Index: /issm/trunk/src/m/classes/clusters/README =================================================================== --- /issm/trunk/src/m/classes/clusters/README (revision 8585) +++ /issm/trunk/src/m/classes/clusters/README (revision 8586) @@ -9,4 +9,4 @@ How to add your cluster? -use an existing cluster script, such as pleiades.m, and rename it to your cluster name. +use an existing cluster script, such as pfe.m, and rename it to your cluster name. update the methods. Index: /issm/trunk/src/m/classes/clusters/astrid.m =================================================================== --- /issm/trunk/src/m/classes/clusters/astrid.m (revision 8585) +++ /issm/trunk/src/m/classes/clusters/astrid.m (revision 8586) @@ -25,142 +25,13 @@ function cluster=astrid(varargin) % {{{1 - %initialize cluster using user settings if provided - if (exist('astrid_settings')==2), astrid_settings; end - - %use provided options to change fields - options=pairoptions(varargin{:}); - for i=1:size(options.list,1), - fieldname=options.list{i,1}; - fieldvalue=options.list{i,2}; - if ismember(fieldname,properties(astrid)), - cluster.(fieldname)=fieldvalue; - else - disp(['''' fieldname ''' is not a property of cluster astrid']); - end - end + disp( '!!! '); + disp( '!!! WARNING'); + disp(['!!! ''astrid'' is now deprecated. Please use the generic cluster instead']); + disp(['!!! ''generic'' uses the same properties as ''astrid'' but the option ''name'' is now mandatory:']); + disp(['!!! Ex: md.cluster=generic(''name'',oshostname,''np'',3);']); + disp( '!!! '); + error('''astrid'' not supported anymore'); end %}}} - function disp(cluster) % {{{1 - % display the object - disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); - disp(sprintf(' name: %s',cluster.name)); - disp(sprintf(' login: %s',cluster.login)); - disp(sprintf(' np: %i',cluster.np)); - disp(sprintf(' port: %i',cluster.port)); - disp(sprintf(' codepath: %s',cluster.codepath)); - disp(sprintf(' executionpath: %s',cluster.executionpath)); - disp(sprintf(' valgrind: %s',cluster.valgrind)); - disp(sprintf(' valgrindlib: %s',cluster.valgrindlib)); - disp(sprintf(' valgrindsup: %s',cluster.valgrindsup)); - end - %}}} - function IsConsistent(cluster) % {{{1 - if cluster.np>16, - error('IsConsistent error message: number of processors should be less than 16!'); - end - if isnan(cluster.np), - error('IsConsistent error message: number of processors should not be NaN!'); - end - end - %}}} - function BuildQueueScript(cluster,md) % {{{1 - - %retrieve parameters - modelname=md.name; - solution_type=md.solution_type; - mem_debug=md.mem_debug; - - %open file for writing: - fid=fopen([modelname '.queue'],'w'); - - %write instructions for launching a job on the cluster - fprintf(fid,'#!/bin/sh\n'); - if mem_debug==0, - if cluster.interactive - fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock ',... - cluster.np,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname); - else - fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog ',... - cluster.np,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - end - else - %fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --gen-suppressions=all --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog ',... - cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - end - - if md.gprof, - fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname); - end - - if ~md.io_gather, - %concatenate the output files: - fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname); - end - - %in interactive mode, create a run file, and errlog and outlog file - if cluster.interactive, - fid=fopen([modelname '.errlog'],'w'); fclose(fid); - fid=fopen([modelname '.outlog'],'w'); fclose(fid); - end - - end - %}}} - function LaunchQueueJob(cluster,md,options)% {{{1 - - %lauch command, to be executed via ssh - launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... - ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue ']; - - if ~strcmpi(options.batch,'yes'), - - %compress the files into one zip. - compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; - if md.qmu_analysis, - compressstring=[compressstring md.name '.qmu.in']; - end - if cluster.interactive, - compressstring=[compressstring ' ' md.name '.errlog ' md.name '.outlog ']; - end - system(compressstring); - - disp('uploading input file and queueing script'); - issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[md.runtimename '.tar.gz']}); - - disp('launching solution sequence on remote cluster'); - issmssh(cluster.name,cluster.login,cluster.port,launchcommand); - else - disp('batch mode requested: not launching job interactively'); - disp('launch solution sequence on remote cluster by hand'); - end - - end %}}} - function Download(cluster,md)% {{{1 - - %some check - if isempty(md.runtimename), - error('pfe Download error message: supply runtime name for results to be loaded!'); - end - - %Figure out the directory where all the files are in: - directory=[cluster.executionpath '/' md.runtimename '/']; - - %What packages are we picking up from remote cluster - packages={[md.name '.outlog'],[md.name '.errlog']}; - if md.qmu_analysis, - packages{end+1}=[md.name '.qmu.err']; - packages{end+1}=[md.name '.qmu.out']; - if isfield(md.qmu_params,'tabular_graphics_data'), - if md.qmu_params.tabular_graphics_data==true, - packages{end+1}='dakota_tabular.dat'; - end - end - else - packages{end+1}=[md.name '.outbin']; - end - - %copy files from cluster to present directory - issmscpin(cluster.name, cluster.login, cluster.port, directory, packages); - end %}}} end end Index: /issm/trunk/src/m/classes/clusters/generic.m =================================================================== --- /issm/trunk/src/m/classes/clusters/generic.m (revision 8585) +++ /issm/trunk/src/m/classes/clusters/generic.m (revision 8586) @@ -1,15 +1,15 @@ -%ASTRID class definition +%GENERIC cluster class definition % % Usage: -% cluster=generic(); -% cluster=generic('np',3); -% cluster=generic('np',3,'name','astrid','login','username'); +% cluster=generic('name','astrid',); +% cluster=generic('name','astrid','np',3); +% cluster=generic('name',oshostname(),'np',3,'login','username'); classdef generic properties (SetAccess=public) % {{{1 - name=oshostname(); + name=''; login=''; - np=feature('numcores'); + np=1; port=0; interactive=1; @@ -23,10 +23,16 @@ methods function cluster=generic(varargin) % {{{1 - + + %use provided options to change fields + options=pairoptions(varargin{:}); + + %get name + if ~exist(options,'name'), error('option ''name'' has not been provided'); end + cluster.name=getfieldvalue(options,'name'); + %initialize cluster using user settings if provided if (exist([cluster.name '_settings'])==2), eval([cluster.name '_settings']); end - %use provided options to change fields - options=pairoptions(varargin{:}); + %OK get other fields for i=1:size(options.list,1), fieldname=options.list{i,1}; @@ -55,6 +61,6 @@ %}}} function IsConsistent(cluster) % {{{1 - if cluster.np>feature('numcores'), - error(['number of processors exceeds number of cores seen by matlab ' num2str(feature('numcores'))]); + if cluster.np<1 + error(['number of processors should be at least 1']); end if isnan(cluster.np), Index: sm/trunk/src/m/classes/clusters/larsen.m =================================================================== --- /issm/trunk/src/m/classes/clusters/larsen.m (revision 8585) +++ (revision ) @@ -1,157 +1,0 @@ -%LARSEN class definition -% -% Usage: -% cluster=larsen(); -% cluster=larsen('np',3); -% cluster=larsen('np',3,'login','username'); - -classdef larsen - properties (SetAccess=public) - % {{{1 - name='larsen' - login=''; - np=7; - port=0; - interactive=1; - codepath=[issmtier() '/bin']; - executionpath=[issmdir() '/execution']; - valgrind=[issmtier() '/externalpackages/valgrind/install/bin/valgrind']; - valgrindlib=[issmtier() '/externalpackages/valgrind/install/lib/libmpidebug.so']; - valgrindsup=[issmtier() '/externalpackages/valgrind/issm.supp']; - %}}} - end - methods - function cluster=larsen(varargin) % {{{1 - options=pairoptions(varargin{:}); - for i=1:size(options.list,1), - fieldname=options.list{i,1}; - fieldvalue=options.list{i,2}; - if ismember(fieldname,properties(larsen)), - cluster.(fieldname)=fieldvalue; - else - disp(['''' fieldname ''' is not a property of cluster larsen']); - end - end - end - %}}} - function disp(cluster) % {{{1 - % display the object - disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); - disp(sprintf(' name: %s',cluster.name)); - disp(sprintf(' login: %s',cluster.login)); - disp(sprintf(' np: %i',cluster.np)); - disp(sprintf(' port: %i',cluster.port)); - disp(sprintf(' codepath: %s',cluster.codepath)); - disp(sprintf(' executionpath: %s',cluster.executionpath)); - disp(sprintf(' valgrind: %s',cluster.valgrind)); - disp(sprintf(' valgrindlib: %s',cluster.valgrindlib)); - disp(sprintf(' valgrindsup: %s',cluster.valgrindsup)); - end - %}}} - function IsConsistent(cluster) % {{{1 - if cluster.np>8, - error('IsConsistent error message: number of processors should be less than 8!'); - end - if isnan(cluster.np), - error('IsConsistent error message: number of processors should not be NaN!'); - end - end - %}}} - function BuildQueueScript(cluster,md) % {{{1 - - %retrieve parameters - modelname=md.name; - solution_type=md.solution_type; - mem_debug=md.mem_debug; - - %open file for writing: - fid=fopen([modelname '.queue'],'w'); - - %write instructions for launching a job on the cluster - fprintf(fid,'#!/bin/sh\n'); - if mem_debug==0, - if cluster.interactive - fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock',... - cluster.np,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname); - else - fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',... - cluster.np,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - end - else - %fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --gen-suppressions=all --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',... - cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - end - - if md.gprof, - fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname); - end - fclose(fid); - - %in interactive mode, create a run file, and errlog and outlog file - if cluster.interactive, - fid=fopen([modelname '.errlog'],'w'); fclose(fid); - fid=fopen([modelname '.outlog'],'w'); fclose(fid); - end - end - %}}} - function LaunchQueueJob(cluster,md,options)% {{{1 - - %lauch command, to be executed via ssh - launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... - ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue ']; - - if ~strcmpi(options.batch,'yes'), - - %compress the files into one zip. - compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; - if md.qmu_analysis, - compressstring=[compressstring md.name '.qmu.in']; - end - if cluster.interactive, - compressstring=[compressstring ' ' md.name '.errlog ' md.name '.outlog ']; - end - system(compressstring); - - disp('uploading input file and queueing script'); - issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); - - disp('launching solution sequence on remote cluster'); - issmssh(md.cluster.name,md.cluster.login,md.cluster.port,launchcommand); - - else - disp('batch mode requested: not launching job interactively'); - disp('launch solution sequence on remote cluster by hand'); - end - - end - %}}} - function Download(cluster,md)% {{{1 - - %some check - if isempty(md.runtimename), - error('pfe Download error message: supply runtime name for results to be loaded!'); - end - - %Figure out the directory where all the files are in: - directory=[cluster.executionpath '/' md.runtimename '/']; - - %What packages are we picking up from remote cluster - packages={[md.name '.outlog'],[md.name '.errlog']}; - if md.qmu_analysis, - packages{end+1}=[md.name '.qmu.err']; - packages{end+1}=[md.name '.qmu.out']; - if isfield(md.qmu_params,'tabular_graphics_data'), - if md.qmu_params.tabular_graphics_data==true, - packages{end+1}='dakota_tabular.dat'; - end - end - else - packages{end+1}=[md.name '.outbin']; - end - - %copy files from cluster to present directory - issmscpin(cluster.name, cluster.login, cluster.port, directory, packages); - end %}}} - end -end Index: sm/trunk/src/m/classes/clusters/maceric.m =================================================================== --- /issm/trunk/src/m/classes/clusters/maceric.m (revision 8585) +++ (revision ) @@ -1,139 +1,0 @@ -%ERICMAC class definition -% -% Usage: -% cluster=ericmac(); -% cluster=ericmac('np',3); -% cluster=ericmac('np',3,'login','username'); - -classdef ericmac - properties (SetAccess=public) - % {{{1 - name='ericmac' - login='larour'; - np=3; - port=0; - codepath=[issmtier() '/bin']; - executionpath=[issmdir() '/execution']; - valgrind=[issmtier() '/externalpackages/valgrind/install/bin/valgrind']; - valgrindlib=[issmtier() '/externalpackages/valgrind/install/lib/libmpidebug.so']; - valgrindsup=[issmtier() '/externalpackages/valgrind/issm.supp']; - %}}} - end - methods - function cluster=ericmac(varargin) % {{{1 - options=pairoptions(varargin{:}); - for i=1:size(options.list,1), - fieldname=options.list{i,1}; - fieldvalue=options.list{i,2}; - if ismember(fieldname,properties(ericmac)), - cluster.(fieldname)=fieldvalue; - else - disp(['''' fieldname ''' is not a property of cluster ericmac']); - end - end - end - %}}} - function disp(cluster) % {{{1 - % display the object - disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); - disp(sprintf(' name: %s',cluster.name)); - disp(sprintf(' login: %s',cluster.login)); - disp(sprintf(' np: %i',cluster.np)); - disp(sprintf(' port: %i',cluster.port)); - disp(sprintf(' codepath: %s',cluster.codepath)); - disp(sprintf(' executionpath: %s',cluster.executionpath)); - disp(sprintf(' valgrind: %s',cluster.valgrind)); - disp(sprintf(' valgrindlib: %s',cluster.valgrindlib)); - disp(sprintf(' valgrindsup: %s',cluster.valgrindsup)); - end - %}}} - function IsConsistent(cluster) % {{{1 - if cluster.np>4, - error('IsConsistent error message: number of processors should be less than 4!'); - end - if isnan(cluster.np), - error('IsConsistent error message: number of processors should not be NaN!'); - end - end - %}}} - function BuildQueueScript(cluster,md) % {{{1 - - %retrieve parameters - modelname=md.name; - solution_type=md.solution_type; - mem_debug=md.mem_debug; - - %open file for writing: - fid=fopen([modelname '.queue'],'w'); - - %write instructions for launching a job on the cluster - fprintf(fid,'#!/bin/sh\n'); - if mem_debug==0, - fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.np,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - else - %fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --gen-suppressions=all --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - end - - %close file - fclose(fid); - - end - %}}} - function LaunchQueueJob(cluster,md,options)% {{{1 - - %lauch command, to be executed via ssh - launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... - ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue ']; - - if ~strcmpi(options.batch,'yes'), - - %compress the files into one zip. - compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; - if md.qmu_analysis, - compressstring=[compressstring md.name '.qmu.in']; - end - system(compressstring); - - disp('uploading input file and queueing script'); - issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); - - disp('launching solution sequence on remote cluster'); - issmssh(md.cluster.name,md.cluster.login,md.cluster.port,launchcommand); - - else - disp('batch mode requested: not launching job interactively'); - disp('launch solution sequence on remote cluster by hand'); - end - - end - %}}} - function Download(cluster,md)% {{{1 - - %some check - if isempty(md.runtimename), - error('pfe Download error message: supply runtime name for results to be loaded!'); - end - - %Figure out the directory where all the files are in: - directory=[cluster.executionpath '/' md.runtimename '/']; - - %What packages are we picking up from remote cluster - packages={[md.name '.outlog'],[md.name '.errlog']}; - if md.qmu_analysis, - packages{end+1}=[md.name '.qmu.err']; - packages{end+1}=[md.name '.qmu.out']; - if isfield(md.qmu_params,'tabular_graphics_data'), - if md.qmu_params.tabular_graphics_data==true, - packages{end+1}='dakota_tabular.dat'; - end - end - else - packages{end+1}=[md.name '.outbin']; - end - - %copy files from cluster to present directory - issmscpin(cluster.name, cluster.login, cluster.port, directory, packages); - end %}}} - end -end Index: sm/trunk/src/m/classes/clusters/machelene.m =================================================================== --- /issm/trunk/src/m/classes/clusters/machelene.m (revision 8585) +++ (revision ) @@ -1,139 +1,0 @@ -%ERICMAC class definition -% -% Usage: -% cluster=machelene(); -% cluster=machelene('np',3); -% cluster=machelene('np',3,'login','username'); - -classdef machelene - properties (SetAccess=public) - % {{{1 - name='machelene' - login='helene'; - np=3; - port=0; - codepath=[issmtier() '/bin']; - executionpath=[issmdir() '/execution']; - valgrind=[issmtier() '/externalpackages/valgrind/install/bin/valgrind']; - valgrindlib=[issmtier() '/externalpackages/valgrind/install/lib/libmpidebug.so']; - valgrindsup=[issmtier() '/externalpackages/valgrind/issm.supp']; - %}}} - end - methods - function cluster=machelene(varargin) % {{{1 - options=pairoptions(varargin{:}); - for i=1:size(options.list,1), - fieldname=options.list{i,1}; - fieldvalue=options.list{i,2}; - if ismember(fieldname,properties(machelene)), - cluster.(fieldname)=fieldvalue; - else - disp(['''' fieldname ''' is not a property of cluster machelene']); - end - end - end - %}}} - function disp(cluster) % {{{1 - % display the object - disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); - disp(sprintf(' name: %s',cluster.name)); - disp(sprintf(' login: %s',cluster.login)); - disp(sprintf(' np: %i',cluster.np)); - disp(sprintf(' port: %i',cluster.port)); - disp(sprintf(' codepath: %s',cluster.codepath)); - disp(sprintf(' executionpath: %s',cluster.executionpath)); - disp(sprintf(' valgrind: %s',cluster.valgrind)); - disp(sprintf(' valgrindlib: %s',cluster.valgrindlib)); - disp(sprintf(' valgrindsup: %s',cluster.valgrindsup)); - end - %}}} - function IsConsistent(cluster) % {{{1 - if cluster.np>4, - error('IsConsistent error message: number of processors should be less than 4!'); - end - if isnan(cluster.np), - error('IsConsistent error message: number of processors should not be NaN!'); - end - end - %}}} - function BuildQueueScript(cluster,md) % {{{1 - - %retrieve parameters - modelname=md.name; - solution_type=md.solution_type; - mem_debug=md.mem_debug; - - %open file for writing: - fid=fopen([modelname '.queue'],'w'); - - %write instructions for launching a job on the cluster - fprintf(fid,'#!/bin/sh\n'); - if mem_debug==0, - fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock ',cluster.np,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname); - else - %fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --gen-suppressions=all --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - end - - %close file - fclose(fid); - - end - %}}} - function LaunchQueueJob(cluster,md,options)% {{{1 - - %lauch command, to be executed via ssh - launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... - ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue ']; - - if ~strcmpi(options.batch,'yes'), - - %compress the files into one zip. - compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; - if md.qmu_analysis, - compressstring=[compressstring md.name '.qmu.in']; - end - system(compressstring); - - disp('uploading input file and queueing script'); - issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); - - disp('launching solution sequence on remote cluster'); - issmssh(md.cluster.name,md.cluster.login,md.cluster.port,launchcommand); - - else - disp('batch mode requested: not launching job interactively'); - disp('launch solution sequence on remote cluster by hand'); - end - - end - %}}} - function Download(cluster,md)% {{{1 - - %some check - if isempty(md.runtimename), - error('pfe Download error message: supply runtime name for results to be loaded!'); - end - - %Figure out the directory where all the files are in: - directory=[cluster.executionpath '/' md.runtimename '/']; - - %What packages are we picking up from remote cluster - packages={[md.name '.outlog'],[md.name '.errlog']}; - if md.qmu_analysis, - packages{end+1}=[md.name '.qmu.err']; - packages{end+1}=[md.name '.qmu.out']; - if isfield(md.qmu_params,'tabular_graphics_data'), - if md.qmu_params.tabular_graphics_data==true, - packages{end+1}='dakota_tabular.dat'; - end - end - else - packages{end+1}=[md.name '.outbin']; - end - - %copy files from cluster to present directory - issmscpin(cluster.name, cluster.login, cluster.port, directory, packages); - end %}}} - end -end Index: sm/trunk/src/m/classes/clusters/macmathieu.m =================================================================== --- /issm/trunk/src/m/classes/clusters/macmathieu.m (revision 8585) +++ (revision ) @@ -1,139 +1,0 @@ -%ERICMAC class definition -% -% Usage: -% cluster=macmathieu(); -% cluster=macmathieu('np',3); -% cluster=macmathieu('np',3,'login','username'); - -classdef macmathieu - properties (SetAccess=public) - % {{{1 - name='macmathieu' - login='mathieu'; - np=3; - port=0; - codepath=[issmtier() '/bin']; - executionpath=[issmdir() '/execution']; - valgrind=[issmtier() '/externalpackages/valgrind/install/bin/valgrind']; - valgrindlib=[issmtier() '/externalpackages/valgrind/install/lib/libmpidebug.so']; - valgrindsup=[issmtier() '/externalpackages/valgrind/issm.supp']; - %}}} - end - methods - function cluster=macmathieu(varargin) % {{{1 - options=pairoptions(varargin{:}); - for i=1:size(options.list,1), - fieldname=options.list{i,1}; - fieldvalue=options.list{i,2}; - if ismember(fieldname,properties(macmathieu)), - cluster.(fieldname)=fieldvalue; - else - disp(['''' fieldname ''' is not a property of cluster macmathieu']); - end - end - end - %}}} - function disp(cluster) % {{{1 - % display the object - disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); - disp(sprintf(' name: %s',cluster.name)); - disp(sprintf(' login: %s',cluster.login)); - disp(sprintf(' np: %i',cluster.np)); - disp(sprintf(' port: %i',cluster.port)); - disp(sprintf(' codepath: %s',cluster.codepath)); - disp(sprintf(' executionpath: %s',cluster.executionpath)); - disp(sprintf(' valgrind: %s',cluster.valgrind)); - disp(sprintf(' valgrindlib: %s',cluster.valgrindlib)); - disp(sprintf(' valgrindsup: %s',cluster.valgrindsup)); - end - %}}} - function IsConsistent(cluster) % {{{1 - if cluster.np>4, - error('IsConsistent error message: number of processors should be less than 4!'); - end - if isnan(cluster.np), - error('IsConsistent error message: number of processors should not be NaN!'); - end - end - %}}} - function BuildQueueScript(cluster,md) % {{{1 - - %retrieve parameters - modelname=md.name; - solution_type=md.solution_type; - mem_debug=md.mem_debug; - - %open file for writing: - fid=fopen([modelname '.queue'],'w'); - - %write instructions for launching a job on the cluster - fprintf(fid,'#!/bin/sh\n'); - if mem_debug==0, - fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock ',cluster.np,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname); - else - %fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --gen-suppressions=all --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - end - - %close file - fclose(fid); - - end - %}}} - function LaunchQueueJob(cluster,md,options)% {{{1 - - %lauch command, to be executed via ssh - launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... - ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue ']; - - if ~strcmpi(options.batch,'yes'), - - %compress the files into one zip. - compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; - if md.qmu_analysis, - compressstring=[compressstring md.name '.qmu.in']; - end - system(compressstring); - - disp('uploading input file and queueing script'); - issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); - - disp('launching solution sequence on remote cluster'); - issmssh(md.cluster.name,md.cluster.login,md.cluster.port,launchcommand); - - else - disp('batch mode requested: not launching job interactively'); - disp('launch solution sequence on remote cluster by hand'); - end - - end - %}}} - function Download(cluster,md)% {{{1 - - %some check - if isempty(md.runtimename), - error('pfe Download error message: supply runtime name for results to be loaded!'); - end - - %Figure out the directory where all the files are in: - directory=[cluster.executionpath '/' md.runtimename '/']; - - %What packages are we picking up from remote cluster - packages={[md.name '.outlog'],[md.name '.errlog']}; - if md.qmu_analysis, - packages{end+1}=[md.name '.qmu.err']; - packages{end+1}=[md.name '.qmu.out']; - if isfield(md.qmu_params,'tabular_graphics_data'), - if md.qmu_params.tabular_graphics_data==true, - packages{end+1}='dakota_tabular.dat'; - end - end - else - packages{end+1}=[md.name '.outbin']; - end - - %copy files from cluster to present directory - issmscpin(cluster.name, cluster.login, cluster.port, directory, packages); - end %}}} - end -end Index: sm/trunk/src/m/classes/clusters/murdo.m =================================================================== --- /issm/trunk/src/m/classes/clusters/murdo.m (revision 8585) +++ (revision ) @@ -1,152 +1,0 @@ -%MURDO class definition -% -% Usage: -% cluster=murdo(); -% cluster=murdo('np',3); -% cluster=murdo('np',3,'login','username'); - -classdef murdo - properties (SetAccess=public) - % {{{1 - name='murdo'; - login='larour'; - np=24; - port=0; - codepath=[issmtier() '/bin']; - executionpath=[issmdir() '/execution']; - valgrind=[issmtier() '/externalpackages/valgrind/install/bin/valgrind']; - valgrindlib=[issmtier() '/externalpackages/valgrind/install/lib/libmpidebug.so']; - valgrindsup=[issmtier() '/externalpackages/valgrind/issm.supp']; - - %}}} - end - methods - function cluster=murdo(varargin) % {{{1 - - %initialize cluster using user settings if provided - if (exist('murdo_settings')==2), murdo_settings; end - - %use provided options to change fields - options=pairoptions(varargin{:}); - for i=1:size(options.list,1), - fieldname=options.list{i,1}; - fieldvalue=options.list{i,2}; - if ismember(fieldname,properties(murdo)), - cluster.(fieldname)=fieldvalue; - else - disp(['''' fieldname ''' is not a property of cluster murdo']); - end - end - end - %}}} - function disp(cluster) % {{{1 - % display the object - disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); - disp(sprintf(' name: %s',cluster.name)); - disp(sprintf(' login: %s',cluster.login)); - disp(sprintf(' np: %i',cluster.np)); - disp(sprintf(' port: %i',cluster.port)); - disp(sprintf(' codepath: %s',cluster.codepath)); - disp(sprintf(' executionpath: %s',cluster.executionpath)); - disp(sprintf(' valgrind: %s',cluster.valgrind)); - disp(sprintf(' valgrindlib: %s',cluster.valgrindlib)); - disp(sprintf(' valgrindsup: %s',cluster.valgrindsup)); - end - %}}} - function IsConsistent(cluster) % {{{1 - if cluster.np>24, - error('IsConsistent error message: number of processors should be less than 24!'); - end - if isnan(cluster.np), - error('IsConsistent error message: number of processors should not be NaN!'); - end - end - %}}} - function BuildQueueScript(cluster,md) % {{{1 - - %retrieve parameters - modelname=md.name; - solution_type=md.solution_type; - mem_debug=md.mem_debug; - - %open file for writing: - fid=fopen([modelname '.queue'],'w'); - - %write instructions for launching a job on the cluster - fprintf(fid,'#!/bin/sh\n'); - if mem_debug==0, - fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - else - %fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --gen-suppressions=all --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - end - - if md.gprof, - fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname); - end - - if ~md.io_gather, - %concatenate the output files: - fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname); - end - - %close file - fclose(fid); - - end - %}}} - function LaunchQueueJob(cluster,md,options)% {{{1 - - %lauch command, to be executed via ssh - launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... - ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue ']; - - if ~strcmpi(options.batch,'yes'), - - %compress the files into one zip. - compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; - if md.qmu_analysis, - compressstring=[compressstring md.name '.qmu.in']; - end - system(compressstring); - - disp('uploading input file and queueing script'); - issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[md.runtimename '.tar.gz']}); - - disp('launching solution sequence on remote cluster'); - issmssh(cluster.name,cluster.login,cluster.port,launchcommand); - else - disp('batch mode requested: not launching job interactively'); - disp('launch solution sequence on remote cluster by hand'); - end - - end %}}} - function Download(cluster,md)% {{{1 - - %some check - if isempty(md.runtimename), - error('pfe Download error message: supply runtime name for results to be loaded!'); - end - - %Figure out the directory where all the files are in: - directory=[cluster.executionpath '/' md.runtimename '/']; - - %What packages are we picking up from remote cluster - packages={[md.name '.outlog'],[md.name '.errlog']}; - if md.qmu_analysis, - packages{end+1}=[md.name '.qmu.err']; - packages{end+1}=[md.name '.qmu.out']; - if isfield(md.qmu_params,'tabular_graphics_data'), - if md.qmu_params.tabular_graphics_data==true, - packages{end+1}='dakota_tabular.dat'; - end - end - else - packages{end+1}=[md.name '.outbin']; - end - - %copy files from cluster to present directory - issmscpin(cluster.name, cluster.login, cluster.port, directory, packages); - end %}}} - end -end Index: sm/trunk/src/m/classes/clusters/ogive.m =================================================================== --- /issm/trunk/src/m/classes/clusters/ogive.m (revision 8585) +++ (revision ) @@ -1,143 +1,0 @@ -%LARSEN class definition -% -% Usage: -% cluster=ogive(); -% cluster=ogive('np',3); -% cluster=ogive('np',3,'login','username'); - -classdef ogive - properties (SetAccess=public) - % {{{1 - name='ogive' - login='larour'; - np=7; - port=0; - codepath=[issmtier() '/bin']; - executionpath=[issmdir() '/execution']; - valgrind=[issmtier() '/externalpackages/valgrind/install/bin/valgrind']; - valgrindlib=[issmtier() '/externalpackages/valgrind/install/lib/libmpidebug.so']; - valgrindsup=[issmtier() '/externalpackages/valgrind/issm.supp']; - %}}} - end - methods - function cluster=ogive(varargin) % {{{1 - options=pairoptions(varargin{:}); - for i=1:size(options.list,1), - fieldname=options.list{i,1}; - fieldvalue=options.list{i,2}; - if ismember(fieldname,properties(ogive)), - cluster.(fieldname)=fieldvalue; - else - disp(['''' fieldname ''' is not a property of cluster ogive']); - end - end - end - %}}} - function disp(cluster) % {{{1 - % display the object - disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); - disp(sprintf(' name: %s',cluster.name)); - disp(sprintf(' login: %s',cluster.login)); - disp(sprintf(' np: %i',cluster.np)); - disp(sprintf(' port: %i',cluster.port)); - disp(sprintf(' codepath: %s',cluster.codepath)); - disp(sprintf(' executionpath: %s',cluster.executionpath)); - disp(sprintf(' valgrind: %s',cluster.valgrind)); - disp(sprintf(' valgrindlib: %s',cluster.valgrindlib)); - disp(sprintf(' valgrindsup: %s',cluster.valgrindsup)); - end - %}}} - function IsConsistent(cluster) % {{{1 - if cluster.np>8, - error('IsConsistent error message: number of processors should be less than 8!'); - end - if isnan(cluster.np), - error('IsConsistent error message: number of processors should not be NaN!'); - end - end - %}}} - function BuildQueueScript(cluster,md) % {{{1 - - %retrieve parameters - modelname=md.name; - solution_type=md.solution_type; - mem_debug=md.mem_debug; - - %open file for writing: - fid=fopen([modelname '.queue'],'w'); - - %write instructions for launching a job on the cluster - fprintf(fid,'#!/bin/sh\n'); - if mem_debug==0, - fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.np,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - else - %fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --gen-suppressions=all --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - end - - if md.gprof, - fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname); - end - - %close file - fclose(fid); - - end - %}}} - function LaunchQueueJob(cluster,md,options)% {{{1 - - %lauch command, to be executed via ssh - launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... - ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue ']; - - if ~strcmpi(options.batch,'yes'), - - %compress the files into one zip. - compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; - if md.qmu_analysis, - compressstring=[compressstring md.name '.qmu.in']; - end - system(compressstring); - - disp('uploading input file and queueing script'); - issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); - - disp('launching solution sequence on remote cluster'); - issmssh(md.cluster.name,md.cluster.login,md.cluster.port,launchcommand); - - else - disp('batch mode requested: not launching job interactively'); - disp('launch solution sequence on remote cluster by hand'); - end - - end - %}}} - function Download(cluster,md)% {{{1 - - %some check - if isempty(md.runtimename), - error('pfe Download error message: supply runtime name for results to be loaded!'); - end - - %Figure out the directory where all the files are in: - directory=[cluster.executionpath '/' md.runtimename '/']; - - %What packages are we picking up from remote cluster - packages={[md.name '.outlog'],[md.name '.errlog']}; - if md.qmu_analysis, - packages{end+1}=[md.name '.qmu.err']; - packages{end+1}=[md.name '.qmu.out']; - if isfield(md.qmu_params,'tabular_graphics_data'), - if md.qmu_params.tabular_graphics_data==true, - packages{end+1}='dakota_tabular.dat'; - end - end - else - packages{end+1}=[md.name '.outbin']; - end - - %copy files from cluster to present directory - issmscpin(cluster.name, cluster.login, cluster.port, directory, packages); - end %}}} - end -end Index: sm/trunk/src/m/classes/clusters/wilkes.m =================================================================== --- /issm/trunk/src/m/classes/clusters/wilkes.m (revision 8585) +++ (revision ) @@ -1,143 +1,0 @@ -%WILKES class definition -% -% Usage: -% cluster=wilkes(); -% cluster=wilkes('np',3); -% cluster=wilkes('np',3,'login','username'); - -classdef wilkes - properties (SetAccess=public) - % {{{1 - name='wilkes' - login=''; - np=7; - port=0; - codepath=[issmtier() '/bin']; - executionpath=[issmdir() '/execution']; - valgrind=[issmtier() '/externalpackages/valgrind/install/bin/valgrind']; - valgrindlib=[issmtier() '/externalpackages/valgrind/install/lib/libmpidebug.so']; - valgrindsup=[issmtier() '/externalpackages/valgrind/issm.supp']; - %}}} - end - methods - function cluster=wilkes(varargin) % {{{1 - options=pairoptions(varargin{:}); - for i=1:size(options.list,1), - fieldname=options.list{i,1}; - fieldvalue=options.list{i,2}; - if ismember(fieldname,properties(wilkes)), - cluster.(fieldname)=fieldvalue; - else - disp(['''' fieldname ''' is not a property of cluster wilkes']); - end - end - end - %}}} - function disp(cluster) % {{{1 - % display the object - disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); - disp(sprintf(' name: %s',cluster.name)); - disp(sprintf(' login: %s',cluster.login)); - disp(sprintf(' np: %i',cluster.np)); - disp(sprintf(' port: %i',cluster.port)); - disp(sprintf(' codepath: %s',cluster.codepath)); - disp(sprintf(' executionpath: %s',cluster.executionpath)); - disp(sprintf(' valgrind: %s',cluster.valgrind)); - disp(sprintf(' valgrindlib: %s',cluster.valgrindlib)); - disp(sprintf(' valgrindsup: %s',cluster.valgrindsup)); - end - %}}} - function IsConsistent(cluster) % {{{1 - if cluster.np>16, - error('IsConsistent error message: number of processors should be less than 16!'); - end - if isnan(cluster.np), - error('IsConsistent error message: number of processors should not be NaN!'); - end - end - %}}} - function BuildQueueScript(cluster,md) % {{{1 - - %retrieve parameters - modelname=md.name; - solution_type=md.solution_type; - mem_debug=md.mem_debug; - - %open file for writing: - fid=fopen([modelname '.queue'],'w'); - - %write instructions for launching a job on the cluster - fprintf(fid,'#!/bin/sh\n'); - if mem_debug==0, - fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.np,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - else - %fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --gen-suppressions=all --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - end - - if md.gprof, - fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname); - end - - %close file - fclose(fid); - - end - %}}} - function LaunchQueueJob(cluster,md,options)% {{{1 - - %lauch command, to be executed via ssh - launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... - ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue ']; - - if ~strcmpi(options.batch,'yes'), - - %compress the files into one zip. - compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; - if md.qmu_analysis, - compressstring=[compressstring md.name '.qmu.in']; - end - system(compressstring); - - disp('uploading input file and queueing script'); - issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); - - disp('launching solution sequence on remote cluster'); - issmssh(md.cluster.name,md.cluster.login,md.cluster.port,launchcommand); - - else - disp('batch mode requested: not launching job interactively'); - disp('launch solution sequence on remote cluster by hand'); - end - - end - %}}} - function Download(cluster,md)% {{{1 - - %some check - if isempty(md.runtimename), - error('pfe Download error message: supply runtime name for results to be loaded!'); - end - - %Figure out the directory where all the files are in: - directory=[cluster.executionpath '/' md.runtimename '/']; - - %What packages are we picking up from remote cluster - packages={[md.name '.outlog'],[md.name '.errlog']}; - if md.qmu_analysis, - packages{end+1}=[md.name '.qmu.err']; - packages{end+1}=[md.name '.qmu.out']; - if isfield(md.qmu_params,'tabular_graphics_data'), - if md.qmu_params.tabular_graphics_data==true, - packages{end+1}='dakota_tabular.dat'; - end - end - else - packages{end+1}=[md.name '.outbin']; - end - - %copy files from cluster to present directory - issmscpin(cluster.name, cluster.login, cluster.port, directory, packages); - end %}}} - end -end