since your domain is small I would first try without MPI, ie. like this:<br>
> > > > > <br>
> > > > > ${somepath}/tools/genmake2 -of ${somepath}/tools/build_options/linux_amd64_ifort -mods ../code<br>
> > > > > make CLEAN && make depend && make<br>
> > > > > <br>
> > > > > - With this non-MPI configuration I would try to run the model. First with useOBCS=.FALSE. (just a few timesteps), and then with .TRUE.<br>
> > > > > <br>
> > > > > - once this works, you can recompile with MPI (if you really need it), like this:<br>
> > > > > <br>
> > > > > ${somepath}/tools/genmake2 -of ${somepath}/tools/build_options/linux_amd64_ifort -mods ../code -mpi<br>
> > > > > make CLEAN && make depend && make<br>
> > > > > (note that the extra flag ???-mpi" is enough)<br>
> > > > > <br>
> > > > > and check if you get the same. For further help, you should record the potential error messages after each step.<br>
> > > > > <br>
> > > > > Martin<br>
> > > > > <br>
> > > > > PS. Some comments about your namelist below:<br>
> > > > > <br>
> > > > > > On 22. Aug 2019, at 12:39, Estanislao Gavilan Pascual-Ahuir <dramauh@hotmail.com> wrote:<br>
> > > > > > <br>
> > > > > > Hi Martin ,<br>
> > > > > > <br>
> > > > > > Before anything thank you so much for your help. I will try to answer all you questions.<br>
> > > > > > <br>
> > > > > > what is the platform, the compiler?<br>
> > > > > > 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<br>
> > > > > > details of the configuration (content of code-directory and namelist files)<br>
> > > > > > I am running a simple simulation with open boundaries. I load the packages gfd, obcs, mnc and diagnostics using the packagesconfig. The frequency of the open boundaries is stated in the data file. This is the data file<br>
> > > > > > Model parameters<br>
> > > > > > # Continuous equation parameters<br>
> > > > > > &PARM01<br>
> > > > > > tRef=23.,23.,<br>
> > > > > > sRef=35.,35.,<br>
> > > > > > selectCoriMap=4,<br>
> > > > > > viscAh=4.E2,<br>
> > > > > with your grid choice (sphericalPolarGrid), the coriolis parameter is computed and these values are not used.<br>
> > > > > > f0=1.E-4,<br>
> > > > > > beta=1.E-11,<br>
> > > > > > rhoNil=1000.,<br>
> > > > > > gBaro=9.81,<br>
> > > > > > rigidLid=.FALSE.,<br>
> > > > > > implicitFreeSurface=.TRUE.,<br>
> > > > > > # momAdvection=.FALSE.,<br>
> > > > > > tempStepping=.FALSE.,<br>
> > > > > > saltStepping=.FALSE.,<br>
> > > > > > &<br>
> > > > > > <br>
> > > > > > # Elliptic solver parameters<br>
> > > > > > &PARM02<br>
> > > > > > cg2dTargetResidual=1.E-7,<br>
> > > > > > cg2dMaxIters=1000,<br>
> > > > > > &<br>
> > > > > > <br>
> > > > > > # Time stepping parameters<br>
> > > > > > &PARM03<br>
> > > > > > nIter0=0,<br>
> > > > > > nTimeSteps=100,<br>
> > > > > > deltaT=1200.0,<br>
> > > > > > pChkptFreq=31104000.0,<br>
> > > > > > chkptFreq=15552000.0,<br>
> > > > > > dumpFreq=15552000.0,<br>
> > > > > # this will give you monitor output every timestep (which is what you want while debugging), later I would set it to something like 20-50 * deltaT<br>
> > > > > > monitorFreq=1200.,<br>
> > > > > > monitorSelect=2,<br>
> > > > > > periodicExternalForcing=.TRUE.,<br>
> > > > > # this means that you will read data each time step. Is that what you want?<br>
> > > > > > externForcingPeriod= 1200.,<br>
> > > > > # with your choice of externForcingPeriod, this requires that you have 1000. records in the file(s)<br>
> > > > > > externForcingCycle = 12000000.,<br>
> > > > > > &<br>
> > > > > > # Gridding parameters<br>
> > > > > > &PARM04<br>
> > > > > > usingSphericalPolarGrid=.TRUE.,<br>
> > > > > # alternatively you can say dxSpacing = 1., dySpacing = 1.,<br>
> > > > > > delX=43*1.,<br>
> > > > > > delY=43*1.,<br>
> > > > > > xgOrigin=-21.,<br>
> > > > > > ygOrigin=-21.,<br>
> > > > > > delR=2*500.,<br>
> > > > > > &<br>
> > > > > > <br>
> > > > > > # Input datasets<br>
> > > > > > &PARM05<br>
> > > > > > bathyFile='bathy_cir.bin'<br>
> > > > > > meridWindFile=,<br>
> > > > > > &<br>
> > > > > > <br>
> > > > > > This is the data.obcs<br>
> > > > > > <br>
> > > > > > # Open-boundaries<br>
> > > > > > &OBCS_PARM01<br>
> > > > > > OBCSfixTopo=.FALSE.,<br>
> > > > > # if I understand the configuration correctly, you have a zonally reentrant channel with wall in the north and the south (python notation: bathy[0+2,:] = 0, and bathy[ny-1,:] = 0, except where you have the open boundaries)? you could actually save
two grid rows (have 40 instead of 43 point in j-direction and set bathy[0,:]=0, bathy[ny,:]=0)<br>
> > > > > > OB_Ieast=0,<br>
> > > > > > OB_Iwest=0,<br>
> > > > > > OB_Jnorth(16:28)=13*41,<br>
> > > > > > OB_Jsouth(16:28)=13*3,<br>
> > > > > > useOBCSprescribe = .TRUE.,<br>
> > > > > These files should be found, if they are in the same directory where you run your model. They should each contain (according to you dimensions and time parameters) for 100 timesteps 100 fields of dimension (nx,nz). For anything above 1000 timesteps,
they should have 1000 fields (because after the 1000ths record, the model starts from the beginning again, according to you externForcingCycle)<br>
> > > > > > OBNvFile = 'OBzonalV.bin',<br>
> > > > > > OBSvFile = 'OBzonalV.bin',<br>
> > > > > > OBNuFile = 'OBmeridU.bin',<br>
> > > > > > OBSuFile = 'OBmeridU.bin???,<br>
> > > > > # same as before this will give you a lot of output. You may want to comment out this line, becasue OBCS_monitorFreq = monitorFreq by default<br>
> > > > > > OBCS_monitorFreq=1200.00,<br>
> > > > > > OBCS_monSelect = 1,<br>
> > > > > > &<br>
> > > > > > <br>
> > > > > > &OBCS_PARM02<br>
> > > > > > &<br>
> > > > > > are you using latest code (some of the flags in the build-option look very outdated ?)?<br>
> > > > > > 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.<br>
> > > > > > <br>
> > > > > > Kind regards,<br>
> > > > > > <br>
> > > > > > Estanislao<br>
> > > > > > <br>
> > > > > <br>
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End of MITgcm-support Digest, Vol 194, Issue 21<br>
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<td style="width: 55px; padding-top: 13px;"><a href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail" target="_blank"><img alt="" width="46" height="29" style="width: 46px; height: 29px;" src="https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif"></a></td>
<td style="width: 470px; padding-top: 12px; color: #41424e; font-size: 13px; font-family: Arial, Helvetica, sans-serif; line-height: 18px;">
Virus-free. <a href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail" target="_blank" style="color: #4453ea;">
www.avast.com</a> </td>
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