Index: sm/trunk/src/m/solutions/dakota/qmuin.m
===================================================================
--- /issm/trunk/src/m/solutions/dakota/qmuin.m	(revision 781)
+++ 	(revision )
@@ -1,86 +1,0 @@
-function md=qmuin(md,package,varargin)
-%INPUT function md=qmuin(md,package,varargin)
-%Create dakota input file for parallel runs
-
-global ISSM_DIR;
-
-% qmudir =['qmu_' datestr(now,'yyyymmdd_HHMMSS')];
-qmudir ='qmu';
-%  qmufile can not be changed unless cielo_ice_script.sh is also changed
-qmufile=md.name;
-ivar   =1;
-iresp  =1;
-imethod=1;
-iparams=1;
-runmpi =false;
-
-%  process any extra input arguments
-
-for i=1:2:nargin-2
-    switch varargin{i}
-        case 'qmudir'
-            qmudir =varargin{i+1};
-            disp(sprintf('qmudir =%s',qmudir));
-        case 'qmufile'
-            qmufile=varargin{i+1};
-            disp(sprintf('qmufile=%s',qmufile));
-        case 'ivar'
-            ivar   =varargin{i+1};
-            disp(sprintf('ivar   =%d',ivara));
-        case 'iresp'
-            iresp  =varargin{i+1};
-            disp(sprintf('iresp  =%d',iresp));
-        case 'imethod'
-            imethod=varargin{i+1};
-            disp(sprintf('imethod=%d',imethod));
-        case 'iparams'
-            iparams=varargin{i+1};
-            disp(sprintf('iparams=%d',iparams));
-        case 'overwrite'
-            overwrite=varargin{i+1};
-            disp(sprintf('overwrite=%s',overwrite));
-        case 'outfiles'
-            outfiles =varargin{i+1};
-            disp(sprintf('outfiles =%s',outfiles));
-        case 'rstfile'
-            rstfile  =varargin{i+1};
-            disp(sprintf('rstfile  =%s',rstfile));
-        case 'rundakota'
-            rundakota=varargin{i+1};
-            disp(sprintf('rundakota=%s',rundakota));
-        case 'runmpi'
-            runmpi =varargin{i+1};
-            disp(sprintf('runmpi =%d',runmpi));
-    end
-end
-
-if exist(qmudir,'dir')
-    if ~exist('overwrite','var')
-        overwrite=input(['Overwrite existing ''' qmudir ''' directory? Y/N [N]: '], 's');
-    end
-    if strncmpi(overwrite,'y',1)
-        system(['rm -rf ' qmudir]);
-%    else
-%        error('Existing ''%s'' directory not overwritten.',qmudir);
-    end
-end
-mkdir(qmudir)
-cd(qmudir)
-
-%create m and in files for dakota
-if (~isfield(md.qmu_params(iparams),'direct') || ...
-    ~md.qmu_params(iparams).direct) && ...
-   (~isfield(md.qmu_params(iparams),'analysis_driver') || ...
-    isempty(md.qmu_params(iparams).analysis_driver))
-    md.qmu_params(iparams).analysis_driver=[ISSM_DIR '/src/m/solutions/dakota/cielo_ice_script.sh'];
-end
-
-dakota_in_data(md.qmu_method(imethod),md.variables(ivar),md.responses(iresp),md.qmu_params(iparams),qmufile,package,md);
-
-
-system(['rm -rf ' md.name '.m']);
-cd ../
-
-%keep ivar iresp for variable and response function handling in marshall routine.
-md.iresp=iresp;
-md.ivar=ivar;
Index: sm/trunk/src/m/solutions/dakota/qmuserial.m
===================================================================
--- /issm/trunk/src/m/solutions/dakota/qmuserial.m	(revision 781)
+++ 	(revision )
@@ -1,184 +1,0 @@
-function md=qmuserial(md,package,varargin)
-%INPUT function md=qmu(md,package)
-%Deal with coupled ISSM or Cielo/ Dakota runs, to do sensitivity analyses.
-
-global ISSM_DIR;
-
-% qmudir =['qmu_' datestr(now,'yyyymmdd_HHMMSS')];
-qmudir ='qmu';
-%  qmufile can not be changed unless cielo_ice_script.sh is also changed
-qmufile='qmu';
-ivar   =1;
-iresp  =1;
-imethod=1;
-iparams=1;
-runmpi =false;
-
-
-%  process any extra input arguments
-
-for i=1:2:nargin-2
-    switch varargin{i}
-        case 'qmudir'
-            qmudir =varargin{i+1};
-            disp(sprintf('qmudir =%s',qmudir));
-        case 'qmufile'
-            qmufile=varargin{i+1};
-            disp(sprintf('qmufile=%s',qmufile));
-        case 'ivar'
-            ivar   =varargin{i+1};
-            disp(sprintf('ivar   =%d',ivara));
-        case 'iresp'
-            iresp  =varargin{i+1};
-            disp(sprintf('iresp  =%d',iresp));
-        case 'imethod'
-            imethod=varargin{i+1};
-            disp(sprintf('imethod=%d',imethod));
-        case 'iparams'
-            iparams=varargin{i+1};
-            disp(sprintf('iparams=%d',iparams));
-        case 'overwrite'
-            overwrite=varargin{i+1};
-            disp(sprintf('overwrite=%s',overwrite));
-        case 'outfiles'
-            outfiles =varargin{i+1};
-            disp(sprintf('outfiles =%s',outfiles));
-        case 'rstfile'
-            rstfile  =varargin{i+1};
-            disp(sprintf('rstfile  =%s',rstfile));
-        case 'rundakota'
-            rundakota=varargin{i+1};
-            disp(sprintf('rundakota=%s',rundakota));
-        case 'runmpi'
-            runmpi =varargin{i+1};
-            disp(sprintf('runmpi =%d',runmpi));
-    end
-end
-
-%first create temporary directory in which we will work
-if exist(qmudir,'dir')
-    if ~exist('overwrite','var')
-        overwrite=input(['Overwrite existing ''' qmudir ''' directory? Y/N [N]: '], 's');
-    end
-    if strncmpi(overwrite,'y',1)
-        system(['rm -rf ' qmudir]);
-%    else
-%        error('Existing ''%s'' directory not overwritten.',qmudir);
-    end
-end
-mkdir(qmudir)
-cd(qmudir)
-system('cp $ISSM_DIR/startup.m .');
-
-%save our model in qmu so that it can be repeatedly used by Dakota.
-save('Qmu.model','md')
-
-%create m and in files for dakota
-if (~isfield(md.qmu_params(iparams),'direct') || ...
-    ~md.qmu_params(iparams).direct) && ...
-   (~isfield(md.qmu_params(iparams),'analysis_driver') || ...
-    isempty(md.qmu_params(iparams).analysis_driver))
-    md.qmu_params(iparams).analysis_driver=[ISSM_DIR '/src/m/solutions/dakota/cielo_ice_script.sh'];
-end
-dakota_in_data(md.qmu_method(imethod),md.variables(ivar),md.responses(iresp),md.qmu_params(iparams),qmufile,package,md);
-
-%  check for existence of results.out files to use
-if exist('results.out.1','file') || exist('results.out.zip','file')
-    if ~exist('outfiles','var')
-        outfiles=input(['Use existing ''results.out'' files? Y/N [N]: '], 's');
-    end
-    if ~strncmpi(outfiles,'y',1)
-        system('rm -f results.out.[1-9]*');
-    else
-        if exist('results.out.zip','file') && ~exist('results.out.1','file')
-            display('Inflating ''results.out.zip'' file.');
-            system('unzip -q results.out.zip');
-        end
-    end
-end
-
-%  check for existence of dakota.rst file to use
-rstflag='';
-if (~exist('outfiles','var') || ~strncmpi(outfiles,'y',1)) && ...
-    exist('dakota.rst','file')
-    if ~exist('rstfile','var')
-        rstfiles=input(['Use existing ''dakota.rst'' file? Y/N [N]: '], 's');
-    end
-    if strncmpi(rstfiles,'y',1)
-        system('rm -f results.out.[1-9]*');
-        system('dakota_restart_util print dakota.rst | grep completed');
-        rstflag=' -read_restart dakota.rst';
-    end
-end
-
-%call dakota
-if ~exist('rundakota','var')
-    rundakota=input(['Run Dakota analysis ''' qmufile '''? Y/N [N]: '], 's');
-end
-if ~strncmpi(rundakota,'y',1)
-    cd ..
-    return
-end
-
-if ~runmpi
-    system(['dakota -i ' qmufile '.in -o ' qmufile '.out -e ' qmufile '.err' rstflag]);
-else
-%  use 'mpd --ncpus=8 &' to initialize mpi and 'mpdringtest' to verify.
-%  exporting MPIRUN_NPROCS sets mpi in dakota.
-%    system('mpd --ncpus=8 &');
-%    system('mpdringtest');
-    system(['export MPIRUN_NPROCS=8;mpirun -np 4 dakota -i ' qmufile '.in -o ' qmufile '.out -e ' qmufile '.err' rstflag]);
-end
-
-%  check to see if dakota returned errors in the err file
-if exist([qmufile '.err'],'file')
-   fide=fopen([qmufile '.err'],'r');
-   fline=fgetl(fide);
-   if ischar(fline)
-       while ischar(fline)
-           disp(sprintf('%s',fline));
-           fline=fgetl(fide);
-       end
-       status=fclose(fide);
-       cd ../
-       error(['Dakota returned error in ''' qmufile '.err'' file.  ''' qmudir ''' directory retained.'])
-    end
-    status=fclose(fide);
-else
-   cd ../
-   error(['Dakota did not generate ''' qmufile '.err'' file.  ''' qmudir ''' directory retained.'])
-end
-
-%parse inputs and results from dakota
-[method,dvar,dresp_in]=dakota_in_parse([qmufile '.in']);
-md.dakotaresults.method   =method;
-md.dakotaresults.dvar     =dvar;
-md.dakotaresults.dresp_in =dresp_in;
-
-[method,dresp_out,scm,pcm,srcm,prcm]=dakota_out_parse([qmufile '.out']);
-md.dakotaresults.dresp_out=dresp_out;
-md.dakotaresults.scm      =scm;
-md.dakotaresults.pcm      =pcm;
-md.dakotaresults.srcm     =srcm;
-md.dakotaresults.prcm     =prcm;
-
-if exist('dakota_tabular.dat','file')
-    [method,dresp_dat                  ]=dakota_out_parse('dakota_tabular.dat');
-    md.dakotaresults.dresp_dat=dresp_dat;
-end
-
-%save input and output files into model
-%md.dakotain =readfile([qmufile '.in']);
-%md.dakotaout=readfile([qmufile '.out']);
-%if exist('dakota_tabular.dat','file')
-%	md.dakotadat=readfile('dakota_tabular.dat');
-%end
-
-%  move all the individual function evalutations into zip files
-system('zip -mq params.in.zip params.in.[1-9]*');
-system('zip -mq results.out.zip results.out.[1-9]*');
-system('zip -mq matlab.out.zip matlab*.out.[1-9]*');
-
-%get out of local directory and erase
-cd ../
-% system(['rm -rf ' qmudir]);