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Hi Martin and <span style="color: rgb(50, 49, 48); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; font-size: 14.6667px; background-color: rgb(255, 255, 255); display: inline !important">Jean-Michel</span></div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span style="color: rgb(50, 49, 48); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; font-size: 14.6667px; background-color: rgb(255, 255, 255); display: inline !important">
I still have the error <b>forrtl: severe (36): attempt to access non-existent record, unit 16, file /bblablabla/run/OBzonalV.bin.
</b>In addition, I saw this message after doing make depend<b> f90mkdepend: no source file found for module this.
</b>I am no sure if this is important.</span></div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span style="color: rgb(50, 49, 48); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; font-size: 14.6667px; background-color: rgb(255, 255, 255); display: inline !important"><br>
</span></div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span style="color: rgb(50, 49, 48); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; font-size: 14.6667px; background-color: rgb(255, 255, 255); display: inline !important">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
<span>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>
</span><span></span></span></div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span style="color: rgb(50, 49, 48); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; font-size: 14.6667px; background-color: rgb(255, 255, 255); display: inline !important"><span><br>
</span></span></div>
<div style=""><span style="font-size: 14.6667px;">Kind regards,</span></div>
<div style=""><span style="font-size: 14.6667px;"><br>
</span></div>
<div style=""><span style="font-size: 14.6667px;">Estanis</span></div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span style="color: rgb(50, 49, 48); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; font-size: 14.6667px; background-color: rgb(255, 255, 255); display: inline !important"><br>
</span></div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span style="color: rgb(50, 49, 48); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; font-size: 14.6667px; background-color: rgb(255, 255, 255); display: inline !important"><b><span style="color: rgb(12, 100, 192);">#!/bin/bash</span><br>
</b>
<div><b><span style="color: rgb(12, 100, 192);">#</span><br>
</b></div>
<div><b><span style="color: rgb(12, 100, 192);"># Tested on uv100.awi.de (SGI UV 100, details:</span><br>
</b></div>
<div><b><span style="color: rgb(12, 100, 192);"># http://www.sgi.com/products/servers/uv/specs.html)</span><br>
</b></div>
<div><b><span style="color: rgb(12, 100, 192);"># a) For more speed, provided your data size does not exceed 2GB you can</span><br>
</b></div>
<div><b><span style="color: rgb(12, 100, 192);"># remove -fPIC which carries a performance penalty of 2-6%.</span><br>
</b></div>
<div><b><span style="color: rgb(12, 100, 192);"># b) You can replace -fPIC with '-mcmodel=medium -shared-intel' which may</span><br>
</b></div>
<div><b><span style="color: rgb(12, 100, 192);"># perform faster than -fPIC and still support data sizes over 2GB per</span><br>
</b></div>
<div><b><span style="color: rgb(12, 100, 192);"># process but all the libraries you link to must be compiled with</span><br>
</b></div>
<div><b><span style="color: rgb(12, 100, 192);"># -fPIC or -mcmodel=medium</span><br>
</b></div>
<div><span style="color: rgb(12, 100, 192);"><b># c) flags adjusted for ifort 12.1.0</b></span><br>
</div>
<div><br>
</div>
<div><b><span style="color: rgb(81, 167, 249);">FC=</span>ifort<br>
</b></div>
<div><b><span style="color: rgb(81, 167, 249);">F90C=</span>ifort<br>
</b></div>
<div><b><span style="color: rgb(81, 167, 249);">CC=</span>icc</b><br>
</div>
<div><b><span style="color: rgb(12, 100, 192);"># requires that all static libraries are available:</span><br>
</b></div>
<div><span style="color: rgb(12, 100, 192);"><b>#LINK='ifort -static'</b></span><br>
</div>
<div><b><span style="color: rgb(81, 167, 249);">LINK=</span>'ifort'</b><br>
</div>
<div><b><span style="color: rgb(12, 100, 192);"># for adjoint runs the default makedepend often cannot handle enough files</span><br>
</b></div>
<div><span style="color: rgb(12, 100, 192);"><b>#MAKEDEPEND=tools_xmakedepend</b></span><br>
</div>
<div><br>
</div>
<div><span style="color: rgb(81, 167, 249);"><b>DEFINES=</b></span><span style="color: rgb(200, 38, 19);"><b>'-DWORDLENGTH=4'</b></span><br>
</div>
<div><span style="color: rgb(81, 167, 249);"><b>CPP=</b></span><span style="color: rgb(200, 38, 19);"><b>'cpp -traditional -P'</b></span><b><br>
</b></div>
<div><span style="color: rgb(81, 167, 249);"><b>F90FIXEDFORMAT=</b></span><span style="color: rgb(200, 38, 19);"><b>'-fixed -Tf'</b></span><b><br>
</b></div>
<div><span style="color: rgb(81, 167, 249);"><b>EXTENDED_SRC_FLAG=</b></span><span style="color: rgb(200, 38, 19);"><b>'-132'</b></span><b><br>
</b></div>
<div><span style="color: rgb(81, 167, 249);"><b>#OMPFLAG=</b></span><span style="color: rgb(200, 38, 19);"><b>'-openmp'</b></span><br>
</div>
<div><br>
</div>
<div><span style="color: rgb(81, 167, 249);"><b>NOOPTFLAGS=</b></span><span style="color: rgb(200, 38, 19);"><b>"-O0 -g -m64"</b></span><b><br>
</b></div>
<div><span style="color: rgb(81, 167, 249);"><b>NOOPTFILES=''</b></span><b><br>
</b></div>
<div><b><br>
</b></div>
<div><span style="color: rgb(81, 167, 249);"><b>MCMODEL=</b></span><span style="color: rgb(200, 38, 19);"><b>'-fPIC'</b></span><br>
</div>
<div><span style="color: rgb(12, 100, 192);"><b># for large memory requirements uncomment this line</b></span><b><br>
</b></div>
<div><span style="color: rgb(12, 100, 192);"><b>#MCMODEL='-mcmodel=medium -shared-intel'</b></span><br>
</div>
<div><br>
</div>
<div><span style="color: rgb(81, 167, 249);"><b>FFLAGS=</b></span><span style="color: rgb(200, 38, 19);"><b>"$FFLAGS -W0 -WB -convert big_endian -assume byterecl $MCMODEL"</b></span><br>
</div>
<div><b><span style="color: rgb(12, 100, 192);">#- might want to use '-r8' for fizhi pkg:</span><br>
</b></div>
<div><span style="color: rgb(12, 100, 192);"><b>#FFLAGS="$FFLAGS -r8"</b></span><br>
</div>
<div><br>
</div>
<div><span style="color: rgb(195, 151, 29);"><b>if test </b></span><span style="color: rgb(200, 38, 19);"><b>"x$IEEE"</b></span><span style="color: rgb(195, 151, 29);"><b> = x ; then </b></span><span style="color: rgb(12, 100, 192);"><b> #- with optimisation:</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b> </b></span><span style="color: rgb(81, 167, 249);"><b>FOPTIM=</b></span><span style="color: rgb(81, 167, 249);"><b>'</b></span><span style="color: rgb(200, 38, 19);"><b>-O3 -align'</b></span><br>
</div>
<div><b><span style="color: rgb(12, 100, 192);"># does not work when -static does not work</span><br>
</b></div>
<div><b><span style="color: rgb(12, 100, 192);"># FOPTIM='-fast -align'</span><br>
</b></div>
<div><b><span style="color: rgb(12, 100, 192);"># instead you can use</span><br>
</b></div>
<div><span style="color: rgb(12, 100, 192);"><b># FOPTIM='-O3 -ipo -align'</b></span><br>
</div>
<div><span style="color: rgb(195, 151, 29);"><b>else</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b> if test </b></span><span style="color: rgb(200, 38, 19);"><b>"x$DEVEL"</b></span><span style="color: rgb(195, 151, 29);"><b> = x ; then </b></span><span style="color: rgb(12, 100, 192);"><b>#- no optimisation
+ IEEE :</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b> </b></span><span style="color: rgb(81, 167, 249);"><b> FOPTIM=</b></span><span style="color: rgb(200, 38, 19);"><b>'-O0 -noalign -fp-model precise'</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> </b></span><span style="color: rgb(12, 100, 192);"><b> # -fltconsistency</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b> else </b></span><span style="color: rgb(12, 100, 192);"><b>#- development/check options:</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b> </b></span><span style="color: rgb(81, 167, 249);"><b>FOPTIM=</b></span><span style="color: rgb(200, 38, 19);"><b>'-O0 -noalign -fp-model precise'</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b> </b></span><span style="color: rgb(81, 167, 249);"><b> FOPTIM=</b></span><span style="color: rgb(200, 38, 19);"><b>"$FOPTIM -g -check all -fpe0 -traceback -ftrapuv -fp-model except -warn all"</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b> fi</b></span><b><br>
</b></div>
<b><span></span></b><span style="color: rgb(195, 151, 29);"><b>fi</b></span><span><br>
</span>
<div><br>
</div>
<div><span style="color: rgb(81, 167, 249);"><b>F90FLAGS=</b></span><span style="color: rgb(200, 38, 19);"><b>$FFLAGS</b></span><b><br>
</b></div>
<div><span style="color: rgb(81, 167, 249);"><b>F90OPTIM=</b></span><span style="color: rgb(200, 38, 19);"><b>$FOPTIM</b></span><b><br>
</b></div>
<div><span style="color: rgb(81, 167, 249);"><b>CFLAGS=</b></span><span style="color: rgb(200, 38, 19);"><b>"-O0 -ip $MCMODEL"</b></span><b><br>
</b></div>
<div><b><br>
</b></div>
<div><span style="color: rgb(81, 167, 249);"><b>INCLUDEDIRS=</b></span><b>''<br>
</b></div>
<div><span style="color: rgb(81, 167, 249);"><b>INCLUDES=</b></span><span style="color: rgb(200, 38, 19);"><b>'-I. -I$NETCDF/include -I/WORK/app/netcdf/4.3.2/01-CF-14/include -I/usr/local/mpi3-dynamic/include'</b></span><b><br>
</b></div>
<div><span style="color: rgb(81, 167, 249);"><b>LIBS=</b></span><span style="color: rgb(200, 38, 19);"><b>'-L$NETCDF/lib -lnetcdff -lnetcdf -I/WORK/app/netcdf/4.3.2/01-CF-14/lib'</b></span><b><br>
</b></div>
<div><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b>if [ </b></span><span style="color: rgb(200, 38, 19);"><b>"x$NETCDF_ROOT"</b></span><span style="color: rgb(195, 151, 29);"><b> != x ] ; then</b></span><b><br>
</b></div>
<div><b> </b><span style="color: rgb(81, 167, 249);"><b> INCLUDEDIRS=</b></span><span style="color: rgb(200, 38, 19);"><b>"${NETCDF_ROOT}/include"</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> </b></span><span style="color: rgb(81, 167, 249);"><b> INCLUDES=</b></span><span style="color: rgb(200, 38, 19);"><b>"-I${NETCDF_ROOT}/include"</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> </b></span><span style="color: rgb(81, 167, 249);"><b>LIBS=</b></span><span style="color: rgb(200, 38, 19);"><b>"-L${NETCDF_ROOT}/lib"</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b>elif [ </b></span><span style="color: rgb(200, 38, 19);"><b>"x$NETCDF_HOME"</b></span><span style="color: rgb(195, 151, 29);"><b> != x ]; then</b></span><b><br>
</b></div>
<div><b> </b><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
INCLUDEDIRS=</b>"${NETCDF_HOME}/include"</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
INCLUDES=</b>"-I${NETCDF_HOME}/include"</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
LIBS=</b>"-L${NETCDF_HOME}/lib"</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b>elif [</b></span><span style="color: rgb(200, 38, 19);"><b> "x$NETCDF_INC"</b></span><span style="color: rgb(195, 151, 29);"><b> != x -a
</b></span><span style="color: rgb(200, 38, 19);"><b>"x$NETCDF_LIB"</b></span><span style="color: rgb(195, 151, 29);"><b> != x ]; then</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> </b></span><span style="color: rgb(81, 167, 249);"><b>NETCDF_INC</b></span><span style="color: rgb(200, 38, 19);"><b>=`echo $NETCDF_INC | sed 's/-I//g'`</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> </b></span><span style="color: rgb(81, 167, 249);"><b>NETCDF_LIB=</b></span><span style="color: rgb(200, 38, 19);"><b>`echo $NETCDF_LIB | sed 's/-L//g'`</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">INCLUDEDIRS=</b>"${NETCDF_INC}"</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
INCLUDES=</b>"-I${NETCDF_INC}"</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
LIBS=</b>"-L${NETCDF_LIB}"</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b><span style="margin: 0px; font-weight: 400; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(195, 151, 29); background-color: rgb(255, 255, 255)"><b>elif
[</b></span><span style="margin: 0px; font-weight: 400; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)"><b><span> </span>"x$NETCDF_INCDIR"</b></span><span style="margin: 0px; font-weight: 400; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(195, 151, 29); background-color: rgb(255, 255, 255)"><b><span> </span>!=
x -a<span> </span></b></span><span style="margin: 0px; font-weight: 400; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)"><b>"x$NETCDF_LIBDIR"</b></span><span style="margin: 0px; font-weight: 400; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(195, 151, 29); background-color: rgb(255, 255, 255)"><b><span> </span>!=
x ]; then</b></span></b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">INCLUDEDIRS=</b>"${NETCDF_INCDIR}"</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
INCLUDES=</b>"-I${NETCDF_INCDIR}"</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
LIBS=</b>"-L${NETCDF_LIBDIR}"</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b>elif test -d /usr/include/netcdf-3 ; then</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">INCLUDEDIRS=</b>'/usr/include/netcdf-3'</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">INCLUDES=</b>'-I/usr/include/netcdf-3'</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">LIBS=</b>'-L/usr/lib/netcdf-3
-L/usr/lib64/netcdf-3'</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b>elif test -d /usr/include/netcdf ; then</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
INCLUDEDIRS=</b>'/usr/include/netcdf'</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
INCLUDES=</b>'-I/usr/include/netcdf'</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b>elif test -d /usr/local/netcdf ; then</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
INCLUDEDIRS=</b>'/usr/include/netcdf/include'</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
INCLUDES=</b>'-I/usr/local/netcdf/include'</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
LIBS=</b>'-L/usr/local/netcdf/lib'</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b>elif test -d /usr/local/include/netcdf.inc ; then</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
INCLUDEDIRS=</b>'/usr/local/include'</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
INCLUDES=</b>'-I/usr/local/include'</b></span><b><br>
</b></div>
<div><span style="color: rgb(200, 38, 19);"><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
LIBS=</b>'-L/usr/local/lib64'</b></span><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b>fi</b></span><b><br>
</b></div>
<div><b><br>
</b></div>
<div><span style="color: rgb(195, 151, 29);"><b>if [ -n "$MPI_INC_DIR" -a "x$MPI" = xtrue ] ; then</b></span><b><br>
</b></div>
<div><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
LIBS=</b></b><span style="color: rgb(200, 38, 19);"><b>"$LIBS -lmpi"</b></span><b><br>
</b></div>
<div><b> <b style="color: rgb(81, 167, 249); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
INCLUDES=</b></b><span style="color: rgb(200, 38, 19);"><b>"$INCLUDES -I$MPI_INC_DIR"</b></span><b><br>
</b></div>
<div><b> <b style="color: rgb(200, 38, 19); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; background-color: rgb(255, 255, 255)">
<b style="color: rgb(81, 167, 249); background-color: rgb(255, 255, 255)">INCLUDEDIRS=</b></b></b><span style="color: rgb(200, 38, 19);"><b>"$INCLUDEDIRS $MPI_INC_DIR"</b></span><b><br>
</b></div>
<div><b> </b><span style="color: rgb(12, 100, 192);"><b>#- used for parallel (MPI) DIVA</b></span><b><br>
</b></div>
<div><b> </b><span style="color: rgb(81, 167, 249);"><b>MPIINCLUDEDIR=</b></span><span style="color: rgb(200, 38, 19);"><b>"$MPI_INC_DIR"</b></span><b><br>
</b></div>
<b><span></span></b></span><span style="color: rgb(195, 151, 29); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; font-size: 14.6667px; background-color: rgb(255, 255, 255); display: inline !important;"><b>fi</b></span></div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt">
<div class="PlainText"><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 packages.config. 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 packages.config. 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>
> MITgcm-support mailing list<br>
> MITgcm-support@mitgcm.org<br>
> <a href="http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support">http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support</a><br>
<br>
<br>
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Subject: Digest Footer<br>
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<br>
End of MITgcm-support Digest, Vol 194, Issue 12<br>
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