Index: /issm/trunk/configure.ac =================================================================== --- /issm/trunk/configure.ac (revision 23393) +++ /issm/trunk/configure.ac (revision 23394) @@ -2,5 +2,5 @@ #AUTOCONF -AC_INIT([Ice Sheet System Model (ISSM)],[4.14],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_INIT([Ice Sheet System Model (ISSM)],[4.15],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure AC_CONFIG_AUX_DIR([./aux-config]) #Put config files in aux-config AC_CONFIG_MACRO_DIR([m4]) #m4 macros are located in m4 Index: /issm/trunk/etc/environment.sh =================================================================== --- /issm/trunk/etc/environment.sh (revision 23393) +++ /issm/trunk/etc/environment.sh (revision 23394) @@ -75,18 +75,10 @@ fi -#legacy mpich2 (To be removed) -MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install" -if [ -d "$MPI_DIR" ]; then - export MPI_DIR - pathprepend "$MPI_DIR/bin" - libpathappend "$MPI_DIR/lib" -fi - MPI_DIR="$ISSM_DIR/externalpackages/mpich/install" if [ -d "$MPI_DIR" ]; then export MPI_DIR export MPI_INC_DIR="$MPI_DIR/include" - pathprepend "$MPI_DIR/bin" - libpathappend "$MPI_DIR/lib" + pathprepend "$MPI_DIR/bin" + libpathprepend "$MPI_DIR/lib" fi @@ -234,12 +226,4 @@ pathprepend "$GMAKE_DIR/bin" -PYTHON_DIR="$ISSM_DIR/externalpackages/python/install" -if [ -d "$PYTHON_DIR" ]; then - export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/lib" - pathprepend "$PYTHON_DIR/bin" - libpathprepend "$PYTHON_DIR/lib" - libpathprepend "$ISSM_DIR/lib" -fi - MODELE_DIR="$ISSM_DIR/externalpackages/modelE/install" pathappend "$MODELE_DIR/src/exec" Index: /issm/trunk/examples/Pig2/DomainOutline.exp =================================================================== --- /issm/trunk/examples/Pig2/DomainOutline.exp (revision 23394) +++ /issm/trunk/examples/Pig2/DomainOutline.exp (revision 23394) @@ -0,0 +1,101 @@ +## Name: +## Icon:0 +# Points Count Value +95 25000.000000 +# X pos Y pos +-1712113.0179281300 -349656.0205056490 +-1711509.1917759699 -349354.1074295690 +-1709240.6586108401 -349354.1074295690 +-1707080.1508345299 -348922.0058743060 +-1705459.7700022999 -347193.5996532570 +-1703083.2114483600 -345249.1426545770 +-1701138.7544496800 -344168.8887664210 +-1698438.1197292900 -343952.8379887900 +-1698006.0181740201 -341900.3556012940 +-1693793.0280102200 -340279.9747690600 +-1691092.3932898301 -339631.8224361670 +-1688391.7585694401 -339415.7716585360 +-1686447.3015707601 -340063.9239914290 +-1683530.6160727399 -341036.1524907690 +-1682558.3875734000 -343304.6856558960 +-1682134.7209454600 -344182.1487658350 +-1682126.2860181299 -345681.2442098390 +-1681072.0444963200 -345932.4393879640 +-1680634.4718407800 -346682.5639403050 +-1680571.9614614199 -348557.8753211580 +-1677446.4424933300 -348370.3441830730 +-1675508.6207331200 -349495.5310115840 +-1676616.9911885399 -353567.0975933760 +-1672991.8601872099 -353799.6175753630 +-1668839.1631938200 -353999.1991486380 +-1667132.2298986400 -355121.4651541420 +-1666069.5534494901 -357496.8595698890 +-1662944.0344814099 -358309.4945015920 +-1660756.1712037399 -358747.0671571240 +-1657922.9836098100 -361682.8074238540 +-1656579.2228470000 -364003.8487410000 +-1653004.8841628900 -364748.0635758530 +-1653442.4568184200 -361622.5446077650 +-1651129.5727820301 -355684.0585683980 +-1648929.2928810001 -350845.9692010000 +-1646260.7698359799 -347802.2804785470 +-1644571.8968503401 -341785.6704672340 +-1643503.3064999001 -340869.0986596620 +-1643190.7546030900 -336680.9032424240 +-1642690.6715682000 -335243.1645171040 +-1641913.0916588283 -332341.0814454452 +-1640683.9739821283 -330436.6112348017 +-1637816.0327364956 -328532.1410241582 +-1635241.2508976001 -328652.8685499910 +-1631765.4107996500 -327017.1790921330 +-1625934.5618617306 -322342.6128395668 +-1620608.3852626982 -320438.1426289233 +-1616101.6204481323 -320438.1426289233 +-1611594.8556335662 -320914.2601815842 +-1607907.5026034669 -321866.4952869060 +-1602991.0318966676 -324723.2006028712 +-1599713.3847588014 -327579.9059188365 +-1593977.5022675355 -328532.1410241582 +-1590699.8551296694 -334721.6692087495 +-1589259.8391499999 -338300.0840570000 +-1588627.0898328500 -343572.9950327750 +-1588056.6000060199 -345432.3563530700 +-1586993.9235568701 -347432.6884926460 +-1589259.8391499999 -349315.9832070000 +-1585493.6744521901 -352996.1122558430 +-1585118.6121760199 -354496.3613605250 +-1585861.9157163899 -356240.3342513760 +-1586368.8197632500 -358747.0671571240 +-1587889.0972700799 -360996.6006787950 +-1586681.3716600600 -363935.4286441500 +-1585806.2263489999 -365748.2296456410 +-1586743.8820394201 -368373.6655788350 +-1586056.2678664399 -370123.9562009640 +-1585493.6744521901 -371124.1222707520 +-1586243.7990045301 -373562.0270658610 +-1414257.6683934701 -327460.5482541260 +-1412220.4351378100 -325972.8942023180 +-1404515.9240538401 -296165.1737279960 +-1387984.9332285200 -267002.0106682320 +-1360067.9373810000 -107884.1934940000 +-1423274.3497420000 -81217.9259650000 +-1402446.7987670000 -45916.9921070000 +-1478343.8065599999 60338.8188030000 +-1503760.4789370000 36334.1837800000 +-1528509.5619775900 63667.6809196406 +-1623055.4918765700 62841.1506965373 +-1725734.5897359999 -61372.6193030000 +-1719614.6457630000 -69022.5492690000 +-1759088.2843859999 -114004.1374660000 +-1755416.3180020000 -117064.1094530000 +-1761230.2647760001 -126856.0198080000 +-1758170.2927900001 -130527.9861920000 +-1762148.2563720001 -135423.9413700000 +-1764902.2311590000 -131445.9777880000 +-1769798.1863370000 -134199.9525750000 +-1775000.1387139999 -131445.9777880000 +-1794277.9622269999 -153477.7760890000 +-1712576.7101950001 -225081.1205660000 +-1729939.5891459100 -335652.4567604720 +-1712113.0179281300 -349656.0205056490 + Index: /issm/trunk/examples/Pig2/FrontRetreat.exp =================================================================== --- /issm/trunk/examples/Pig2/FrontRetreat.exp (revision 23394) +++ /issm/trunk/examples/Pig2/FrontRetreat.exp (revision 23394) @@ -0,0 +1,17 @@ +## Name:FrontRetreat +## Icon:0 +# Points Count Value +11 1.000000 +# X pos Y pos +-1626858.6376043619 -327176.4356578548 +-1605190.4936934854 -325911.1425827671 +-1604716.0087903275 -316263.2828852235 +-1607088.4333061168 -312625.5652943464 +-1612465.9288752396 -311676.5954880306 +-1618476.0709819060 -312467.4036599604 +-1624011.7281854146 -313890.8583694341 +-1626858.6376043619 -315788.7979820656 +-1627807.6074106777 -319268.3539385567 +-1628756.5772169936 -322589.7482606619 +-1626858.6376043619 -327176.4356578548 + Index: /issm/trunk/examples/Pig2/Pig.par =================================================================== --- /issm/trunk/examples/Pig2/Pig.par (revision 23394) +++ /issm/trunk/examples/Pig2/Pig.par (revision 23394) @@ -0,0 +1,118 @@ +% Parameters to change/Try +friction_coefficient = 10; % default [10] +Temp_change = 0; % default [0 K] + +%Name and Coordinate system +md.miscellaneous.name='PIG'; +md.mesh.epsg=3031; + +%NetCdf Loading +disp(' Loading SeaRISE data from NetCDF'); +ncdata='../Data/Antarctica_5km_withshelves_v0.75.nc'; +x1 = ncread(ncdata,'x1'); +y1 = ncread(ncdata,'y1'); +usrf = ncread(ncdata,'usrf')'; +topg = ncread(ncdata,'topg')'; +temp = ncread(ncdata,'presartm')'; +smb = ncread(ncdata,'presprcp')'; +gflux = ncread(ncdata,'bheatflx_fox')'; + +%Geometry +disp(' Interpolating surface and ice base'); +md.geometry.base = InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); +md.geometry.surface = InterpFromGridToMesh(x1,y1,usrf,md.mesh.x,md.mesh.y,0); +clear usrf, topg; + +disp(' Constructing thickness'); +md.geometry.thickness=md.geometry.surface-md.geometry.base; + +%ensure hydrostatic equilibrium on ice shelf: +di=md.materials.rho_ice/md.materials.rho_water; + +%Get the node numbers of floating nodes +pos=find(md.mask.groundedice_levelset<0); + +%apply a flotation criterion on the precedingly defined nodes and +%redefine base and thickness accordingly +md.geometry.thickness(pos)=1/(1-di)*md.geometry.surface(pos); +md.geometry.base(pos)=md.geometry.surface(pos)-md.geometry.thickness(pos); +md.geometry.hydrostatic_ratio=ones(md.mesh.numberofvertices,1); %For Dakota + +%Set min thickness to 1 meter +pos0=find(md.geometry.thickness<=1); +md.geometry.thickness(pos0)=1; +md.geometry.surface=md.geometry.thickness+md.geometry.base; +md.geometry.bed=md.geometry.base; +md.geometry.bed(pos)=md.geometry.base(pos)-1000; + +%Initialization parameters +disp(' Interpolating temperatures'); +md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15+Temp_change; +clear temp; + +disp(' Loading velocities data from NetCDF'); +nsidc_vel='../Data/Antarctica_ice_velocity.nc'; +xmin = ncreadatt(nsidc_vel,'/','xmin'); +ymax = ncreadatt(nsidc_vel,'/','ymax'); +spacing = ncreadatt(nsidc_vel,'/','spacing'); +nx = double(ncreadatt(nsidc_vel,'/','nx')); +ny = double(ncreadatt(nsidc_vel,'/','ny')); +velx = double(ncread(nsidc_vel,'vx')); +vely = double(ncread(nsidc_vel,'vy')); +% Read coordinates +xmin = strtrim(xmin); +xmin = str2num(xmin(1:end-2)); +ymax = strtrim(ymax); +ymax = str2num(ymax(1:end-2)); +spacing = strtrim(spacing); +spacing = str2num(spacing(1:end-2)); +% Build the coordinates +x2=xmin+(0:1:nx)'*spacing; +y2=(ymax-ny*spacing)+(0:1:ny)'*spacing; + +disp(' Set observed velocities') +md.initialization.vx=InterpFromGridToMesh(x2,y2,flipud(velx'),md.mesh.x,md.mesh.y,0); +md.initialization.vy=InterpFromGridToMesh(x2,y2,flipud(vely'),md.mesh.x,md.mesh.y,0); +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.vel=sqrt(md.initialization.vx.^2+md.initialization.vy.^2); +clear velx vely; + +disp(' Set Pressure'); +md.initialization.pressure=md.materials.rho_ice*md.constants.g*md.geometry.thickness; + +disp(' Construct ice rheological properties'); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_B=paterson(md.initialization.temperature); + +%Forcings +disp(' Interpolating surface mass balance'); +mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance=mass_balance*md.materials.rho_water/md.materials.rho_ice; +clear smb; + +disp(' Set geothermal heat flux'); +md.basalforcings.geothermalflux=InterpFromGridToMesh(x1,y1,gflux,md.mesh.x,md.mesh.y,0); +clear gflux; + +%Friction and inversion set up +disp(' Construct basal friction parameters'); +md.friction.coefficient=friction_coefficient*ones(md.mesh.numberofvertices,1); +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +%no friction applied on floating ice +pos=find(md.mask.groundedice_levelset<0); +md.friction.coefficient(pos)=0; +md.groundingline.migration='SubelementMigration'; + +md.inversion=m1qn3inversion(); +md.inversion.vx_obs=md.initialization.vx; +md.inversion.vy_obs=md.initialization.vy; +md.inversion.vel_obs=md.initialization.vel; + +disp(' Set boundary conditions'); +md=SetMarineIceSheetBC(md); +md.basalforcings.floatingice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.thermal.spctemperature = md.initialization.temperature; +md.masstransport.spcthickness = NaN*ones(md.mesh.numberofvertices,1); Index: /issm/trunk/examples/Pig2/runme.m =================================================================== --- /issm/trunk/examples/Pig2/runme.m (revision 23394) +++ /issm/trunk/examples/Pig2/runme.m (revision 23394) @@ -0,0 +1,231 @@ +steps=[1:8]; + +if any(steps==1) %Mesh Generation #1 + + %Mesh parameters + domain =['./DomainOutline.exp']; + hinit=5000; % element size for the initial mesh + hmax=40000; % maximum element size of the final mesh + hmin=4000; % minimum element size of the final mesh + gradation=1.7; % maximum size ratio between two neighboring elements + err=8; % maximum error between interpolated and control field + + % Generate an initial uniform mesh (resolution = hinit m) + md=bamg(model,'domain',domain,'hmax',hinit); + + % Get necessary data to build up the velocity grid + nsidc_vel='../Data/Antarctica_ice_velocity.nc'; + xmin = strsplit(ncreadatt(nsidc_vel,'/','xmin')); xmin = str2num(xmin{2}); + ymax = strsplit(ncreadatt(nsidc_vel,'/','ymax')); ymax = str2num(ymax{2}); + spacing = strsplit(ncreadatt(nsidc_vel,'/','spacing')); spacing = str2num(spacing{2}); + nx = double(ncreadatt(nsidc_vel,'/','nx')); + ny = double(ncreadatt(nsidc_vel,'/','ny')); + vx = double(ncread(nsidc_vel,'vx')); + vy = double(ncread(nsidc_vel,'vy')); + + % Build the coordinates + x=xmin+(0:1:nx)'*spacing; + y=(ymax-ny*spacing)+(0:1:ny)'*spacing; + + % Interpolate velocities onto coarse mesh + vx_obs=InterpFromGridToMesh(x,y,flipud(vx'),md.mesh.x,md.mesh.y,0); + vy_obs=InterpFromGridToMesh(x,y,flipud(vy'),md.mesh.x,md.mesh.y,0); + vel_obs=sqrt(vx_obs.^2+vy_obs.^2); + clear vx vy x y; + + % Adapt the mesh to minimize error in velocity interpolation + md=bamg(md,'hmax',hmax,'hmin',hmin,'gradation',gradation,'field',vel_obs,'err',err); + + % Plot and save model + plotmodel(md,'data','mesh') + save ./Models/PIG_Mesh_generation md; +end + +if any(steps==2) %Masks #2 + + md = loadmodel('./Models/PIG_Mesh_generation'); + + % Load SeaRISe dataset for Antarctica http://websrv.cs.umt.edu/isis/index.php/Present_Day_Antarctica + searise='../Data/Antarctica_5km_withshelves_v0.75.nc'; + + %read thickness mask from SeaRISE + x1=double(ncread(searise,'x1')); + y1=double(ncread(searise,'y1')); + thkmask=double(ncread(searise,'thkmask')); + + %interpolate onto our mesh vertices + groundedice=double(InterpFromGridToMesh(x1,y1,thkmask',md.mesh.x,md.mesh.y,0)); + groundedice(groundedice<=0)=-1; + clear thkmask; + + %fill in the md.mask structure + md.mask.groundedice_levelset=groundedice; %ice is grounded for mask equal one + md.mask.ice_levelset=-1*ones(md.mesh.numberofvertices,1);%ice is present when negatvie + + plotmodel(md,'data',md.mask.groundedice_levelset,'title','grounded/floating','data',md.mask.ice_levelset,'title','ice/no-ice') + + save ./Models/PIG_SetMask md; +end + +if any(steps==3) %Parameterization #3 + + md = loadmodel('./Models/PIG_SetMask'); + md = setflowequation(md,'SSA','all'); + md = parameterize(md,'./Pig.par'); + + save ./Models/PIG_Parameterization md; +end + +if any(steps==4) %Rheology B inversion + + md = loadmodel('./Models/PIG_Parameterization'); + + % Control general + md.inversion.iscontrol=1; + md.inversion.maxsteps=40; + md.inversion.maxiter=40; + md.inversion.dxmin=0.1; + md.inversion.gttol=1.0e-6; + md.verbose=verbose('control',true); + + % Cost functions + md.inversion.cost_functions=[101 103 502]; + md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,3); + md.inversion.cost_functions_coefficients(:,1)=1000; + md.inversion.cost_functions_coefficients(:,2)=1; + md.inversion.cost_functions_coefficients(:,3)=1.e-16; + + % Controls + md.inversion.control_parameters={'MaterialsRheologyBbar'}; + md.inversion.min_parameters=md.materials.rheology_B; + md.inversion.max_parameters=md.materials.rheology_B; + pos = find(md.mask.groundedice_levelset<0); + md.inversion.min_parameters(pos) = cuffey(273); + md.inversion.max_parameters(pos) = cuffey(200); + + % Additional parameters + md.stressbalance.restol=0.01; + md.stressbalance.reltol=0.1; + md.stressbalance.abstol=NaN; + + % Solve + md.cluster=generic('name',oshostname,'np',2); + mds=extract(md,md.mask.groundedice_levelset<0); + mds=solve(mds,'Stressbalance'); + + % Update model rheology_B accordingly + md.materials.rheology_B(mds.mesh.extractedvertices)=mds.results.StressbalanceSolution.MaterialsRheologyBbar; + plotmodel(md,'data',md.materials.rheology_B) + + % Save model + save ./Models/PIG_Control_B md; +end + +if any(steps==5) %drag inversion + + md = loadmodel('./Models/PIG_Control_B'); + + % Cost functions + md.inversion.cost_functions=[101 103 501]; + md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,3); + md.inversion.cost_functions_coefficients(:,1)=2000; + md.inversion.cost_functions_coefficients(:,2)=1; + md.inversion.cost_functions_coefficients(:,3)=8e-7; + + % Controls + md.inversion.control_parameters={'FrictionCoefficient'}; + md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); + md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); + + % Solve + md=solve(md,'Stressbalance'); + + % Update model friction fields accordingly + md.friction.coefficient=md.results.StressbalanceSolution.FrictionCoefficient; + + %Plot and save + plotmodel(md,... + 'data',md.initialization.vel,'title','Observed velocity',... + 'data',md.results.StressbalanceSolution.Vel,'title','Modeled Velocity',... + 'data',md.geometry.base,'title','Bed elevation',... + 'data',md.results.StressbalanceSolution.FrictionCoefficient,'title','Friction Coefficient',... + 'colorbar#all','on','colorbartitle#1-2','(m/yr)',... + 'caxis#1-2',([1.5,4000]),... + 'colorbartitle#3','(m)', 'log#1-2',10); + save ./Models/PIG_Control_drag md; +end + +if any(steps==6) %Transient Run #1 + + md = loadmodel('../Pig/Models/PIG_Control_drag'); + + md.inversion.iscontrol=0; + md.transient.ismasstransport=1; + md.transient.isstressbalance=1; + md.transient.isgroundingline=1; + md.transient.ismovingfront=0; + md.transient.isthermal=0; + md.verbose.solution=1; + md.timestepping.time_step=0.1; + md.timestepping.final_time=10; + md.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'}; + + %Set melt to 25 m/yr under floating ice + md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); + md.basalforcings.floatingice_melting_rate=25*ones(md.mesh.numberofvertices,1); + + + md=solve(md,'Transient'); + time = cell2mat({md.results.TransientSolution(:).time}); + V_control = cell2mat({md.results.TransientSolution(:).IceVolumeAboveFloatation}); + plot(time,V_control); legend({'Control run'}); + + % Save model + save ./Models/PIG_Transient md; +end + +if any(steps==7) %High Melt #2 + md = loadmodel('./Models/PIG_Transient'); + + %Set melt to 60 m/yr under floating ice + md.basalforcings.floatingice_melting_rate=60*ones(md.mesh.numberofvertices,1); + + md=solve(md,'Transient'); + V_melt = cell2mat({md.results.TransientSolution(:).IceVolumeAboveFloatation}); + plot(time,[V_control',V_melt']); legend({'Control run','High melt'}); + + save ./Models/PIG_HighMelt md; +end + +if any(steps==8) %Ice Front retreat + md = loadmodel('./Models/PIG_Transient'); + + pos = find(ContourToNodes(md.mesh.x,md.mesh.y,'FrontRetreat.exp',2)); + md.mask.ice_levelset(pos) = +1; %Deactivate nodes in retreated area + + md=solve(md,'Transient'); + V_retreat = cell2mat({md.results.TransientSolution(:).IceVolumeAboveFloatation}); + plot(time,[V_control',V_melt',V_retreat']); legend({'Control run','High melt','Retreat'}); + + save ./Models/PIG_FrontRetreat md; +end + +if any(steps==9) %High surface mass balance #3 + %Load model from PIG_Transient + %... + + %Change surface mass balance (x2) + %... + + %Solve + %... + + %Get volume time series + %... + + %plot + plot(time,[V_control',V_melt',V_retreat',V_smb']); legend({'Control run','High melt','Retreat','SMB'}); + + %Save model + save ./Models/PIG_SMB md; +end Index: sm/trunk/externalpackages/README =================================================================== --- /issm/trunk/externalpackages/README (revision 23393) +++ (revision ) @@ -1,22 +1,0 @@ -To install all the ISSM libraries: - -1/ go into each library folder and type install.sh . - -2/ There is no guarantee the compilation will work on all systems. A lot of tweaking of the -install.sh files will probably be involved. Especially, the configuration part of the install. - -Update: -now install.sh can call configure.sh for the most complex libraries, ie Petsc and Dakota. For those -libraries, go in the configs/ directory, pick up the correct configuration file and copy it to the top -folder of the library compilation. Tweak if necessary. - -machine characteristics: - --astrid: linux 64 bits --castor: altix 64 bits --cosmos: JPL cluster 32 bits --macmathieu: iMac 24" 2009 32 bits --macbookmathieu: MacBook Pro 13" 2010; OS X 10.6.7; 2.4GHz Intel Core 2 Duo 64 bits --maceric: MacBook Pro 15" 2010 32 bits --ogive: Mac Pro 2008 32 bits --pleiades: AMES cluster Index: /issm/trunk/externalpackages/adjointmpi/install-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/adjointmpi/install-pleiades.sh (revision 23394) +++ /issm/trunk/externalpackages/adjointmpi/install-pleiades.sh (revision 23394) @@ -0,0 +1,25 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +#Almost the same as adjoinable mpi but some adaptations to CoDiPack +svn co https://github.com/michel2323/AdjointMPI.git/branches/doubleFixMaster src +mkdir install + +cd src +autoreconf -fi + ./configure \ + --prefix="$ISSM_DIR/externalpackages/adjointmpi/install" \ + --with-mpi-root="/nasa/sgi/mpt/2.15r20/" \ + CXXFLAGS="-O2 -fPIC" CFLAGS="-O2 -fPIC" + +#Compile adjoinablempi +make clean +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/adjointmpi/install.sh =================================================================== --- /issm/trunk/externalpackages/adjointmpi/install.sh (revision 23394) +++ /issm/trunk/externalpackages/adjointmpi/install.sh (revision 23394) @@ -0,0 +1,25 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +#Almost the same as adjoinable mpi but some adaptations to CoDiPack +svn co https://github.com/michel2323/AdjointMPI.git/branches/doubleFixMaster src +mkdir install + +cd src +autoreconf -fi + ./configure \ + --prefix="$ISSM_DIR/externalpackages/adjointmpi/install" \ + --with-mpi-root="$ISSM_DIR/externalpackages/mpich/install" \ + CXXFLAGS="-O2 -fPIC" CFLAGS="-O2 -fPIC" + +#Compile adjoinablempi +make clean +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/codipack/install.sh =================================================================== --- /issm/trunk/externalpackages/codipack/install.sh (revision 23394) +++ /issm/trunk/externalpackages/codipack/install.sh (revision 23394) @@ -0,0 +1,8 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install + +#Download development version +svn co https://github.com/SciCompKL/CoDiPack.git/trunk install Index: /issm/trunk/externalpackages/medipack/install.sh =================================================================== --- /issm/trunk/externalpackages/medipack/install.sh (revision 23394) +++ /issm/trunk/externalpackages/medipack/install.sh (revision 23394) @@ -0,0 +1,8 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install + +#Download development version +svn co https://github.com/SciCompKL/MeDiPack/trunk install Index: /issm/trunk/externalpackages/petsc/install-3.9-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.9-macosx64.sh (revision 23394) +++ /issm/trunk/externalpackages/petsc/install-3.9-macosx64.sh (revision 23394) @@ -0,0 +1,34 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.9.3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.9.3.tar.gz' 'petsc-3.9.3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.9.3.tar.gz +mv petsc-3.9.3/* src/ +rm -rf petsc-3.9.3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=1 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-shared-libraries=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-mumps=1 \ + --download-scalapack=1 + +#Compile and intall +make +make install Index: /issm/trunk/jenkins/jenkins.sh =================================================================== --- /issm/trunk/jenkins/jenkins.sh (revision 23393) +++ /issm/trunk/jenkins/jenkins.sh (revision 23394) @@ -324,8 +324,8 @@ #concatenate reports cd $ISSM_DIR/nightlylog/ -echo 'CHECKING NIGHTLYLOG DIRECTORY' -echo '-----------------------------' -ls -la -echo '-----------------------------' +#echo 'CHECKING NIGHTLYLOG DIRECTORY' +#echo '-----------------------------' +#ls -la +#echo '-----------------------------' if [ -f matlab_log.log ]; then Index: /issm/trunk/jenkins/linux64_caladan_ad =================================================================== --- /issm/trunk/jenkins/linux64_caladan_ad (revision 23393) +++ /issm/trunk/jenkins/linux64_caladan_ad (revision 23394) @@ -32,5 +32,4 @@ mpich install-3.2-linux64.sh petsc install-3.7-linux64.sh - metis install-5.0.1-linux64.sh triangle install-linux64.sh gsl install-linux64.sh Index: /issm/trunk/jenkins/linux64_caladan_ampi =================================================================== --- /issm/trunk/jenkins/linux64_caladan_ampi (revision 23393) +++ /issm/trunk/jenkins/linux64_caladan_ampi (revision 23394) @@ -41,5 +41,4 @@ mpich install-3.2-linux64.sh petsc install-3.7-linux64.sh - metis install-5.0.1-linux64.sh triangle install-linux64.sh gsl install-linux64.sh Index: /issm/trunk/jenkins/linux64_ross_ad =================================================================== --- /issm/trunk/jenkins/linux64_ross_ad (revision 23393) +++ /issm/trunk/jenkins/linux64_ross_ad (revision 23394) @@ -37,5 +37,4 @@ mpich install-3.2-linux64.sh petsc install-3.7-linux64.sh - metis install-5.0.1-linux64.sh triangle install-linux64.sh gsl install-linux64.sh Index: /issm/trunk/jenkins/linux64_ross_ampi =================================================================== --- /issm/trunk/jenkins/linux64_ross_ampi (revision 23393) +++ /issm/trunk/jenkins/linux64_ross_ampi (revision 23394) @@ -44,5 +44,4 @@ mpich install-3.2-linux64.sh petsc install-3.7-linux64.sh - metis install-5.0.1-linux64.sh triangle install-linux64.sh gsl install-linux64.sh Index: /issm/trunk/jenkins/linux64_ross_codi =================================================================== --- /issm/trunk/jenkins/linux64_ross_codi (revision 23394) +++ /issm/trunk/jenkins/linux64_ross_codi (revision 23394) @@ -0,0 +1,70 @@ +# +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#MATLAB path +MATLAB_PATH="/usr/local/MATLAB/R2015a" + +#ISSM CONFIGURATION +ISSM_CONFIG='--prefix=$ISSM_DIR\ + --without-kriging \ + --without-kml \ + --without-GiaIvins \ + --without-Love \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-matlab-dir=$MATLAB_PATH \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpifort -lmpi" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-numthreads=4 \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \ + --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \ + --with-codipack-dir="$ISSM_DIR/externalpackages/codipack/install" \ + --enable-tape-alloc \ + --with-cxxoptflags="-DAD_TYPE=codi::RealReverse" \ + --with-adjointmpi-dir="$ISSM_DIR/externalpackages/adjointmpi/install" \ + --enable-development \ + --enable-debugging ' + +#PYTHON and MATLAB testing +MATLAB_TEST=1 +PYTHON_TEST=0 + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#List of external pakages to be installed and their installation scripts +EXTERNALPACKAGES="autotools install.sh + cmake install.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh + triangle install-linux64.sh + gsl install-linux64.sh + m1qn3 install.sh + adjointmpi install.sh + codipack install.sh + shell2junit install.sh" + +#-----------------# +# 4: test options # +#-----------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=5 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=1 + +#Nightly run options. The matlab routine runme.m will be called +#as follows: runme($MATLAB_NROPTIONS). The options must be understandable +#by Matlab and runme.m +#ex: "'id',[101 102 103]" +MATLAB_NROPTIONS="'benchmark','all','id',[3015,3119,3480]" +PYTHON_NROPTIONS="--benchmark='all' -i 3015 3119 3480" Index: /issm/trunk/jenkins/linux64_ross_dakota =================================================================== --- /issm/trunk/jenkins/linux64_ross_dakota (revision 23393) +++ /issm/trunk/jenkins/linux64_ross_dakota (revision 23394) @@ -11,4 +11,6 @@ --disable-static \ --with-matlab-dir=$MATLAB_PATH \ + --with-python-dir=/usr \ + --with-python-numpy-dir=/home/jenkins/.local/lib/python2.7/site-packages/numpy \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ @@ -30,5 +32,5 @@ #PYTHON and MATLAB testing MATLAB_TEST=1 -PYTHON_TEST=0 +PYTHON_TEST=1 #-----------------------------------# @@ -63,4 +65,4 @@ #by Matlab and runme.m #ex: "'id',[101 102 103]" -PYTHON_NROPTIONS="--exclude 243 701 702 435" +PYTHON_NROPTIONS="--exclude 243 701 702 435 --include_name 'Dakota'" MATLAB_NROPTIONS="'exclude',[243,701,702,435]" Index: /issm/trunk/jenkins/linux64_ross_python =================================================================== --- /issm/trunk/jenkins/linux64_ross_python (revision 23393) +++ /issm/trunk/jenkins/linux64_ross_python (revision 23394) @@ -10,9 +10,10 @@ ISSM_CONFIG='--prefix=$ISSM_DIR \ --disable-static \ + --with-matlab-dir=$MATLAB_PATH \ --with-python-dir=/usr \ --with-python-numpy-dir=/home/jenkins/.local/lib/python2.7/site-packages/numpy \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lmpifort" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lmpicxx -lmpifort" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -21,5 +22,5 @@ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ - --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran" \ --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \ --with-numthreads=4 \ @@ -50,8 +51,8 @@ #number of cpus used in ISSM installation and compilation (one is usually #safer as some packages are very sensitive to parallel compilation) -NUMCPUS_INSTALL=10 +NUMCPUS_INSTALL=5 #number of cpus used in the nightly runs. -NUMCPUS_RUN=5 +NUMCPUS_RUN=3 #Nightly run options. The matlab routine runme.m will be called Index: /issm/trunk/jenkins/macosx_pine-island =================================================================== --- /issm/trunk/jenkins/macosx_pine-island (revision 23393) +++ /issm/trunk/jenkins/macosx_pine-island (revision 23394) @@ -5,5 +5,5 @@ #MATLAB path -MATLAB_PATH="/Applications/MATLAB_R2015b.app/" +MATLAB_PATH="/Applications/MATLAB_R2015b.app" #ISSM CONFIGURATION @@ -48,5 +48,5 @@ #number of cpus used in the nightly runs. -NUMCPUS_RUN=2 +NUMCPUS_RUN=4 #Nightly run options. The matlab routine runme.m will be called Index: /issm/trunk/jenkins/macosx_pine-island_dakota =================================================================== --- /issm/trunk/jenkins/macosx_pine-island_dakota (revision 23393) +++ /issm/trunk/jenkins/macosx_pine-island_dakota (revision 23394) @@ -5,9 +5,11 @@ #MATLAB path -MATLAB_PATH="/Applications/MATLAB_R2015b.app/" +MATLAB_PATH="/Applications/MATLAB_R2015b.app" -#ISSM CONFIGURATION +#ISSM CONFIGURATION ISSM_CONFIG='--prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_PATH \ + --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ + --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ @@ -27,5 +29,5 @@ #PYTHON and MATLAB testing MATLAB_TEST=1 -PYTHON_TEST=0 +PYTHON_TEST=1 #-----------------------------------# @@ -54,10 +56,10 @@ #number of cpus used in the nightly runs. -NUMCPUS_RUN=2 +NUMCPUS_RUN=4 #Nightly run options. The matlab routine runme.m will be called #as follows: runme($MATLAB_NROPTIONS). The options must be understandable #by Matlab and runme.m -#ex: "'id',[101 102 103]" ERRORS ARE LARGE FOR: 418 420 -PYTHON_NROPTIONS="" +#ex: "'id',[101 102 103]" ERRORS ARE LARGE FOR: 418 420 +PYTHON_NROPTIONS="--exclude 119 243 514 701 702 703 234 235 418 420 --include_name 'Dakota'" MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,703,234,235,418,420]" Index: /issm/trunk/jenkins/macosx_pine-island_dakota_static =================================================================== --- /issm/trunk/jenkins/macosx_pine-island_dakota_static (revision 23393) +++ /issm/trunk/jenkins/macosx_pine-island_dakota_static (revision 23394) @@ -4,7 +4,7 @@ #MATLAB path -MATLAB_PATH="/Applications/MATLAB_R2015b.app/" +MATLAB_PATH="/Applications/MATLAB_R2015b.app" -#ISSM CONFIGURATION +#ISSM CONFIGURATION ISSM_CONFIG='--prefix=$ISSM_DIR \ --disable-static \ @@ -56,5 +56,5 @@ #number of cpus used in the nightly runs. -NUMCPUS_RUN=2 +NUMCPUS_RUN=4 #Nightly run options. The matlab routine runme.m will be called @@ -62,5 +62,5 @@ #by Matlab and runme.m #ex: "'id',[101 102 103]" -## bamg mesh FS +## bamg mesh FS #PYTHON_NROPTIONS="--exclude_name 'Dakota'" #MATLAB_NROPTIONS="'exclude',[243,701,702,703,435,IdFromString('Dakota')]" Index: /issm/trunk/jenkins/macosx_pine-island_examples =================================================================== --- /issm/trunk/jenkins/macosx_pine-island_examples (revision 23393) +++ /issm/trunk/jenkins/macosx_pine-island_examples (revision 23394) @@ -5,7 +5,7 @@ #MATLAB path -MATLAB_PATH="/Applications/MATLAB_R2015b.app/" +MATLAB_PATH="/Applications/MATLAB_R2015b.app" -#ISSM CONFIGURATION +#ISSM CONFIGURATION ISSM_CONFIG='--prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_PATH \ Index: /issm/trunk/m4/issm_options.m4 =================================================================== --- /issm/trunk/m4/issm_options.m4 (revision 23393) +++ /issm/trunk/m4/issm_options.m4 (revision 23394) @@ -9,5 +9,5 @@ dnl ISSM's internal options dnl Build info{{{ - + dnl build date AC_PATH_PROGS(DATE, date) @@ -153,5 +153,5 @@ AC_MSG_CHECKING(for wrappers compilation) AM_CONDITIONAL([WRAPPERS], [test x$WRAPPERS_VALUE = xyes]) - AC_MSG_RESULT($WRAPPERS_VALUE) + AC_MSG_RESULT($WRAPPERS_VALUE) dnl }}} dnl Extensions{{{ @@ -251,5 +251,5 @@ fi fi - AC_SUBST([OSLIBS]) + AC_SUBST([OSLIBS]) AC_MSG_RESULT(done) dnl }}} @@ -281,21 +281,21 @@ AC_DEFINE([_HAVE_MATLAB_],[1],[with matlab in ISSM src]) - + dnl 4. get MEXLIB MEXLINK and MEXEXT (experimental) except for windows AC_MSG_CHECKING([matlab's mex compilation flags]) case "${host_os}" in - *cygwin*) + *cygwin*) if test $VENDOR = intel-win7-32; then - MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" + MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win32/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" MEXEXT=`$MATLAB_ROOT/bin/mexext.bat` MEXEXT=".$MEXEXT" elif test $VENDOR = intel-win7-64; then - MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" - MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" + MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" + MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" MEXEXT=".mexw64" elif test $VENDOR = MSVC-Win64 || test $VENDOR = MSVC-Win64-par; then - MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" - MEXLINK="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" + MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" + MEXLINK="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" MATLABINCL="-I`cygpath -m $MATLAB_ROOT/extern/include/`" MEXEXT=".mexw64" @@ -311,5 +311,5 @@ echo "#include " > conftest.cpp echo "void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){}" >> conftest.cpp - $MATLAB_ROOT/bin/mex -v -lmex conftest.cpp > conftest.tmp 2>&1 + $MATLAB_ROOT/bin/mex -v -lmex conftest.cpp > conftest.tmp 2>&1 rm -f conftest.cpp MEXLINK=$(cat conftest.tmp | grep LDFLAGS | sed -e "s/LDFLAGS ://g") @@ -333,5 +333,5 @@ MATLABWRAPPEREXT=$MEXEXT AC_SUBST([MATLABWRAPPEREXT]) - AC_SUBST([MEXLIB]) + AC_SUBST([MEXLIB]) AC_SUBST([MEXLINK]) fi @@ -345,5 +345,5 @@ AC_ARG_WITH([javascript], AS_HELP_STRING([--with-javascript], [compile javascript wrappers? default is no.]), - [JAVASCRIPT=$withval],[JAVASCRIPT="no"]) + [JAVASCRIPT=$withval],[JAVASCRIPT="no"]) dnl Check whether javascript wrappers are desired @@ -364,5 +364,5 @@ AC_ARG_WITH([triangle-dir], AS_HELP_STRING([--with-triangle-dir=DIR], [triangle root directory.]), - [TRIANGLE_ROOT=$withval],[TRIANGLE_ROOT="no"]) + [TRIANGLE_ROOT=$withval],[TRIANGLE_ROOT="no"]) dnl Check whether triangle is enabled @@ -394,5 +394,5 @@ if test "x$HAVE_JAVASCRIPT" = "xyes"; then dnl go to the bit code, not the library. - TRIANGLELIB=$TRIANGLE_ROOT/triangle.o + TRIANGLELIB=$TRIANGLE_ROOT/triangle.o else TRIANGLELIB=$TRIANGLE_ROOT/triangle.a @@ -402,5 +402,5 @@ if test "x$HAVE_JAVASCRIPT" = "xyes"; then dnl go to the bit code, not the library. - TRIANGLELIB=$TRIANGLE_ROOT/triangle.o + TRIANGLELIB=$TRIANGLE_ROOT/triangle.o else TRIANGLELIB=$TRIANGLE_ROOT/triangle.a @@ -416,5 +416,5 @@ AC_ARG_WITH([boost-dir], AS_HELP_STRING([--with-boost-dir=DIR], [boost root directory.]), - [BOOST_ROOT=$withval],[BOOST_ROOT="no"]) + [BOOST_ROOT=$withval],[BOOST_ROOT="no"]) dnl Check whether boost is enabled @@ -443,6 +443,6 @@ AC_ARG_WITH([dakota-dir], AS_HELP_STRING([--with-dakota-dir=DIR], [dakota root directory.]), - [DAKOTA_ROOT=$withval],[DAKOTA_ROOT="no"]) - + [DAKOTA_ROOT=$withval],[DAKOTA_ROOT="no"]) + dnl Check whether dakota is enabled AC_MSG_CHECKING([for dakota]) @@ -573,5 +573,5 @@ AC_ARG_WITH([python-dir], AS_HELP_STRING([--with-python-dir=DIR], [python root directory.]), - [PYTHON_ROOT=$withval],[PYTHON_ROOT="no"]) + [PYTHON_ROOT=$withval],[PYTHON_ROOT="no"]) dnl Check whether python is enabled @@ -592,10 +592,10 @@ if test "x$HAVE_PYTHON" = "xyes"; then AC_MSG_CHECKING([for python version]) - dnl Query Python for its version number.  Getting [:3] seems to be the + dnl Query Python for its version number. Getting [:3] seems to be the dnl best way to do this; it's what "site.py" does in the standard library. PYTHON_VERSION=$($PYTHON_ROOT/bin/python -c "import sys; print sys.version[[:3]]") AC_MSG_RESULT($PYTHON_VERSION) - dnl recover major + dnl recover major PYTHON_MAJOR=${PYTHON_VERSION%.*} AC_DEFINE_UNQUOTED([_PYTHON_MAJOR_],$PYTHON_MAJOR,[python version major]) @@ -643,6 +643,11 @@ AC_ARG_WITH([python-numpy-dir], AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory.]), - [PYTHON_NUMPY_ROOT=$withval],[PYTHON_NUMPY_ROOT="no"]) - + [PYTHON_NUMPY_ROOT=$withval],[PYTHON_NUMPY_ROOT="no"]) + + dnl you can find numpy by typing + dnl >>> import numpy + dnl >>> numpy.__file__ + dnl '/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/__init__.pyc' + dnl Check whether numpy is enabled AC_MSG_CHECKING(for python-numpy) @@ -667,6 +672,6 @@ AC_ARG_WITH([chaco-dir], AS_HELP_STRING([--with-chaco-dir=DIR], [chaco root directory.]), - [CHACO_ROOT=$withval],[CHACO_ROOT="no"]) - + [CHACO_ROOT=$withval],[CHACO_ROOT="no"]) + dnl Check whether chaco is enabled AC_MSG_CHECKING([for chaco]) @@ -694,5 +699,5 @@ AC_ARG_WITH([scotch-dir], AS_HELP_STRING([--with-scotch-dir=DIR], [scotch root directory.]), - [SCOTCH_ROOT=$withval],[SCOTCH_ROOT="no"]) + [SCOTCH_ROOT=$withval],[SCOTCH_ROOT="no"]) dnl Check whether scotch is enabled @@ -708,5 +713,5 @@ AC_MSG_RESULT($HAVE_SCOTCH) AM_CONDITIONAL([SCOTCH],[test x$HAVE_SCOTCH = xyes]) - + dnl scotch libraries if test "x$HAVE_SCOTCH" = "xyes"; then @@ -721,5 +726,5 @@ AC_ARG_WITH([esmf-dir], AS_HELP_STRING([--with-esmf-dir=DIR], [esmf root directory.]), - [ESMF_ROOT=$withval],[ESMF_ROOT="no"]) + [ESMF_ROOT=$withval],[ESMF_ROOT="no"]) dnl Check whether esmf is enabled @@ -734,5 +739,5 @@ fi AC_MSG_RESULT($HAVE_ESMF) - + dnl esmf headers and libraries if test "x$HAVE_ESMF" == "xyes"; then @@ -745,8 +750,47 @@ AM_CONDITIONAL([ESMF], [test x$HAVE_ESMF = xyes]) dnl }}} + dnl codipack{{{ + AC_ARG_WITH([codipack-dir], + AS_HELP_STRING([--with-codipack-dir=DIR], [CoDiPack root directory.]), + [CODIPACK_ROOT=$withval],[CODIPACK_ROOT="no"]) + + dnl Check whether codipack is enabled + AC_MSG_CHECKING([for CoDiPack]) + if test "x$CODIPACK_ROOT" = "xno" ; then + HAVE_CODIPACK=no + else + HAVE_CODIPACK=yes + if ! test -d "$CODIPACK_ROOT"; then + AC_MSG_ERROR([codipack directory provided ($CODIPACK_ROOT) does not exist]); + fi + fi + AC_MSG_RESULT($HAVE_CODIPACK) + + dnl codipack headers and libraries + if test "x$HAVE_CODIPACK" == "xyes"; then + CODIPACKINCL="-I$CODIPACK_ROOT/include" + AC_DEFINE([_HAVE_CODIPACK_],[1],[with codipack in ISSM src]) + AC_DEFINE([_HAVE_AD_],[1],[with AD in ISSM src]) + AC_SUBST([CODIPACKINCL]) + fi + AM_CONDITIONAL([CODIPACK], [test x$HAVE_CODIPACK = xyes]) + AM_COND_IF(CODIPACK,[CXXFLAGS+=" -std=c++11"]) + dnl }}} + dnl tapeallocation {{{ + AC_ARG_ENABLE([tape-alloc], dnl feature + AS_HELP_STRING([--enable-tape-alloc],[turn tape allocation support on]), + [enable_tape_alloc=$enableval], [enable_tape_alloc=no]) + + dnl check whether enabled + AC_MSG_CHECKING(for tape memory allocation) + if test "x$enable_tape_alloc" = xyes; then + AC_DEFINE([_AD_TAPE_ALLOC_],[1],[Macro to enable a priori tape allocation for AD]) + fi + AC_MSG_RESULT($enable_tape_alloc) + dnl }}} dnl adolc{{{ AC_ARG_WITH([adolc-dir], AS_HELP_STRING([--with-adolc-dir=DIR], [adolc root directory.]), - [ADOLC_ROOT=$withval],[ADOLC_ROOT="no"]) + [ADOLC_ROOT=$withval],[ADOLC_ROOT="no"]) dnl Check whether adolc is enabled @@ -761,5 +805,5 @@ fi AC_MSG_RESULT($HAVE_ADOLC) - + dnl adolc headers and libraries if test "x$HAVE_ADOLC" == "xyes"; then @@ -773,11 +817,11 @@ fi AM_CONDITIONAL([ADOLC], [test x$HAVE_ADOLC = xyes]) - AM_COND_IF(ADOLC,[CXXFLAGS+=" -std=c++11"]) + AM_COND_IF(ADOLC,[CXXFLAGS+=" -std=c++11"]) dnl }}} dnl adolc-version{{{ AC_ARG_WITH([adolc-version], AS_HELP_STRING([--with-adolc-version=number], [adolc version.]), - [ADOLC_VERSION=$withval],[ADOLC_VERSION=2]) - AC_MSG_CHECKING(for adolc-version) + [ADOLC_VERSION=$withval],[ADOLC_VERSION=2]) + AC_MSG_CHECKING(for adolc-version) AC_DEFINE_UNQUOTED([_ADOLC_VERSION_],$ADOLC_VERSION,[ADOLC version]) @@ -787,5 +831,5 @@ AC_ARG_WITH([adic2-dir], AS_HELP_STRING([--with-adic2-dir=DIR], [adic2 root directory.]), - [ADIC2_ROOT=$withval],[ADIC2_ROOT="no"]) + [ADIC2_ROOT=$withval],[ADIC2_ROOT="no"]) dnl Check whether adic2 is enabled @@ -815,5 +859,5 @@ AS_HELP_STRING([--with-atlas-dir=DIR],[atlas root directory]), [ATLAS_ROOT=$withval],[ATLAS_ROOT="no"]) - + dnl Check whether atlas is enabled AC_MSG_CHECKING(for atlas and cblas libraries) @@ -836,8 +880,8 @@ ;; *linux*) - ATLASLIB=-L"$ATLAS_ROOT/lib -lcblas -latlas -lm " + ATLASLIB=-L"$ATLAS_ROOT/lib -lcblas -latlas -lm " ;; *darwin*) - ATLASLIB=-L"$ATLAS_ROOT/lib -lcblas -latlas -lm" + ATLASLIB=-L"$ATLAS_ROOT/lib -lcblas -latlas -lm" ;; esac @@ -849,5 +893,5 @@ AC_ARG_WITH([gsl-dir], AS_HELP_STRING([--with-gsl-dir=DIR], [gsl root directory.]), - [GSL_ROOT=$withval],[GSL_ROOT="no"]) + [GSL_ROOT=$withval],[GSL_ROOT="no"]) dnl Check whether gsl is enabled @@ -862,5 +906,5 @@ fi AC_MSG_RESULT($HAVE_GSL) - + dnl gsl headers and libraries if test "x$HAVE_GSL" == "xyes"; then @@ -877,8 +921,8 @@ AM_CONDITIONAL([GSL], [test x$HAVE_GSL = xyes]) dnl }}} - dnl adjoinable-mpi{{{ + dnl ampi (ADOLC){{{ AC_ARG_WITH([ampi-dir], AS_HELP_STRING([--with-ampi-dir=DIR], [adjoinable mpi root directory.]), - [AMPI_ROOT=$withval],[AMPI_ROOT="no"]) + [AMPI_ROOT=$withval],[AMPI_ROOT="no"]) dnl Check whether ampi is enabled @@ -893,5 +937,5 @@ fi AC_MSG_RESULT($HAVE_AMPI) - + dnl ampi headers and libraries if test "x$HAVE_AMPI" == "xyes"; then @@ -912,8 +956,73 @@ AM_CONDITIONAL([AMPI], [test x$HAVE_AMPI = xyes]) dnl }}} + dnl adjointmpi (CoDiPack){{{ + AC_ARG_WITH([adjointmpi-dir], + AS_HELP_STRING([--with-adjointmpi-dir=DIR], [adjoinable mpi root directory.]), + [ADJOINTMPI_ROOT=$withval],[ADJOINTMPI_ROOT="no"]) + + dnl Check whether adjointmpi is enabled + AC_MSG_CHECKING([for adjointmpi]) + if test "x$ADJOINTMPI_ROOT" = "xno" ; then + HAVE_ADJOINTMPI=no + else + HAVE_ADJOINTMPI=yes + if ! test -d "$ADJOINTMPI_ROOT"; then + AC_MSG_ERROR([adjointmpi directory provided ($ADJOINTMPI_ROOT) does not exist]); + fi + fi + AC_MSG_RESULT($HAVE_ADJOINTMPI) + + dnl adjointmpi headers and libraries + if test "x$HAVE_ADJOINTMPI" == "xyes"; then + if test "x$CODIPACK_ROOT" == "xno"; then + AC_MSG_ERROR([cannot run adjoint mpi without CoDiPack]); + fi + ADJOINTMPIINCL="-I$ADJOINTMPI_ROOT/include" + ADJOINTMPILIB="-L$ADJOINTMPI_ROOT/lib -lAMPI" + dnl Also set _HAVE_AMPI_, because the interface is (almost) the + dnl same as for adjoinable mpi... + AC_DEFINE([_HAVE_AMPI_],[1],[with adjoint mpi in ISSM src]) + AC_DEFINE([_HAVE_ADJOINTMPI_],[1],[with adjoint mpi in ISSM src]) + AC_SUBST([ADJOINTMPIINCL]) + AC_SUBST([ADJOINTMPILIB]) + fi + AM_CONDITIONAL([ADJOINTMPI], [test x$HAVE_ADJOINTMPI = xyes]) + dnl }}} + dnl medipack (CoDiPack, ADOLC dev){{{ + AC_ARG_WITH([medipack-dir], + AS_HELP_STRING([--with-medipack-dir=DIR], [MeDiPack root directory.]), + [MEDIPACK_ROOT=$withval],[MEDIPACK_ROOT="no"]) + + dnl Check whether medipack is enabled + AC_MSG_CHECKING([for medipack]) + if test "x$MEDIPACK_ROOT" = "xno" ; then + HAVE_MEDIPACK=no + else + HAVE_MEDIPACK=yes + if ! test -d "$MEDIPACK_ROOT"; then + AC_MSG_ERROR([medipack directory provided ($MEDIPACK_ROOT) does not exist]); + fi + fi + AC_MSG_RESULT($HAVE_MEDIPACK) + + dnl medipack headers and libraries + if test "x$HAVE_MEDIPACK" == "xyes"; then + if test "x$CODIPACK_ROOT" == "xno"; then + AC_MSG_ERROR([cannot run MeDiPack without CoDiPack]); + fi + MEDIPACKINCL="-I$MEDIPACK_ROOT/include -I$MEDIPACK_ROOT/src" + dnl Also set _HAVE_AMPI_, because the interface is (almost) the + dnl same as for adjoinable mpi... + AC_DEFINE([_HAVE_AMPI_],[1],[with adjoint mpi in ISSM src]) + AC_DEFINE([_HAVE_MEDIPACK_],[1],[with MeDiPack in ISSM src]) + AC_SUBST([MEDIPACKINCL]) + fi + AM_CONDITIONAL([MEDIPACK], [test x$HAVE_MEDIPACK = xyes]) + + dnl }}} dnl rose{{{ AC_ARG_WITH([rose-dir], AS_HELP_STRING([--with-rose-dir=DIR], [rose root directory.]), - [ROSE_ROOT=$withval],[ROSE_ROOT="no"]) + [ROSE_ROOT=$withval],[ROSE_ROOT="no"]) dnl Check whether rose is enabled @@ -941,5 +1050,5 @@ dnl mpi{{{ AC_MSG_CHECKING(for mpi) - + AC_ARG_WITH([mpi-include], AS_HELP_STRING([--with-mpi-include=DIR],[mpi include directory, necessary for parallel build]), @@ -954,5 +1063,5 @@ [MPI_LIBFLAGS=$withval],[MPI_LIBFLAGS=""]) - + if test -z "$MPI_INCLUDE" ; then HAVE_MPI=no @@ -980,5 +1089,5 @@ if test x$IS_WINDOWS = xyes; then MPIINCL=/I"$MPI_INCLUDE" - else + else MPIINCL=-I"$MPI_INCLUDE" fi @@ -996,5 +1105,5 @@ AS_HELP_STRING([--with-petsc-dir=DIR],[PETSc root directory, necessary for parallel build]), [PETSC_ROOT=$withval],[PETSC_ROOT="no"]) - + dnl Check whether petsc is enabled AC_MSG_CHECKING([for petsc]) @@ -1033,5 +1142,5 @@ AC_MSG_RESULT(no) fi - + AC_ARG_WITH([petsc-arch], AS_HELP_STRING([--with-petsc-arch=DIR],[PETSc arch, necessary for PETSc < 3.0]), @@ -1050,5 +1159,5 @@ PETSCINCL+=" $PETSC_ROOT/include/$PETSC_ARCH" fi - + case "${host_os}" in *cygwin*) @@ -1069,5 +1178,5 @@ if test "x$host_os_version" = "x3.0.101-0.31.1_1.0502.8394-cray_gem_s" ; then PETSCLIB="-L$PETSC_ROOT/lib -lcraypetsc_gnu_real -lmetis" - fi + fi ;; *darwin*) @@ -1122,8 +1231,8 @@ if test "$METIS_VERSION" = "4" ; then - METISINCL=-I"$METIS_ROOT/Lib" + METISINCL=-I"$METIS_ROOT/Lib" case "${host_os}" in *cygwin*) - METISINCL="/I`cygpath -m $METIS_ROOT/Lib`" + METISINCL="/I`cygpath -m $METIS_ROOT/Lib`" METISLIB="-Wl,/link -Wl,/LIBPATH:`cygpath -m $METIS_ROOT` -Wl,libmetis.lib" ;; @@ -1150,5 +1259,5 @@ ;; esac - METISINCL=-I"$METIS_ROOT/include" + METISINCL=-I"$METIS_ROOT/include" AC_DEFINE([_METIS_VERSION_],[5],[ Metis version number]) fi @@ -1164,5 +1273,5 @@ AC_ARG_WITH([tao-dir], AS_HELP_STRING([--with-tao-dir=DIR], [tao root directory.]), - [TAO_ROOT=$withval],[TAO_ROOT="no"]) + [TAO_ROOT=$withval],[TAO_ROOT="no"]) dnl Check whether tao is enabled @@ -1199,5 +1308,5 @@ AC_ARG_WITH([m1qn3-dir], AS_HELP_STRING([--with-m1qn3-dir=DIR], [m1qn3 root directory.]), - [M1QN3_ROOT=$withval],[M1QN3_ROOT="no"]) + [M1QN3_ROOT=$withval],[M1QN3_ROOT="no"]) dnl Check whether m1qn3 is enabled @@ -1212,8 +1321,8 @@ fi AC_MSG_RESULT($HAVE_M1QN3) - + dnl m1qn3 headers and libraries if test "x$HAVE_M1QN3" == "xyes"; then - M1QN3LIB="$M1QN3_ROOT/libm1qn3.a $M1QN3_ROOT//libddot.a" + M1QN3LIB="$M1QN3_ROOT/libm1qn3.a $M1QN3_ROOT/libddot.a" AC_DEFINE([_HAVE_M1QN3_],[1],[with M1QN3 in ISSM src]) AC_SUBST([M1QN3LIB]) @@ -1223,5 +1332,5 @@ AC_ARG_WITH([proj4-dir], AS_HELP_STRING([--with-proj4-dir=DIR], [proj4 root directory.]), - [PROJ4_ROOT=$withval],[PROJ4_ROOT="no"]) + [PROJ4_ROOT=$withval],[PROJ4_ROOT="no"]) dnl Check whether proj4 is enabled @@ -1236,5 +1345,5 @@ fi AC_MSG_RESULT($HAVE_PROJ4) - + dnl proj4 headers and libraries if test "x$HAVE_PROJ4" == "xyes"; then @@ -1251,5 +1360,5 @@ AS_HELP_STRING([--with-slepc-dir=DIR],[slepc root directory]), [SLEPC_ROOT=$withval],[SLEPC_ROOT="no"]) - + dnl Check whether slepc is enabled AC_MSG_CHECKING([for slepc]) @@ -1263,5 +1372,5 @@ fi AC_MSG_RESULT($HAVE_SLEPC) - + dnl slepc headers and libraries if test "x$HAVE_SLEPC" == "xyes"; then @@ -1277,5 +1386,5 @@ AS_HELP_STRING([--with-shapelib-dir=DIR], [shapelib root directory]), [SHAPELIB_ROOT=$withval],[SHAPELIB_ROOT="no"]) - + dnl Check whether shapelib is enabled AC_MSG_CHECKING([for shapelib]) @@ -1289,5 +1398,5 @@ fi AC_MSG_RESULT($HAVE_SHAPELIB) - + dnl shapelib headers and libraries if test "x$HAVE_SHAPELIB" == "xyes"; then @@ -1309,5 +1418,5 @@ AS_HELP_STRING([--with-scalapack-lib=LIBS],[scalapack libraries to include]), [SCALAPACKLIB=$withval],[SCALAPACKLIB="no"]) - + dnl Check whether scalapack is enabled AC_MSG_CHECKING([for scalapack]) @@ -1329,5 +1438,5 @@ fi AC_MSG_RESULT($HAVE_SCALAPACK) - + dnl scalapack headers and libraries if test "x$HAVE_SCALAPACK" = "xyes"; then @@ -1340,5 +1449,5 @@ AS_HELP_STRING([--with-blas-lapack-dir=DIR],[blas-lapack root directory]), [BLASLAPACK_ROOT=$withval],[BLASLAPACK_ROOT="no"]) - + dnl Check whether blas-lapack is enabled AC_MSG_CHECKING([for blas-lapack]) @@ -1352,5 +1461,5 @@ fi AC_MSG_RESULT($HAVE_BLASLAPACK) - + dnl blas-lapack headers and libraries if test "x$HAVE_BLASLAPACK" == "xyes"; then @@ -1362,8 +1471,8 @@ ;; *linux*) - BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " + BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " ;; *darwin*) - BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " + BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " ;; esac @@ -1393,17 +1502,17 @@ dnl plapack{{{ AC_MSG_CHECKING(for plapack) - + AC_ARG_WITH([plapack-lib], AS_HELP_STRING([--with-plapack-lib = lib],[plapack library]), [PLAPACK_LIB=$withval],[PLAPACK_LIB=""]) - + AC_ARG_WITH([plapack-include], AS_HELP_STRING([--with-plapack-include = include], [plapack include ]), [PLAPACK_INCLUDE=$withval],[PLAPACK_INCLUDE=""]) - + if test -n "$PLAPACK_LIB"; then if test -n "$PLAPACK_INCLUDE"; then - + HAVE_PLAPACK=yes PLAPACKINCL="$PLAPACK_INCLUDE" @@ -1424,5 +1533,5 @@ AS_HELP_STRING([--with-mumps-dir=DIR],[mumps root directory]), [MUMPS_ROOT=$withval],[MUMPS_ROOT="no"]) - + dnl Check whether mumps is enabled AC_MSG_CHECKING([for mumps]) @@ -1436,5 +1545,5 @@ fi AC_MSG_RESULT($HAVE_MUMPS) - + dnl mumps headers and libraries if test "x$HAVE_MUMPS" == "xyes"; then @@ -1455,5 +1564,5 @@ if test "x$HAVE_MUMPS" != "xyes"; then AC_MSG_CHECKING(for mumps2 (stand alone)) - + AC_ARG_WITH([mumps2-include], AS_HELP_STRING([--with-mumps2-include=DIR],[mumps2 include directory, necessary for parallel build]), @@ -1464,5 +1573,5 @@ [MUMPS_LIBFLAGS=$withval],[MUMPS_LIBFLAGS=""]) - + if test -z "$MUMPS_INCLUDE" ; then HAVE_MUMPS=no @@ -1490,5 +1599,5 @@ AS_HELP_STRING([--with-blacs-dir=DIR],[blacs root directory]), [BLACS_ROOT=$withval],[BLACS_ROOT="no"]) - + dnl Check whether blacs is enabled AC_MSG_CHECKING([for blacs]) @@ -1502,5 +1611,5 @@ fi AC_MSG_RESULT($HAVE_BLACS) - + dnl blacs headers and libraries if test "x$HAVE_BLACS" == "xyes"; then @@ -1516,5 +1625,5 @@ AS_HELP_STRING([--with-hypre-dir=DIR],[hypre root directory]), [HYPRE_ROOT=$withval],[HYPRE_ROOT="no"]) - + dnl Check whether hypre is enabled AC_MSG_CHECKING([for hypre]) @@ -1590,5 +1699,5 @@ fi dnl }}} -dnl superlu{{{ +dnl superlu{{{ AC_ARG_WITH([superlu-dir], AS_HELP_STRING([--with-superlu-dir=DIR],[superlu root directory]), @@ -1606,5 +1715,5 @@ fi AC_MSG_RESULT($HAVE_SUPERLU) - + dnl superlu headers and libraries if test "x$HAVE_SUPERLU" == "xyes"; then @@ -1616,5 +1725,5 @@ fi dnl }}} -dnl spooles{{{ +dnl spooles{{{ AC_ARG_WITH([spooles-dir], AS_HELP_STRING([--with-spooles-dir=DIR],[spooles root directory]), @@ -1632,5 +1741,5 @@ fi AC_MSG_RESULT($HAVE_SPOOLES) - + dnl spooles headers and libraries if test "x$HAVE_SPOOLES" == "xyes"; then @@ -1642,5 +1751,5 @@ fi dnl }}} -dnl pastix{{{ +dnl pastix{{{ AC_ARG_WITH([pastix-dir], AS_HELP_STRING([--with-pastix-dir=DIR],[pastix root directory]), @@ -1658,5 +1767,5 @@ fi AC_MSG_RESULT($HAVE_PASTIX) - + dnl pastix headers and libraries if test "x$HAVE_PASTIX" == "xyes"; then @@ -1672,5 +1781,5 @@ AS_HELP_STRING([--with-ml-dir=DIR],[ml root directory]), [ML_ROOT=$withval],[ML_ROOT="no"]) - + dnl Check whether ml is enabled AC_MSG_CHECKING([for ml]) @@ -1684,5 +1793,5 @@ fi AC_MSG_RESULT($HAVE_ML) - + dnl ml headers and libraries if test "x$HAVE_ML" == "xyes"; then @@ -1698,5 +1807,5 @@ AS_HELP_STRING([--with-umfpack-dir=DIR],[UMFPACK root directory]), [UMFPACK_ROOT=$withval],[UMFPACK_ROOT="no"]) - + dnl Check whether umfpack is enabled AC_MSG_CHECKING([for umfpack]) @@ -1710,5 +1819,5 @@ fi AC_MSG_RESULT($HAVE_UMFPACK) - + dnl umfpack headers and libraries if test "x$HAVE_UMFPACK" == "xyes"; then @@ -1738,6 +1847,6 @@ AC_ARG_WITH([math77-dir], AS_HELP_STRING([--with-math77-dir=DIR], [math77 root directory.]), - [MATH77_ROOT=$withval],[MATH77_ROOT="no"]) - + [MATH77_ROOT=$withval],[MATH77_ROOT="no"]) + dnl Check whether math77 is enabled AC_MSG_CHECKING([for math77]) @@ -1751,5 +1860,5 @@ fi AC_MSG_RESULT($HAVE_MATH77) - + dnl math77 headers and libraries if test "x$HAVE_MATH77" == "xyes"; then @@ -1762,5 +1871,5 @@ AC_ARG_WITH([fortran], AS_HELP_STRING([--with-fortran = YES], [do we compile fortran code (default is yes)]), - [FORTRAN=$withval],[FORTRAN=yes]) + [FORTRAN=$withval],[FORTRAN=yes]) AC_MSG_CHECKING(for fortran compilation) if test "x$FORTRAN" = "xyes"; then @@ -1830,5 +1939,5 @@ AC_ARG_WITH([meteoio-dir], AS_HELP_STRING([--with-meteoio-dir=DIR], [use meteoio in conjunction with snowpack model.]), - [METEOIO_ROOT=$withval],[METEOIO_ROOT="no"]) + [METEOIO_ROOT=$withval],[METEOIO_ROOT="no"]) dnl Check whether meteoio is enabled @@ -1843,5 +1952,5 @@ fi AC_MSG_RESULT($HAVE_METEOIO) - + dnl meteoio headers and libraries if test "x$HAVE_METEOIO" == "xyes"; then @@ -1858,5 +1967,5 @@ AC_ARG_WITH([snowpack-dir], AS_HELP_STRING([--with-snowpack-dir=DIR], [use snowpack for surface mass balance model.]), - [SNOWPACK_ROOT=$withval],[SNOWPACK_ROOT="no"]) + [SNOWPACK_ROOT=$withval],[SNOWPACK_ROOT="no"]) dnl Check whether snowpack is enabled @@ -1871,5 +1980,5 @@ fi AC_MSG_RESULT($HAVE_SNOWPACK) - + dnl snowpack headers and libraries if test "x$HAVE_SNOWPACK" == "xyes"; then @@ -1886,5 +1995,5 @@ AC_ARG_WITH([neopz-dir], AS_HELP_STRING([--with-neopz-dir=DIR], [neopz root directory.]), - [NEOPZ_ROOT=$withval],[NEOPZ_ROOT="no"]) + [NEOPZ_ROOT=$withval],[NEOPZ_ROOT="no"]) dnl Check whether neopz is enabled @@ -1899,5 +2008,5 @@ fi AC_MSG_RESULT($HAVE_NEOPZ) - + dnl neopz headers and libraries if test "x$HAVE_NEOPZ" == "xyes"; then @@ -1938,5 +2047,5 @@ AC_ARG_WITH([bamg], AS_HELP_STRING([--with-bamg = YES],[compile with bamg capabilities (default is yes)]), - [BAMG=$withval],[BAMG=yes]) + [BAMG=$withval],[BAMG=yes]) AC_MSG_CHECKING(for bamg capability compilation) @@ -1952,5 +2061,5 @@ AC_ARG_WITH([ocean], AS_HELP_STRING([--with-ocean = YES],[compile with ice/ocean coupling (default is no)]), - [OCEAN=$withval],[OCEAN=no]) + [OCEAN=$withval],[OCEAN=no]) AC_MSG_CHECKING(for ice/ocean capability compilation) @@ -1966,5 +2075,5 @@ AC_ARG_WITH([kml], AS_HELP_STRING([--with-kml = YES],[compile with kml capabilities (default is no)]), - [KML=$withval],[KML=no]) + [KML=$withval],[KML=no]) AC_MSG_CHECKING(for kml capability compilation) @@ -1980,5 +2089,5 @@ AC_ARG_WITH([kriging], AS_HELP_STRING([--with-kriging = YES],[compile with kriging capabilities (default is yes)]), - [KRIGING=$withval],[KRIGING=yes]) + [KRIGING=$withval],[KRIGING=yes]) AC_MSG_CHECKING(for kriging capability compilation) @@ -1997,5 +2106,5 @@ AC_ARG_WITH([ios], AS_HELP_STRING([--with-ios = YES], [compile with iOS capabilities (default is no, alternatives are yes)]), - [IOS=$withval],[IOS=no]) + [IOS=$withval],[IOS=no]) AC_MSG_CHECKING(for iOS compilation) @@ -2016,5 +2125,5 @@ AC_ARG_WITH([android], AS_HELP_STRING([--with-android = EXE], [compile with android capabilities (default is no, alternatives are exe and jni)]), - [ANDROID=$withval],[ANDROID=no]) + [ANDROID=$withval],[ANDROID=no]) AC_MSG_CHECKING(for android capability compilation) @@ -2043,7 +2152,7 @@ AC_ARG_WITH([android-ndk], AS_HELP_STRING([--with-android-ndk=DIR], [android-ndk root directory.]), - [ANDROID_NDK_ROOT=$withval],[ANDROID_NDK_ROOT=""]) + [ANDROID_NDK_ROOT=$withval],[ANDROID_NDK_ROOT=""]) AC_MSG_CHECKING(with android ndk) - + if test -d "$ANDROID_NDK_ROOT"; then dnl defaults @@ -2061,8 +2170,8 @@ dnl other options dnl optimization{{{ - dnl bypass standard optimization -g -O2 ? + dnl bypass standard optimization -g -O2 ? AC_ARG_WITH([cxxoptflags], AS_HELP_STRING([--with-cxxoptflags = CXXOPTFLAGS], [optimization using CXX flags, ex: --with-cxxoptflags=-march=opteron -O3]), - [CXXOPTFLAGS=$withval],[CXXOPTFLAGS="-g -O2 -fPIC"]) + [CXXOPTFLAGS=$withval],[CXXOPTFLAGS="-g -O2 -fPIC"]) AC_MSG_CHECKING(for c++ optimization flags) AC_SUBST([CXXOPTFLAGS]) @@ -2079,5 +2188,5 @@ MULTITHREADINLIB="" if test "$NUMTHREADS_VALUE" != "1"; then - + MULTITHREADINGLIB="-lpthread -lrt" case "${host_os}" in @@ -2094,12 +2203,19 @@ AC_DEFINE([_MULTITHREADING_],[1],[with numthreads enabled]) fi + dnl check that it is an integer + if [[ "$NUMTHREADS_VALUE" -eq "$NUMTHREADS_VALUE" 2> /dev/null ]] ; then + dnl cool we have an integer + : + else + AC_MSG_ERROR([Number of threads provided ($NUMTHREADS_VALUE) is not an integer]); + fi AC_DEFINE_UNQUOTED([_NUMTHREADS_],[$NUMTHREADS_VALUE],[number of threads]) AC_SUBST([MULTITHREADINGLIB]) - AC_MSG_RESULT($NUMTHREADS_VALUE) + AC_MSG_RESULT($NUMTHREADS_VALUE) dnl }}} dnl 64bit {{{ AC_ARG_WITH([64bit-indices], AS_HELP_STRING([--with-64bit-indices = bool], [use 64 bit integers, default 0, ex: --with-64bit-indices=1]), - [USE_64BIT_INDICES=$withval],[USE_64BIT_INDICES=0]) + [USE_64BIT_INDICES=$withval],[USE_64BIT_INDICES=0]) AC_MSG_CHECKING(for 64 bit indices) @@ -2132,5 +2248,5 @@ AC_MSG_ERROR([need fortran compiler to compile GiaIvins (or use --without-GiaIvins )]); fi - + dnl check that fortran is provided if Love is on if test "$HAVE_LOVE" = "yes" && test "$HAVE_FORTRAN" = "no" ; then @@ -2142,5 +2258,5 @@ AC_MSG_ERROR([need mpi if using the metis partitioner!]); fi - + dnl check that if we run adolc, we don't compile krigging.exe if test "$HAVE_ADOLC" = "yes" && test "$HAVE_KRIGING" = "yes" ; then @@ -2151,4 +2267,10 @@ AC_MSG_ERROR([cannot compile ISSM with both PETSc and adolc]); fi + if test "$HAVE_ADOLC" = "yes" && test "$HAVE_CODIPACK" = "yes" ; then + AC_MSG_ERROR([cannot compile ISSM with both ADOLC and CoDiPack]); + fi + if test "$HAVE_ADJOINTMPI" = "yes" && test "$HAVE_MEDIPACK" = "yes" ; then + AC_MSG_ERROR([cannot compile ISSM with both MeDiPack and AdjointMPI]); + fi dnl check that if we run meteoio, we have snowpack also if test "$HAVE_METEOIO" = "yes" && test "$HAVE_SNOWPACK" = "no" ; then Index: /issm/trunk/src/c/Makefile.am =================================================================== --- /issm/trunk/src/c/Makefile.am (revision 23393) +++ /issm/trunk/src/c/Makefile.am (revision 23394) @@ -1,3 +1,3 @@ -AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJ4INCL@ +AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @CODIPACKINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJ4INCL@ AUTOMAKE_OPTIONS = subdir-objects @@ -51,8 +51,11 @@ ./modules/BamgTriangulatex/BamgTriangulatex.cpp -#do not include AmrBamg with ADOLC +#do not include AmrBamg with AD if ADOLC else +if CODIPACK +else issm_sources += ./classes/AmrBamg.cpp +endif endif endif @@ -172,4 +175,5 @@ ./shared/Elements/PrintArrays.cpp\ ./shared/Elements/PddSurfaceMassBalance.cpp\ + ./shared/Elements/PddSurfaceMassBalanceSicopolis.cpp\ ./shared/Elements/ComputeDelta18oTemperaturePrecipitation.cpp\ ./shared/Elements/ComputeMungsmTemperaturePrecipitation.cpp\ @@ -320,4 +324,12 @@ ./classes/Inputs/TetraInput.cpp #}}} +#ADJOINTMPI/MeDiPack sources {{{ +if ADJOINTMPI +issm_sources += ./toolkits/codipack/ampi_interface.cpp +endif +if MEDIPACK +issm_sources += ./toolkits/codipack/ampi_interface.cpp +endif +# }}} #DAKOTA sources {{{ if DAKOTA @@ -632,5 +644,5 @@ if !WINDOWS if !STANDALONE_LIBRARIES -libISSMCore_la_LIBADD = $(PETSCLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) +libISSMCore_la_LIBADD = $(PETSCLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) if FORTRAN libISSMCore_la_LIBADD += $(FLIBS) $(FORTRANLIB) @@ -714,5 +726,5 @@ #External packages -LDADD += $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(PETSCLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(AMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJ4LIB) +LDADD += $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(PETSCLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJ4LIB) if FORTRAN Index: /issm/trunk/src/c/analyses/EnthalpyAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/EnthalpyAnalysis.cpp (revision 23393) +++ /issm/trunk/src/c/analyses/EnthalpyAnalysis.cpp (revision 23394) @@ -43,6 +43,7 @@ int smb_model; iomodel->FindConstant(&smb_model,"md.smb.model"); - if(smb_model==SMBpddEnum) isdynamic=true; - if(smb_model==SMBd18opddEnum) isdynamic=true; + if(smb_model==SMBpddEnum) isdynamic=true; + if(smb_model==SMBd18opddEnum) isdynamic=true; + if(smb_model==SMBpddSicopolisEnum) isdynamic=true; } @@ -1200,4 +1201,6 @@ _assert_((Hc+Ht)>0.); lambda = Hc/(Hc+Ht); + _assert_(lambda>=0.); + _assert_(lambda<=1.); kappa = kappa_c*kappa_t/(lambda*kappa_t+(1.-lambda)*kappa_c); // ==(lambda/kappa_c + (1.-lambda)/kappa_t)^-1 } Index: /issm/trunk/src/c/analyses/ExtrapolationAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/ExtrapolationAnalysis.cpp (revision 23393) +++ /issm/trunk/src/c/analyses/ExtrapolationAnalysis.cpp (revision 23394) @@ -65,5 +65,5 @@ femmodel->SetCurrentConfiguration(ExtrapolationAnalysisEnum); - if(VerboseSolution()) _printf0_("extrapolation of " << EnumToStringx(extvar_enum) << ": call computational core:\n"); + if(VerboseSolution()) _printf0_(" extrapolation of " << EnumToStringx(extvar_enum) << ":\n"); solutionsequence_linear(femmodel); Index: /issm/trunk/src/c/analyses/FreeSurfaceBaseAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/FreeSurfaceBaseAnalysis.cpp (revision 23393) +++ /issm/trunk/src/c/analyses/FreeSurfaceBaseAnalysis.cpp (revision 23394) @@ -80,5 +80,4 @@ iomodel->FetchDataToInput(elements,"md.mask.ice_levelset",MaskIceLevelsetEnum); iomodel->FetchDataToInput(elements,"md.basalforcings.groundedice_melting_rate",BasalforcingsGroundediceMeltingRateEnum,0.); - iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum); iomodel->FetchDataToInput(elements,"md.initialization.vx",VxEnum); iomodel->FetchDataToInput(elements,"md.initialization.vy",VyEnum); @@ -89,4 +88,29 @@ iomodel->FetchDataToInput(elements,"md.mesh.vertexonbase",MeshVertexonbaseEnum); iomodel->FetchDataToInput(elements,"md.mesh.vertexonsurface",MeshVertexonsurfaceEnum); + } + + /*Get what we need for ocean-induced basal melting*/ + int basalforcing_model; + iomodel->FindConstant(&basalforcing_model,"md.basalforcings.model"); + switch(basalforcing_model){ + case FloatingMeltRateEnum: + iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum); + break; + case LinearFloatingMeltRateEnum: + break; + case MismipFloatingMeltRateEnum: + break; + case MantlePlumeGeothermalFluxEnum: + break; + case SpatialLinearFloatingMeltRateEnum: + iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); + iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); + iomodel->FetchDataToInput(elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); + break; + case BasalforcingsPicoEnum: + iomodel->FetchDataToInput(elements,"md.basalforcings.basin_id",BasalforcingsPicoBasinIdEnum); + break; + default: + _error_("Basal forcing model "<FindParam(&dt,TimesteppingTimeStepEnum); basalelement ->FindParam(&dt,HydrologydtEnum); - - Input* epl_thick_input = basalelement->GetInput(HydrologydcEplThicknessHydrostepEnum); _assert_(epl_thick_input); - Input* sed_head_input = basalelement->GetInput(SedimentHeadHydrostepEnum); _assert_(sed_head_input); - Input* epl_head_input = basalelement->GetInput(EplHeadHydrostepEnum); _assert_(epl_head_input); - Input* water_input = basalelement->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(water_input); - Input* residual_input = basalelement->GetInput(SedimentHeadResidualEnum); _assert_(residual_input); - Input* base_input = basalelement->GetInput(BaseEnum); _assert_(base_input); + basalelement ->FindParam(&smb_model,SmbEnum); + + Input* epl_thick_input = basalelement->GetInput(HydrologydcEplThicknessHydrostepEnum); _assert_(epl_thick_input); + Input* sed_head_input = basalelement->GetInput(SedimentHeadHydrostepEnum); _assert_(sed_head_input); + Input* epl_head_input = basalelement->GetInput(EplHeadHydrostepEnum); _assert_(epl_head_input); + Input* basal_melt_input = basalelement->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(basal_melt_input); + Input* residual_input = basalelement->GetInput(SedimentHeadResidualEnum); _assert_(residual_input); + Input* base_input = basalelement->GetInput(BaseEnum); _assert_(base_input); if(dt!= 0.){ old_wh_input = basalelement->GetInput(EplHeadOldEnum); _assert_(old_wh_input); } + if(smb_model==SMBgradientscomponentsEnum){ + surface_runoff_input = basalelement->GetInput(SmbRunoffEnum); _assert_(surface_runoff_input); + } + /* Start looping on the number of gaussian points: */ Gauss* gauss = basalelement->NewGauss(2); @@ -355,6 +362,8 @@ /*Loading term*/ - water_input->GetInputValue(&water_load,gauss); - scalar = Jdet*gauss->weight*(water_load); + basal_melt_input->GetInputValue(&water_load,gauss); + if(surface_runoff_input) surface_runoff_input->GetInputValue(&runoff_value,gauss); + else runoff_value = 0.; + scalar = Jdet*gauss->weight*(water_load+runoff_value); //scalar = Jdet*gauss->weight*(water_load)/epl_transmitivity; if(dt!=0.) scalar = scalar*dt; @@ -524,4 +533,5 @@ IssmDouble EPLgrad2; IssmDouble EPL_N; + IssmDouble opening,closing; femmodel->parameters->FindParam(&domaintype,DomainTypeEnum); @@ -589,7 +599,12 @@ EPLgrad2 = (epl_slopeX[i]*epl_slopeX[i])+(epl_slopeY[i]*epl_slopeY[i]); /*And proceed to the real thing*/ - thickness[i] = old_thickness[i]/(1.0 - -((rho_water*gravity*epl_conductivity*EPLgrad2*dt)/(rho_ice*latentheat)) - +((2.0*A*dt*pow(EPL_N,n))/(pow(n,n)))); + opening=(rho_water*gravity*epl_conductivity*EPLgrad2*dt)/(rho_ice*latentheat); + closing=(2.0*A*dt*pow(EPL_N,n))/(pow(n,n)); + /*implicit*/ + thickness[i] = old_thickness[i]/(1.0-opening+closing); + /*explicit*/ + //thickness[i] = old_thickness[i]*(1.0+opening-closing); + /*centered*/ + //thickness[i] = old_thickness[i]*(1.0+opening-closing)/(1.0-opening+closing); /*Take care of otherthikening*/ if(thickness[i]>max_thick){ @@ -688,24 +703,20 @@ if(old_active[i]>0.){ vec_mask->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); - /* If epl thickness gets under colapse thickness, close the layer */ - if(epl_thickness[i]SetValue(basalelement->nodes[i]->Sid(),0.,INS_VAL); recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); } - /* //If epl head gets under base elevation, close the layer */ - /* else if(eplhead[i]<(base[i]-1.0e-8)){ */ - /* vec_mask->SetValue(basalelement->nodes[i]->Sid(),0.,INS_VAL); */ - /* recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); */ - /* } */ - } - /*If node is now closed bring its thickness back to initial*/ + } if (old_active[i]==0.){ - epl_thickness[i]=init_thick; /*Activate if we have a residual from sediment*/ if(residual[i]>0.){ vec_mask->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); - if(old_active[i]==0.){ - recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); - } + recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); + } + else{ + /*If node is now closed bring its thickness back to initial*/ + epl_thickness[i]=init_thick; + vec_mask->SetValue(basalelement->nodes[i]->Sid(),0.,INS_VAL); } } Index: /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 23393) +++ /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 23394) @@ -10,5 +10,4 @@ return 1; }/*}}}*/ - void HydrologyDCInefficientAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ @@ -29,4 +28,6 @@ /*retrieve some parameters: */ + bool issmb; + iomodel->FindConstant(&issmb,"md.transient.issmb"); iomodel->FindConstant(&hydrology_model,"md.hydrology.model"); @@ -63,4 +64,8 @@ parameters->AddObject(new DoubleParam(HydrologydcSedimentlimitEnum,sedimentlimit)); } + if(!issmb){ + parameters->AddObject(iomodel->CopyConstantObject("md.smb.model",SmbEnum)); + } + /*Requested outputs*/ iomodel->FindConstant(&requestedoutputs,&numoutputs,"md.hydrology.requested_outputs"); @@ -69,5 +74,4 @@ iomodel->DeleteData(&requestedoutputs,numoutputs,"md.hydrology.requested_outputs"); }/*}}}*/ - void HydrologyDCInefficientAnalysis::UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/ @@ -105,11 +109,10 @@ iomodel->FetchDataToInput(elements,"md.mesh.vertexonsurface",MeshVertexonsurfaceEnum); } - if(isefficientlayer){ iomodel->FetchDataToInput(elements,"md.hydrology.mask_eplactive_node",HydrologydcMaskEplactiveNodeEnum); iomodel->FetchDataToInput(elements,"md.initialization.epl_head",EplHeadHydrostepEnum); } -}/*}}}*/ - + +}/*}}}*/ void HydrologyDCInefficientAnalysis::CreateNodes(Nodes* nodes,IoModel* iomodel){/*{{{*/ @@ -127,5 +130,4 @@ iomodel->DeleteData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); }/*}}}*/ - void HydrologyDCInefficientAnalysis::CreateConstraints(Constraints* constraints,IoModel* iomodel){/*{{{*/ @@ -137,5 +139,4 @@ IoModelToConstraintsx(constraints,iomodel,"md.hydrology.spcsediment_head",HydrologyDCInefficientAnalysisEnum,P1Enum); }/*}}}*/ - void HydrologyDCInefficientAnalysis::CreateLoads(Loads* loads, IoModel* iomodel){/*{{{*/ @@ -172,14 +173,11 @@ _error_("not implemented"); }/*}}}*/ - ElementVector* HydrologyDCInefficientAnalysis::CreateDVector(Element* element){/*{{{*/ /*Default, return NULL*/ return NULL; }/*}}}*/ - ElementMatrix* HydrologyDCInefficientAnalysis::CreateJacobianMatrix(Element* element){/*{{{*/ _error_("Not implemented"); }/*}}}*/ - ElementMatrix* HydrologyDCInefficientAnalysis::CreateKMatrix(Element* element){/*{{{*/ @@ -307,5 +305,4 @@ return Ke; }/*}}}*/ - ElementVector* HydrologyDCInefficientAnalysis::CreatePVector(Element* element){/*{{{*/ @@ -342,12 +339,14 @@ /*Intermediaries */ bool active_element,isefficientlayer; + int smb_model; IssmDouble dt,scalar,sediment_storing; IssmDouble water_head,sediment_transmitivity; - IssmDouble water_load,transfer; + IssmDouble water_load,runoff_value,transfer; IssmDouble Jdet; IssmDouble *xyz_list = NULL; Input* active_element_input = NULL; - Input* old_wh_input = NULL; + Input* old_wh_input = NULL; + Input* surface_runoff_input = NULL; /*Fetch number of nodes and dof for this finite element*/ @@ -361,16 +360,21 @@ basalelement->GetVerticesCoordinates(&xyz_list); //basalelement->FindParam(&dt,TimesteppingTimeStepEnum); - basalelement ->FindParam(&dt,HydrologydtEnum); + basalelement->FindParam(&dt,HydrologydtEnum); basalelement->FindParam(&isefficientlayer,HydrologydcIsefficientlayerEnum); - - Input* sed_head_input = basalelement->GetInput(SedimentHeadHydrostepEnum); - Input* epl_head_input = basalelement->GetInput(EplHeadHydrostepEnum); - Input* base_input = basalelement->GetInput(BaseEnum); - Input* water_input = basalelement->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(water_input); - Input* SedTrans_input = basalelement->GetInput(HydrologydcSedimentTransmitivityEnum); _assert_(SedTrans_input); + basalelement->FindParam(&smb_model,SmbEnum); + + Input* sed_head_input = basalelement->GetInput(SedimentHeadHydrostepEnum); + Input* epl_head_input = basalelement->GetInput(EplHeadHydrostepEnum); + Input* base_input = basalelement->GetInput(BaseEnum); + Input* basal_melt_input = basalelement->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(basal_melt_input); + Input* SedTrans_input = basalelement->GetInput(HydrologydcSedimentTransmitivityEnum); _assert_(SedTrans_input); if(dt!= 0.){ old_wh_input = basalelement->GetInput(SedimentHeadOldEnum); _assert_(old_wh_input); } + if(smb_model==SMBgradientscomponentsEnum){ + surface_runoff_input = basalelement->GetInput(SmbRunoffEnum); _assert_(surface_runoff_input); + } + /*Transfer related Inputs*/ if(isefficientlayer){ @@ -388,6 +392,8 @@ /*Loading term*/ if(!isefficientlayer){ - water_input->GetInputValue(&water_load,gauss); - scalar = Jdet*gauss->weight*(water_load); + basal_melt_input->GetInputValue(&water_load,gauss); + if(surface_runoff_input) surface_runoff_input->GetInputValue(&runoff_value,gauss); + else runoff_value = 0.; + scalar = Jdet*gauss->weight*(water_load+runoff_value); //scalar = Jdet*gauss->weight*(water_load)/sediment_transmitivity; if(dt!=0.) scalar = scalar*dt; @@ -400,6 +406,8 @@ active_element_input->GetInputValue(&active_element); if(!active_element){ - water_input->GetInputValue(&water_load,gauss); - scalar = Jdet*gauss->weight*(water_load); + basal_melt_input->GetInputValue(&water_load,gauss); + if(surface_runoff_input) surface_runoff_input->GetInputValue(&runoff_value,gauss); + else runoff_value = 0.; + scalar = Jdet*gauss->weight*(water_load+runoff_value); //scalar = Jdet*gauss->weight*(water_load)/sediment_transmitivity; if(dt!=0.) scalar = scalar*dt; @@ -444,5 +452,4 @@ return pe; }/*}}}*/ - void HydrologyDCInefficientAnalysis::GetB(IssmDouble* B,Element* element,IssmDouble* xyz_list,Gauss* gauss){/*{{{*/ /*Compute B matrix. B=[B1 B2 B3] where Bi is of size 3*NDOF2. @@ -472,13 +479,10 @@ xDelete(dbasis); }/*}}}*/ - void HydrologyDCInefficientAnalysis::GetSolutionFromInputs(Vector* solution,Element* element){/*{{{*/ element->GetSolutionFromInputsOneDof(solution,SedimentHeadHydrostepEnum); }/*}}}*/ - void HydrologyDCInefficientAnalysis::GradientJ(Vector* gradient,Element* element,int control_type,int control_index){/*{{{*/ _error_("Not implemented yet"); }/*}}}*/ - void HydrologyDCInefficientAnalysis::InputUpdateFromSolution(IssmDouble* solution,Element* element){/*{{{*/ @@ -514,5 +518,4 @@ /*Use the dof list to index into the solution vector: */ - /*need to introduce thawed test herre*/ for(int i=0;iGetInput(HydrologydcMaskThawedEltEnum); _assert_(thawed_element_input); + thawed_element_input->GetInputValue(&thawed_element); + for(int i=0;iGetNode(i)); if(values[i]>h_max) { @@ -551,7 +562,6 @@ residual[i] = 0.; } - //adding base in min to take into account heads under bed wich don't change N - //pressure[i]=(rho_ice*g*thickness[i])-(rho_freshwater*g*(max((min(h_max,values[i])-base[i]),0.0))); pressure[i]=(rho_ice*g*thickness[i])-(rho_freshwater*g*(values[i]-base[i])); + } xDelete(thickness); @@ -575,10 +585,8 @@ } }/*}}}*/ - void HydrologyDCInefficientAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ /*Default, do nothing*/ return; }/*}}}*/ - IssmDouble HydrologyDCInefficientAnalysis::SedimentStoring(Element* element,Gauss* gauss,Input* sed_head_input, Input* base_input){/*{{{*/ int unconf_scheme; @@ -620,5 +628,4 @@ return sediment_storing; }/*}}}*/ - IssmDouble HydrologyDCInefficientAnalysis::SedimentTransmitivity(Element* element,Gauss* gauss,Input* sed_head_input, Input* base_input,Input* SedTrans_input){/*{{{*/ int unconf_scheme; @@ -630,7 +637,5 @@ IssmDouble base_elev,prestep_head,water_sheet; IssmDouble sediment_thickness = element->GetMaterialParameter(HydrologydcSedimentThicknessEnum); - bool isthermal; - - element->FindParam(&isthermal,TransientIsthermalEnum); + element->FindParam(&unconf_scheme,HydrologydcUnconfinedFlagEnum); SedTrans_input->GetInputValue(&FullLayer_transmitivity,gauss); @@ -657,5 +662,4 @@ return sediment_transmitivity; }/*}}}*/ - void HydrologyDCInefficientAnalysis::GetHydrologyDCInefficientHmax(IssmDouble* ph_max,Element* element, Node* innode){/*{{{*/ @@ -693,5 +697,4 @@ } /*}}}*/ - IssmDouble HydrologyDCInefficientAnalysis::GetHydrologyKMatrixTransfer(Element* element){/*{{{*/ @@ -715,5 +718,4 @@ return transfer; }/*}}}*/ - IssmDouble HydrologyDCInefficientAnalysis::GetHydrologyPVectorTransfer(Element* element, Gauss* gauss, Input* epl_head_input){/*{{{*/ @@ -740,5 +742,4 @@ return transfer; }/*}}}*/ - void HydrologyDCInefficientAnalysis::ElementizeEplMask(FemModel* femmodel){/*{{{*/ @@ -759,6 +760,5 @@ } }/*}}}*/ - -void HydrologyDCInefficientAnalysis::HydrologyIDSGetMask(Vector* vec_mask, Element* element){ +void HydrologyDCInefficientAnalysis::HydrologyIDSGetMask(Vector* vec_mask, Element* element){/*{{{*/ bool active_element; int domaintype; @@ -801,5 +801,5 @@ xDelete(meltingrate); xDelete(groundedice); -} +}/*}}}*/ void HydrologyDCInefficientAnalysis::ElementizeIdsMask(FemModel* femmodel){/*{{{*/ @@ -820,5 +820,4 @@ } }/*}}}*/ - void HydrologyDCInefficientAnalysis::HydrologyIdsGetActive(Vector* active_vec, Element* element){/*{{{*/ /*Constants*/ Index: /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp (revision 23393) +++ /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp (revision 23394) @@ -131,5 +131,5 @@ femmodel->SetCurrentConfiguration(LevelsetAnalysisEnum); - if(VerboseSolution()) _printf0_("call computational core:\n"); + if(VerboseSolution()) _printf0_(" call computational core:\n"); if(stabilization==4){ solutionsequence_fct(femmodel); Index: /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp (revision 23393) +++ /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp (revision 23394) @@ -124,5 +124,4 @@ bool isoceancoupling; bool issmb; - int basalforcingsmodel; /*Fetch data needed: */ @@ -133,5 +132,4 @@ iomodel->FindConstant(&isoceancoupling,"md.transient.isoceancoupling"); iomodel->FindConstant(&issmb,"md.transient.issmb"); - iomodel->FindConstant(&basalforcingsmodel,"md.basalforcings.model"); /*Finite element type*/ @@ -158,9 +156,4 @@ iomodel->FetchDataToInput(elements,"md.mask.groundedice_levelset",MaskGroundediceLevelsetEnum); iomodel->FetchDataToInput(elements,"md.basalforcings.groundedice_melting_rate",BasalforcingsGroundediceMeltingRateEnum); - if (basalforcingsmodel==SpatialLinearFloatingMeltRateEnum){ - iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); - iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); - iomodel->FetchDataToInput(elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); - } iomodel->FetchDataToInput(elements,"md.initialization.vx",VxEnum); iomodel->FetchDataToInput(elements,"md.initialization.vy",VyEnum); @@ -181,4 +174,9 @@ break; case MantlePlumeGeothermalFluxEnum: + break; + case SpatialLinearFloatingMeltRateEnum: + iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); + iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); + iomodel->FetchDataToInput(elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); break; case BasalforcingsPicoEnum: @@ -631,7 +629,7 @@ }/*}}}*/ void MasstransportAnalysis::GetB(IssmDouble* B,Element* element,int dim,IssmDouble* xyz_list,Gauss* gauss){/*{{{*/ - /*Compute B matrix. B=[B1 B2 B3] where Bi is of size 3*NDOF2. + /*Compute B matrix. B=[B1 B2 B3] where Bi is of size 3*NDOF2. * For node i, Bi can be expressed in the actual coordinate system - * by: + * by: * Bi=[ N ] * [ N ] @@ -659,7 +657,7 @@ }/*}}}*/ void MasstransportAnalysis::GetBprime(IssmDouble* Bprime,Element* element,int dim,IssmDouble* xyz_list,Gauss* gauss){/*{{{*/ - /*Compute B' matrix. B'=[B1' B2' B3'] where Bi' is of size 3*NDOF2. + /*Compute B' matrix. B'=[B1' B2' B3'] where Bi' is of size 3*NDOF2. * For node i, Bi' can be expressed in the actual coordinate system - * by: + * by: * Bi_prime=[ dN/dx ] * [ dN/dy ] Index: /issm/trunk/src/c/analyses/SmbAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/SmbAnalysis.cpp (revision 23393) +++ /issm/trunk/src/c/analyses/SmbAnalysis.cpp (revision 23394) @@ -5,4 +5,7 @@ #include "../modules/modules.h" +// FIX +#include "./shared/io/Print/Print.h" + /*Model processing*/ void SmbAnalysis::CreateConstraints(Constraints* constraints,IoModel* iomodel){/*{{{*/ @@ -21,5 +24,5 @@ int smb_model; - bool isdelta18o,ismungsm,isd18opd,issetpddfac,isprecipscaled,istemperaturescaled; + bool isdelta18o,ismungsm,isd18opd,issetpddfac,isprecipscaled,istemperaturescaled,isfirnwarming; /*Update elements: */ @@ -35,5 +38,4 @@ /*Figure out smb model: */ iomodel->FindConstant(&smb_model,"md.smb.model"); - switch(smb_model){ case SMBforcingEnum: @@ -88,4 +90,14 @@ } break; + case SMBpddSicopolisEnum: + iomodel->FetchDataToInput(elements,"md.smb.s0p",SmbS0pEnum); + iomodel->FetchDataToInput(elements,"md.smb.s0t",SmbS0tEnum); + iomodel->FindConstant(&isfirnwarming,"md.smb.isfirnwarming"); + iomodel->FetchDataToInput(elements,"md.smb.smb_corr",SmbSmbCorrEnum); + iomodel->FetchDataToInput(elements,"md.smb.precipitation",SmbPrecipitationEnum); + iomodel->FetchDataToInput(elements,"md.smb.monthlytemperatures",SmbMonthlytemperaturesEnum); + iomodel->FetchDataToInput(elements,"md.smb.precipitation_anomaly",SmbPrecipitationsAnomalyEnum); + iomodel->FetchDataToInput(elements,"md.smb.temperature_anomaly",SmbTemperaturesAnomalyEnum); + break; case SMBd18opddEnum: iomodel->FindConstant(&istemperaturescaled,"md.smb.istemperaturescaled"); @@ -139,4 +151,10 @@ iomodel->FetchDataToInput(elements,"md.smb.refreeze",SmbRefreezeEnum,0.); break; + case SMBgradientscomponentsEnum: + iomodel->FetchDataToInput(elements,"md.smb.accualti",SmbAccualtiEnum); + iomodel->FetchDataToInput(elements,"md.smb.accugrad",SmbAccugradEnum); + iomodel->FetchDataToInput(elements,"md.smb.runoffalti",SmbRunoffaltiEnum); + iomodel->FetchDataToInput(elements,"md.smb.runoffgrad",SmbRunoffgradEnum); + break; default: _error_("Surface mass balance model "<AddObject(iomodel->CopyConstantObject("md.smb.isfirnwarming",SmbIsfirnwarmingEnum)); + break; case SMBd18opddEnum: parameters->AddObject(iomodel->CopyConstantObject("md.smb.ismungsm",SmbIsmungsmEnum)); @@ -246,4 +267,18 @@ /*Nothing to add to parameters*/ break; + case SMBgradientscomponentsEnum: + parameters->AddObject(iomodel->CopyConstantObject("md.smb.accualti",SmbAccualtiEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.accugrad",SmbAccugradEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.runoffalti",SmbRunoffaltiEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.runoffgrad",SmbRunoffgradEnum)); + + iomodel->FetchData(&temp,&N,&M,"md.smb.accuref"); _assert_(N==2); + parameters->AddObject(new TransientParam(SmbAccurefEnum,&temp[0],&temp[M],interp,M)); + iomodel->DeleteData(temp,"md.smb.accuref"); + + iomodel->FetchData(&temp,&N,&M,"md.smb.runoffref"); _assert_(N==2); + parameters->AddObject(new TransientParam(SmbRunoffrefEnum,&temp[0],&temp[M],interp,M)); + iomodel->DeleteData(temp,"md.smb.runoffref"); + break; default: _error_("Surface mass balance model "<FetchDataToInput(elements,"md.initialization.pressure",PressureEnum,0.); - iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum,0.); + + /*Add basal forcings to compute melt rate*/ + int basalforcing_model; + iomodel->FindConstant(&basalforcing_model,"md.basalforcings.model"); + switch(basalforcing_model){ + case FloatingMeltRateEnum: + iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum); + break; + case LinearFloatingMeltRateEnum: + break; + case MismipFloatingMeltRateEnum: + break; + case MantlePlumeGeothermalFluxEnum: + break; + case SpatialLinearFloatingMeltRateEnum: + iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); + iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); + iomodel->FetchDataToInput(elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); + break; + case BasalforcingsPicoEnum: + iomodel->FetchDataToInput(elements,"md.basalforcings.basin_id",BasalforcingsPicoBasinIdEnum); + break; + default: + _error_("Basal forcing model "<FetchDataToInput(elements,"md.friction.till_friction_angle",FrictionTillFrictionAngleEnum); iomodel->FetchDataToInput(elements,"md.friction.sediment_compressibility_coefficient",FrictionSedimentCompressibilityCoefficientEnum); + iomodel->FetchDataToInput(elements,"md.hydrology.watercolumn_max",HydrologyWatercolumnMaxEnum); + iomodel->FetchDataToInput(elements,"md.initialization.watercolumn",WatercolumnEnum,0.); break; default: @@ -945,7 +971,9 @@ int solver_type; PetscOptionsDetermineSolverType(&solver_type); + if(solver_type==FSSolverEnum) is_schur_cg_solver = true; #endif + if(is_schur_cg_solver) solutionsequence_schurcg(femmodel); @@ -3270,13 +3298,12 @@ element->NodalFunctionsPressure(pbasis,gauss); - if(dim==3){ + if(dim==3 || dim==2){ /*Pressure mass matrix*/ for(int k=0;kvalues[(3*vnumnodes+k)*numdof+3*vnumnodes+j] += gauss->weight*Jdet*(pbasis[j]*pbasis[k]); + Ke->values[(dim*vnumnodes+k)*numdof+dim*vnumnodes+j] += gauss->weight*Jdet*(pbasis[j]*pbasis[k]); } } - } - else{ + }else{ _error_("STOP"); } @@ -3289,4 +3316,61 @@ return Ke; }/*}}}*/ +ElementMatrix* StressbalanceAnalysis::CreateSchurPrecondMatrix(Element* element){/*{{{*/ + + /*Intermediaries*/ + int i,dim; + IssmDouble viscosity,FSreconditioning,Jdet; + IssmDouble *xyz_list = NULL; + + /*Get problem dimension*/ + element->FindParam(&dim,DomainDimensionEnum); + + /*Fetch number of nodes and dof for this finite element*/ + int vnumnodes = element->NumberofNodesVelocity(); + int pnumnodes = element->NumberofNodesPressure(); + int numdof = vnumnodes*dim + pnumnodes; + + /*Initialize Element matrix and vectors*/ + ElementMatrix* Ke = element->NewElementMatrix(FSvelocityEnum); + IssmDouble* pbasis = xNew(pnumnodes); + + /*Retrieve all inputs and parameters*/ + element->GetVerticesCoordinates(&xyz_list); + //element->FindParam(&FSreconditioning,StressbalanceFSreconditioningEnum); + Input* vx_input=element->GetInput(VxEnum); _assert_(vx_input); + Input* vy_input=element->GetInput(VyEnum); _assert_(vy_input); + Input* vz_input = NULL; + if(dim==3){vz_input=element->GetInput(VzEnum); _assert_(vz_input);} + + + /* Start looping on the number of gaussian points: */ + Gauss* gauss = element->NewGauss(5); + for(int ig=gauss->begin();igend();ig++){ + gauss->GaussPoint(ig); + + element->JacobianDeterminant(&Jdet,xyz_list,gauss); + element->NodalFunctionsPressure(pbasis,gauss); + element->material->ViscosityFS(&viscosity,dim,xyz_list,gauss,vx_input,vy_input,vz_input); + + + if(dim==3 || dim==2){ + /*Pressure mass matrix*/ + for(int k=0;kvalues[(dim*vnumnodes+k)*numdof+dim*vnumnodes+j] += gauss->weight*1./viscosity*Jdet*(pbasis[j]*pbasis[k]); + } + } + }else{ + _error_("STOP"); + } + } + + /*Clean up and return*/ + delete gauss; + xDelete(xyz_list); + xDelete(pbasis); + return Ke; +}/*}}}*/ + ElementMatrix* StressbalanceAnalysis::CreateKMatrixFSViscousLA(Element* element){/*{{{*/ Index: /issm/trunk/src/c/analyses/StressbalanceAnalysis.h =================================================================== --- /issm/trunk/src/c/analyses/StressbalanceAnalysis.h (revision 23393) +++ /issm/trunk/src/c/analyses/StressbalanceAnalysis.h (revision 23394) @@ -75,4 +75,5 @@ ElementMatrix* CreateKMatrixFSViscousXTH(Element* element); ElementMatrix* CreatePressureMassMatrix(Element* element); + ElementMatrix* CreateSchurPrecondMatrix(Element* element); ElementVector* CreatePVectorFS(Element* element); ElementVector* CreatePVectorFSFriction(Element* element); Index: /issm/trunk/src/c/analyses/StressbalanceVerticalAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/StressbalanceVerticalAnalysis.cpp (revision 23393) +++ /issm/trunk/src/c/analyses/StressbalanceVerticalAnalysis.cpp (revision 23394) @@ -111,6 +111,31 @@ } iomodel->FetchDataToInput(elements,"md.basalforcings.groundedice_melting_rate",BasalforcingsGroundediceMeltingRateEnum); - iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum,0.); //iomodel->FetchDataToInput(elements,"md.smb.mass_balance",SmbMassBalanceEnum); + + + /*Add basal forcings to compute melt rate*/ + int basalforcing_model; + iomodel->FindConstant(&basalforcing_model,"md.basalforcings.model"); + switch(basalforcing_model){ + case FloatingMeltRateEnum: + iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum); + break; + case LinearFloatingMeltRateEnum: + break; + case MismipFloatingMeltRateEnum: + break; + case MantlePlumeGeothermalFluxEnum: + break; + case SpatialLinearFloatingMeltRateEnum: + iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); + iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); + iomodel->FetchDataToInput(elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); + break; + case BasalforcingsPicoEnum: + iomodel->FetchDataToInput(elements,"md.basalforcings.basin_id",BasalforcingsPicoBasinIdEnum); + break; + default: + _error_("Basal forcing model "<FetchDataToInput(elements,"md.initialization.vx",VxEnum,0.); iomodel->FetchDataToInput(elements,"md.initialization.vy",VyEnum,0.); Index: /issm/trunk/src/c/analyses/ThermalAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/ThermalAnalysis.cpp (revision 23393) +++ /issm/trunk/src/c/analyses/ThermalAnalysis.cpp (revision 23394) @@ -33,6 +33,7 @@ int smb_model; iomodel->FindConstant(&smb_model,"md.smb.model"); - if(smb_model==SMBpddEnum) isdynamic=true; - if(smb_model==SMBd18opddEnum) isdynamic=true; + if(smb_model==SMBpddEnum) isdynamic=true; + if(smb_model==SMBd18opddEnum) isdynamic=true; + if(smb_model==SMBpddSicopolisEnum) isdynamic=true; } else{ Index: /issm/trunk/src/c/classes/Elements/Element.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/Element.cpp (revision 23393) +++ /issm/trunk/src/c/classes/Elements/Element.cpp (revision 23394) @@ -653,4 +653,74 @@ xDelete(tmp); +} +/*}}}*/ +void Element::SmbGradCompParameterization(void){/*{{{*/ + + /*Are we on the base? If not, return*/ + if(!IsOnBase()) return; + int numvertices = this->GetNumberOfVertices(); + + int i; + IssmDouble accuref, runoffref; //reference values at given altitude + IssmDouble accualti, runoffalti; //reference altitudes + IssmDouble accugrad, runoffgrad; //gradients from reference altitude + IssmDouble rho_water, rho_ice; + IssmDouble time; + + IssmDouble* smb = xNew(numvertices); + IssmDouble* surf = xNew(numvertices); + IssmDouble* accu = xNew(numvertices); + IssmDouble* runoff = xNew(numvertices); + + /*Get material parameters :*/ + rho_water=this->matpar->GetMaterialParameter(MaterialsRhoSeawaterEnum); + rho_ice=this->matpar->GetMaterialParameter(MaterialsRhoIceEnum); + + /*Recover parameters*/ + parameters->FindParam(&time,TimeEnum); + parameters->FindParam(&accualti,SmbAccualtiEnum); + parameters->FindParam(&accugrad,SmbAccugradEnum); + parameters->FindParam(&runoffalti,SmbRunoffaltiEnum); + parameters->FindParam(&runoffgrad,SmbRunoffgradEnum); + + /*Recover reference values at current time*/ + parameters->FindParam(&accuref,SmbAccurefEnum,time); + parameters->FindParam(&runoffref,SmbRunoffrefEnum,time); + + /*Recover surface elevation*/ + GetInputListOnVertices(&surf[0],SurfaceEnum); + + /*Compute the temperature and precipitation*/ + for(int iv=0;ivObjectEnum()){ + case TriaEnum: + this->inputs->AddInput(new TriaInput(SmbMassBalanceEnum,&smb[0],P1Enum)); + this->inputs->AddInput(new TriaInput(SmbRunoffEnum,&runoff[0],P1Enum)); + break; + case PentaEnum: + this->inputs->AddInput(new PentaInput(SmbMassBalanceEnum,&smb[0],P1Enum)); + this->inputs->AddInput(new PentaInput(SmbRunoffEnum,&runoff[0],P1Enum)); + this->InputExtrude(SmbMassBalanceEnum,-1); + this->InputExtrude(SmbRunoffEnum,-1); + break; + case TetraEnum: + this->inputs->AddInput(new TetraInput(SmbMassBalanceEnum,&smb[0],P1Enum)); + this->inputs->AddInput(new TetraInput(SmbRunoffEnum,&runoff[0],P1Enum)); + this->InputExtrude(SmbMassBalanceEnum,-1); + this->InputExtrude(SmbRunoffEnum,-1); + break; + default: _error_("Not implemented yet"); + } + /* this->AddInput(SmbMassBalanceEnum,smb,P1Enum); */ + /* this->AddInput(SmbRunoffEnum,runoff,P1Enum); */ + /*clean-up*/ + xDelete(surf); + xDelete(accu); + xDelete(runoff); + xDelete(smb); } /*}}}*/ @@ -2561,4 +2631,169 @@ } /*}}}*/ +void Element::PositiveDegreeDaySicopolis(bool isfirnwarming){/*{{{*/ + + /* General FIXMEs: get Tmelting point, pddicefactor, pddsnowfactor, sigma from parameters/user input */ + + int numvertices = this->GetNumberOfVertices(); + + int i; + IssmDouble* smb=xNew(numvertices); // surface mass balance + IssmDouble* melt=xNew(numvertices); // melting comp. of surface mass balance + IssmDouble* accu=xNew(numvertices); // accuumulation comp. of surface mass balance + IssmDouble* melt_star=xNew(numvertices); + IssmDouble* monthlytemperatures=xNew(12*numvertices); + IssmDouble* monthlyprec=xNew(12*numvertices); + IssmDouble* yearlytemperatures=xNew(numvertices); memset(yearlytemperatures, 0., numvertices*sizeof(IssmDouble)); + IssmDouble* s=xNew(numvertices); // actual surface height + IssmDouble* s0p=xNew(numvertices); // reference elevation for precip. + IssmDouble* s0t=xNew(numvertices); // reference elevation for temperature + IssmDouble* smbcorr=xNew(numvertices); // surface mass balance correction; will be added after pdd call + IssmDouble* p_ampl=xNew(numvertices); // precip anomaly + IssmDouble* t_ampl=xNew(numvertices); // remperature anomaly + IssmDouble rho_water,rho_ice,desfac,rlaps; + IssmDouble inv_twelve=1./12.; //factor for monthly average + IssmDouble time,yts,time_yr; + + /*Get material parameters :*/ + rho_water=this->matpar->GetMaterialParameter(MaterialsRhoSeawaterEnum); + rho_ice=this->matpar->GetMaterialParameter(MaterialsRhoIceEnum); + + /*Get parameters for height corrections*/ + desfac=this->matpar->GetMaterialParameter(SmbDesfacEnum); + rlaps=this->matpar->GetMaterialParameter(SmbRlapsEnum); + + /*Recover monthly temperatures and precipitation*/ + Input* input=this->inputs->GetInput(SmbMonthlytemperaturesEnum); _assert_(input); + Input* input2=this->inputs->GetInput(SmbPrecipitationEnum); _assert_(input2); + /*Recover smb correction term */ + Input* input3=this->inputs->GetInput(SmbSmbCorrEnum); _assert_(input3); + + /* Get time */ + this->parameters->FindParam(&time,TimeEnum); + this->parameters->FindParam(&yts,ConstantsYtsEnum); + time_yr=floor(time/yts)*yts; + + /* Set parameters for finrnwarming */ + IssmDouble MU_0 = 9.7155; //Firn-warming correction, in (d*deg C)/(mm WE) + IssmDouble mu = MU_0*(1000.0*86400.0)*(rho_ice/rho_water); // (d*deg C)/(mm WE) --> (s*deg C)/(m IE) + + /*loop over vertices: */ + Gauss* gauss=this->NewGauss(); + for(int month=0;month<12;month++){ + for(int iv=0;ivGaussVertex(iv); + input->GetInputValue(&monthlytemperatures[iv*12+month],gauss,(month+1)/12.*yts); + monthlytemperatures[iv*12+month]=monthlytemperatures[iv*12+month]-273.15; // conversion from Kelvin to celcius for PDD module + input2->GetInputValue(&monthlyprec[iv*12+month],gauss,(month+1)/12.*yts); + monthlyprec[iv*12+month]=monthlyprec[iv*12+month]*yts; + } + } + + /*Recover info at the vertices: */ + GetInputListOnVertices(&s[0],SurfaceEnum); + GetInputListOnVertices(&s0p[0],SmbS0pEnum); + GetInputListOnVertices(&s0t[0],SmbS0tEnum); + GetInputListOnVertices(&smbcorr[0],SmbSmbCorrEnum); + GetInputListOnVertices(&t_ampl[0],SmbTemperaturesAnomalyEnum); + GetInputListOnVertices(&p_ampl[0],SmbPrecipitationsAnomalyEnum); + + /*measure the surface mass balance*/ + for (int iv = 0; iv=melt[iv]){ + yearlytemperatures[iv]= yearlytemperatures[iv]+mu*(melt_star[iv]-melt[iv]); + } + else{ + yearlytemperatures[iv]= yearlytemperatures[iv]; + } + } + if (yearlytemperatures[iv]>273.15) yearlytemperatures[iv]=273.15; + } + + switch(this->ObjectEnum()){ + case TriaEnum: + // this->inputs->AddInput(new TriaInput(TemperatureEnum,&yearlytemperatures[0],P1Enum)); + this->inputs->AddInput(new TriaInput(TemperaturePDDEnum,&yearlytemperatures[0],P1Enum)); + this->inputs->AddInput(new TriaInput(SmbMassBalanceEnum,&smb[0],P1Enum)); + this->inputs->AddInput(new TriaInput(SmbAccumulationEnum,&accu[0],P1Enum)); + this->inputs->AddInput(new TriaInput(SmbMeltEnum,&melt[0],P1Enum)); + break; + case PentaEnum: + bool isthermal; + this->parameters->FindParam(&isthermal,TransientIsthermalEnum); + if(isthermal){ + bool isenthalpy; + this->parameters->FindParam(&isenthalpy,ThermalIsenthalpyEnum); + if(IsOnSurface()){ + /*Here, we want to change the BC of the thermal model, keep + * the temperatures as they are for the base of the penta and + * use yearlytemperatures for the top*/ + GetInputListOnVertices(&s[0],TemperatureEnum); + yearlytemperatures[0] = s[0]; + yearlytemperatures[1] = s[1]; + yearlytemperatures[2] = s[2]; + this->inputs->AddInput(new PentaInput(TemperatureEnum,&yearlytemperatures[0],P1Enum)); + if(isenthalpy){ + /*Convert that to enthalpy for the enthalpy model*/ + IssmDouble enthalpy[6]; + GetInputListOnVertices(&enthalpy[0],EnthalpyEnum); + ThermalToEnthalpy(&enthalpy[3],yearlytemperatures[3],0.,0.); + ThermalToEnthalpy(&enthalpy[4],yearlytemperatures[4],0.,0.); + ThermalToEnthalpy(&enthalpy[5],yearlytemperatures[5],0.,0.); + this->inputs->AddInput(new PentaInput(EnthalpyEnum,&enthalpy[0],P1Enum)); + } + } + } + this->inputs->AddInput(new PentaInput(SmbMassBalanceEnum,&smb[0],P1Enum)); + this->inputs->AddInput(new PentaInput(TemperaturePDDEnum,&yearlytemperatures[0],P1Enum)); + this->inputs->AddInput(new PentaInput(SmbAccumulationEnum,&accu[0],P1Enum)); + this->inputs->AddInput(new PentaInput(SmbMeltEnum,&melt[0],P1Enum)); + this->InputExtrude(TemperaturePDDEnum,-1); + this->InputExtrude(SmbMassBalanceEnum,-1); + this->InputExtrude(SmbAccumulationEnum,-1); + this->InputExtrude(SmbMeltEnum,-1); + break; + case TetraEnum: + if(IsOnSurface()){ + GetInputListOnVertices(&s[0],TemperatureEnum); + yearlytemperatures[0] = s[0]; + yearlytemperatures[1] = s[1]; + yearlytemperatures[2] = s[2]; + this->inputs->AddInput(new TetraInput(TemperatureEnum,&yearlytemperatures[0],P1Enum)); + } + this->inputs->AddInput(new TetraInput(SmbMassBalanceEnum,&smb[0],P1Enum)); + this->inputs->AddInput(new TetraInput(TemperaturePDDEnum,&yearlytemperatures[0],P1Enum)); + this->InputExtrude(TemperaturePDDEnum,-1); + this->InputExtrude(SmbMassBalanceEnum,-1); + break; + default: _error_("Not implemented yet"); + } + + /*clean-up*/ + delete gauss; + xDelete(monthlytemperatures); + xDelete(monthlyprec); + xDelete(smb); + xDelete(melt); + xDelete(accu); + xDelete(yearlytemperatures); + xDelete(s); + xDelete(s0t); + xDelete(s0p); + xDelete(t_ampl); + xDelete(p_ampl); + xDelete(smbcorr); + xDelete(melt_star); +} +/*}}}*/ IssmDouble Element::PureIceEnthalpy(IssmDouble pressure){/*{{{*/ return this->matpar->PureIceEnthalpy(pressure); @@ -2568,6 +2803,6 @@ /*Some intputs need to be computed, even if they are already in inputs, they might not be up to date!*/ switch(output_enum){ - case ViscousHeatingEnum: this->ViscousHeatingCreateInput(); break; - case StressMaxPrincipalEnum: this->StressMaxPrincipalCreateInput(); break; + case ViscousHeatingEnum: this->ViscousHeatingCreateInput(); break; + case StressMaxPrincipalEnum: this->StressMaxPrincipalCreateInput(); break; case StressTensorxxEnum: case StressTensorxyEnum: @@ -2582,5 +2817,5 @@ case StrainRateyzEnum: case StrainRatezzEnum: - case StrainRateeffectiveEnum: this->ComputeStrainRate(); break; + case StrainRateeffectiveEnum: this->ComputeStrainRate(); break; case DeviatoricStressxxEnum: case DeviatoricStressxyEnum: @@ -3133,5 +3368,8 @@ } - #ifndef _HAVE_ADOLC_ //we want to avoid the round operation at all cost. Not differentiable. + #if defined(_HAVE_AD_) + /*we want to avoid the round operation at all cost. Not differentiable.*/ + _error_("not implemented yet"); + #else dMass = sumMass + sumR + sumW - sumP - sumEC - initMass - sumMassAdd; dMass = round(dMass * 100.0)/100.0; Index: /issm/trunk/src/c/classes/Elements/Element.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Element.h (revision 23393) +++ /issm/trunk/src/c/classes/Elements/Element.h (revision 23394) @@ -1,7 +1,7 @@ /*!\file: Element.h * \brief abstract class for Element object - * This class is a place holder for the Tria and the Penta elements. + * This class is a place holder for the Tria and the Penta elements. * It is derived from Element, so DataSets can contain them. - */ + */ #ifndef _ELEMENT_H_ @@ -50,5 +50,5 @@ int element_type; - public: + public: /*Constructors/Destructores*/ Element(); @@ -68,4 +68,5 @@ void Delta18oParameterization(void); void Delta18opdParameterization(void); + void SmbGradCompParameterization(void); IssmDouble Divergence(void); void dViscositydBFS(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input); @@ -130,14 +131,14 @@ void InputUpdateFromConstant(int constant, int name); void InputUpdateFromConstant(bool constant, int name); - bool IsFloating(); + bool IsFloating(); bool IsIceInElement(); bool IsLandInElement(); bool IsWaterInElement(); - void LinearFloatingiceMeltingRate(); - void SpatialLinearFloatingiceMeltingRate(); - void MantlePlumeGeothermalFlux(); + void LinearFloatingiceMeltingRate(); + void SpatialLinearFloatingiceMeltingRate(); + void MantlePlumeGeothermalFlux(); void MarshallElement(char** pmarshalled_data,int* pmarshalled_data_size, int marshall_direction,int numanalyses); void MigrateGroundingLine(IssmDouble* sheet_ungrounding); - void MismipFloatingiceMeltingRate(); + void MismipFloatingiceMeltingRate(); void MungsmtpParameterization(void); ElementMatrix* NewElementMatrix(int approximation_enum=NoneApproximationEnum); @@ -145,4 +146,5 @@ ElementVector* NewElementVector(int approximation_enum=NoneApproximationEnum); void PositiveDegreeDay(IssmDouble* pdds,IssmDouble* pds,IssmDouble signorm,bool ismungsm,bool issetpddfac); + void PositiveDegreeDaySicopolis(bool isfirnwarming); IssmDouble PureIceEnthalpy(IssmDouble pressure); void ResultInterpolation(int* pinterpolation,int*nodesperelement,int* parray_size, int output_enum); @@ -240,5 +242,5 @@ virtual bool IsFaceOnBoundary(void)=0; virtual bool IsIcefront(void)=0; - virtual bool IsNodeOnShelfFromFlags(IssmDouble* flags)=0; + virtual bool IsNodeOnShelfFromFlags(IssmDouble* flags)=0; virtual bool IsOnBase()=0; virtual bool IsOnSurface()=0; @@ -330,5 +332,5 @@ virtual IssmDouble OceanAverage(IssmDouble* Sg)=0; virtual IssmDouble OceanArea(void)=0; - virtual void SealevelriseMomentOfInertia(IssmDouble* dI_list,IssmDouble* Sg_old,IssmDouble eartharea)=0; + virtual void SealevelriseMomentOfInertia(IssmDouble* dI_list,IssmDouble* Sg_old,IssmDouble eartharea)=0; virtual void SealevelriseEustatic(Vector* pSgi,IssmDouble* peustatic,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble oceanarea,IssmDouble eartharea)=0; virtual void SealevelriseNonEustatic(Vector* pSgo,IssmDouble* Sg_old,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble eartharea)=0; Index: /issm/trunk/src/c/classes/ExternalResults/GenericExternalResult.h =================================================================== --- /issm/trunk/src/c/classes/ExternalResults/GenericExternalResult.h (revision 23393) +++ /issm/trunk/src/c/classes/ExternalResults/GenericExternalResult.h (revision 23394) @@ -622,5 +622,5 @@ /*Specific instantiations for IssmDouble*: */ -#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) //We hook off this specific specialization when not running ADOLC, otherwise we get a redeclaration with the next specialization. +#if defined(_HAVE_AD_) && !defined(_WRAPPERS_) //We hook off this specific specialization when not running ADOLC, otherwise we get a redeclaration with the next specialization. template <> inline GenericExternalResult::~GenericExternalResult(){ /*{{{*/ xDelete(result_name); @@ -709,5 +709,5 @@ return new GenericExternalResult*>(this->id,StringToEnumx(this->result_name),this->value,this->step,this->time); } /*}}}*/ -#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) //We hook off this specific specialization when not running ADOLC, otherwise we get a redeclaration with the next specialization. +#if defined(_HAVE_AD_) && !defined(_WRAPPERS_) //We hook off this specific specialization when not running ADOLC, otherwise we get a redeclaration with the next specialization. template <> inline void GenericExternalResult*>::WriteData(FILE* fid,bool io_gather){ /*{{{*/ Index: /issm/trunk/src/c/classes/FemModel.cpp =================================================================== --- /issm/trunk/src/c/classes/FemModel.cpp (revision 23393) +++ /issm/trunk/src/c/classes/FemModel.cpp (revision 23394) @@ -17,4 +17,9 @@ #include "../shared/Enum/Enum.h" #include "../analyses/analyses.h" + +#if _HAVE_CODIPACK_ +#include // for output of the CoDiPack tape +extern CoDi_global codi_global; +#endif /*module includes: {{{*/ @@ -84,11 +89,11 @@ this->parameters->FindParam(&amr_frequency,TransientAmrFrequencyEnum); this->parameters->FindParam(&amr_frequency,TransientAmrFrequencyEnum); - #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) this->amr = NULL; #endif - #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) this->amrbamg = NULL; #endif - #if !defined(_HAVE_ADOLC_) + #if !defined(_HAVE_AD_) if(amr_frequency && solution_type==TransientSolutionEnum){ /*Verifications. AMR supports SSA, P1 and horizontal 2D domain*/ @@ -147,8 +152,8 @@ profiler->Stop(MPROCESSOR); - #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) this->amr = NULL; #endif - #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) this->amrbamg = NULL; #endif @@ -184,9 +189,9 @@ if(results)delete results; - #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) if(amr)delete amr; #endif - #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) if(amrbamg)delete amrbamg; #endif @@ -254,8 +259,12 @@ /*Before we delete the profiler, report statistics for this run: */ profiler->Stop(TOTAL); //final tagging + _printf0_("\n"); - _printf0_(" "<TotalTime(MPROCESSOR) << "\n"); - _printf0_(" "<TotalTime(CORE) << "\n"); - _printf0_(" "<TotalTime(SOLVER) << "\n"); + _printf0_(" "<TotalTime(MPROCESSOR) << "\n"); + /*Total times*/ + _printf0_(" "<TotalTime(CORE) << "\n"); + + /*Linear solver only*/ + _printf0_(" "<TotalTime(SOLVER) << " ("<TotalTime(SOLVER)/profiler->TotalTime(CORE)*100.<<"%)\n"); _printf0_("\n"); _printf0_(" Total elapsed time: " @@ -319,8 +328,8 @@ /*AMR, no copy for now*/ - #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) this->amr = NULL; #endif - #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) this->amrbamg = NULL; #endif @@ -853,8 +862,23 @@ solution_memory=profiler->Memory(CORE); - _printf0_("Core solution elapsed time : " << solution_time << " Seconds\n"); - _printf0_("Core solution number of flops : " << solution_flops << " Flops\n"); - _printf0_("Core solution memory used : " << solution_memory << " Bytes\n"); - + _printf0_("\nCore solution profiling\n"); + _printf0_(" elapsed time : " << solution_time << " Seconds\n"); + _printf0_(" number of flops : " << solution_flops << " Flops\n"); + _printf0_(" memory used : " << solution_memory << " Bytes\n"); + + /*Individual cores*/ + _printf0_("Individual core profiling\n"); + if(profiler->Used(THERMALCORE)) _printf0_(" "<TotalTime(THERMALCORE) << " sec\n"); + if(profiler->Used(HYDROLOGYCORE)) _printf0_(" "<TotalTime(HYDROLOGYCORE) << " sec\n"); + if(profiler->Used(STRESSBALANCECORE)) _printf0_(" "<TotalTime(STRESSBALANCECORE) << " sec\n"); + if(profiler->Used(DAMAGECORE)) _printf0_(" "<TotalTime(DAMAGECORE) << " sec\n"); + if(profiler->Used(MOVINGFRONTCORE)) _printf0_(" "<TotalTime(MOVINGFRONTCORE) << " sec\n"); + if(profiler->Used(MASSTRANSPORTCORE)) _printf0_(" "<TotalTime(MASSTRANSPORTCORE) << " sec\n"); + if(profiler->Used(SMBCORE)) _printf0_(" "<TotalTime(SMBCORE) << " sec\n"); + if(profiler->Used(GROUNDINGLINECORE)) _printf0_(" "<TotalTime(GROUNDINGLINECORE) << " sec\n"); + if(profiler->Used(GIACORE)) _printf0_(" "<TotalTime(GIACORE) << " sec\n"); + if(profiler->Used(ESACORE)) _printf0_(" "<TotalTime(ESACORE) << " sec\n"); + if(profiler->Used(SLRCORE)) _printf0_(" "<TotalTime(SLRCORE) << " sec\n"); + /*Add to results: */ results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingSolutionTimeEnum, solution_time)); @@ -862,13 +886,15 @@ results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentFlopsEnum, solution_flops)); - #ifdef _HAVE_ADOLC_ - solution_time=profiler->TotalTime(ADCORE); - solution_flops=profiler->TotalFlops(ADCORE); - solution_memory=profiler->Memory(ADCORE); - - _printf0_("AD Solution elapsed time : " << solution_time << " Seconds\n"); - _printf0_("AD Solution number of flops : " << solution_flops << " Flops\n"); - _printf0_("AD Solution memory used : " << solution_memory << " Bytes\n"); + #ifdef _HAVE_AD_ + solution_time = profiler->TotalTime(ADCORE); + solution_flops = profiler->TotalFlops(ADCORE); + solution_memory = profiler->Memory(ADCORE); + + _printf0_("AD profiling\n"); + _printf0_(" elapsed time : " << solution_time << " Seconds\n"); + _printf0_(" number of flops : " << solution_flops << " Flops\n"); + _printf0_(" memory used : " << solution_memory << " Bytes\n"); #endif + _printf0_("\n"); } @@ -1824,9 +1850,13 @@ if(isautodiff){ - #ifdef _HAVE_ADOLC_ + #ifdef _HAVE_AD_ parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); parameters->FindParam(&dependent_objects,AutodiffDependentObjectsEnum); if(num_dependents){ dependents=xNew(num_dependents); + + #if defined(_HAVE_CODIPACK_) + auto& tape_codi = IssmDouble::getGlobalTape(); + #endif /*Go through our dependent variables, and compute the response:*/ @@ -1835,5 +1865,11 @@ dep->Responsex(&output_value,this); if (my_rank==0) { - output_value>>=dependents[i]; + #if defined(_HAVE_CODIPACK_) + tape_codi.registerOutput(output_value); + dependents[i] = output_value.getValue(); + codi_global.output_indices.push_back(output_value.getGradientData()); + #else + output_value>>=dependents[i]; + #endif } } @@ -2509,5 +2545,5 @@ /*AMR*/ -#if !defined(_HAVE_ADOLC_) +#ifndef _HAVE_AD_ void FemModel::ReMesh(void){/*{{{*/ @@ -2528,9 +2564,9 @@ this->parameters->FindParam(&amrtype,AmrTypeEnum); switch(amrtype){ - #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) case AmrNeopzEnum: this->ReMeshNeopz(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; #endif - #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) case AmrBamgEnum: this->ReMeshBamg(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; #endif @@ -4884,5 +4920,5 @@ #endif -#if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) +#if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) void FemModel::ReMeshBamg(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist){/*{{{*/ @@ -5210,5 +5246,5 @@ #endif -#if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) +#if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) void FemModel::ReMeshNeopz(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist){/*{{{*/ Index: /issm/trunk/src/c/classes/FemModel.h =================================================================== --- /issm/trunk/src/c/classes/FemModel.h (revision 23393) +++ /issm/trunk/src/c/classes/FemModel.h (revision 23394) @@ -20,8 +20,8 @@ class Profiler; class Elements; -#if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) +#if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) #include "./AdaptiveMeshRefinement.h" #endif -#if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) +#if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) #include "./AmrBamg.h" #endif @@ -51,9 +51,9 @@ //FIXME: do we want only one class and have virtual functions? or keep 2 classes, at least rename AdaptiveMeshRefinement -> AmrNeopz - #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) AdaptiveMeshRefinement *amr; //adaptive mesh refinement object. It keeps coarse mesh and execute refinement process #endif - #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) AmrBamg *amrbamg; //adaptive mesh refinement object. It keeps coarse mesh and execute refinement process #endif @@ -164,5 +164,5 @@ /*AMR*/ - #if !defined(_HAVE_ADOLC_) + #if !defined(_HAVE_AD_) void ReMesh(void); void BedrockFromMismipPlus(void); @@ -191,5 +191,5 @@ #endif - #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) void ReMeshBamg(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); void InitializeAdaptiveRefinementBamg(void); @@ -199,5 +199,5 @@ #endif - #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) void ReMeshNeopz(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); void InitializeAdaptiveRefinementNeopz(void); Index: /issm/trunk/src/c/classes/IoModel.cpp =================================================================== --- /issm/trunk/src/c/classes/IoModel.cpp (revision 23393) +++ /issm/trunk/src/c/classes/IoModel.cpp (revision 23394) @@ -27,4 +27,9 @@ #include "../shared/io/io.h" #include "../shared/shared.h" + +#ifdef _HAVE_CODIPACK_ +extern CoDi_global codi_global; +#include // for output of the CoDiPack tape +#endif /*IoConstant class and methods*/ @@ -431,5 +436,6 @@ if(trace || (autodiff && !iscontrol)){ - #ifdef _HAVE_ADOLC_ + #ifdef _HAVE_AD_ + // FIXME codi here we should be able to execute codi version as normal this->FetchData(&num_independent_objects,"md.autodiff.num_independent_objects"); if(num_independent_objects){ @@ -460,5 +466,5 @@ #else /*if we asked for AD computations, we have a problem!: */ - _error_("Cannot carry out AD mode computations without support of ADOLC compiled in!"); + _error_("Cannot carry out AD mode computations without support of ADOLC or CoDiPack compiled in!"); #endif } @@ -1702,5 +1708,5 @@ if(X) Xcount=*pXcount; - #ifdef _HAVE_ADOLC_ //cannot come here unless you are running AD mode, from DeclaredIndependents: + #ifdef _HAVE_AD_ //cannot come here unless you are running AD mode, from DeclaredIndependents: /*output: */ @@ -1719,10 +1725,22 @@ /*Now, before we even broadcast this to other nodes, declare the scalar as an independent variable!. If we *have been supplied an X vector, use it instead of what we just read: */ - if(X){ - scalar<<=X[Xcount]; - } - else{ - scalar<<=pscalar; - } + #if defined(_HAVE_CODIPACK_) + // FIXME codi here we just assign instead of using "operator <<=" + if(X){ + scalar=X[Xcount]; + } else { + scalar=pscalar; + } + auto& tape_codi = IssmDouble::getGlobalTape(); + tape_codi.registerInput(scalar); + codi_global.input_indices.push_back(scalar.getGradientData()); + #else + if(X){ + scalar<<=X[Xcount]; + } + else{ + scalar<<=pscalar; + } + #endif } @@ -1744,5 +1762,5 @@ if(X) Xcount=*pXcount; - #ifdef _HAVE_ADOLC_ //cannot come here unless you are running AD mode, from DeclaredIndependents: + #ifdef _HAVE_AD_ //cannot come here unless you are running AD mode, from DeclaredIndependents: /*Intermediaries*/ @@ -1785,10 +1803,29 @@ /*Now, before we even broadcast this to other nodes, declare the whole matrix as a independent variable! If we have been supplied an X vector, use it instead of what we just read: */ - if(X){ - for(int i=0;iAddDataIndependent(new IoData(matrix,code,layout,M,N,data_name)); @@ -2472,5 +2511,7 @@ /*recover my_rank:*/ my_rank=IssmComm::GetRank(); - _assert_(strncmp(data_name,mddot,3)==0); + if(strncmp(data_name,mddot,3)!=0){ + _error_("Cannot fetch \""<FetchData(&keep,"md.autodiff.keep"); @@ -2579,7 +2621,35 @@ int skipFileDeletion=1; trace_on(my_rank,keepTaylors,reCast(obufsize),reCast(lbufsize),reCast(cbufsize),reCast(tbufsize),skipFileDeletion); + + #elif defined(_HAVE_CODIPACK_) + //fprintf(stderr, "*** Codipack IoModel::StartTrace\n"); + /* + * FIXME codi + * - ADOL-C variant uses fine grained tracing with various arguments + * - ADOL-C variant sets a garbage collection parameter for its tape + * -> These parameters are not read for the CoDiPack ISSM version! + */ + auto& tape_codi = IssmDouble::getGlobalTape(); + tape_codi.setActive(); + #if _AD_TAPE_ALLOC_ + //alloc_profiler.Tag(StartInit, true); + IssmDouble x_t(1.0), y_t(1.0); + tape_codi.registerInput(y_t); + int codi_allocn = 0; + this->FetchData(&codi_allocn,"md.autodiff.tapeAlloc"); + for(int i = 0;i < codi_allocn;++i) { + x_t = y_t * y_t; + } + /* + std::stringstream out_s; + IssmDouble::getGlobalTape().printStatistics(out_s); + _printf0_("StartTrace::Tape Statistics : TapeAlloc count=[" << codi_allocn << "]\n" << out_s.str()); + */ + tape_codi.reset(); + //alloc_profiler.Tag(FinishInit, true); #endif - } - -} -/*}}}*/ + #endif + } + +} +/*}}}*/ Index: /issm/trunk/src/c/classes/Materials/Matpar.cpp =================================================================== --- /issm/trunk/src/c/classes/Materials/Matpar.cpp (revision 23393) +++ /issm/trunk/src/c/classes/Materials/Matpar.cpp (revision 23394) @@ -107,9 +107,13 @@ iomodel->FindConstant(&this->rlapslgm,"md.smb.rlapslgm"); break; + case SMBpddSicopolisEnum: + iomodel->FindConstant(&this->desfac,"md.smb.desfac"); + iomodel->FindConstant(&this->rlaps,"md.smb.rlaps"); + break; case SMBd18opddEnum: iomodel->FindConstant(&this->desfac,"md.smb.desfac"); iomodel->FindConstant(&this->rlaps,"md.smb.rlaps"); iomodel->FindConstant(&this->rlapslgm,"md.smb.rlapslgm"); - iomodel->FindConstant(&this->dpermil,"md.smb.dpermil"); + iomodel->FindConstant(&this->dpermil,"md.smb.dpermil"); case SMBgradientsEnum: /*Nothing to add*/ @@ -125,4 +129,7 @@ break; case SMBmeltcomponentsEnum: + /*Nothing to add*/ + break; + case SMBgradientscomponentsEnum: /*Nothing to add*/ break; @@ -170,9 +177,9 @@ break; case MaterialsEnum: - //we have several types of materials. Retrieve this info first: + //we have several types of materials. Retrieve this info first: iomodel->FetchData(&nature,&nnat,&dummy,"md.materials.nature"); - //go through list of materials, and create constant parameters accordingly: - for(int i=0;iFindConstant(&this->rlapslgm,"md.smb.rlapslgm"); break; + case SMBpddSicopolisEnum: + iomodel->FindConstant(&this->desfac,"md.smb.desfac"); + iomodel->FindConstant(&this->rlaps,"md.smb.rlaps"); + break; case SMBd18opddEnum: iomodel->FindConstant(&this->desfac,"md.smb.desfac"); iomodel->FindConstant(&this->rlaps,"md.smb.rlaps"); iomodel->FindConstant(&this->rlapslgm,"md.smb.rlapslgm"); - iomodel->FindConstant(&this->dpermil,"md.smb.dpermil"); + iomodel->FindConstant(&this->dpermil,"md.smb.dpermil"); case SMBgradientsEnum: /*Nothing to add*/ @@ -233,5 +244,5 @@ default: _error_("Surface mass balance model "<FindConstant(&this->sediment_compressibility,"md.hydrology.sediment_compressibility"); @@ -350,5 +361,5 @@ this->Echo(); -} +} /*}}}*/ void Matpar::Echo(void){/*{{{*/ @@ -381,16 +392,16 @@ _printf_(" sediment_porosity: " << sediment_porosity << "\n"); _printf_(" sediment_thickness: " << sediment_thickness << "\n"); - _printf_(" water_compressibility: " << water_compressibility << "\n"); - _printf_(" epl_compressibility: " << epl_compressibility << "\n"); - _printf_(" epl_porosity: " << epl_porosity << "\n"); - _printf_(" epl_init_thickness: " << epl_init_thickness << "\n"); - _printf_(" epl_colapse_thickness: " << epl_colapse_thickness << "\n"); - _printf_(" epl_max_thickness: " << epl_max_thickness << "\n"); - _printf_(" epl_conductivity: " << epl_conductivity << "\n"); - _printf_(" lithosphere_shear_modulus: " << lithosphere_shear_modulus << "\n"); - _printf_(" lithosphere_density: " << lithosphere_density << "\n"); - _printf_(" mantle_shear_modulus: " << mantle_shear_modulus << "\n"); - _printf_(" mantle_density: " << mantle_density << "\n"); - _printf_(" earth_density: " << earth_density << "\n"); + _printf_(" water_compressibility: " << water_compressibility << "\n"); + _printf_(" epl_compressibility: " << epl_compressibility << "\n"); + _printf_(" epl_porosity: " << epl_porosity << "\n"); + _printf_(" epl_init_thickness: " << epl_init_thickness << "\n"); + _printf_(" epl_colapse_thickness: " << epl_colapse_thickness << "\n"); + _printf_(" epl_max_thickness: " << epl_max_thickness << "\n"); + _printf_(" epl_conductivity: " << epl_conductivity << "\n"); + _printf_(" lithosphere_shear_modulus: " << lithosphere_shear_modulus << "\n"); + _printf_(" lithosphere_density: " << lithosphere_density << "\n"); + _printf_(" mantle_shear_modulus: " << mantle_shear_modulus << "\n"); + _printf_(" mantle_density: " << mantle_density << "\n"); + _printf_(" earth_density: " << earth_density << "\n"); return; } @@ -512,5 +523,5 @@ this->dpermil=constant; break; - default: + default: break; } Index: /issm/trunk/src/c/classes/Numberedcostfunction.cpp =================================================================== --- /issm/trunk/src/c/classes/Numberedcostfunction.cpp (revision 23393) +++ /issm/trunk/src/c/classes/Numberedcostfunction.cpp (revision 23394) @@ -149,6 +149,8 @@ _error_("not supported"); } + _printf0_("#"< inline void GenericOption::Get(IssmPDouble** pvalue){ /*{{{*/ Index: /issm/trunk/src/c/classes/Params/Parameters.cpp =================================================================== --- /issm/trunk/src/c/classes/Params/Parameters.cpp (revision 23393) +++ /issm/trunk/src/c/classes/Params/Parameters.cpp (revision 23394) @@ -92,5 +92,5 @@ } /*}}}*/ -void Parameters::DeepEcho(void){/*{{{*/ +void Parameters::DeepEcho(void){/*{{{*/ for(int i=0;iparams[i]) this->params[i]->DeepEcho(); @@ -99,5 +99,5 @@ } /*}}}*/ -void Parameters::Echo(void){/*{{{*/ +void Parameters::Echo(void){/*{{{*/ for(int i=0;iparams[i]) this->params[i]->Echo(); @@ -139,5 +139,5 @@ /*Recover enum of object first: */ - MARSHALLING(obj_enum); + MARSHALLING(obj_enum); if(obj_enum==DoubleParamEnum){ @@ -200,5 +200,5 @@ fileparam->Marshall(pmarshalled_data,pmarshalled_data_size,marshall_direction); delete fileparam; - /* No need to add this object, the pointer is not valid + /* No need to add this object, the pointer is not valid The FemModel should reset all FileParams in the restart function */ } @@ -426,4 +426,40 @@ } /*}}}*/ +void Parameters::FindParamAndMakePassive(IssmPDouble* pscalar,int param_enum){ _assert_(this);/*{{{*/ + _assert_(param_enum>ParametersSTARTEnum); + _assert_(param_enumparams[index]) _error_("Parameter " << EnumToStringx(param_enum) <<" not set"); + this->params[index]->GetParameterValue(&intermediary); + + /*cast to "passive"*/ + *pscalar=reCast(intermediary); +} +/*}}}*/ +void Parameters::FindParamAndMakePassive(IssmPDouble** pvec,int* pM, int param_enum){ _assert_(this);/*{{{*/ + + _assert_(param_enum>ParametersSTARTEnum); + _assert_(param_enumparams[index]) _error_("Parameter " << EnumToStringx(param_enum) <<" not set"); + this->params[index]->GetParameterValue(&vector,&n); + + /*Make output passive*/ + IssmPDouble* output = xNew(n); + for(int i=0;i(vector[i]); + + /*assign output pointers*/ + if(pvec) *pvec = output; + if(pM) *pM = n; +}/*}}}*/ void Parameters::FindParamInDataset(IssmDouble** pIssmDoublearray,int* pM,int* pN,int dataset_type,int enum_type){/*{{{*/ _assert_(this); @@ -613,5 +649,5 @@ char* OptionsFromAnalysis(char** pouttoolkit,Parameters* parameters,int analysis_type){ /*{{{*/ - /* figure out ISSM options for current analysis, return a string. */ + /* figure out ISSM options for current analysis, return a string. */ /*output: */ @@ -631,6 +667,6 @@ parameters->FindParam(&strings,&numanalyses,ToolkitsOptionsStringsEnum); - parameters->FindParam(&toolkits,&dummy,ToolkitsTypesEnum); _assert_(dummy==numanalyses); - parameters->FindParam(&analyses,&dummy,ToolkitsOptionsAnalysesEnum); _assert_(dummy==numanalyses); + parameters->FindParam(&toolkits,&dummy,ToolkitsTypesEnum); _assert_(dummy==numanalyses); + parameters->FindParam(&analyses,&dummy,ToolkitsOptionsAnalysesEnum); _assert_(dummy==numanalyses); if(numanalyses==0)return NULL; //we did not find petsc options, don't bother. @@ -674,14 +710,14 @@ xDelete(analyses); return outstring; -} +} /*}}}*/ void ToolkitsOptionsFromAnalysis(Parameters* parameters,int analysis_type){ /*{{{*/ /*!\file: ToolkitsOptionsFromAnalysis.cpp - * \brief: for each analysis, setup the issmoptions string. - * This is mainly for the case where we run our toolkits using petsc. In this case, we need to - * plug our toolkits options directly into the petsc options database. This is the case for each analysis type + * \brief: for each analysis, setup the issmoptions string. + * This is mainly for the case where we run our toolkits using petsc. In this case, we need to + * plug our toolkits options directly into the petsc options database. This is the case for each analysis type * and parameters - */ + */ char* options = NULL; @@ -695,5 +731,5 @@ #ifdef _HAVE_PETSC_ - /*In case we are using PETSC, we do not rely on issmoptions. Instead, we dump issmoptions into the Petsc + /*In case we are using PETSC, we do not rely on issmoptions. Instead, we dump issmoptions into the Petsc * options database: */ #if (_PETSC_MINOR_>=7) @@ -717,20 +753,2 @@ } /*}}}*/ - -/*Specific case with ADOL-C, we might need to get double params for m1qn3*/ -#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) -void Parameters::FindParamAndMakePassive(double* pscalar,int param_enum){ _assert_(this);/*{{{*/ - _assert_(param_enum>ParametersSTARTEnum); - _assert_(param_enumparams[index]) _error_("Parameter " << EnumToStringx(param_enum) <<" not set"); - this->params[index]->GetParameterValue(&intermediary); - - /*cast to "passive"*/ - *pscalar=reCast(intermediary); -} -/*}}}*/ -#endif Index: /issm/trunk/src/c/classes/Params/Parameters.h =================================================================== --- /issm/trunk/src/c/classes/Params/Parameters.h (revision 23393) +++ /issm/trunk/src/c/classes/Params/Parameters.h (revision 23394) @@ -52,4 +52,6 @@ void FindParam(FILE** pfid,int enum_type); void FindParam(DataSet** pdataset, int enum_type); + void FindParamAndMakePassive(IssmPDouble* pscalar, int enum_type); + void FindParamAndMakePassive(IssmPDouble** pvec,int* pM,int enum_type); void FindParamInDataset(IssmDouble** pIssmDoublearray,int* pM,int* pN,int dataset_type,int enum_type); @@ -70,9 +72,4 @@ Param* FindParamObject(int enum_type); - /*Specific instantiations for IssmDouble*: */ - #if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) - void FindParamAndMakePassive(double* pscalar, int enum_type); - #endif - }; Index: /issm/trunk/src/c/classes/Profiler.cpp =================================================================== --- /issm/trunk/src/c/classes/Profiler.cpp (revision 23393) +++ /issm/trunk/src/c/classes/Profiler.cpp (revision 23394) @@ -15,5 +15,5 @@ /*Profiler constructors and destructors:*/ Profiler::Profiler(){/*{{{*/ - for(int i=0;itime[i] = 0.; this->time_start[i] = 0.; @@ -23,4 +23,5 @@ this->memory_start[i] = 0.; this->running[i] = false; + this->used[i] = false; } } /*}}}*/ @@ -32,5 +33,5 @@ Profiler* output=new Profiler(); - for(int i=0;itime[i] =this->time[i]; output->flops[i] =this->flops[i]; @@ -49,5 +50,5 @@ _printf_("Profiler:\n"); - for(int i=0;iflops[i]<<"\n"); @@ -70,11 +71,11 @@ MARSHALLING_ENUM(ProfilerEnum); pointer = &this->time[0]; - MARSHALLING_DYNAMIC(pointer,IssmPDouble,MAXIMUMSIZE); + MARSHALLING_DYNAMIC(pointer,IssmPDouble,MAXPROFSIZE); pointer = &this->flops[0]; - MARSHALLING_DYNAMIC(pointer,IssmPDouble,MAXIMUMSIZE); + MARSHALLING_DYNAMIC(pointer,IssmPDouble,MAXPROFSIZE); pointer = &this->memory[0]; - MARSHALLING_DYNAMIC(pointer,IssmPDouble,MAXIMUMSIZE); + MARSHALLING_DYNAMIC(pointer,IssmPDouble,MAXPROFSIZE); bpointer = &this->running[0]; - MARSHALLING_DYNAMIC(bpointer,bool,MAXIMUMSIZE); + MARSHALLING_DYNAMIC(bpointer,bool,MAXPROFSIZE); } /*}}}*/ @@ -88,5 +89,5 @@ /*Get tag*/ _assert_(tag>=0); - _assert_(tagrunning[tag]) _error_("Tag "<=0); - _assert_(tagrunning[tag]) _error_("Tag "<=0); - _assert_(tagrunning[tag]) _error_("Tag "<=0); - _assert_(tagrunning[tag]) _error_("Tag "<time: */ _assert_(tag>=0); - _assert_(tagtime_start[tag] = t; this->flops_start[tag] = f; @@ -174,4 +175,5 @@ /*turn on running*/ this->running[tag] = true; + this->used[tag] = true; }/*}}}*/ void Profiler::Stop(int tag,bool dontmpisync){/*{{{*/ @@ -179,5 +181,5 @@ /*Check tag*/ _assert_(tag>=0); - _assert_(tagrunning[tag]) _error_("Tag "<time: */ _assert_(tag>=0); - _assert_(tagtime[tag] += t - this->time_start[tag]; this->flops[tag] += f - this->flops_start[tag]; @@ -214,2 +216,9 @@ this->running[tag] = false; }/*}}}*/ +bool Profiler::Used(int tag){/*{{{*/ + + /*Check tag*/ + _assert_(tag>=0); + _assert_(tagused[tag]; +}/*}}}*/ Index: /issm/trunk/src/c/classes/Profiler.h =================================================================== --- /issm/trunk/src/c/classes/Profiler.h (revision 23393) +++ /issm/trunk/src/c/classes/Profiler.h (revision 23394) @@ -11,21 +11,33 @@ /*Macros*/ -#define TOTAL 0 /*Profiling Total time */ -#define MPROCESSOR 1 /*Profiling Model processor*/ -#define CORE 2 /*Profiling solution */ -#define SOLVER 3 /*Profiling solution */ -#define ADCORE 4 /*Profiling AD */ -#define MAXIMUMSIZE 5 +#define TOTAL 0 /*Profiling Total time */ +#define MPROCESSOR 1 /*Profiling Model processor*/ +#define CORE 2 /*Profiling solution */ +#define SOLVER 3 /*Profiling solution */ +#define ADCORE 4 /*Profiling AD */ +#define THERMALCORE 5 /*Profiling THERMAL */ +#define HYDROLOGYCORE 6 /*Profiling HYDROLOGY */ +#define STRESSBALANCECORE 7 /*Profiling STRESSBALANCE */ +#define DAMAGECORE 8 /*Profiling DAMAGE */ +#define MOVINGFRONTCORE 9 /*Profiling MOVINGFRONT */ +#define MASSTRANSPORTCORE 10 /*Profiling MASSTRANSPORT */ +#define SMBCORE 11 /*Profiling SMB */ +#define GROUNDINGLINECORE 12 /*Profiling GROUDINGLINE MIGRATION */ +#define GIACORE 13 /*Profiling GIA */ +#define ESACORE 14 /*Profiling ESA */ +#define SLRCORE 15 /*Profiling SLR */ +#define MAXPROFSIZE 16 /*Used to initialize static arrays*/ class Profiler: public Object{ public: - IssmPDouble flops[MAXIMUMSIZE]; - IssmPDouble flops_start[MAXIMUMSIZE]; - IssmPDouble memory[MAXIMUMSIZE]; - IssmPDouble memory_start[MAXIMUMSIZE]; - IssmPDouble time[MAXIMUMSIZE]; - IssmPDouble time_start[MAXIMUMSIZE]; - bool running[MAXIMUMSIZE]; + IssmPDouble flops[MAXPROFSIZE]; + IssmPDouble flops_start[MAXPROFSIZE]; + IssmPDouble memory[MAXPROFSIZE]; + IssmPDouble memory_start[MAXPROFSIZE]; + IssmPDouble time[MAXPROFSIZE]; + IssmPDouble time_start[MAXPROFSIZE]; + bool running[MAXPROFSIZE]; + bool used[MAXPROFSIZE]; /*Profiler constructors, destructors */ @@ -48,6 +60,7 @@ int TotalTimeModSec(int tag); IssmPDouble Memory(int tag); - void Start(int tagenum,bool dontmpisync=false); - void Stop(int tagenum,bool dontmpisync=false); + void Start(int tagenum,bool dontmpisync=true); /*Do not call MPI barrier by default to save some ms*/ + void Stop(int tagenum, bool dontmpisync=true); /*Do not call MPI barrier by default to save some ms*/ + bool Used(int tagenum); }; Index: /issm/trunk/src/c/cores/ad_core.cpp =================================================================== --- /issm/trunk/src/c/cores/ad_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/ad_core.cpp (revision 23394) @@ -19,4 +19,7 @@ /*}}}*/ +#ifdef _HAVE_CODIPACK_ +CoDi_global codi_global = {}; +#endif void ad_core(FemModel* femmodel){ @@ -41,5 +44,5 @@ if(isautodiff && !iscontrol){ - #ifdef _HAVE_ADOLC_ + #if defined(_HAVE_ADOLC_) if(VerboseAutodiff())_printf0_(" start ad core\n"); @@ -318,4 +321,65 @@ xDelete(axp); xDelete(driver); + + #elif defined(_HAVE_CODIPACK_) + if(VerboseAutodiff())_printf0_(" start CoDiPack ad core\n"); + + /*First, stop tracing: */ + auto& tape_codi = IssmDouble::getGlobalTape(); + tape_codi.setPassive(); + + if(VerboseAutodiff()){ /*{{{*/ + if(my_rank == 0) { + // FIXME codi "just because" for now + tape_codi.printStatistics(std::cout); + codi_global.print(std::cout); + } + } + + /*retrieve parameters: */ + femmodel->parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); + femmodel->parameters->FindParam(&num_independents,AutodiffNumIndependentsEnum); + + /*if no dependents, no point in running a driver: */ + if(!(num_dependents*num_independents)) return; + + /*Branch according to AD driver: */ + femmodel->parameters->FindParam(&driver,AutodiffDriverEnum); + if(VerboseAutodiff())_printf0_(" driver: " << driver << "\n"); + + if (strcmp(driver,"fos_reverse")==0) { /*{{{*/ + if(VerboseAutodiff())_printf0_(" CoDiPack fos_reverse\n"); + int aDepIndex=0; + double *weightVectorTimesJac=NULL; + + /*retrieve direction index: */ + femmodel->parameters->FindParam(&aDepIndex,AutodiffFosReverseIndexEnum); + if (my_rank==0) { + if (aDepIndex<0 || aDepIndex>=num_dependents + || codi_global.output_indices.size() <= aDepIndex){ + _error_("index value for AutodiffFosReverseIndexEnum should be in [0,num_dependents-1]"); + } + tape_codi.setGradient(codi_global.output_indices[aDepIndex], 1.0); + } + + tape_codi.evaluate(); + + weightVectorTimesJac=xNew(num_independents); + /*call driver: */ + auto in_size = codi_global.input_indices.size(); + for(size_t i = 0; i < in_size; ++i) { + weightVectorTimesJac[i] = tape_codi.getGradient(codi_global.input_indices[i]); + } + + /*add to results*/ + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,AutodiffJacobianEnum,weightVectorTimesJac,num_independents,1,0,0.0)); + + /*free resources :*/ + xDelete(weightVectorTimesJac); + } /*}}}*/ + else _error_("driver: " << driver << " not yet supported!"); + + if(VerboseAutodiff())_printf0_(" end CoDiPack ad core\n"); + xDelete(driver); #else _error_("Should not be requesting AD drivers when an AD library is not available!"); Index: /issm/trunk/src/c/cores/adgradient_core.cpp =================================================================== --- /issm/trunk/src/c/cores/adgradient_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/adgradient_core.cpp (revision 23394) @@ -48,5 +48,5 @@ if(isautodiff){ - #ifdef _HAVE_ADOLC_ + #if defined(_HAVE_ADOLC_) if(VerboseAutodiff())_printf0_(" start ad core\n"); @@ -182,4 +182,7 @@ xDelete(totalgradient); xDelete(axp); /*}}}*/ + + #elif defined(_HAVE_CODIPACK_) + fprintf(stderr, "*** Codipack adgradient_core()\n"); #else _error_("Should not be requesting AD drivers when an AD library is not available!"); Index: /issm/trunk/src/c/cores/adjointstressbalance_core.cpp =================================================================== --- /issm/trunk/src/c/cores/adjointstressbalance_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/adjointstressbalance_core.cpp (revision 23394) @@ -31,7 +31,18 @@ if(VerboseSolution()) _printf0_(" computing velocities\n"); femmodel->SetCurrentConfiguration(StressbalanceAnalysisEnum); + + bool is_schur_cg_solver = false; + #ifdef _HAVE_PETSC_ + int solver_type; + PetscOptionsDetermineSolverType(&solver_type); + + if(solver_type==FSSolverEnum) is_schur_cg_solver = true; + #endif + if(isFS){ if (fe_FS==LATaylorHoodEnum || fe_FS==LACrouzeixRaviartEnum) solutionsequence_la(femmodel); + else if(is_schur_cg_solver) + solutionsequence_schurcg(femmodel); else solutionsequence_nonlinear(femmodel,conserve_loads); Index: /issm/trunk/src/c/cores/balancethickness_core.cpp =================================================================== --- /issm/trunk/src/c/cores/balancethickness_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/balancethickness_core.cpp (revision 23394) @@ -21,5 +21,5 @@ femmodel->parameters->FindParam(&save_results,SaveResultsEnum); - if(VerboseSolution()) _printf0_("call computational core:\n"); + if(VerboseSolution()) _printf0_(" call computational core:\n"); solutionsequence_linear(femmodel); Index: /issm/trunk/src/c/cores/balancevelocity_core.cpp =================================================================== --- /issm/trunk/src/c/cores/balancevelocity_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/balancevelocity_core.cpp (revision 23394) @@ -27,5 +27,5 @@ solutionsequence_linear(femmodel); - if(VerboseSolution()) _printf0_("call computational core:\n"); + if(VerboseSolution()) _printf0_(" call computational core:\n"); femmodel->SetCurrentConfiguration(BalancevelocityAnalysisEnum); solutionsequence_linear(femmodel); Index: /issm/trunk/src/c/cores/control_core.cpp =================================================================== --- /issm/trunk/src/c/cores/control_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/control_core.cpp (revision 23394) @@ -81,6 +81,6 @@ IssmDouble *XL = NULL; IssmDouble *XU = NULL; - GetVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); - GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + GetVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); + GetVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); for(long i=0;iXU[i]) X0[i]=XU[i]; @@ -97,5 +97,5 @@ femmodel->OutputControlsx(&femmodel->results); - #ifdef _HAVE_ADOLC_ + #ifdef _HAVE_AD_ IssmPDouble* J_passive=xNew(nsteps); for(int i=0;i(J[i]); @@ -134,6 +134,6 @@ IssmDouble *XL = NULL; IssmDouble *XU = NULL; - GetVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); - GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + GetVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); + GetVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); for(long i=0;iXU[i]) X[i]=XU[i]; @@ -143,5 +143,6 @@ /*Update control input*/ SetControlInputsFromVectorx(femmodel,X); - + + /*solve forward: */ switch(solution_type){ @@ -150,8 +151,21 @@ stressbalance_core(femmodel); //We need a 3D velocity!! (vz is required for the next thermal run) break; - case StressbalanceSolutionEnum: + case StressbalanceSolutionEnum:{ femmodel->SetCurrentConfiguration(StressbalanceAnalysisEnum); - solutionsequence_nonlinear(femmodel,conserve_loads); - break; + + bool is_schur_cg_solver = false; + #ifdef _HAVE_PETSC_ + int solver_type; + PetscOptionsDetermineSolverType(&solver_type); + if(solver_type==FSSolverEnum) is_schur_cg_solver = true; + #endif + + if(is_schur_cg_solver){ + solutionsequence_schurcg(femmodel); + }else{ + solutionsequence_nonlinear(femmodel,conserve_loads); + } + } + break; case BalancethicknessSolutionEnum: femmodel->SetCurrentConfiguration(BalancethicknessAnalysisEnum); @@ -211,6 +225,6 @@ IssmDouble *XL = NULL; IssmDouble *XU = NULL; - GetVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); - GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + GetVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); + GetVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); for(long i=0;iXU[i]) X[i]=XU[i]; Index: /issm/trunk/src/c/cores/controlad_core.cpp =================================================================== --- /issm/trunk/src/c/cores/controlad_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/controlad_core.cpp (revision 23394) @@ -11,4 +11,5 @@ #include "../solutionsequences/solutionsequences.h" +/*This file is probably never used!*/ #if defined (_HAVE_M1QN3_) & defined (_HAVE_ADOLC_) /*m1qn3 prototypes {{{*/ Index: /issm/trunk/src/c/cores/controladm1qn3_core.cpp =================================================================== --- /issm/trunk/src/c/cores/controladm1qn3_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/controladm1qn3_core.cpp (revision 23394) @@ -11,6 +11,11 @@ #include "../solutionsequences/solutionsequences.h" -#if defined (_HAVE_M1QN3_) && defined(_HAVE_ADOLC_) -/*m1qn3 prototypes*/ +#ifdef _HAVE_CODIPACK_ +extern CoDi_global codi_global; +#include // for output of the CoDiPack tape +#endif + +#if defined (_HAVE_M1QN3_) && defined(_HAVE_AD_) +/*m1qn3 prototypes {{{*/ extern "C" void *ctonbe_; // DIS mode : Conversion extern "C" void *ctcabe_; // DIS mode : Conversion @@ -31,8 +36,10 @@ int* i; } m1qn3_struct; +/*}}}*/ /*m1qm3 functions*/ void simul_starttrace(FemModel* femmodel){/*{{{*/ + #if defined(_HAVE_ADOLC_) /*Retrive ADOLC parameters*/ IssmDouble gcTriggerRatio; @@ -57,114 +64,48 @@ int my_rank=IssmComm::GetRank(); trace_on(my_rank,keepTaylors,reCast(obufsize),reCast(lbufsize),reCast(cbufsize),reCast(tbufsize),skipFileDeletion); + + #elif defined(_HAVE_CODIPACK_) + + //fprintf(stderr, "*** Codipack IoModel::StartTrace\n"); + /* + * FIXME codi + * - ADOL-C variant uses fine grained tracing with various arguments + * - ADOL-C variant sets a garbage collection parameter for its tape + * -> These parameters are not read for the CoDiPack ISSM version! + */ + auto& tape_codi = IssmDouble::getGlobalTape(); + tape_codi.setActive(); + #if _AD_TAPE_ALLOC_ + //alloc_profiler.Tag(StartInit, true); + IssmDouble x_t(1.0), y_t(1.0); + tape_codi.registerInput(y_t); + int codi_allocn = 0; + femmodel->parameters->FindParam(&codi_allocn,AutodiffTapeAllocEnum); + for(int i = 0;i < codi_allocn;++i) { + x_t = y_t * y_t; + } + /* + std::stringstream out_s; + IssmDouble::getGlobalTape().printStatistics(out_s); + _printf0_("StartTrace::Tape Statistics : TapeAlloc count=[" << codi_allocn << "]\n" << out_s.str()); + */ + tape_codi.reset(); + //alloc_profiler.Tag(FinishInit, true); + #else + tape_codi.reset(); + #endif + + #else + _error_("not implemented"); + #endif }/*}}}*/ -void simul_ad(long* indic,long* n,double* X,double* pf,double* G,long izs[1],float rzs[1],void* dzs){/*{{{*/ - - /*Get rank*/ - int my_rank=IssmComm::GetRank(); - - /*Recover Arguments*/ - m1qn3_struct *input_struct = (m1qn3_struct*)dzs; - - FemModel* femmodel = input_struct->femmodel; - int num_responses,num_controls,numberofvertices,solution_type; - femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); - int* N = NULL; - int N_add = 0; - int* control_enum = NULL; - - if (solution_type == TransientSolutionEnum){ - femmodel = input_struct->femmodel->copy(); - } - - IssmPDouble* Jlist = input_struct->Jlist; - int JlistM = input_struct->M; - int JlistN = input_struct->N; - int* Jlisti = input_struct->i; - int intn = (int)*n; - - /*Recover some parameters*/ - IssmDouble* scaling_factors = NULL; - femmodel->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum); - femmodel->parameters->FindParam(&num_controls,InversionNumControlParametersEnum); - femmodel->parameters->FindParam(&scaling_factors,NULL,InversionControlScalingFactorsEnum); - femmodel->parameters->FindParam(&N,NULL,ControlInputSizeNEnum); - femmodel->parameters->FindParam(&control_enum,NULL,InversionControlParametersEnum); - numberofvertices=femmodel->vertices->NumberOfVertices(); - - /*Constrain input vector and update controls*/ - double *XL = NULL; - double *XU = NULL; - GetPassiveVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); - GetPassiveVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); - - N_add = 0; - for (int c=0;c(scaling_factors[c]); - if(X[index]>XU[index]) X[index]=XU[index]; - if(X[index](intn,"t"); -#else - IssmDouble* aX=xNew(intn); -#endif - if(my_rank==0){ - for(int i=0;i(aX); - - /*Compute solution (forward)*/ - void (*solutioncore)(FemModel*)=NULL; - CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); - solutioncore(femmodel); - - /*Reset the time to zero for next optimization*/ - if(solution_type==TransientSolutionEnum){ - IssmDouble restart_time; - femmodel->parameters->FindParam(&restart_time,TimesteppingStartTimeEnum); - femmodel->parameters->SetParam(restart_time,TimeEnum); - - } - - /*Get Dependents*/ - IssmDouble output_value; - int num_dependents; - IssmPDouble *dependents; - DataSet* dependent_objects=NULL; - IssmDouble J=0.; - femmodel->parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); - femmodel->parameters->FindParam(&dependent_objects,AutodiffDependentObjectsEnum); - - /*Go through our dependent variables, and compute the response:*/ - dependents=xNew(num_dependents); - for(int i=0;iSize();i++){ - DependentObject* dep=(DependentObject*)dependent_objects->GetObjectByOffset(i); - if(solution_type==TransientSolutionEnum) output_value = dep->GetValue(); - if(solution_type!=TransientSolutionEnum) dep->Responsex(&output_value,femmodel); - if (my_rank==0) { - output_value>>=dependents[i]; - J+=output_value; - } - } - - /*Turning off trace tape*/ +void simul_stoptrace(){/*{{{*/ + + #if defined(_HAVE_ADOLC_) trace_off(); -time_t now = time(NULL); -if(my_rank==0) _printf_("\nTIME: "<femmodel; + int num_responses,num_controls,solution_type; + femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); + + /*In transient, we need to make sure we do not modify femmodel at each iteration, make a copy*/ + if(solution_type == TransientSolutionEnum) femmodel = input_struct->femmodel->copy(); + + IssmPDouble* Jlist = input_struct->Jlist; + int JlistM = input_struct->M; + int JlistN = input_struct->N; + int* Jlisti = input_struct->i; + int intn = (int)*n; + + /*Recover some parameters*/ + IssmDouble *scaling_factors = NULL; + int *N = NULL; + int *control_enum = NULL; + femmodel->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum); + femmodel->parameters->FindParam(&num_controls,InversionNumControlParametersEnum); + femmodel->parameters->FindParam(&scaling_factors,NULL,InversionControlScalingFactorsEnum); + femmodel->parameters->FindParam(&N,NULL,ControlInputSizeNEnum); + femmodel->parameters->FindParam(&control_enum,NULL,InversionControlParametersEnum); + int numberofvertices=femmodel->vertices->NumberOfVertices(); + + /*Constrain input vector and update controls*/ + double *XL = NULL; + double *XU = NULL; + GetPassiveVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); + GetPassiveVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + + int N_add = 0; + for (int c=0;c(scaling_factors[c]); + if(X[index]>XU[index]) X[index]=XU[index]; + if(X[index](intn,"t"); +#else + IssmDouble* aX=xNew(intn); +#endif + + #if defined(_HAVE_ADOLC_) + if(my_rank==0){ + for(int i=0;i(aX); + + /*Compute solution (forward)*/ + void (*solutioncore)(FemModel*)=NULL; + CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); + solutioncore(femmodel); + + /*Reset the time to zero for next optimization*/ + if(solution_type==TransientSolutionEnum){ + IssmDouble restart_time; + femmodel->parameters->FindParam(&restart_time,TimesteppingStartTimeEnum); + femmodel->parameters->SetParam(restart_time,TimeEnum); + + } + + /*Get Dependents*/ + IssmDouble output_value; + int num_dependents; + IssmPDouble *dependents; + DataSet* dependent_objects=NULL; + IssmDouble J=0.; + femmodel->parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); + femmodel->parameters->FindParam(&dependent_objects,AutodiffDependentObjectsEnum); + + /*Go through our dependent variables, and compute the response:*/ + dependents=xNew(num_dependents); + #if defined(_HAVE_CODIPACK_) + codi_global.output_indices.clear(); + #endif + for(int i=0;iSize();i++){ + DependentObject* dep=(DependentObject*)dependent_objects->GetObjectByOffset(i); + if(solution_type==TransientSolutionEnum) output_value = dep->GetValue(); + if(solution_type!=TransientSolutionEnum) dep->Responsex(&output_value,femmodel); + if(my_rank==0) { + + #if defined(_HAVE_CODIPACK_) + tape_codi.registerOutput(output_value); + dependents[i] = output_value.getValue(); + codi_global.output_indices.push_back(output_value.getGradientData()); + + #elif defined(_HAVE_ADOLC_) + output_value>>=dependents[i]; + + #else + _error_("not suppoted"); + #endif + J+=output_value; + } + } + + /*Turning off trace tape*/ + simul_stoptrace(); + //time_t now = time(NULL); + //if(my_rank==0) _printf_("\nTIME: "<(num_independents); /*if no dependents, no point in running a driver: */ @@ -229,4 +322,7 @@ int num_dependents_old = num_dependents; int num_independents_old = num_independents; + + #if defined(_HAVE_ADOLC_) + /*Get gradient for ADOLC {{{*/ if(my_rank!=0){ num_dependents = 0; @@ -243,6 +339,4 @@ /* Ok, now we are going to call the fos_reverse in a loop on the index, from 0 to num_dependents, so * as to generate num_dependents gradients: */ - totalgradient=xNewZeroInit(num_independents_old); - for(int aDepIndex=0;aDepIndex(num_dependents); + if(my_rank==0){ + if(aDepIndex<0 || aDepIndex>=num_dependents || codi_global.output_indices.size() <= aDepIndex){ + _error_("index value for AutodiffFosReverseIndexEnum should be in [0,num_dependents-1]"); + } + tape_codi.setGradient(codi_global.output_indices[aDepIndex],1.0); + } + tape_codi.evaluate(); + + /*Get gradient for this dependent */ + weightVectorTimesJac=xNew(num_independents); + auto in_size = codi_global.input_indices.size(); + for(size_t i = 0; i < in_size; ++i) { + _assert_(i(J); -/* - IssmDouble* test = xNew(intn); - femmodel->parameters->FindParam(&test,NULL,InversionXBestEnum); - for(int i=0;i<10;i++)_printf_("X "<(intn); -*/ if(*indic==0){ /*dry run, no gradient required*/ @@ -341,4 +466,6 @@ xDelete(XU); xDelete(XL); + xDelete(control_enum); + xDelete(N); xDelete(scaling_factors); xDelete(totalgradient); @@ -394,10 +521,5 @@ /*Get initial guess*/ - Vector *Xpetsc = NULL; - - GetPassiveVectorFromControlInputsx(&Xpetsc,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); - X = Xpetsc->ToMPISerial(); - Xpetsc->GetSize(&intn); - delete Xpetsc; + GetPassiveVectorFromControlInputsx(&X,&intn,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); //_assert_(intn==numberofvertices*num_controls); @@ -458,6 +580,6 @@ double *XL = NULL; double *XU = NULL; - GetPassiveVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); - GetPassiveVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + GetPassiveVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); + GetPassiveVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); N_add = 0; @@ -479,5 +601,5 @@ aX[i] = reCast(X[i]); aG[i] = reCast(G[i]); - } + } ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,aG); @@ -538,4 +660,4 @@ #else -void controladm1qn3_core(FemModel* femmodel){_error_("M1QN3 or ADOLC not installed");} +void controladm1qn3_core(FemModel* femmodel){_error_("M1QN3 or ADOLC/CoDiPack not installed");} #endif //_HAVE_M1QN3_ Index: /issm/trunk/src/c/cores/controlm1qn3_core.cpp =================================================================== --- /issm/trunk/src/c/cores/controlm1qn3_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/controlm1qn3_core.cpp (revision 23394) @@ -11,6 +11,6 @@ #include "../solutionsequences/solutionsequences.h" -#if defined (_HAVE_M1QN3_) && !defined(_HAVE_ADOLC_) -/*m1qn3 prototypes*/ +#if defined (_HAVE_M1QN3_) +/*m1qn3 prototypes {{{*/ extern "C" void *ctonbe_; // DIS mode : Conversion extern "C" void *ctcabe_; // DIS mode : Conversion @@ -28,21 +28,22 @@ /*Use struct to provide arguments*/ typedef struct{ - FemModel * femmodel; - IssmDouble* Jlist; + FemModel * femmodel; + IssmPDouble* Jlist; int M; int N; int* i; } m1qn3_struct; - -void controlm1qn3_core(FemModel* femmodel){ +/*}}}*/ + +void controlm1qn3_core(FemModel* femmodel){/*{{{*/ /*Intermediaries*/ - long omode; - double f,dxmin,gttol; - int maxsteps,maxiter; - int intn,numberofvertices,num_controls,num_cost_functions,solution_type; - IssmDouble *scaling_factors = NULL; - IssmDouble *X = NULL; - IssmDouble *G = NULL; + long omode; + double f,dxmin,gttol; + int maxsteps,maxiter; + int intn,numberofvertices,num_controls,num_cost_functions,solution_type; + double *scaling_factors = NULL; + double *X = NULL; + double *G = NULL; /*Recover some parameters*/ @@ -52,7 +53,7 @@ femmodel->parameters->FindParam(&maxsteps,InversionMaxstepsEnum); femmodel->parameters->FindParam(&maxiter,InversionMaxiterEnum); - femmodel->parameters->FindParam(&dxmin,InversionDxminEnum); - femmodel->parameters->FindParam(>tol,InversionGttolEnum); - femmodel->parameters->FindParam(&scaling_factors,NULL,InversionControlScalingFactorsEnum); + femmodel->parameters->FindParamAndMakePassive(&dxmin,InversionDxminEnum); + femmodel->parameters->FindParamAndMakePassive(>tol,InversionGttolEnum); + femmodel->parameters->FindParamAndMakePassive(&scaling_factors,NULL,InversionControlScalingFactorsEnum); femmodel->parameters->SetParam(false,SaveResultsEnum); numberofvertices=femmodel->vertices->NumberOfVertices(); @@ -77,9 +78,5 @@ /*Get initial guess*/ - Vector *Xpetsc = NULL; - GetVectorFromControlInputsx(&Xpetsc,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); - X = Xpetsc->ToMPISerial(); - Xpetsc->GetSize(&intn); - delete Xpetsc; + GetPassiveVectorFromControlInputsx(&X,&intn,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); _assert_(intn==numberofvertices*num_controls); @@ -111,5 +108,5 @@ mystruct.M = maxiter; mystruct.N = num_cost_functions+1; - mystruct.Jlist = xNewZeroInit(mystruct.M*mystruct.N); + mystruct.Jlist = xNewZeroInit(mystruct.M*mystruct.N); mystruct.i = xNewZeroInit(1); @@ -127,4 +124,5 @@ &reverse,&indic,izs,rzs,(void*)&mystruct); + /*Print exit flag*/ switch(int(omode)){ case 0: _printf0_(" Stop requested (indic = 0)\n"); break; @@ -140,8 +138,8 @@ /*Constrain solution vector*/ - IssmDouble *XL = NULL; - IssmDouble *XU = NULL; - GetVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); - GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + double *XL = NULL; + double *XU = NULL; + GetPassiveVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); + GetPassiveVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); for(int c=0;c(intn); + IssmDouble* aG=xNew(intn); + for(int i=0;i(X[i]); + aG[i] = reCast(G[i]); + } + ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,aG); + SetControlInputsFromVectorx(femmodel,aX); + xDelete(aX); + xDelete(aG); + #else SetControlInputsFromVectorx(femmodel,X); ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,G); + #endif + femmodel->OutputControlsx(&femmodel->results); femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,JEnum,mystruct.Jlist,(*mystruct.i),mystruct.N,0,0)); @@ -173,13 +187,11 @@ xDelete(mystruct.Jlist); xDelete(mystruct.i); -} - -/*Cost function definition*/ -void simul(long* indic,long* n,double* X,double* pf,double* G,long izs[1],float rzs[1],void* dzs){ +}/*}}}*/ +void simul(long* indic,long* n,double* X,double* pf,double* G,long izs[1],float rzs[1],void* dzs){/*{{{*/ /*Recover Arguments*/ m1qn3_struct *input_struct = (m1qn3_struct*)dzs; FemModel *femmodel = input_struct->femmodel; - IssmDouble *Jlist = input_struct->Jlist; + IssmPDouble *Jlist = input_struct->Jlist; int JlistM = input_struct->M; int JlistN = input_struct->N; @@ -188,16 +200,16 @@ /*Recover some parameters*/ int num_responses,num_controls,numberofvertices,solution_type; - IssmDouble* scaling_factors = NULL; + double* scaling_factors = NULL; femmodel->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum); femmodel->parameters->FindParam(&num_controls,InversionNumControlParametersEnum); - femmodel->parameters->FindParam(&scaling_factors,NULL,InversionControlScalingFactorsEnum); + femmodel->parameters->FindParamAndMakePassive(&scaling_factors,NULL,InversionControlScalingFactorsEnum); femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); numberofvertices=femmodel->vertices->NumberOfVertices(); /*Constrain input vector and update controls*/ - IssmDouble *XL = NULL; - IssmDouble *XU = NULL; - GetVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); - GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + double *XL = NULL; + double *XU = NULL; + GetPassiveVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); + GetPassiveVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); for(int c=0;c(*n); + for(int i=0;i<*n;i++) aX[i] = reCast(X[i]); + SetControlInputsFromVectorx(femmodel,aX); + xDelete(aX); + #else SetControlInputsFromVectorx(femmodel,X); + #endif /*Compute solution and adjoint*/ @@ -222,9 +241,11 @@ /*Compute objective function*/ IssmDouble* Jtemp = NULL; - femmodel->CostFunctionx(pf,&Jtemp,NULL); + IssmDouble J; + femmodel->CostFunctionx(&J,&Jtemp,NULL); + *pf = reCast(J); _printf0_("f(x) = "<(Jtemp[i]); Jlist[(*Jlisti)*JlistN+num_responses] = *pf; xDelete(Jtemp); @@ -239,6 +260,6 @@ *Jlisti = (*Jlisti) +1; - xDelete(XU); - xDelete(XL); + xDelete(XU); + xDelete(XL); return; } @@ -251,5 +272,5 @@ IssmDouble* G2 = NULL; Gradjx(&G2,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); - for(long i=0;i<*n;i++) G[i] = -G2[i]; + for(long i=0;i<*n;i++) G[i] = -reCast(G2[i]); xDelete(G2); @@ -275,12 +296,10 @@ /*Clean-up and return*/ *Jlisti = (*Jlisti) +1; - xDelete(XU); - xDelete(XL); - xDelete(scaling_factors); -} + xDelete(XU); + xDelete(XL); + xDelete(scaling_factors); +}/*}}}*/ #else -void controlm1qn3_core(FemModel* femmodel){ - _error_("M1QN3 not installed"); -} +void controlm1qn3_core(FemModel* femmodel){_error_("M1QN3 not installed");} #endif //_HAVE_M1QN3_ Index: /issm/trunk/src/c/cores/controlvalidation_core.cpp =================================================================== --- /issm/trunk/src/c/cores/controlvalidation_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/controlvalidation_core.cpp (revision 23394) @@ -9,19 +9,157 @@ #include "../modules/modules.h" +#ifdef _HAVE_CODIPACK_ +extern CoDi_global codi_global; +#include // for output of the CoDiPack tape +#endif + +#ifdef _HAVE_AD_ +void simul_starttrace2(FemModel* femmodel){/*{{{*/ + + #if defined(_HAVE_ADOLC_) + /*Retrive ADOLC parameters*/ + IssmDouble gcTriggerRatio; + IssmDouble gcTriggerMaxSize; + IssmDouble obufsize; + IssmDouble lbufsize; + IssmDouble cbufsize; + IssmDouble tbufsize; + femmodel->parameters->FindParam(&gcTriggerRatio,AutodiffGcTriggerRatioEnum); + femmodel->parameters->FindParam(&gcTriggerMaxSize,AutodiffGcTriggerMaxSizeEnum); + femmodel->parameters->FindParam(&obufsize,AutodiffObufsizeEnum); + femmodel->parameters->FindParam(&lbufsize,AutodiffLbufsizeEnum); + femmodel->parameters->FindParam(&cbufsize,AutodiffCbufsizeEnum); + femmodel->parameters->FindParam(&tbufsize,AutodiffTbufsizeEnum); + + /*Set garbage collection parameters: */ + setStoreManagerControl(reCast(gcTriggerRatio),reCast(gcTriggerMaxSize)); + + /*Start trace: */ + int skipFileDeletion=1; + int keepTaylors=1; + int my_rank=IssmComm::GetRank(); + trace_on(my_rank,keepTaylors,reCast(obufsize),reCast(lbufsize),reCast(cbufsize),reCast(tbufsize),skipFileDeletion); + + #elif defined(_HAVE_CODIPACK_) + + //fprintf(stderr, "*** Codipack IoModel::StartTrace\n"); + /* + * FIXME codi + * - ADOL-C variant uses fine grained tracing with various arguments + * - ADOL-C variant sets a garbage collection parameter for its tape + * -> These parameters are not read for the CoDiPack ISSM version! + */ + auto& tape_codi = IssmDouble::getGlobalTape(); + tape_codi.setActive(); + #if _AD_TAPE_ALLOC_ + //alloc_profiler.Tag(StartInit, true); + IssmDouble x_t(1.0), y_t(1.0); + tape_codi.registerInput(y_t); + int codi_allocn = 0; + femmodel->parameters->FindParam(&codi_allocn,AutodiffTapeAllocEnum); + for(int i = 0;i < codi_allocn;++i) { + x_t = y_t * y_t; + } + /* + std::stringstream out_s; + IssmDouble::getGlobalTape().printStatistics(out_s); + _printf0_("StartTrace::Tape Statistics : TapeAlloc count=[" << codi_allocn << "]\n" << out_s.str()); + */ + tape_codi.reset(); + //alloc_profiler.Tag(FinishInit, true); + #else + tape_codi.reset(); + #endif + + #else + _error_("not implemented"); + #endif +}/*}}}*/ +void simul_stoptrace2(){/*{{{*/ + + #if defined(_HAVE_ADOLC_) + trace_off(); + if(VerboseAutodiff()){ /*{{{*/ + + #ifdef _HAVE_ADOLC_ + int my_rank=IssmComm::GetRank(); + size_t tape_stats[15]; + tapestats(my_rank,tape_stats); //reading of tape statistics + int commSize=IssmComm::GetSize(); + int *sstats=new int[7]; + sstats[0]=tape_stats[NUM_OPERATIONS]; + sstats[1]=tape_stats[OP_FILE_ACCESS]; + sstats[2]=tape_stats[NUM_LOCATIONS]; + sstats[3]=tape_stats[LOC_FILE_ACCESS]; + sstats[4]=tape_stats[NUM_VALUES]; + sstats[5]=tape_stats[VAL_FILE_ACCESS]; + sstats[6]=tape_stats[TAY_STACK_SIZE]; + int *rstats=NULL; + if (my_rank==0) rstats=new int[commSize*7]; + ISSM_MPI_Gather(sstats,7,ISSM_MPI_INT,rstats,7,ISSM_MPI_INT,0,IssmComm::GetComm()); + if (my_rank==0) { + int offset=50; + int rOffset=(commSize/10)+1; + _printf_(" ADOLC statistics: \n"); + _printf_(" "<file":"") << "\n"); + _printf_(" locations: entry size " << sizeof(locint) << " Bytes\n"); + _printf_(" "<file":"") << "\n"); + _printf_(" constant values: entry size " << sizeof(double) << " Bytes\n"); + _printf_(" "<file":"") << "\n"); + _printf_(" Taylor stack: entry size " << sizeof(revreal) << " Bytes\n"); + _printf_(" "<tape_stats[TAY_BUFFER_SIZE]?" ->file":"") << "\n"); + delete []rstats; + } + delete [] sstats; + #endif + + #ifdef _HAVE_CODIPACK_ + #ifdef _AD_TAPE_ALLOC_ + //_printf_("Allocation time P(" << my_rank << "): " << alloc_profiler.DeltaTime(StartInit, FinishInit) << "\n"); + #endif + std::stringstream out_s; + IssmDouble::getGlobalTape().printStatistics(out_s); + _printf0_("CoDiPack Profiling::Tape Statistics :\n" << out_s.str()); + #endif + } /*}}}*/ + + #elif defined(_HAVE_CODIPACK_) + auto& tape_codi = IssmDouble::getGlobalTape(); + tape_codi.setPassive(); + if(VerboseAutodiff()){ + int my_rank=IssmComm::GetRank(); + if(my_rank == 0) { + // FIXME codi "just because" for now + tape_codi.printStatistics(std::cout); + codi_global.print(std::cout); + } + } + #else + _error_("not implemented"); + #endif +}/*}}}*/ +#endif + void controlvalidation_core(FemModel* femmodel){ int solution_type,n; int num_responses; - IssmDouble j0,j,yts; + IssmDouble j0,j; IssmDouble Ialpha,exponent,alpha; IssmDouble* scaling_factors = NULL; IssmDouble* jlist = NULL; - IssmDouble *G = NULL; - IssmDouble *X = NULL; - IssmDouble *X0= NULL; - - /*Solution and Adjoint core pointer*/ - void (*solutioncore)(FemModel*) = NULL; - void (*adjointcore)(FemModel*) = NULL; + int my_rank=IssmComm::GetRank(); /*Recover parameters used throughout the solution*/ @@ -29,19 +167,92 @@ femmodel->parameters->SetParam(false,SaveResultsEnum); femmodel->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum); - femmodel->parameters->FindParam(&yts,ConstantsYtsEnum); femmodel->parameters->FindParam(&scaling_factors,NULL,InversionControlScalingFactorsEnum); /*Get initial guess*/ - Vector *Xpetsc = NULL; - GetVectorFromControlInputsx(&Xpetsc,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); - Xpetsc->GetSize(&n); - X0 = Xpetsc->ToMPISerial(); - delete Xpetsc; - - /*Allocate current vector*/ - X = xNew(n); + IssmPDouble* X0 = NULL; + GetPassiveVectorFromControlInputsx(&X0,&n,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); + + /*Allocate vectors*/ + IssmDouble* X = xNew(n); + IssmPDouble* G = xNew(n); /*out of solution_type, figure out solution core and adjoint function pointer*/ + void (*solutioncore)(FemModel*)=NULL; CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); + + #if defined(_HAVE_ADOLC_) + /*{{{*/ + IssmDouble* aX=xNew(n); + if(my_rank==0){ + for(int i=0;i(n); + auto& tape_codi = IssmDouble::getGlobalTape(); + codi_global.input_indices.clear(); + if(my_rank==0){ + for (int i=0;iparameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); + femmodel->parameters->FindParam(&dependent_objects,AutodiffDependentObjectsEnum); + + /*Go through our dependent variables, and compute the response:*/ + dependents=xNew(num_dependents); + codi_global.output_indices.clear(); + for(int i=0;iSize();i++){ + DependentObject* dep=(DependentObject*)dependent_objects->GetObjectByOffset(i); + if(solution_type==TransientSolutionEnum){ + output_value = dep->GetValue(); + } + else{ + dep->Responsex(&output_value,femmodel); + } + _printf0_("=== output ="<0.); + simul_stoptrace2(); + /*initialize direction index in the weights vector: */ + if(my_rank==0){ + tape_codi.setGradient(codi_global.output_indices[0],1.0); + } + tape_codi.evaluate(); + + /*Get gradient for this dependent */ + auto in_size = codi_global.input_indices.size(); + for(size_t i = 0; i < in_size; ++i) { + G[i] = tape_codi.getGradient(codi_global.input_indices[i]); + } + #else + /*{{{*/ + void (*adjointcore)(FemModel*) = NULL; AdjointCorePointerFromSolutionEnum(&adjointcore,solution_type); @@ -59,4 +270,6 @@ Gradjx(&G,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); for(int i=0;iSize();i++){ + DependentObject* dep=(DependentObject*)dependent_objects->GetObjectByOffset(i); + if(solution_type==TransientSolutionEnum){ + output_value = dep->GetValue(); + } + else{ + dep->Responsex(&output_value,femmodel); + } + j+=output_value; + } + #else femmodel->CostFunctionx(&j,NULL,NULL); + #endif IssmDouble Den = 0.; for(int i=0;i0.); _printf0_(" " << setw(11) << setprecision (5)<(2*num); for(int i=0;i<2*num;i++) J_passive[i]=reCast(output[i]); femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,JEnum,J_passive,num,2,0,0)); xDelete(J_passive); + IssmDouble* aG=xNew(n); + for(int i=0;ielements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,aG); + xDelete(aG); #else femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,JEnum,output,num,2,0,0)); + ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,G); #endif - ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,G); femmodel->OutputControlsx(&femmodel->results); /*Clean up and return*/ xDelete(output); - xDelete(G); + xDelete(G); xDelete(X); - xDelete(X0); + xDelete(X0); xDelete(scaling_factors); } Index: /issm/trunk/src/c/cores/damage_core.cpp =================================================================== --- /issm/trunk/src/c/cores/damage_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/damage_core.cpp (revision 23394) @@ -11,5 +11,8 @@ void damage_core(FemModel* femmodel){ - + + /*Start profiler*/ + femmodel->profiler->Start(DAMAGECORE); + /*intermediary*/ bool save_results; @@ -48,3 +51,6 @@ xDelete(requested_outputs); } + + /*End profiler*/ + femmodel->profiler->Stop(DAMAGECORE); } Index: /issm/trunk/src/c/cores/esa_core.cpp =================================================================== --- /issm/trunk/src/c/cores/esa_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/esa_core.cpp (revision 23394) @@ -11,4 +11,7 @@ void esa_core(FemModel* femmodel){ /*{{{*/ + + /*Start profiler*/ + femmodel->profiler->Start(ESACORE); Vector *U_radial = NULL; @@ -112,4 +115,7 @@ if(numoutputs){for(int i=0;i(requested_outputs[i]);} xDelete(requested_outputs);} } + + /*End profiler*/ + femmodel->profiler->Stop(ESACORE); } Index: /issm/trunk/src/c/cores/gia_core.cpp =================================================================== --- /issm/trunk/src/c/cores/gia_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/gia_core.cpp (revision 23394) @@ -10,4 +10,7 @@ #include "../solutionsequences/solutionsequences.h" void gia_core(FemModel* femmodel){ + + /*Start profiler*/ + femmodel->profiler->Start(GIACORE); Vector *wg = NULL; @@ -56,3 +59,6 @@ xDelete(x); xDelete(y); + + /*End profiler*/ + femmodel->profiler->Stop(GIACORE); } Index: /issm/trunk/src/c/cores/hydrology_core.cpp =================================================================== --- /issm/trunk/src/c/cores/hydrology_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/hydrology_core.cpp (revision 23394) @@ -11,4 +11,7 @@ void hydrology_core(FemModel* femmodel){ + + /*Start profiler*/ + femmodel->profiler->Start(HYDROLOGYCORE); /*intermediary*/ @@ -47,5 +50,4 @@ /*intermediary: */ bool isefficientlayer; - bool isthermal; int step,hydroslices; IssmDouble time,init_time,hydrotime,yts; @@ -59,5 +61,4 @@ femmodel->parameters->FindParam(&yts,ConstantsYtsEnum); - femmodel->parameters->FindParam(&isthermal,TransientIsthermalEnum); /*first we exclude frozen nodes of the solved nodes*/ femmodel->SetCurrentConfiguration(HydrologyDCInefficientAnalysisEnum); @@ -150,3 +151,6 @@ xDelete(requested_outputs); } + + /*End profiler*/ + femmodel->profiler->Stop(HYDROLOGYCORE); } Index: /issm/trunk/src/c/cores/masstransport_core.cpp =================================================================== --- /issm/trunk/src/c/cores/masstransport_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/masstransport_core.cpp (revision 23394) @@ -11,4 +11,7 @@ void masstransport_core(FemModel* femmodel){ + + /*Start profiler*/ + femmodel->profiler->Start(MASSTRANSPORTCORE); /*parameters: */ @@ -81,3 +84,6 @@ /*Free ressources:*/ if(numoutputs){for(int i=0;i(requested_outputs[i]);} xDelete(requested_outputs);} + + /*profiler*/ + femmodel->profiler->Stop(MASSTRANSPORTCORE); } Index: /issm/trunk/src/c/cores/movingfront_core.cpp =================================================================== --- /issm/trunk/src/c/cores/movingfront_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/movingfront_core.cpp (revision 23394) @@ -11,4 +11,7 @@ void movingfront_core(FemModel* femmodel){ + + /*Start profiler*/ + femmodel->profiler->Start(MOVINGFRONTCORE); /* intermediaries */ @@ -98,3 +101,6 @@ femmodel->RequestedOutputsx(&femmodel->results,&outputs[0],1); } + + /*End profiler*/ + femmodel->profiler->Stop(MOVINGFRONTCORE); } Index: /issm/trunk/src/c/cores/sealevelrise_core.cpp =================================================================== --- /issm/trunk/src/c/cores/sealevelrise_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/sealevelrise_core.cpp (revision 23394) @@ -13,4 +13,7 @@ void sealevelrise_core(FemModel* femmodel){ /*{{{*/ + /*Start profiler*/ + femmodel->profiler->Start(SLRCORE); + /*Parameters, variables:*/ bool save_results; @@ -54,4 +57,7 @@ /*requested dependents: */ if(solution_type==SealevelriseSolutionEnum)femmodel->RequestedDependentsx(); + + /*End profiler*/ + femmodel->profiler->Stop(SLRCORE); } /*}}}*/ Index: /issm/trunk/src/c/cores/smb_core.cpp =================================================================== --- /issm/trunk/src/c/cores/smb_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/smb_core.cpp (revision 23394) @@ -11,5 +11,8 @@ void smb_core(FemModel* femmodel){ - + + /*Start profiler*/ + femmodel->profiler->Start(SMBCORE); + /*parameters: */ Analysis* analysis=NULL; @@ -45,3 +48,6 @@ /*Free ressources:*/ if(numoutputs){for(int i=0;i(requested_outputs[i]);} xDelete(requested_outputs);} + + /*End profiler*/ + femmodel->profiler->Stop(SMBCORE); } Index: /issm/trunk/src/c/cores/stressbalance_core.cpp =================================================================== --- /issm/trunk/src/c/cores/stressbalance_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/stressbalance_core.cpp (revision 23394) @@ -12,4 +12,7 @@ void stressbalance_core(FemModel* femmodel){ + + /*Start profiler*/ + femmodel->profiler->Start(STRESSBALANCECORE); /*parameters: */ @@ -37,5 +40,4 @@ if(VerboseSolution()) _printf0_(" computing new velocity\n"); - /*Compute slopes if necessary */ if(isSIA || (isFS && domaintype==Domain2DverticalEnum)) surfaceslope_core(femmodel); @@ -73,4 +75,8 @@ /*Compute vertical velocities*/ if (domaintype==Domain3DEnum && (isSIA || isSSA || isL1L2 || isHO)){ + + /*We need basal melt rates for vertical velocity*/ + bmb_core(femmodel); + analysis = new StressbalanceVerticalAnalysis(); analysis->Core(femmodel); @@ -87,3 +93,6 @@ /*Free ressources:*/ if(numoutputs){for(int i=0;i(requested_outputs[i]);} xDelete(requested_outputs);} + + /*End profiler*/ + femmodel->profiler->Stop(STRESSBALANCECORE); } Index: /issm/trunk/src/c/cores/thermal_core.cpp =================================================================== --- /issm/trunk/src/c/cores/thermal_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/thermal_core.cpp (revision 23394) @@ -12,5 +12,8 @@ void thermal_core(FemModel* femmodel){ - + + /*Start profiler*/ + femmodel->profiler->Start(THERMALCORE); + /*intermediary*/ bool save_results,isenthalpy; @@ -52,4 +55,6 @@ /*Free ressources:*/ if(numoutputs){for(int i=0;i(requested_outputs[i]);} xDelete(requested_outputs);} - + + /*End profiler*/ + femmodel->profiler->Stop(THERMALCORE); } Index: /issm/trunk/src/c/cores/transient_core.cpp =================================================================== --- /issm/trunk/src/c/cores/transient_core.cpp (revision 23393) +++ /issm/trunk/src/c/cores/transient_core.cpp (revision 23394) @@ -70,5 +70,5 @@ if(numoutputs) femmodel->parameters->FindParam(&requested_outputs,&numoutputs,TransientRequestedOutputsEnum); - #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) if(amr_frequency){ femmodel->parameters->FindParam(&amr_restart,AmrRestartEnum); @@ -78,5 +78,5 @@ if(isoceancoupling){ /*{{{*/ - #ifndef _HAVE_ADOLC_ + #ifndef _HAVE_AD_ if(VerboseSolution()) _printf0_(" ocean coupling: initialization \n"); int my_rank; @@ -180,5 +180,5 @@ for(int i=0;i0.) icebase_oceangrid[i]=+9999.; xDelete(icemask_oceangrid); - + if(my_rank==0){ ISSM_MPI_Send(icebase_oceangrid,ngrids_ocean,ISSM_MPI_DOUBLE,0,10001008,tomitgcmcomm); @@ -247,5 +247,5 @@ if(isoceancoupling){ /*{{{*/ - #ifndef _HAVE_ADOLC_ + #ifndef _HAVE_AD_ if(VerboseSolution()) _printf0_(" ocean coupling: exchanging information\n"); int my_rank; @@ -371,10 +371,12 @@ femmodel->parameters->FindParam(&smb_model,SmbEnum); if(isenthalpy){ - if(smb_model==SMBpddEnum) ResetBoundaryConditions(femmodel,EnthalpyAnalysisEnum); - if(smb_model==SMBd18opddEnum) ResetBoundaryConditions(femmodel,EnthalpyAnalysisEnum); + if(smb_model==SMBpddEnum) ResetBoundaryConditions(femmodel,EnthalpyAnalysisEnum); + if(smb_model==SMBd18opddEnum) ResetBoundaryConditions(femmodel,EnthalpyAnalysisEnum); + if(smb_model==SMBpddSicopolisEnum) ResetBoundaryConditions(femmodel,EnthalpyAnalysisEnum); } else{ - if(smb_model==SMBpddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); - if(smb_model==SMBd18opddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); + if(smb_model==SMBpddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); + if(smb_model==SMBd18opddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); + if(smb_model==SMBpddSicopolisEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); } } @@ -382,4 +384,7 @@ } + /*shifting smb position to have runoff value*/ + if(issmb) smb_core(femmodel); + if(ishydrology) hydrology_core(femmodel); @@ -391,6 +396,5 @@ /* from here on, prepare geometry for next time step*/ - - if(issmb) smb_core(femmodel); + //if(issmb) smb_core(femmodel); if(ismasstransport){ @@ -401,4 +405,8 @@ if(isgroundingline){ + + /*Start profiler*/ + femmodel->profiler->Start(GROUNDINGLINECORE); + if(VerboseSolution()) _printf0_(" computing new grounding line position\n"); GroundinglineMigrationx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); @@ -410,4 +418,7 @@ femmodel->parameters->SetParam(SurfaceEnum,InputToExtrudeEnum); extrudefrombase_core(femmodel); + + /*Stop profiler*/ + femmodel->profiler->Stop(GROUNDINGLINECORE); if(save_results){ @@ -453,5 +464,5 @@ if(amr_frequency){ - #if !defined(_HAVE_ADOLC_) + #if !defined(_HAVE_AD_) if(save_results) femmodel->WriteMeshInResults(); if(step%amr_frequency==0 && time -void CoordinateSystemTransformx(IssmDouble** px_dest,IssmDouble** py_dest,IssmDouble* x_src,IssmDouble* y_src,int size,const char* str_src,const char* str_dst){ +void CoordinateSystemTransformx(double** px_dest,double** py_dest,double* x_src,double* y_src,int size,const char* str_src,const char* str_dst){ #if !defined(_HAVE_PROJ4_) @@ -17,6 +17,6 @@ /*Allocate output and initialize values as src*/ _assert_(size>0); - IssmDouble* x_dest = xNew(size); - IssmDouble* y_dest = xNew(size); + double* x_dest = xNew(size); + double* y_dest = xNew(size); for(int i=0;i* vec_vector=NULL; + /*Get PETSc vector*/ GetVectorFromControlInputsx( &vec_vector, elements,nodes, vertices, loads, materials, parameters,data); + + /*Serialize*/ + vec_vector->GetSize(&N); IssmDouble* vector=vec_vector->ToMPISerial(); - - /*Free ressources:*/ delete vec_vector; /*Assign output pointers:*/ *pvector=vector; + if(pN) *pN=N; }/*}}}*/ /*For autodiff, we sometimes need to cast our vectors to passive*/ -#ifdef _HAVE_ADOLC_ -void GetPassiveVectorFromControlInputsx(Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,const char* data){/*{{{*/ - - /*Get active vector first*/ - Vector* activevector=NULL; - Vector* vector=NULL; - int size; - - /*Retrieve some parameters*/ - GetVectorFromControlInputsx(&activevector, elements,nodes, vertices, loads, materials, parameters,data); - - /*Serialize vector*/ - activevector->GetSize(&size); - IssmDouble* dactivevector=activevector->ToMPISerial(); - - /*Cast to passive*/ - vector=new Vector(size); - for(int i=0;iSetValue(i,reCast(dactivevector[i]),INS_VAL); - } - vector->Assemble(); - - /*Assign output pointers:*/ - delete activevector; - xDelete(dactivevector); - *pvector=vector; - -}/*}}}*/ -void GetPassiveVectorFromControlInputsx(IssmPDouble** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, const char* data){/*{{{*/ +#ifdef _HAVE_AD_ +void GetPassiveVectorFromControlInputsx(IssmPDouble** pvector,int* pN, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, const char* data){/*{{{*/ /*Get active vector first*/ @@ -144,15 +121,11 @@ xDelete(dactivevector); *pvector=vector; + if(pN) *pN=size; }/*}}}*/ #else -void GetPassiveVectorFromControlInputsx(Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,const char* data){/*{{{*/ +void GetPassiveVectorFromControlInputsx(IssmPDouble** pvector,int* pN, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, const char* data){/*{{{*/ - GetVectorFromControlInputsx(pvector, elements,nodes, vertices, loads, materials, parameters,data); - -}/*}}}*/ -void GetPassiveVectorFromControlInputsx(IssmPDouble** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, const char* data){/*{{{*/ - - GetVectorFromControlInputsx(pvector, elements,nodes, vertices, loads, materials, parameters,data); + GetVectorFromControlInputsx(pvector,pN,elements,nodes, vertices, loads, materials, parameters,data); }/*}}}*/ #endif Index: /issm/trunk/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h =================================================================== --- /issm/trunk/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h (revision 23393) +++ /issm/trunk/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h (revision 23394) @@ -9,8 +9,7 @@ /* local prototypes: */ void GetVectorFromControlInputsx( Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); -void GetVectorFromControlInputsx( IssmDouble** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); +void GetVectorFromControlInputsx( IssmDouble** pvector,int* pN, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); -void GetPassiveVectorFromControlInputsx(Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); -void GetPassiveVectorFromControlInputsx(double** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); +void GetPassiveVectorFromControlInputsx(double** pvector,int* pN, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); #endif /* _GETVECTORFROMCONTROLINPUTSXX_H */ Index: /issm/trunk/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 23393) +++ /issm/trunk/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 23394) @@ -73,7 +73,36 @@ xDelete(options); /*}}}*/ + #elif _HAVE_CODIPACK_ + //fprintf(stderr, "*** Codipack CreateParametersAutodiff()\n"); + /*initialize a placeholder to store solver pointers: {{{*/ + /*Solver pointers depend on what type of solver we are implementing: */ + options=OptionsFromAnalysis(&toolkit,parameters,DefaultAnalysisEnum); + ToolkitOptions::Init(toolkit,options); + xDelete(toolkit); + + switch(IssmSolverTypeFromToolkitOptions()){ + case MumpsEnum:{ + #ifndef _HAVE_MUMPS_ + _error_("CoDiPack: requesting mumps solver without MUMPS being compiled in!"); + #endif + break; + } + case GslEnum: { + #ifndef _HAVE_GSL_ + _error_("CoDiPack: requesting GSL solver without GSL being compiled in!"); + #endif + break; + } + default: + _error_("solver type not supported yet!"); + } + /*Free ressources: */ + xDelete(options); + #endif + #if defined(_HAVE_AD_) if(isautodiff){ - /*Copy some parameters from IoModel to parameters dataset: {{{*/ + #if defined(_HAVE_ADOLC_) + /*Copy some parameters from IoModel to parameters dataset*/ parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.obufsize",AutodiffObufsizeEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.cbufsize",AutodiffCbufsizeEnum)); @@ -82,5 +111,12 @@ parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.gcTriggerRatio",AutodiffGcTriggerRatioEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.gcTriggerMaxSize",AutodiffGcTriggerMaxSizeEnum)); - /*}}}*/ + + #elif defined(_HAVE_CODIPACK_) + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.tapeAlloc",AutodiffTapeAllocEnum)); + + #else + _error_("not supported yet"); + #endif + /*retrieve driver: {{{*/ iomodel->FindConstant(&autodiff_driver,"md.autodiff.driver"); @@ -88,4 +124,8 @@ if(strcmp(autodiff_driver,"fos_forward")==0){ +#if _HAVE_CODIPACK_ + // FIXME codi support Foward Mode (scalar) + _error_("Foward Mode (scalar) not supported yet!"); +#endif parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.fos_forward_index",AutodiffFosForwardIndexEnum)); } @@ -94,4 +134,8 @@ } else if(strcmp(autodiff_driver,"fov_forward")==0){ +#if _HAVE_CODIPACK_ + // FIXME codi support Foward Mode (vector) + _error_("Foward Mode (vector) not supported yet!"); +#endif /*Retrieve list of indices: */ iomodel->FetchData(&indices,&num_indices,&dummy,"md.autodiff.fov_forward_indices"); Index: /issm/trunk/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp (revision 23393) +++ /issm/trunk/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp (revision 23394) @@ -9,5 +9,4 @@ #include "../ModelProcessorx.h" -#if !defined(_HAVE_ADOLC_) void UpdateElementsAndMaterialsControl(Elements* elements,Parameters* parameters,Materials* materials, IoModel* iomodel){ /*Intermediary*/ @@ -20,4 +19,12 @@ char **controls = NULL; char **cost_functions = NULL; + + /*Fetch parameters: */ + bool isautodiff; + iomodel->FindConstant(&isautodiff,"md.autodiff.isautodiff"); + if(isautodiff){ + UpdateElementsAndMaterialsControlAD(elements,parameters,materials,iomodel); + return; + } /*Fetch parameters: */ @@ -126,7 +133,7 @@ xDelete(controls); } -#else -void UpdateElementsAndMaterialsControl(Elements* elements,Parameters* parameters,Materials* materials, IoModel* iomodel){ - +void UpdateElementsAndMaterialsControlAD(Elements* elements,Parameters* parameters,Materials* materials, IoModel* iomodel){ + + #if defined(_HAVE_AD_) /*Intermediaries*/ int num_independent_objects,M,N,M_par,N_par; @@ -222,7 +229,10 @@ xDelete(independents_fullmax); xDelete(start_point); + xDelete(control_sizes); /*Step2: create cost functions (dependents)*/ return; +#else + _error_("AD not compiled"); +#endif } -#endif Index: /issm/trunk/src/c/modules/ModelProcessorx/CreateNodes.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CreateNodes.cpp (revision 23393) +++ /issm/trunk/src/c/modules/ModelProcessorx/CreateNodes.cpp (revision 23394) @@ -32,5 +32,5 @@ for(j=0;j<3;j++){ if(my_nodes[3*i+j]){ - nodes->AddObject(new Node(id0+3*i+j+1,id0+3*i+j,lid++,iomodel->elements[+3*i+j]-1,iomodel,analysis,approximation)); + nodes->AddObject(new Node(id0+3*i+j+1,id0+3*i+j,lid++,iomodel->elements[3*i+j]-1,iomodel,analysis,approximation)); } Index: /issm/trunk/src/c/modules/ModelProcessorx/CreateParameters.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 23393) +++ /issm/trunk/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 23394) @@ -374,5 +374,5 @@ ParseToolkitsOptionsx(parameters,toolkitsoptionsfid); - #ifdef _HAVE_ADOLC_ + #ifdef _HAVE_AD_ if(VerboseMProcessor()) _printf0_(" starting autodiff parameters \n"); CreateParametersAutodiff(parameters,iomodel); Index: /issm/trunk/src/c/modules/ModelProcessorx/ModelProcessorx.h =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/ModelProcessorx.h (revision 23393) +++ /issm/trunk/src/c/modules/ModelProcessorx/ModelProcessorx.h (revision 23394) @@ -19,4 +19,5 @@ void CreateOutputDefinitions(Elements* elements, Parameters* parameters,IoModel* iomodel); void UpdateElementsAndMaterialsControl(Elements* elements,Parameters* parameters,Materials* materials, IoModel* iomodel); +void UpdateElementsAndMaterialsControlAD(Elements* elements,Parameters* parameters,Materials* materials, IoModel* iomodel); void UpdateElementsAndMaterialsDakota(Elements* elements,Materials* materials, IoModel* iomodel); void UpdateElementsTransient(Elements* elements,Parameters* parameters,IoModel* iomodel,int analysis_type); Index: /issm/trunk/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp =================================================================== --- /issm/trunk/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp (revision 23393) +++ /issm/trunk/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp (revision 23394) @@ -33,4 +33,6 @@ xDelete(control_type); + xDelete(M); + xDelete(N); } else{ Index: /issm/trunk/src/c/modules/SurfaceMassBalancex/Gembx.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceMassBalancex/Gembx.cpp (revision 23393) +++ /issm/trunk/src/c/modules/SurfaceMassBalancex/Gembx.cpp (revision 23394) @@ -62,5 +62,5 @@ //into specified top structure depth (zTop). Also make sure top grid cell //structure length (dzTop) is greater than 5 cm - #ifndef _HAVE_ADOLC_ //avoid the round operation check! + #ifndef _HAVE_AD_ //avoid the round operation check! if (dgpTop != round(dgpTop)){ _error_("top grid cell structure length does not go evenly into specified top structure depth, adjust dzTop or zTop"); @@ -425,9 +425,9 @@ // spectral range: // 0.3 - 0.8um - IssmDouble a0 = fmin(0.98, 1 - 1.58 *pow(gsz,0.5)); + IssmDouble a0 = min(0.98, 1 - 1.58 *pow(gsz,0.5)); // 0.8 - 1.5um - IssmDouble a1 = fmax(0, 0.95 - 15.4 *pow(gsz,0.5)); + IssmDouble a1 = max(0., 0.95 - 15.4 *pow(gsz,0.5)); // 1.5 - 2.8um - IssmDouble a2 = fmax(0.127, 0.88 + 346.3*gsz - 32.31*pow(gsz,0.5)); + IssmDouble a2 = max(0.127, 0.88 + 346.3*gsz - 32.31*pow(gsz,0.5)); // broadband surface albedo @@ -667,5 +667,5 @@ // NS: 2.16.18 divided dt by scaling factor, default set to 1/11 for stability dt=1e12; - for(int i=0;i 1/2 @@ -752,5 +752,5 @@ // less when Ts is taken as the mean of the x top grid cells. Ts = (T[0] + T[1])/2.0; - Ts = fmin(CtoK,Ts); // don't allow Ts to exceed 273.15 K (0 degC) + Ts = min(CtoK,Ts); // don't allow Ts to exceed 273.15 K (0 degC) //TURBULENT HEAT FLUX @@ -767,5 +767,5 @@ // do not allow Ri to exceed 0.19 - Ri = fmin(Ri, 0.19); + Ri = min(Ri, 0.19); // calculate momentum 'coefM' stability factor @@ -947,9 +947,9 @@ // spectral albedos: // 0.3 - 0.8um - IssmDouble a0 = fmin(0.98, 1.0 - 1.58 *pow(gsz[0],0.5)); + IssmDouble a0 = min(0.98, 1.0 - 1.58 *pow(gsz[0],0.5)); // 0.8 - 1.5um - IssmDouble a1 = fmax(0.0, 0.95 - 15.4 *pow(gsz[0],0.5)); + IssmDouble a1 = max(0.0, 0.95 - 15.4 *pow(gsz[0],0.5)); // 1.5 - 2.8um - IssmDouble a2 = fmax(0.127, 0.88 + 346.3*gsz[0] - 32.31*pow(gsz[0],0.5)); + IssmDouble a2 = max(0.127, 0.88 + 346.3*gsz[0] - 32.31*pow(gsz[0],0.5)); // separate net shortwave radiative flux into spectral ranges @@ -1204,5 +1204,5 @@ mass_diff = mass - massinit - P; - #ifndef _HAVE_ADOLC_ //avoid round operation. only check in forward mode. + #ifndef _HAVE_AD_ //avoid round operation. only check in forward mode. mass_diff = round(mass_diff * 100.0)/100.0; if (mass_diff > 0) _error_("mass not conserved in accumulation function"); @@ -1323,9 +1323,9 @@ // calculate temperature excess above 0 deg C exsT=xNewZeroInit(n); - for(int i=0;i(n); for(int i=0;i(n); for(int i=0;i 0.0 + Ttol ){ @@ -1380,8 +1380,8 @@ T[i+1] = surpE[i]/m[i+1]/CI + T[i+1]; - exsT[i+1] = fmax(0.0, T[i+1] - CtoK) + exsT[i+1]; - T[i+1] = fmin(CtoK, T[i+1]); - - surpT[i+1] = fmax(0.0, exsT[i+1] - LF/CI); + exsT[i+1] = max(0.0, T[i+1] - CtoK) + exsT[i+1]; + T[i+1] = min(CtoK, T[i+1]); + + surpT[i+1] = max(0.0, exsT[i+1] - LF/CI); surpE[i+1] = surpT[i+1] * CI * m[i+1]; @@ -1394,9 +1394,9 @@ // convert temperature excess to melt [kg] - for(int i=0;iW[i]-Wtol ){ dW[i]= -1*W[i]; @@ -1474,6 +1474,6 @@ if (dW[i] < 0.0-Wtol){ // excess pore water dMax = (dIce - d[i])*dz_0; // maximum refreeze - IssmDouble maxF2 = fmin(dMax, maxF[i]-F1); // maximum refreeze - F2 = fmin(-1*dW[i], maxF2); // pore water refreeze + IssmDouble maxF2 = min(dMax, maxF[i]-F1); // maximum refreeze + F2 = min(-1*dW[i], maxF2); // pore water refreeze m[i] = m[i] + F2; // mass after refreeze d[i] = m[i]/dz_0; @@ -1753,5 +1753,5 @@ /*only in forward mode! avoid round in AD mode as it is not differentiable: */ - #ifndef _HAVE_ADOLC_ + #ifndef _HAVE_AD_ dm = round((mSum0 - mSum1 + mAdd)*100.0)/100.0; dE = round(sumE0 - sumE1 - sumER + addE); @@ -1915,6 +1915,6 @@ c0arth = 0.07 * H; c1arth = 0.03 * H; - M0 = fmax(1.435 - (0.151 * log(C)),0.25); - M1 = fmax(2.366 - (0.293 * log(C)),0.25); + M0 = max(1.435 - (0.151 * log(C)),0.25); + M1 = max(2.366 - (0.293 * log(C)),0.25); c0 = M0*c0arth; c1 = M1*c1arth; @@ -1926,6 +1926,6 @@ c0arth = 0.07 * H; c1arth = 0.03 * H; - M0 = fmax(1.042 - (0.0916 * log(C)),0.25); - M1 = fmax(1.734 - (0.2039 * log(C)),0.25); + M0 = max(1.042 - (0.0916 * log(C)),0.25); + M1 = max(1.734 - (0.2039 * log(C)),0.25); c0 = M0*c0arth; c1 = M1*c1arth; @@ -2021,5 +2021,5 @@ // do not allow Ri to exceed 0.19 - Ri = fmin(Ri, 0.19); + Ri = min(Ri, 0.19); // calculate momentum 'coefM' stability factor Index: /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp (revision 23393) +++ /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp (revision 23394) @@ -1,4 +1,4 @@ /*!\file SurfaceMassBalancex - * \brief: calculates SMB + * \brief: calculates SMB */ @@ -105,5 +105,5 @@ for(v=0;vela[v]){ + if(s[v]>ela[v]){ smb[v]=b_pos[v]*(s[v]-ela[v]); } @@ -167,5 +167,5 @@ // INPUT: surface elevation (m): hd(NA) // monthly mean surface sealevel temperature (degrees C): vTempsea(NA - // ,NTIME) + // ,NTIME) // monthly mean precip rate (m/yr water equivalent): vPrec(NA,NTIME) // OUTPUT: mass-balance (m/yr ice): agd(NA) @@ -174,5 +174,5 @@ int i, it, jj, itm; IssmDouble DT = 0.02, sigfac, snormfac; - IssmDouble signorm = 5.5; // signorm : sigma of the temperature distribution for a normal day + IssmDouble signorm = 5.5; // signorm : sigma of the temperature distribution for a normal day IssmDouble siglim; // sigma limit for the integration which is equal to 2.5 sigmanorm IssmDouble signormc = signorm - 0.5; // sigma of the temperature distribution for cloudy day @@ -180,5 +180,5 @@ IssmDouble tstep, tsint, tint, tstepc; int NPDMAX = 1504, NPDCMAX = 1454; - //IssmDouble pdds[NPDMAX]={0}; + //IssmDouble pdds[NPDMAX]={0}; //IssmDouble pds[NPDCMAX]={0}; IssmDouble pddt, pd ; // pd : snow/precip fraction, precipitation falling as snow @@ -193,6 +193,6 @@ Element *element = NULL; - pdds=xNew(NPDMAX+1); - pds=xNew(NPDCMAX+1); + pdds=xNew(NPDMAX+1); + pds=xNew(NPDCMAX+1); // Get ismungsm parameter @@ -216,5 +216,5 @@ if(itm >= NPDMAX) _error_("increase NPDMAX in massBalance.cpp"); - for(it = 0; it < itm; it++){ + for(it = 0; it < itm; it++){ // tstar = REAL(it)*DT-siglim; tstar = it*DT-siglim; @@ -262,4 +262,15 @@ xDelete(pds); }/*}}}*/ +void PositiveDegreeDaySicopolisx(FemModel* femmodel){/*{{{*/ + + bool isfirnwarming; + femmodel->parameters->FindParam(&isfirnwarming,SmbIsfirnwarmingEnum); + + for(int i=0;ielements->Size();i++){ + Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); + element->PositiveDegreeDaySicopolis(isfirnwarming); + } + +}/*}}}*/ void SmbHenningx(FemModel* femmodel){/*{{{*/ @@ -346,7 +357,7 @@ /*Allocate all arrays*/ int numvertices = element->GetNumberOfVertices(); - IssmDouble* acc = xNew(numvertices); + IssmDouble* acc = xNew(numvertices); IssmDouble* evap = xNew(numvertices); - IssmDouble* runoff = xNew(numvertices); + IssmDouble* runoff = xNew(numvertices); IssmDouble* smb = xNew(numvertices); @@ -388,5 +399,5 @@ int numvertices = element->GetNumberOfVertices(); IssmDouble* acc = xNew(numvertices); - IssmDouble* evap = xNew(numvertices); + IssmDouble* evap = xNew(numvertices); IssmDouble* melt = xNew(numvertices); IssmDouble* refreeze = xNew(numvertices); @@ -414,2 +425,15 @@ }/*}}}*/ +void SmbGradientsComponentsx(FemModel* femmodel){/*{{{*/ + + // void SurfaceMassBalancex(hd,agd,ni){ + // INPUT parameters: ni: working size of arrays + // INPUT: surface elevation (m): hd(NA) + // OUTPUT: mass-balance (m/yr ice): agd(NA) + + for(int i=0;ielements->Size();i++){ + Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); + element->SmbGradCompParameterization(); + } + +}/*}}}*/ Index: /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h =================================================================== --- /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h (revision 23393) +++ /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h (revision 23394) @@ -1,5 +1,5 @@ /*!\file: SurfaceMassBalancex.h * \brief header file for SMB - */ + */ #ifndef _SurfaceMassBalancex_H @@ -16,11 +16,12 @@ void Delta18opdParameterizationx(FemModel* femmodel); void PositiveDegreeDayx(FemModel* femmodel); +void PositiveDegreeDaySicopolisx(FemModel* femmodel); void SmbHenningx(FemModel* femmodel); void SmbComponentsx(FemModel* femmodel); -void SmbMeltComponentsx(FemModel* femmodel); - +void SmbMeltComponentsx(FemModel* femmodel); +void SmbGradientsComponentsx(FemModel* femmodel); /*GEMB: */ void Gembx(FemModel* femmodel); -void GembgridInitialize(IssmDouble** pdz, int* psize, IssmDouble zTop, IssmDouble dzTop, IssmDouble zMax, IssmDouble zY); +void GembgridInitialize(IssmDouble** pdz, int* psize, IssmDouble zTop, IssmDouble dzTop, IssmDouble zMax, IssmDouble zY); IssmDouble Marbouty(IssmDouble T, IssmDouble d, IssmDouble dT); void grainGrowth(IssmDouble** pre, IssmDouble** pgdn, IssmDouble** pgsp, IssmDouble* T,IssmDouble* dz,IssmDouble* d, IssmDouble* W,IssmDouble smb_dt,int m,int aIdx, int sid); @@ -28,5 +29,5 @@ void shortwave(IssmDouble** pswf, int swIdx, int aIdx, IssmDouble dsw, IssmDouble as, IssmDouble* d, IssmDouble* dz, IssmDouble* re, IssmDouble dIce, int m, int sid); void thermo(IssmDouble* pEC, IssmDouble** T, IssmDouble* dz, IssmDouble* d, IssmDouble* swf, IssmDouble dlw, IssmDouble Ta, IssmDouble V, IssmDouble eAir, IssmDouble pAir, IssmDouble teValue, IssmDouble Ws, IssmDouble dt0, int m, IssmDouble Vz, IssmDouble Tz, IssmDouble thermo_scaling, IssmDouble dIce, int sid); -void accumulation(IssmDouble** pT, IssmDouble** pdz, IssmDouble** pd, IssmDouble** pW, IssmDouble** pa, IssmDouble** pre, IssmDouble** pgdn, IssmDouble** pgsp, int* pm, int aIdx,IssmDouble Ta, IssmDouble P, IssmDouble dzMin, IssmDouble aSnow, IssmDouble dIce, int sid); +void accumulation(IssmDouble** pT, IssmDouble** pdz, IssmDouble** pd, IssmDouble** pW, IssmDouble** pa, IssmDouble** pre, IssmDouble** pgdn, IssmDouble** pgsp, int* pm, int aIdx,IssmDouble Ta, IssmDouble P, IssmDouble dzMin, IssmDouble aSnow, IssmDouble dIce, int sid); void melt(IssmDouble* pM, IssmDouble* pR, IssmDouble* pmAdd, IssmDouble* pdz_add, IssmDouble** pT, IssmDouble** pd, IssmDouble** pdz, IssmDouble** pW, IssmDouble** pa, IssmDouble** pre, IssmDouble** pgdn, IssmDouble** pgsp, int* pn, IssmDouble dzMin, IssmDouble zMax, IssmDouble zMin, IssmDouble zTop, IssmDouble dIce, int sid); void densification(IssmDouble** pd,IssmDouble** pdz, IssmDouble* T, IssmDouble* re, int denIdx, IssmDouble C, IssmDouble dt, IssmDouble Tmean, IssmDouble dIce, int m, int sid); Index: /issm/trunk/src/c/shared/Elements/PddSurfaceMassBalanceSicopolis.cpp =================================================================== --- /issm/trunk/src/c/shared/Elements/PddSurfaceMassBalanceSicopolis.cpp (revision 23394) +++ /issm/trunk/src/c/shared/Elements/PddSurfaceMassBalanceSicopolis.cpp (revision 23394) @@ -0,0 +1,137 @@ +/* file: PddSurfaceMassBlanceSicopolis.cpp + Calculating the surface mass balance using the adapted PDD routine from SICOPOLIS. + */ + +#include "./elements.h" +#include "../Numerics/numerics.h" +#include "../Exceptions/exceptions.h" + +IssmDouble PddSurfaceMassBalanceSicopolis(IssmDouble* monthlytemperatures, IssmDouble* monthlyprec, + IssmDouble* melt, IssmDouble* accu, IssmDouble* melt_star, IssmDouble* t_ampl, IssmDouble* p_ampl, + IssmDouble yts, IssmDouble s, IssmDouble desfac, + IssmDouble s0t, IssmDouble s0p, IssmDouble rlaps, + IssmDouble rho_water,IssmDouble rho_ice){ + + int imonth; // month counter + IssmDouble B; // output: surface mass balance (m/a IE), melt+accumulation + IssmDouble frac_solid, snowfall, rainfall, runoff; + IssmDouble saccu; // yearly surface accumulation (m/a IE) + IssmDouble smelt; // yearly melt (m/a IE) + IssmDouble smelt_star; // yearly ... + IssmDouble precip; // total precipitation during 1 year + IssmDouble sconv; //rhow_rain/rhoi / 12 months + IssmDouble st; // elevation between altitude of the temp record and current altitude + IssmDouble sp; // elevation between altitude of the prec record and current altitude + IssmDouble q; // q is desert/elev. fact + IssmDouble pdd; // pdd factor (a * degC) + IssmDouble tstar; // monthly temp. after lapse rate correction (degC) + IssmDouble precip_star; // monthly precip after correction (m/a IE) + IssmDouble beta1 = 2.73; // 3 mm IE/(d*deg C), ablation factor for snow per positive degree day. + IssmDouble beta2 = 7.28; // 8 mm IE/(d*deg C), ablation factor for ice per pdd (Braithwaite 1995 from tarasov 2002). + IssmDouble Pmax = 0.6; + IssmDouble inv_twelve=1./12.; + + sconv=(rho_water/rho_ice); //rhow_rain/rhoi + + /* FIXME betas shoud be user input */ + beta1=beta1*(0.001*365)*sconv; // (mm WE)/(d*deg C) --> (m IE)/(a*deg C) + beta2=beta2*(0.001*365)*sconv; // (mm WE)/(d*deg C) --> (m IE)/(a*deg C) + + /* initalize fields */ + precip=0.0; + tstar=0.0; + snowfall=0.0; + pdd=0.0; + /* seasonal loop */ + for(imonth=0;imonth<12;imonth++){ + + /********* Surface temperature correction *******/ + st=(s-s0t)/1000.; + + // FIXME rlaps ?? + rlaps=-6.309e-03+(-5.426e-03-(-6.309e-03))*sin((imonth+1-4)*PI/6.0)*1000.0; + monthlytemperatures[imonth]=monthlytemperatures[imonth]-rlaps*st;//*max(st,1e-3); + tstar=monthlytemperatures[imonth]+t_ampl[0]; + + /********* Precipitation correction *************/ + /* Ref: Vizcaino et al 2010; DOI 10.1007/s00382-009-0591-y */ + if(s0p<2000.0) + q=exp(desfac*(max(s,2000.0)-2000.0)); + else + q=exp(desfac*(max(s,2000.0)-s0p)); + + precip_star=q*monthlyprec[imonth]*sconv*p_ampl[0]*yts; // convert precip from m/s -> m/a + precip=precip+precip_star*inv_twelve; + + /********* compute PDD **************************/ + /* Ref: Calov & Greve 2005 Journal of Glaciology, Vol. 51, No. 172, 2005, Correspondence */ + IssmDouble s_stat=5.0; + IssmDouble inv_sqrt2pi =1.0/sqrt(2.0*PI); + IssmDouble inv_s_stat =1.0/s_stat; + IssmDouble inv_sqrt2 =1.0/sqrt(2.0); + + #if !defined(_HAVE_ADOLC_) + pdd=pdd+(s_stat*inv_sqrt2pi*exp(-0.5*pow(tstar*inv_s_stat,2)) + +0.5*tstar*erfc(-tstar*inv_s_stat*inv_sqrt2))*inv_twelve; + #else + _error_("Cannot differentiate erfc, talk to ADOLC folks (http://functions.wolfram.com/GammaBetaErf/Erfc/20/01/)"); + #endif + + /*Partition of precip in solid and liquid parts, Bales et al. (2009) */ + IssmDouble temp_rain=7.2; // Threshold monthly mean temperature for + // precipitation = 101% rain, in deg C + IssmDouble temp_snow=-11.6; // Threshold monthly mean temperature for + // precipitation = 100% snow, in deg C + + IssmDouble coeff1=5.4714e-01; // Coefficients + IssmDouble coeff2=-9.1603e-02; // of + IssmDouble coeff3=-3.314e-03; // the + IssmDouble coeff4= 4.66e-04; // fifth-order + IssmDouble coeff5=3.8e-05; // polynomial + IssmDouble coeff6=6.0e-07; // fit + + if(tstar>=temp_rain) + frac_solid = 0.0; + else if(tstar<=temp_snow) + frac_solid = 1.0; + else{ + frac_solid=coeff1+tstar*(coeff2 + +tstar*(coeff3+tstar*(coeff4+tstar*(coeff5+tstar*coeff6)))); + } + + snowfall=snowfall+precip_star*frac_solid*inv_twelve; + } + /* end of seasonal loop */ + + rainfall=precip-snowfall; + if(snowfall<0.0) snowfall=0.0; // correction of + if(rainfall<0.0) rainfall=0.0; // negative values + + if(rainfall<=(Pmax*snowfall)){ + if((rainfall+beta1*pdd)<=(Pmax*snowfall)) { + smelt_star = rainfall+beta1*pdd; + smelt = 0.0; + runoff = smelt; + } + else{ + smelt_star = Pmax*snowfall; + smelt = beta2*(pdd-(smelt_star-rainfall)/beta1); + runoff = smelt; + } + } + else{ + smelt_star = Pmax*snowfall; + smelt = beta2*pdd; + runoff = smelt+rainfall-Pmax*snowfall; + } + + saccu = precip; + + /* asign output*/ + melt[0]=runoff/yts; + accu[0]=saccu/yts; + melt_star[0]=smelt_star/yts; + B=(saccu-runoff)/yts; + + return B; +} Index: /issm/trunk/src/c/shared/Elements/PrintArrays.cpp =================================================================== --- /issm/trunk/src/c/shared/Elements/PrintArrays.cpp (revision 23393) +++ /issm/trunk/src/c/shared/Elements/PrintArrays.cpp (revision 23394) @@ -12,5 +12,5 @@ _printf_("\n"); } -#ifdef _HAVE_ADOLC_ +#ifdef _HAVE_AD_ void printarray(IssmDouble* array,int lines,int cols){ _printf_("\n"); Index: /issm/trunk/src/c/shared/Elements/elements.h =================================================================== --- /issm/trunk/src/c/shared/Elements/elements.h (revision 23393) +++ /issm/trunk/src/c/shared/Elements/elements.h (revision 23394) @@ -24,4 +24,8 @@ IssmDouble TdiffTime,IssmDouble sealevTime,IssmDouble pddsnowfac,IssmDouble pddicefac, IssmDouble rho_water, IssmDouble rho_ice); +IssmDouble PddSurfaceMassBalanceSicopolis(IssmDouble* monthlytemperatures, IssmDouble* monthlyprec, + IssmDouble* melt, IssmDouble* accu, IssmDouble* melt_star, IssmDouble* t_ampl, IssmDouble* p_ampl, + IssmDouble yts, IssmDouble s, IssmDouble desfac,IssmDouble s0t, + IssmDouble s0p, IssmDouble rlaps, IssmDouble rho_water, IssmDouble rho_ice); void ComputeDelta18oTemperaturePrecipitation(IssmDouble Delta18oSurfacePresent, IssmDouble Delta18oSurfaceLgm, IssmDouble Delta18oSurfaceTime, IssmDouble Delta18oPresent, IssmDouble Delta18oLgm, IssmDouble Delta18oTime, @@ -42,5 +46,5 @@ /*Print arrays*/ void printarray(IssmPDouble* array,int lines,int cols=1); -#if _HAVE_ADOLC_ && !defined(_WRAPPERS_) +#if _HAVE_AD_ && !defined(_WRAPPERS_) void printarray(IssmDouble* array,int lines,int cols=1); #endif Index: /issm/trunk/src/c/shared/Enum/EnumDefinitions.h =================================================================== --- /issm/trunk/src/c/shared/Enum/EnumDefinitions.h (revision 23393) +++ /issm/trunk/src/c/shared/Enum/EnumDefinitions.h (revision 23394) @@ -53,4 +53,5 @@ AutodiffNumIndependentsEnum, AutodiffObufsizeEnum, + AutodiffTapeAllocEnum, AutodiffTbufsizeEnum, AutodiffXpEnum, @@ -272,4 +273,7 @@ SettingsSolverResidueThresholdEnum, SettingsWaitonlockEnum, + SmbAccualtiEnum, + SmbAccugradEnum, + SmbAccurefEnum, SmbAdThreshEnum, SmbAIceEnum, @@ -290,4 +294,5 @@ SmbIsdensificationEnum, SmbIsgraingrowthEnum, + SmbIsfirnwarmingEnum, SmbIsmeltEnum, SmbIsmungsmEnum, @@ -302,4 +307,7 @@ SmbPfacEnum, SmbRequestedOutputsEnum, + SmbRunoffaltiEnum, + SmbRunoffgradEnum, + SmbRunoffrefEnum, SmbSealevEnum, SmbSwIdxEnum, @@ -526,7 +534,7 @@ SealevelNEsaRateEnum, SealevelRSLRateEnum, - SealevelUEsaEnum, + SealevelUEsaEnum, SealevelRSLEustaticRateEnum, - SealevelNEsaEnum, + SealevelNEsaEnum, SealevelUGiaEnum, SealevelNGiaEnum, @@ -577,4 +585,5 @@ SmbPEnum, SmbPrecipitationEnum, + SmbPrecipitationsAnomalyEnum, SmbPrecipitationsLgmEnum, SmbPrecipitationsPresentdayEnum, @@ -588,5 +597,7 @@ SmbSizeiniEnum, SmbSmbrefEnum, + SmbSmbCorrEnum, SmbTaEnum, + SmbTemperaturesAnomalyEnum, SmbTemperaturesLgmEnum, SmbTemperaturesPresentdayEnum, @@ -1095,4 +1106,6 @@ SMBmeltcomponentsEnum, SMBpddEnum, + SMBpddSicopolisEnum, + SMBgradientscomponentsEnum, SmbRlapsEnum, SmbRlapslgmEnum, Index: /issm/trunk/src/c/shared/Enum/EnumToStringx.cpp =================================================================== --- /issm/trunk/src/c/shared/Enum/EnumToStringx.cpp (revision 23393) +++ /issm/trunk/src/c/shared/Enum/EnumToStringx.cpp (revision 23394) @@ -61,4 +61,5 @@ case AutodiffNumIndependentsEnum : return "AutodiffNumIndependents"; case AutodiffObufsizeEnum : return "AutodiffObufsize"; + case AutodiffTapeAllocEnum : return "AutodiffTapeAlloc"; case AutodiffTbufsizeEnum : return "AutodiffTbufsize"; case AutodiffXpEnum : return "AutodiffXp"; @@ -280,4 +281,7 @@ case SettingsSolverResidueThresholdEnum : return "SettingsSolverResidueThreshold"; case SettingsWaitonlockEnum : return "SettingsWaitonlock"; + case SmbAccualtiEnum : return "SmbAccualti"; + case SmbAccugradEnum : return "SmbAccugrad"; + case SmbAccurefEnum : return "SmbAccuref"; case SmbAdThreshEnum : return "SmbAdThresh"; case SmbAIceEnum : return "SmbAIce"; @@ -298,4 +302,5 @@ case SmbIsdensificationEnum : return "SmbIsdensification"; case SmbIsgraingrowthEnum : return "SmbIsgraingrowth"; + case SmbIsfirnwarmingEnum : return "SmbIsfirnwarming"; case SmbIsmeltEnum : return "SmbIsmelt"; case SmbIsmungsmEnum : return "SmbIsmungsm"; @@ -310,4 +315,7 @@ case SmbPfacEnum : return "SmbPfac"; case SmbRequestedOutputsEnum : return "SmbRequestedOutputs"; + case SmbRunoffaltiEnum : return "SmbRunoffalti"; + case SmbRunoffgradEnum : return "SmbRunoffgrad"; + case SmbRunoffrefEnum : return "SmbRunoffref"; case SmbSealevEnum : return "SmbSealev"; case SmbSwIdxEnum : return "SmbSwIdx"; @@ -583,4 +591,5 @@ case SmbPEnum : return "SmbP"; case SmbPrecipitationEnum : return "SmbPrecipitation"; + case SmbPrecipitationsAnomalyEnum : return "SmbPrecipitationsAnomaly"; case SmbPrecipitationsLgmEnum : return "SmbPrecipitationsLgm"; case SmbPrecipitationsPresentdayEnum : return "SmbPrecipitationsPresentday"; @@ -594,5 +603,7 @@ case SmbSizeiniEnum : return "SmbSizeini"; case SmbSmbrefEnum : return "SmbSmbref"; + case SmbSmbCorrEnum : return "SmbSmbCorr"; case SmbTaEnum : return "SmbTa"; + case SmbTemperaturesAnomalyEnum : return "SmbTemperaturesAnomaly"; case SmbTemperaturesLgmEnum : return "SmbTemperaturesLgm"; case SmbTemperaturesPresentdayEnum : return "SmbTemperaturesPresentday"; @@ -1099,4 +1110,6 @@ case SMBmeltcomponentsEnum : return "SMBmeltcomponents"; case SMBpddEnum : return "SMBpdd"; + case SMBpddSicopolisEnum : return "SMBpddSicopolis"; + case SMBgradientscomponentsEnum : return "SMBgradientscomponents"; case SmbRlapsEnum : return "SmbRlaps"; case SmbRlapslgmEnum : return "SmbRlapslgm"; Index: /issm/trunk/src/c/shared/Enum/StringToEnumx.cpp =================================================================== --- /issm/trunk/src/c/shared/Enum/StringToEnumx.cpp (revision 23393) +++ /issm/trunk/src/c/shared/Enum/StringToEnumx.cpp (revision 23394) @@ -61,4 +61,5 @@ else if (strcmp(name,"AutodiffNumIndependents")==0) return AutodiffNumIndependentsEnum; else if (strcmp(name,"AutodiffObufsize")==0) return AutodiffObufsizeEnum; + else if (strcmp(name,"AutodiffTapeAlloc")==0) return AutodiffTapeAllocEnum; else if (strcmp(name,"AutodiffTbufsize")==0) return AutodiffTbufsizeEnum; else if (strcmp(name,"AutodiffXp")==0) return AutodiffXpEnum; @@ -136,9 +137,9 @@ else if (strcmp(name,"FrictionLaw")==0) return FrictionLawEnum; else if (strcmp(name,"FrictionPseudoplasticityExponent")==0) return FrictionPseudoplasticityExponentEnum; - else if (strcmp(name,"FrictionThresholdSpeed")==0) return FrictionThresholdSpeedEnum; else stage=2; } if(stage==2){ - if (strcmp(name,"FrictionDelta")==0) return FrictionDeltaEnum; + if (strcmp(name,"FrictionThresholdSpeed")==0) return FrictionThresholdSpeedEnum; + else if (strcmp(name,"FrictionDelta")==0) return FrictionDeltaEnum; else if (strcmp(name,"FrictionVoidRatio")==0) return FrictionVoidRatioEnum; else if (strcmp(name,"GiaCrossSectionShape")==0) return GiaCrossSectionShapeEnum; @@ -259,9 +260,9 @@ else if (strcmp(name,"SealevelriseFluidLove")==0) return SealevelriseFluidLoveEnum; else if (strcmp(name,"SealevelriseGElastic")==0) return SealevelriseGElasticEnum; - else if (strcmp(name,"SealevelriseGeodetic")==0) return SealevelriseGeodeticEnum; else stage=3; } if(stage==3){ - if (strcmp(name,"SealevelriseGeodeticRunFrequency")==0) return SealevelriseGeodeticRunFrequencyEnum; + if (strcmp(name,"SealevelriseGeodetic")==0) return SealevelriseGeodeticEnum; + else if (strcmp(name,"SealevelriseGeodeticRunFrequency")==0) return SealevelriseGeodeticRunFrequencyEnum; else if (strcmp(name,"SealevelriseHElastic")==0) return SealevelriseHElasticEnum; else if (strcmp(name,"SealevelriseHoriz")==0) return SealevelriseHorizEnum; @@ -286,4 +287,7 @@ else if (strcmp(name,"SettingsSolverResidueThreshold")==0) return SettingsSolverResidueThresholdEnum; else if (strcmp(name,"SettingsWaitonlock")==0) return SettingsWaitonlockEnum; + else if (strcmp(name,"SmbAccualti")==0) return SmbAccualtiEnum; + else if (strcmp(name,"SmbAccugrad")==0) return SmbAccugradEnum; + else if (strcmp(name,"SmbAccuref")==0) return SmbAccurefEnum; else if (strcmp(name,"SmbAdThresh")==0) return SmbAdThreshEnum; else if (strcmp(name,"SmbAIce")==0) return SmbAIceEnum; @@ -304,4 +308,5 @@ else if (strcmp(name,"SmbIsdensification")==0) return SmbIsdensificationEnum; else if (strcmp(name,"SmbIsgraingrowth")==0) return SmbIsgraingrowthEnum; + else if (strcmp(name,"SmbIsfirnwarming")==0) return SmbIsfirnwarmingEnum; else if (strcmp(name,"SmbIsmelt")==0) return SmbIsmeltEnum; else if (strcmp(name,"SmbIsmungsm")==0) return SmbIsmungsmEnum; @@ -316,4 +321,7 @@ else if (strcmp(name,"SmbPfac")==0) return SmbPfacEnum; else if (strcmp(name,"SmbRequestedOutputs")==0) return SmbRequestedOutputsEnum; + else if (strcmp(name,"SmbRunoffalti")==0) return SmbRunoffaltiEnum; + else if (strcmp(name,"SmbRunoffgrad")==0) return SmbRunoffgradEnum; + else if (strcmp(name,"SmbRunoffref")==0) return SmbRunoffrefEnum; else if (strcmp(name,"SmbSealev")==0) return SmbSealevEnum; else if (strcmp(name,"SmbSwIdx")==0) return SmbSwIdxEnum; @@ -375,5 +383,8 @@ else if (strcmp(name,"TransientIsmovingfront")==0) return TransientIsmovingfrontEnum; else if (strcmp(name,"TransientIsoceancoupling")==0) return TransientIsoceancouplingEnum; - else if (strcmp(name,"TransientIsslr")==0) return TransientIsslrEnum; + else stage=4; + } + if(stage==4){ + if (strcmp(name,"TransientIsslr")==0) return TransientIsslrEnum; else if (strcmp(name,"TransientIssmb")==0) return TransientIssmbEnum; else if (strcmp(name,"TransientIsstressbalance")==0) return TransientIsstressbalanceEnum; @@ -383,8 +394,5 @@ else if (strcmp(name,"Velocity")==0) return VelocityEnum; else if (strcmp(name,"WorldComm")==0) return WorldCommEnum; - else stage=4; - } - if(stage==4){ - if (strcmp(name,"ParametersEND")==0) return ParametersENDEnum; + else if (strcmp(name,"ParametersEND")==0) return ParametersENDEnum; else if (strcmp(name,"InputsSTART")==0) return InputsSTARTEnum; else if (strcmp(name,"Adjoint")==0) return AdjointEnum; @@ -498,5 +506,8 @@ else if (strcmp(name,"Ice")==0) return IceEnum; else if (strcmp(name,"IceMaskNodeActivation")==0) return IceMaskNodeActivationEnum; - else if (strcmp(name,"Input")==0) return InputEnum; + else stage=5; + } + if(stage==5){ + if (strcmp(name,"Input")==0) return InputEnum; else if (strcmp(name,"InversionCostFunctionsCoefficients")==0) return InversionCostFunctionsCoefficientsEnum; else if (strcmp(name,"InversionSurfaceObs")==0) return InversionSurfaceObsEnum; @@ -506,8 +517,5 @@ else if (strcmp(name,"InversionVyObs")==0) return InversionVyObsEnum; else if (strcmp(name,"LevelsetfunctionSlopeX")==0) return LevelsetfunctionSlopeXEnum; - else stage=5; - } - if(stage==5){ - if (strcmp(name,"LevelsetfunctionSlopeY")==0) return LevelsetfunctionSlopeYEnum; + else if (strcmp(name,"LevelsetfunctionSlopeY")==0) return LevelsetfunctionSlopeYEnum; else if (strcmp(name,"LoadingforceX")==0) return LoadingforceXEnum; else if (strcmp(name,"LoadingforceY")==0) return LoadingforceYEnum; @@ -595,4 +603,5 @@ else if (strcmp(name,"SmbP")==0) return SmbPEnum; else if (strcmp(name,"SmbPrecipitation")==0) return SmbPrecipitationEnum; + else if (strcmp(name,"SmbPrecipitationsAnomaly")==0) return SmbPrecipitationsAnomalyEnum; else if (strcmp(name,"SmbPrecipitationsLgm")==0) return SmbPrecipitationsLgmEnum; else if (strcmp(name,"SmbPrecipitationsPresentday")==0) return SmbPrecipitationsPresentdayEnum; @@ -606,5 +615,7 @@ else if (strcmp(name,"SmbSizeini")==0) return SmbSizeiniEnum; else if (strcmp(name,"SmbSmbref")==0) return SmbSmbrefEnum; + else if (strcmp(name,"SmbSmbCorr")==0) return SmbSmbCorrEnum; else if (strcmp(name,"SmbTa")==0) return SmbTaEnum; + else if (strcmp(name,"SmbTemperaturesAnomaly")==0) return SmbTemperaturesAnomalyEnum; else if (strcmp(name,"SmbTemperaturesLgm")==0) return SmbTemperaturesLgmEnum; else if (strcmp(name,"SmbTemperaturesPresentday")==0) return SmbTemperaturesPresentdayEnum; @@ -618,5 +629,8 @@ else if (strcmp(name,"SmbVz")==0) return SmbVzEnum; else if (strcmp(name,"SmbW")==0) return SmbWEnum; - else if (strcmp(name,"SmbWini")==0) return SmbWiniEnum; + else stage=6; + } + if(stage==6){ + if (strcmp(name,"SmbWini")==0) return SmbWiniEnum; else if (strcmp(name,"SmbZMax")==0) return SmbZMaxEnum; else if (strcmp(name,"SmbZMin")==0) return SmbZMinEnum; @@ -629,8 +643,5 @@ else if (strcmp(name,"StrainRatexy")==0) return StrainRatexyEnum; else if (strcmp(name,"StrainRatexz")==0) return StrainRatexzEnum; - else stage=6; - } - if(stage==6){ - if (strcmp(name,"StrainRateyy")==0) return StrainRateyyEnum; + else if (strcmp(name,"StrainRateyy")==0) return StrainRateyyEnum; else if (strcmp(name,"StrainRateyz")==0) return StrainRateyzEnum; else if (strcmp(name,"StrainRatezz")==0) return StrainRatezzEnum; @@ -741,5 +752,8 @@ else if (strcmp(name,"DatasetInput")==0) return DatasetInputEnum; else if (strcmp(name,"DataSetParam")==0) return DataSetParamEnum; - else if (strcmp(name,"DefaultAnalysis")==0) return DefaultAnalysisEnum; + else stage=7; + } + if(stage==7){ + if (strcmp(name,"DefaultAnalysis")==0) return DefaultAnalysisEnum; else if (strcmp(name,"DefaultCalving")==0) return DefaultCalvingEnum; else if (strcmp(name,"DegreeOfChannelization")==0) return DegreeOfChannelizationEnum; @@ -752,8 +766,5 @@ else if (strcmp(name,"Domain3Dsurface")==0) return Domain3DsurfaceEnum; else if (strcmp(name,"DoubleArrayInput")==0) return DoubleArrayInputEnum; - else stage=7; - } - if(stage==7){ - if (strcmp(name,"DoubleExternalResult")==0) return DoubleExternalResultEnum; + else if (strcmp(name,"DoubleExternalResult")==0) return DoubleExternalResultEnum; else if (strcmp(name,"DoubleInput")==0) return DoubleInputEnum; else if (strcmp(name,"DoubleMatArrayParam")==0) return DoubleMatArrayParamEnum; @@ -864,5 +875,8 @@ else if (strcmp(name,"LambdaS")==0) return LambdaSEnum; else if (strcmp(name,"LATaylorHood")==0) return LATaylorHoodEnum; - else if (strcmp(name,"LevelsetAnalysis")==0) return LevelsetAnalysisEnum; + else stage=8; + } + if(stage==8){ + if (strcmp(name,"LevelsetAnalysis")==0) return LevelsetAnalysisEnum; else if (strcmp(name,"LevelsetfunctionPicard")==0) return LevelsetfunctionPicardEnum; else if (strcmp(name,"LinearFloatingMeltRate")==0) return LinearFloatingMeltRateEnum; @@ -875,8 +889,5 @@ else if (strcmp(name,"LoveKernelsImag")==0) return LoveKernelsImagEnum; else if (strcmp(name,"LoveKernelsReal")==0) return LoveKernelsRealEnum; - else stage=8; - } - if(stage==8){ - if (strcmp(name,"LoveKi")==0) return LoveKiEnum; + else if (strcmp(name,"LoveKi")==0) return LoveKiEnum; else if (strcmp(name,"LoveKr")==0) return LoveKrEnum; else if (strcmp(name,"LoveLi")==0) return LoveLiEnum; @@ -987,5 +998,8 @@ else if (strcmp(name,"Outputdefinition37")==0) return Outputdefinition37Enum; else if (strcmp(name,"Outputdefinition38")==0) return Outputdefinition38Enum; - else if (strcmp(name,"Outputdefinition39")==0) return Outputdefinition39Enum; + else stage=9; + } + if(stage==9){ + if (strcmp(name,"Outputdefinition39")==0) return Outputdefinition39Enum; else if (strcmp(name,"Outputdefinition3")==0) return Outputdefinition3Enum; else if (strcmp(name,"Outputdefinition40")==0) return Outputdefinition40Enum; @@ -998,8 +1012,5 @@ else if (strcmp(name,"Outputdefinition47")==0) return Outputdefinition47Enum; else if (strcmp(name,"Outputdefinition48")==0) return Outputdefinition48Enum; - else stage=9; - } - if(stage==9){ - if (strcmp(name,"Outputdefinition49")==0) return Outputdefinition49Enum; + else if (strcmp(name,"Outputdefinition49")==0) return Outputdefinition49Enum; else if (strcmp(name,"Outputdefinition4")==0) return Outputdefinition4Enum; else if (strcmp(name,"Outputdefinition50")==0) return Outputdefinition50Enum; @@ -1110,5 +1121,8 @@ else if (strcmp(name,"SMBcomponents")==0) return SMBcomponentsEnum; else if (strcmp(name,"SMBd18opdd")==0) return SMBd18opddEnum; - else if (strcmp(name,"SmbDesfac")==0) return SmbDesfacEnum; + else stage=10; + } + if(stage==10){ + if (strcmp(name,"SmbDesfac")==0) return SmbDesfacEnum; else if (strcmp(name,"SmbDpermil")==0) return SmbDpermilEnum; else if (strcmp(name,"SmbDzAdd")==0) return SmbDzAddEnum; @@ -1121,9 +1135,8 @@ else if (strcmp(name,"SMBhenning")==0) return SMBhenningEnum; else if (strcmp(name,"SmbMAdd")==0) return SmbMAddEnum; - else stage=10; - } - if(stage==10){ - if (strcmp(name,"SMBmeltcomponents")==0) return SMBmeltcomponentsEnum; + else if (strcmp(name,"SMBmeltcomponents")==0) return SMBmeltcomponentsEnum; else if (strcmp(name,"SMBpdd")==0) return SMBpddEnum; + else if (strcmp(name,"SMBpddSicopolis")==0) return SMBpddSicopolisEnum; + else if (strcmp(name,"SMBgradientscomponents")==0) return SMBgradientscomponentsEnum; else if (strcmp(name,"SmbRlaps")==0) return SmbRlapsEnum; else if (strcmp(name,"SmbRlapslgm")==0) return SmbRlapslgmEnum; Index: /issm/trunk/src/c/shared/MemOps/MemOps.cpp =================================================================== --- /issm/trunk/src/c/shared/MemOps/MemOps.cpp (revision 23393) +++ /issm/trunk/src/c/shared/MemOps/MemOps.cpp (revision 23394) @@ -16,5 +16,5 @@ #if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) template <> adouble* xNew(unsigned int size, const char* const contig) { - if (*contig == 't') + if (contig[0] == 't' || contig[0] == 'c') ensureContiguousLocations(size); Index: /issm/trunk/src/c/shared/Numerics/extrema.cpp =================================================================== --- /issm/trunk/src/c/shared/Numerics/extrema.cpp (revision 23393) +++ /issm/trunk/src/c/shared/Numerics/extrema.cpp (revision 23394) @@ -11,16 +11,20 @@ #include "./types.h" +#ifndef _HAVE_CODIPACK_// already defined in codipack headers IssmDouble min(IssmDouble a,IssmDouble b){ if (ab)return a; else return b; } +#endif int max(int a,int b){ if (a>b)return a; @@ -28,5 +32,5 @@ } -#ifdef _HAVE_ADOLC_ +#ifdef _HAVE_AD_ IssmPDouble min(IssmPDouble a,IssmPDouble b){ if (a int xIsInf (const adouble& X){ return std::isinf(X.getValue()); } #endif + +#if defined(_HAVE_CODIPACK_) && !defined(_WRAPPERS_) +template <> int xIsNan (const IssmDouble& X){ + return std::isnan(X.getValue()); +} +template <> int xIsInf (const IssmDouble& X){ + return std::isinf(X.getValue()); +} +#endif Index: /issm/trunk/src/c/shared/Numerics/isnan.h =================================================================== --- /issm/trunk/src/c/shared/Numerics/isnan.h (revision 23393) +++ /issm/trunk/src/c/shared/Numerics/isnan.h (revision 23394) @@ -33,3 +33,9 @@ #endif +#if defined(_HAVE_CODIPACK_) && !defined(_WRAPPERS_) +#include "./types.h" +template <> int xIsNan (const IssmDouble& X); +template <> int xIsInf (const IssmDouble& X); #endif + +#endif Index: /issm/trunk/src/c/shared/Numerics/numerics.h =================================================================== --- /issm/trunk/src/c/shared/Numerics/numerics.h (revision 23393) +++ /issm/trunk/src/c/shared/Numerics/numerics.h (revision 23394) @@ -20,8 +20,11 @@ #include "./OptPars.h" +#if !defined(_HAVE_CODIPACK_) +// already defined in codipack headers IssmDouble min(IssmDouble a,IssmDouble b); IssmDouble max(IssmDouble a,IssmDouble b); +#endif -#ifdef _HAVE_ADOLC_ +#ifdef _HAVE_AD_ IssmPDouble min(IssmPDouble a,IssmPDouble b); IssmPDouble max(IssmPDouble a,IssmPDouble b); Index: /issm/trunk/src/c/shared/Numerics/recast.h =================================================================== --- /issm/trunk/src/c/shared/Numerics/recast.h (revision 23393) +++ /issm/trunk/src/c/shared/Numerics/recast.h (revision 23394) @@ -15,5 +15,5 @@ #endif -#if !defined(_HAVE_ADOLC_) || defined(_WRAPPERS_) +#if !defined(_HAVE_AD_) || defined(_WRAPPERS_) template To reCast(const From& from) { @@ -34,7 +34,14 @@ * partial specialization */ +#ifdef _HAVE_ADOLC_ template struct ForPartialSpecialization { static To reCast(const adouble& from ) { return (To) (from.getValue());} }; +#endif +#ifdef _HAVE_CODIPACK_ +template struct ForPartialSpecialization { + static To reCast(const IssmDouble& from ) { return (To) (from.getValue());} +}; +#endif #endif Index: /issm/trunk/src/c/shared/Numerics/types.h =================================================================== --- /issm/trunk/src/c/shared/Numerics/types.h (revision 23393) +++ /issm/trunk/src/c/shared/Numerics/types.h (revision 23394) @@ -22,13 +22,18 @@ #if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) +/*ADOLC typedefs*/ #include "adolc/adolc.h" -// for active variables -typedef adouble IssmDouble; -// for passive variables -typedef double IssmPDouble; +typedef adouble IssmDouble; /*for active variables*/ +typedef double IssmPDouble; /*for passive variables*/ + +#elif defined(_HAVE_CODIPACK_) && !defined(_WRAPPERS_) +/*CoDiPack typedefs*/ +#include +typedef codi::RealReverse IssmDouble; +typedef double IssmPDouble; + +/*Non-AD typedefs*/ #else -// see above -typedef double IssmDouble; -// see above +typedef double IssmDouble; typedef IssmDouble IssmPDouble; #endif Index: /issm/trunk/src/c/shared/io/Marshalling/IoCodeConversions.cpp =================================================================== --- /issm/trunk/src/c/shared/io/Marshalling/IoCodeConversions.cpp (revision 23393) +++ /issm/trunk/src/c/shared/io/Marshalling/IoCodeConversions.cpp (revision 23394) @@ -173,4 +173,6 @@ case 8: return SMBgembEnum; case 9: return SMBgradientselaEnum; + case 10: return SMBpddSicopolisEnum; + case 11: return SMBgradientscomponentsEnum; default: _error_("Marshalled SMB code \""<* Kff,Vector* pf,Vector* uf,Vector* old_uf,IssmDouble eps_res,IssmDouble eps_rel,IssmDouble eps_abs){ +void convergence(bool* pconverged, Matrix* Kff,Vector* pf,Vector* uf,Vector* old_uf,IssmDouble eps_res,IssmDouble eps_rel,IssmDouble eps_abs){/*{{{*/ /*output*/ @@ -34,6 +34,9 @@ } + /*Display solver caracteristics*/ if (VerboseConvergence()){ + + /*compute KUF = KU - F = K*U - F*/ @@ -136,3 +139,5 @@ /*assign output*/ *pconverged=converged; -} +}/*}}}*/ + + Index: /issm/trunk/src/c/solutionsequences/solutionsequence_hydro_nonlinear.cpp =================================================================== --- /issm/trunk/src/c/solutionsequences/solutionsequence_hydro_nonlinear.cpp (revision 23393) +++ /issm/trunk/src/c/solutionsequences/solutionsequence_hydro_nonlinear.cpp (revision 23394) @@ -190,10 +190,12 @@ Reduceloadx(pf,Kfs,ys); delete Kfs; delete uf_epl; + femmodel->profiler->Start(SOLVER); Solverx(&uf_epl,Kff,pf,uf_epl_sub_iter,df,femmodel->parameters); femmodel->profiler->Stop(SOLVER); + delete Kff; delete pf; delete df; delete uf_epl_sub_iter; - uf_epl_sub_iter=uf_epl->Duplicate(); + uf_epl_sub_iter=uf_epl->Duplicate();_assert_(uf_epl_sub_iter); uf_epl->Copy(uf_epl_sub_iter); delete ug_epl; @@ -215,6 +217,4 @@ _error_(" maximum number of EPL iterations (" << hydro_maxiter << ") exceeded"); } - //If there is some colapse go through sediment again - /* if(ThickCountparameters); femmodel->profiler->Stop(SOLVER); + Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);delete ys; @@ -86,5 +87,5 @@ } } - + /*Increase count: */ count++; Index: /issm/trunk/src/c/solutionsequences/solutionsequence_schurcg.cpp =================================================================== --- /issm/trunk/src/c/solutionsequences/solutionsequence_schurcg.cpp (revision 23393) +++ /issm/trunk/src/c/solutionsequences/solutionsequence_schurcg.cpp (revision 23394) @@ -10,16 +10,473 @@ #include "../analyses/analyses.h" + #ifdef _HAVE_PETSC_ -void SchurCGSolver(Vector** puf,Mat Kff,Mat Mff,Vec pf, Vec uf0,Vec df,Parameters* parameters){/*{{{*/ + + +void SchurCGSolver(Vector** puf,Mat Kff,Vec pf, Vec uf0,IS isv,IS isp,Parameters* parameters){/*{{{*/ + + Mat A, B, BT; /* Saddle point block matrices */ + Mat IP; /* Preconditioner matrix */ + Mat IP2; + int nu, np; /* No of. free nodes in velocity / pressure space */ + Vec p,uold,unew; /* Solution vectors for pressure / vel. */ + Vec tmpu, tmpp, rhsu,rhsp; /* temp. vectors, arbitrary RHS in vel. / pressure space */ + Vec gold,gnew,wold,wnew,chi,thetaold,thetanew,eta; /* CG intermediaries */ + Vec f1,f2; /* RHS of the global system */ + double rho,gamma,tmpScalar; /* Step sizes, arbitrary double */ + KSP kspu,kspp; /* KSP contexts for vel. / pressure systems*/ + KSPConvergedReason reason; /* Convergence reason for troubleshooting */ + int its; /* No. of iterations for troubleshooting */ + double initRnorm, rnorm, TOL; /* residual norms, STOP tolerance */ + PC pcu,pcp; /* Preconditioner contexts pertaining the KSP contexts*/ + PetscViewer viewer; /* Viewer for troubleshooting */ + IssmPDouble t1,t2; /* Time measurement for bottleneck analysis */ + + /*STOP tolerance for the rel. residual*/ + TOL = 0.4; /*Initialize output*/ - Vec uf = NULL; - - _error_("not implemented yet"); + Vector* out_uf=new Vector(uf0); + + /* Extract block matrices from the saddle point matrix */ + /* [ A B ] = Kff + * [ B^T 0 ] + * */ + #if (_PETSC_MAJOR_==3) && (_PETSC_MINOR_>=8) + MatCreateSubMatrix(Kff,isv,isv,MAT_INITIAL_MATRIX,&A); + MatCreateSubMatrix(Kff,isv,isp,MAT_INITIAL_MATRIX,&B); + MatCreateSubMatrix(Kff,isp,isv,MAT_INITIAL_MATRIX,&BT); + #else + MatGetSubMatrix(Kff,isv,isv,MAT_INITIAL_MATRIX,&A); + MatGetSubMatrix(Kff,isv,isp,MAT_INITIAL_MATRIX,&B); + MatGetSubMatrix(Kff,isp,isv,MAT_INITIAL_MATRIX,&BT); + #endif + + /* Extract preconditioner matrix on the pressure space*/ + #if (_PETSC_MAJOR_==3) && (_PETSC_MINOR_>=8) + MatCreateSubMatrix(Kff,isp,isp,MAT_INITIAL_MATRIX,&IP); + #else + MatGetSubMatrix(Kff,isp,isp,MAT_INITIAL_MATRIX,&IP); + #endif + + /* Get number of velocity / pressure nodes */ + MatGetSize(B,&nu,&np); + + /* Extract initial guesses for uold and pold */ + VecCreate(IssmComm::GetComm(),&p);VecSetSizes(p,PETSC_DECIDE,np);VecSetFromOptions(p); + VecAssemblyBegin(p);VecAssemblyEnd(p); + VecCreate(IssmComm::GetComm(),&uold);VecSetSizes(uold,PETSC_DECIDE,nu);VecSetFromOptions(uold); + VecAssemblyBegin(uold);VecAssemblyEnd(uold); + + VecGetSubVector(out_uf->pvector->vector,isv,&uold); + VecGetSubVector(out_uf->pvector->vector,isp,&p); + + + /* Set up intermediaries */ + VecDuplicate(uold,&f1);VecSet(f1,0.0); + VecDuplicate(p,&f2);VecSet(f2,0.0); + VecDuplicate(uold,&tmpu);VecSet(tmpu,0.0); + VecDuplicate(p,&tmpp);VecSet(tmpp,0.0); + VecDuplicate(p,&rhsp);VecSet(rhsp,0.0); + VecDuplicate(uold,&rhsu);VecSet(rhsu,0.0); + VecDuplicate(p,&gold);VecSet(gold,0.0); + VecDuplicate(p,&wnew);VecSet(wnew,0.0); + VecDuplicate(uold,&chi);VecSet(chi,0.0); + VecDuplicate(p,&thetanew);VecSet(thetanew,0.0); + VecDuplicate(p,&thetaold);VecSet(thetaold,0.0); + VecDuplicate(p,&eta);VecSet(eta,0.0); + + /* Get global RHS (for each block sub-problem respectively)*/ + VecGetSubVector(pf,isv,&f1); + VecGetSubVector(pf,isp,&f2); + + /* ------------------------------------------------------------ */ + + /* Generate initial value for the velocity from the pressure */ + /* a(u0,v) = f1(v)-b(p0,v) i.e. Au0 = F1-Bp0 */ + /* u0 = u_DIR on \Gamma_DIR */ + + /* Create KSP context */ + KSPCreate(IssmComm::GetComm(),&kspu); + #if (_PETSC_MAJOR_==3) && (_PETSC_MINOR_>=5) + KSPSetOperators(kspu,A,A); + #else + KSPSetOperators(kspu,A,A,DIFFERENT_NONZERO_PATTERN); + #endif + KSPSetType(kspu,KSPCG); + KSPSetInitialGuessNonzero(kspu,PETSC_TRUE); + //KSPSetTolerances(kspu,1e-12,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT); + //KSPMonitorSet(kspu,KSPMonitorDefault,NULL,NULL); + KSPGetPC(kspu,&pcu); + PCSetType(pcu,PCSOR); + KSPSetUp(kspu); + + + /* Create RHS */ + /* RHS = F1-B * pold */ + VecScale(p,-1.);MatMultAdd(B,p,f1,rhsu);VecScale(p,-1.); + + /* Go solve Au0 = F1-Bp0*/ + KSPSolve(kspu,rhsu,uold); + + + /* Set up u_new */ + VecDuplicate(uold,&unew);VecCopy(uold,unew); + VecAssemblyBegin(unew);VecAssemblyEnd(unew); + + + + /* ------------------------------------------------------------- */ + + /*Get initial residual*/ + /*(1/mu(x) * g0, q) = b(q,u0) - (f2,q) i.e. IP * g0 = BT * u0 - F2*/ + + /* Create KSP context */ + KSPCreate(IssmComm::GetComm(),&kspp); + #if (_PETSC_MAJOR_==3) && (_PETSC_MINOR_>=5) + KSPSetOperators(kspp,IP,IP); + #else + KSPSetOperators(kspp,IP,IP,DIFFERENT_NONZERO_PATTERN); + #endif + + /* Create RHS */ + /* RHS = BT * uold - F2 */ + VecScale(f2,-1.);MatMultAdd(BT,uold,f2,rhsp);VecScale(f2,-1.); + + /* Set KSP & PC options */ + KSPSetType(kspp,KSPCG); + KSPSetInitialGuessNonzero(kspp,PETSC_TRUE); + KSPGetPC(kspp,&pcp); + PCSetType(pcp,PCJACOBI); + /* Note: Systems in the pressure space are cheap, so we can afford a better tolerance */ + KSPSetTolerances(kspp,1e-10,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT); + KSPSetUp(kspp); + + /* Go solve */ + KSPSolve(kspp,rhsp,gold); + + /*Initial residual*/ + VecNorm(gold,NORM_INFINITY,&initRnorm); + + /* Further setup */ + VecDuplicate(gold,&gnew);VecCopy(gold,gnew); + VecAssemblyBegin(gnew);VecAssemblyEnd(gnew); + + + /* ------------------------------------------------------------ */ + + /*Set initial search direction*/ + /*w0 = g0*/ + VecDuplicate(gold,&wold);VecCopy(gold,wold); + VecAssemblyBegin(wold);VecAssemblyEnd(wold); + + /*Realizing the step size part 1: thetam */ + /*IP * theta = BT * uold - F2*/ + VecScale(f2,-1.);MatMultAdd(BT,uold,f2,rhsp);VecScale(f2,-1.); + KSPSolve(kspp,rhsp,thetaold); + + + /* Count number of iterations */ + int count = 0; + + /* CG iteration*/ + for(;;){ + + /*Realizing the step size part 2: chim */ + /*a(chim,v) = -b(wm,v) i.e. A * chim = -B * wm */ + /*chim_DIR = 0*/ + VecScale(wold,-1.);MatMult(B,wold,rhsu);VecScale(wold,-1.); + KSPSolve(kspu,rhsu,chi); + + /*Realizing the step size part 3: etam */ + MatMult(BT,chi,rhsp); + KSPSolve(kspp,rhsp,eta); + + /* ---------------------------------------------------------- */ + + + /*Set step size*/ + /*rhom = [(wm)^T * IP^-1 * (BT * um - F2)]/[(wm)^T * IP^-1 * BT * chim]*/ + VecDot(wold,thetaold,&rho); + VecDot(wold,eta,&tmpScalar); + rho = rho/tmpScalar; + + + /* ---------------------------------------------------------- */ + + + /*Pressure update*/ + /*p(m+1) = pm - rhom * wm*/ + VecAXPY(p,-1.*rho,wold); + + + /*Velocity update*/ + /*u(m+1) = um - rhom * chim*/ + VecWAXPY(unew,-1.*rho,chi,uold); + + + /* ---------------------------------------------------------- */ + + /*Theta update*/ + /*IP * theta = BT * uold - F2*/ + VecScale(f2,-1.);MatMultAdd(BT,unew,f2,rhsp);VecScale(f2,-1.); + KSPSolve(kspp,rhsp,thetanew); + + + /* ---------------------------------------------------------- */ + + /*Residual update*/ + /*g(m+1) = gm - rhom * BT * chim*/ + VecWAXPY(gnew,-1.*rho,eta,gold); + + /* ---------------------------------------------------------- */ + + + /*BREAK if norm(g(m+0),2) < TOL or pressure space has been full searched*/ + VecNorm(gnew,NORM_INFINITY,&rnorm); + if(rnorm < TOL*initRnorm) + break; + else if(rnorm > 100*initRnorm) + _error_("Solver diverged. This shouldn't happen\n"); + //else + // PetscPrintf(PETSC_COMM_WORLD,"rel. residual at step %d: %g, at TOL = %g\n",count,rnorm/initRnorm,TOL); + + + + + if(count > np-1) break; + + + /* ---------------------------------------------------------- */ + + + /*Directional update*/ + /*gamma = [g(m+1)^T * theta(m+1)]/[g(m)^T * thetam]*/ + VecDot(gnew,thetanew,&gamma); + VecDot(gold,thetaold,&tmpScalar); + gamma = gamma/tmpScalar; + + /*w(m+1) = g(m+1) + gamma * w(m)*/ + VecWAXPY(wnew,gamma,wold,gnew); + + /* Assign new to old iterates */ + VecCopy(wnew,wold);VecCopy(gnew,gold);VecCopy(unew,uold);VecCopy(thetanew,thetaold); + + count++; + } + + + /* Restore pressure and velocity sol. vectors to its global form */ + VecRestoreSubVector(out_uf->pvector->vector,isv,&unew); + VecRestoreSubVector(out_uf->pvector->vector,isp,&p); /*return output pointer*/ - Vector* out_uf=new Vector(uf); - VecFree(&uf); *puf=out_uf; + + + /* Cleanup */ + KSPDestroy(&kspu);KSPDestroy(&kspp); + + MatDestroy(&A);MatDestroy(&B);MatDestroy(&BT);MatDestroy(&IP); + + VecDestroy(&p);VecDestroy(&uold);VecDestroy(&unew);VecDestroy(&rhsu);VecDestroy(&rhsp); + VecDestroy(&gold);VecDestroy(&gnew);VecDestroy(&wold);VecDestroy(&wnew);VecDestroy(&chi); + VecDestroy(&tmpp);VecDestroy(&tmpu);VecDestroy(&f1);VecDestroy(&f2);VecDestroy(&eta); + VecDestroy(&thetanew);VecDestroy(&thetaold); + +}/*}}}*/ +void convergence_schurcg(bool* pconverged, Matrix* Kff,Vector* pf,Vector* uf,Vector* old_uf,IssmDouble eps_res,IssmDouble eps_rel,IssmDouble eps_abs,IS isv,IS isp){/*{{{*/ + + /*output*/ + bool converged=false; + + /*intermediary*/ + //Vector* KU=NULL; + //Vector* KUF=NULL; + //Vector* KUold=NULL; + //Vector* KUoldF=NULL; + Vector* duf=NULL; + IssmDouble ndu,nduinf,nu; + IssmDouble nKUF; + IssmDouble nKUoldF; + IssmDouble nF; + IssmDouble solver_residue,res; + int analysis_type; + + Mat A, B, BT; + Vec u,p,uold,pold,f1,f2,tmp,res1,res2; + int n_u,n_p; + double rnorm1, rnorm2; + + + if(VerboseModule()) _printf0_(" checking convergence\n"); + + /*If uf is NULL in input, f-set is nil, model is fully constrained, therefore converged from + * the get go: */ + if(uf->IsEmpty()){ + *pconverged=true; + return; + } + + /* Note: SchurCG also constructs the Schur preconditioner and stores it in the free block of Kff */ + /* [A B] + * Kff = | | + * [B^T IP] + * To calculate the residual, only the necessary blocks need to be extracted */ + + /*Extract A, B, B^T */ + #if (_PETSC_MAJOR_==3) && (_PETSC_MINOR_>=8) + MatCreateSubMatrix(Kff->pmatrix->matrix,isv,isv,MAT_INITIAL_MATRIX,&A); + MatCreateSubMatrix(Kff->pmatrix->matrix,isv,isp,MAT_INITIAL_MATRIX,&B); + MatCreateSubMatrix(Kff->pmatrix->matrix,isp,isv,MAT_INITIAL_MATRIX,&BT); + #else + MatGetSubMatrix(Kff->pmatrix->matrix,isv,isv,MAT_INITIAL_MATRIX,&A); + MatGetSubMatrix(Kff->pmatrix->matrix,isv,isp,MAT_INITIAL_MATRIX,&B); + MatGetSubMatrix(Kff->pmatrix->matrix,isp,isv,MAT_INITIAL_MATRIX,&BT); + #endif + + /*no. of free nodes in velocity/pressure space*/ + MatGetSize(B,&n_u,&n_p); + + /*Extract values corresponding to the free velocity/pressure nodes*/ + VecCreate(IssmComm::GetComm(),&p);VecSetSizes(p,PETSC_DECIDE,n_p);VecSetFromOptions(p); + VecAssemblyBegin(p);VecAssemblyEnd(p); + VecCreate(IssmComm::GetComm(),&u);VecSetSizes(u,PETSC_DECIDE,n_u);VecSetFromOptions(u); + VecAssemblyBegin(u);VecAssemblyEnd(u); + + VecGetSubVector(uf->pvector->vector,isv,&u); + VecGetSubVector(uf->pvector->vector,isp,&p); + + + /*Extract values of the RHS corresponding to the first/second block*/ + VecDuplicate(u,&f1);VecSet(f1,1.0); + VecDuplicate(p,&f2);VecSet(f2,1.0); + VecGetSubVector(pf->pvector->vector,isv,&f1); + VecGetSubVector(pf->pvector->vector,isp,&f2); + + /*Allocate intermediaries*/ + VecDuplicate(u,&res1);VecSet(res1,1.0); + VecDuplicate(u,&tmp);VecSet(tmp,1.0); + VecDuplicate(p,&res2);VecSet(res2,1.0); + + + /*Display solver caracteristics*/ + if (VerboseConvergence()){ + + /*Calculate res1 = A*u + B*p - f1*/ + VecScale(f1,-1.);MatMultAdd(A,u,f1,tmp);MatMultAdd(B,p,tmp,res1);VecScale(f1,-1.); + /*Calculate res2 = B^T * u - f2*/ + VecScale(f2,-1.);MatMultAdd(BT,u,f2,res2);VecScale(f2,-1.); + + + /*compute norm(res1), norm(res2), norm(F) and residue*/ + VecNorm(res1,NORM_2,&rnorm1);VecNorm(res2,NORM_2,&rnorm2); + nKUF=sqrt(rnorm1*rnorm1 + rnorm2*rnorm2); + nF=pf->Norm(NORM_TWO); + solver_residue=nKUF/nF; + _printf0_("\n" << " solver residue: norm(KU-F)/norm(F)=" << solver_residue << "\n"); + if(xIsNan(solver_residue)){ + //Kff->Echo(); + } + + } + /*clean up*/ + VecRestoreSubVector(uf->pvector->vector,isv,&u); + VecRestoreSubVector(uf->pvector->vector,isp,&p); + + /*Extract values corresponding to velocity/pressure on the old solution*/ + VecGetSubVector(old_uf->pvector->vector,isv,&uold); + VecGetSubVector(old_uf->pvector->vector,isp,&pold); + + + /*Force equilibrium (Mandatory)*/ + + /*Calculate res1 = A*uold + B*pold - f1*/ + VecScale(f1,-1.);MatMultAdd(A,uold,f1,tmp);MatMultAdd(B,pold,tmp,res1);VecScale(f1,-1.); + /*Calculate res2 = B^T * uold - f2*/ + VecScale(f2,-1.);MatMultAdd(BT,uold,f2,res2);VecScale(f2,-1.); + + /*compute norm(res1), norm(res2), norm(F) and residue*/ + VecNorm(res1,NORM_2,&rnorm1);VecNorm(res2,NORM_2,&rnorm2); + nKUoldF=sqrt(rnorm1*rnorm1 + rnorm2*rnorm2); + nF=pf->Norm(NORM_TWO); + res=nKUoldF/nF; + if (xIsNan(res)){ + _printf0_("norm nf = " << nF << "f and norm kuold = " << nKUoldF << "f\n"); + _error_("mechanical equilibrium convergence criterion is NaN!"); + } + + MatDestroy(&A);MatDestroy(&B);MatDestroy(&BT); + VecRestoreSubVector(pf->pvector->vector,isv,&f1); + VecRestoreSubVector(pf->pvector->vector,isp,&f2); + VecDestroy(&res1);VecDestroy(&res2);VecDestroy(&tmp); + VecRestoreSubVector(old_uf->pvector->vector,isv,&uold); + VecRestoreSubVector(old_uf->pvector->vector,isp,&pold); + + + + //print + if(res "<(eps_rel) || (VerboseConvergence())){ + + //compute norm(du)/norm(u) + duf=old_uf->Duplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); + ndu=duf->Norm(NORM_TWO); nu=old_uf->Norm(NORM_TWO); + + if (xIsNan(ndu) || xIsNan(nu)) _error_("convergence criterion is NaN!"); + + //clean up + delete duf; + + //print + if (!xIsNan(eps_rel)){ + if((ndu/nu) " << eps_rel*100 << " %\n"); + converged=false; + } + } + else _printf0_(setw(50) << left << " Convergence criterion: norm(du)/norm(u)" << ndu/nu*100 << " %\n"); + + } + + /*Absolute criterion (Optional) = max(du)*/ + if (!xIsNan(eps_abs) || (VerboseConvergence())){ + + //compute max(du) + duf=old_uf->Duplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); + ndu=duf->Norm(NORM_TWO); nduinf=duf->Norm(NORM_INF); + if (xIsNan(ndu) || xIsNan(nu)) _error_("convergence criterion is NaN!"); + + //clean up + delete duf; + + //print + if (!xIsNan(eps_abs)){ + if ((nduinf) " << eps_abs << "\n"); + converged=false; + } + } + else _printf0_(setw(50) << left << " Convergence criterion: max(du)" << nduinf << "\n"); + + } + + /*assign output*/ + *pconverged=converged; }/*}}}*/ void solutionsequence_schurcg(FemModel* femmodel){/*{{{*/ @@ -32,8 +489,7 @@ Vector* old_uf = NULL; Vector* pf = NULL; - Vector* pf0 = NULL; Vector* df = NULL; Vector* ys = NULL; - Matrix* Mff = NULL; + /*parameters:*/ @@ -49,5 +505,5 @@ femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); femmodel->UpdateConstraintsx(); - + int size; int count=0; bool converged=false; @@ -69,34 +525,44 @@ /*Get stiffness matrix and Load vector*/ SystemMatricesx(&Kff,&Kfs,&pf,&df,NULL,femmodel); - pf0=pf->Duplicate(); pf->Copy(pf0); CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); Reduceloadx(pf, Kfs, ys); delete Kfs; /*Create mass matrix*/ - int fsize; Kff->GetSize(&fsize,&fsize); - Mff=new Matrix(fsize,fsize,100,4); StressbalanceAnalysis* analysis = new StressbalanceAnalysis(); /*Get complete stiffness matrix without penalties*/ for(int i=0;ielements->Size();i++){ Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); - ElementMatrix* Me = analysis->CreatePressureMassMatrix(element); - if(Me) Me->AddToGlobal(Mff,NULL); - delete Me; + ElementMatrix* Ie = analysis->CreateSchurPrecondMatrix(element); + if(Ie) Ie->AddToGlobal(Kff,NULL); + delete Ie; } - Mff->Assemble(); + Kff->Assemble(); delete analysis; + + /*Obtain index sets for velocity and pressure components */ + IS isv = NULL; + IS isp = NULL; + #if _PETSC_MAJOR_==3 + /*Make indices out of doftypes: */ + if(!(df->pvector->vector))_error_("need doftypes for FS solver!\n"); + DofTypesToIndexSet(&isv,&isp,df->pvector->vector,FSSolverEnum); + #else + _error_("Petsc 3.X required"); + #endif + /*Solve*/ femmodel->profiler->Start(SOLVER); _assert_(Kff->type==PetscMatType); + SchurCGSolver(&uf, Kff->pmatrix->matrix, - Mff->pmatrix->matrix, pf->pvector->vector, old_uf->pvector->vector, - df->pvector->vector, + isv, + isp, femmodel->parameters); femmodel->profiler->Stop(SOLVER); - delete pf0; delete Mff; + /*Merge solution from f set to g set*/ @@ -104,6 +570,7 @@ /*Check for convergence and update inputs accordingly*/ - convergence(&converged,Kff,pf,uf,old_uf,eps_res,eps_rel,eps_abs); delete Kff; delete pf; delete df; + convergence_schurcg(&converged,Kff,pf,uf,old_uf,eps_res,eps_rel,eps_abs,isv,isp); delete Kff; delete pf; delete df; count++; + if(count>=max_nonlinear_iterations){ _printf0_(" maximum number of nonlinear iterations (" << max_nonlinear_iterations << ") exceeded\n"); @@ -128,4 +595,5 @@ }/*}}}*/ + #else void solutionsequence_schurcg(FemModel* femmodel){_error_("PETSc needs to be installed");} Index: /issm/trunk/src/c/toolkits/codipack/CoDiPackCommon.hpp =================================================================== --- /issm/trunk/src/c/toolkits/codipack/CoDiPackCommon.hpp (revision 23394) +++ /issm/trunk/src/c/toolkits/codipack/CoDiPackCommon.hpp (revision 23394) @@ -0,0 +1,90 @@ +/* + * CoDiPackCommon.hpp + * + * Created on: Mai 30, 2016 + * Author: sagebaum + */ + +#ifndef _CODIPACK_COMMON_HPP_ +#define _CODIPACK_COMMON_HPP_ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile without HAVE_CONFIG_H symbol! run configure first!" +#endif + +#if defined(_HAVE_CODIPACK_) +#include "codi.hpp" + +template +inline void getVectorPrimal(const Real* vec, Passive* pasVec, int n) { + for(int i = 0; i < n; ++i) { + pasVec[i]=vec[i].getValue(); + } +} + +template +inline void setVectorPrimal(Real* vec, const Passive* pasVec, int n) { + for(int i = 0; i < n; ++i) { + vec[i].value() = pasVec[i]; + } +} + +template +inline void getVectorGradData(const Real* vec, Data* dataVec, int n) { + for(int i = 0; i < n; ++i) { + dataVec[i]=vec[i].getGradientData(); + } +} + +template +inline void getVectorPrimalAndGradData(const Real* vec, Passive* pasVec, Data* dataVec, int n) { + for(int i = 0; i < n; ++i) { + pasVec[i]=vec[i].getValue(); + dataVec[i]=vec[i].getGradientData(); + } +} + +template +inline void getPrimalAndGradData(const Real& value, Passive& pas, Data& data) { + pas=value.getValue(); + data=value.getGradientData(); +} + +template +inline void registerVector(Real* vec, Data* dataVec, int n) { + typename Real::TapeType& tape = Real::getGlobalTape(); + + for(int i = 0; i < n; ++i) { + tape.registerInput(vec[i]); + dataVec[i]=vec[i].getGradientData(); + } +} + +template +inline void getVectorAdjoint(Tape& tape, const Data* dataVec, Adjoint* adjVec, int n) { + for(int i = 0; i < n; ++i) { + Data index = dataVec[i]; + adjVec[i] = tape.getGradient(index); + tape.gradient(index) = 0.0; + } +} + +template +inline void updateVectorAdjoint(Tape& tape, const Data* dataVec, const Adjoint* adjVec, int n) { + for(int i = 0; i < n; ++i) { + Data index = dataVec[i]; + tape.gradient(index) += adjVec[i]; + } +} + +template +inline void updateAdjoint(Tape& tape, const Data& data, const Adjoint& adj) { + Data index = data; + tape.gradient(index) += adj; +} + +#endif + +#endif Index: /issm/trunk/src/c/toolkits/codipack/CoDiPackGlobal.h =================================================================== --- /issm/trunk/src/c/toolkits/codipack/CoDiPackGlobal.h (revision 23394) +++ /issm/trunk/src/c/toolkits/codipack/CoDiPackGlobal.h (revision 23394) @@ -0,0 +1,40 @@ +/* + * CoDiPackGlobal.h + * + * Created on: Jul 20, 2016 + * Author: a_h_ck + */ + +#ifndef SRC_C_TOOLKITS_CODIPACK_CODIPACKGLOBAL_H_ +#define SRC_C_TOOLKITS_CODIPACK_CODIPACKGLOBAL_H_ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#if defined(_HAVE_CODIPACK_) + +#include +#include + +struct CoDi_global { + std::vector input_indices; + std::vector output_indices; + + void print(std::ostream& out) const { + out << "-------------------------------------\nCoDi_global:\n in = [ "; + for(auto& in_index : input_indices) { + out << in_index << " "; + } + out << "]\n out = [ "; + for(auto& out_index : output_indices) { + out << out_index << " "; + } + out << "]\n-------------------------------------\n"; + } +}; + +#endif /* _HAVE_CODIPACK_ */ +#endif /* SRC_C_TOOLKITS_CODIPACK_CODIPACKGLOBAL_H_ */ Index: /issm/trunk/src/c/toolkits/codipack/ampi_interface.cpp =================================================================== --- /issm/trunk/src/c/toolkits/codipack/ampi_interface.cpp (revision 23394) +++ /issm/trunk/src/c/toolkits/codipack/ampi_interface.cpp (revision 23394) @@ -0,0 +1,14 @@ +#ifdef HAVE_CONFIG_H +#include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#if defined(_HAVE_ADJOINTMPI_) +#include "externals/ampi_interface_realreverse.cpp" +#elif defined(_HAVE_MEDIPACK_) +#include "medi/medi.cpp" +#else +#error "Cannot compile without MeDiPack and AdjointMpi" +#endif + Index: /issm/trunk/src/c/toolkits/codipack/codipackincludes.h =================================================================== --- /issm/trunk/src/c/toolkits/codipack/codipackincludes.h (revision 23394) +++ /issm/trunk/src/c/toolkits/codipack/codipackincludes.h (revision 23394) @@ -0,0 +1,11 @@ +/* \file codipackincludes.h + * \brief all includes for CoDiPack layer + */ + +#ifndef _COIDPACK_INCLUDES_H_ +#define _COIDPACK_INCLUDES_H_ + +#include "./CoDiPackCommon.hpp" +#include "./CoDiPackGlobal.h" + +#endif Index: /issm/trunk/src/c/toolkits/gsl/DenseGslSolve.cpp =================================================================== --- /issm/trunk/src/c/toolkits/gsl/DenseGslSolve.cpp (revision 23393) +++ /issm/trunk/src/c/toolkits/gsl/DenseGslSolve.cpp (revision 23394) @@ -14,4 +14,5 @@ #include "../../classes/Params/Parameters.h" #include "../adolc/adolcincludes.h" +#include "../codipack/codipackincludes.h" #include "./gslincludes.h" @@ -251,2 +252,149 @@ /*}}}*/ #endif + +#ifdef _HAVE_CODIPACK_ +void SolverxSeq_codi_b(void* tape_in,void* data_in,void* ra) {/*{{{*/ + + /*recast data_in and tape*/ + codi::DataStore* data = (codi::DataStore*)data_in; + //IssmDouble::TapeType& tape = (IssmDouble::TapeType&)tape_in; + IssmDouble::TapeType& tape = IssmDouble::getGlobalTape(); + + IssmDouble::Real* valueATrans; + IssmDouble::GradientData* indexATrans; + IssmDouble::GradientData* indexB; + IssmDouble::Real* valueX; + IssmDouble::GradientData* indexX; + int n; + + data->getData(valueATrans); + data->getData(indexATrans); + data->getData(indexB); + data->getData(valueX); + data->getData(indexX); + data->getData(n); + + + // create the adjoint vector for x and reset the adjoint values on the tape + IssmDouble::GradientValue* adjX = xNew(n); + getVectorAdjoint(tape, indexX, adjX, n); + + IssmDouble::GradientValue* sol = xNew(n); + SolverxSeq(sol, valueATrans, adjX, n); + + updateVectorAdjoint(tape, indexB, sol, n); + for(int i=0; igetData(valueATrans); + data->getData(indexATrans); + data->getData(indexB); + data->getData(valueX); + data->getData(indexX); + data->getData(n); + + xDelete(valueATrans); + xDelete(indexATrans); + xDelete(indexB); + xDelete(valueX); + xDelete(indexX); +} +/*}}}*/ +void SolverxSeq(IssmDouble *X,IssmDouble *A,IssmDouble *B,int n, Parameters* parameters){/*{{{*/ + IssmDouble::TapeType& tape = IssmDouble::getGlobalTape(); + codi::DataStore* dataHandler = NULL; + + if(tape.isActive()) { + dataHandler = new codi::DataStore(); + + // create the index vector and the double data for A and B + IssmDouble::Real* valueATrans = xNew(n*n); + IssmDouble::GradientData* indexATrans = xNew(n*n); + + // read the data for matrix in a transposed fashion + for (int i=0; i(n); + getVectorGradData(B, indexB, n); + + dataHandler->addData(valueATrans); + dataHandler->addData(indexATrans); + dataHandler->addData(indexB); + } + + // unpack the primal values from the matrix and the vector + IssmDouble::Real* valueA = xNew(n*n); + IssmDouble::Real* valueB = xNew(n); + // read the data from A and B + getVectorPrimal(A, valueA, n*n); + getVectorPrimal(B, valueB, n); + + // create the placeholder for X and solve the system + IssmDouble::Real* valueX = xNew(n); + SolverxSeq(valueX, valueA, valueB, n); + + // pack the values into x + setVectorPrimal(X, valueX, n); + + if(tape.isActive()) { + // create the index vector X and register x as active variables + IssmDouble::GradientData* indexX = xNew(n); + registerVector(X, indexX, n); + + dataHandler->addData(valueX); + dataHandler->addData(indexX); + + // store other arguments + dataHandler->addData(n); + + tape.pushExternalFunctionHandle(&SolverxSeq_codi_b, dataHandler, &SolverxSeq_codi_delete); + } else { + // if the tape is active valueX is stored in the dataHandler and deleted in the reverse sweep + xDelete(valueX); + } + + xDelete(valueB); + xDelete(valueA); +} +/*}}}*/ +void DenseGslSolve(/*output*/ IssmDouble** px,/*stiffness matrix:*/ IssmDouble* Kff, int Kff_M, int Kff_N, /*right hand side load vector: */ IssmDouble* pf, int pf_M, Parameters* parameters){ /*{{{*/ + + /*Intermediary: */ + + if(Kff_N!=pf_M)_error_("Right hand side vector of size " << pf_M << ", when matrix is of size " << Kff_M << "-" << Kff_N << " !"); + if(Kff_M!=Kff_N)_error_("Stiffness matrix should be square!"); + + IssmDouble *x = xNew(Kff_N,"t"); + + SolverxSeq(x,Kff,pf,Kff_N,parameters); + + /*allocate output pointers: */ + *px=x; +} +/*}}}*/ +#endif Index: /issm/trunk/src/c/toolkits/issm/IssmToolkitUtils.cpp =================================================================== --- /issm/trunk/src/c/toolkits/issm/IssmToolkitUtils.cpp (revision 23393) +++ /issm/trunk/src/c/toolkits/issm/IssmToolkitUtils.cpp (revision 23394) @@ -86,16 +86,15 @@ int IssmSolverTypeFromToolkitOptions(void){ /*{{{*/ - char* solver_type=NULL; int solver_type_enum; - int num_procs=0; bool isparallel=false; /*first, figure out if we are running in parallel: */ - num_procs=IssmComm::GetSize(); + int num_procs=IssmComm::GetSize(); if(num_procs>1)isparallel=true; /*retrieve solver type as a string, from the Toolkits Options database, similar to what Petsc does. Actually, *we try and stick with the Petsc vector types: */ - solver_type=ToolkitOptions::GetToolkitOptionValue("solver_type"); + char* solver_type=ToolkitOptions::GetToolkitOptionValue("solver_type"); + if(!solver_type) _error_("Solver not set"); if (strcmp(solver_type,"mumps")==0){ Index: /issm/trunk/src/c/toolkits/mpi/issmmpi.cpp =================================================================== --- /issm/trunk/src/c/toolkits/mpi/issmmpi.cpp (revision 23393) +++ /issm/trunk/src/c/toolkits/mpi/issmmpi.cpp (revision 23394) @@ -42,5 +42,5 @@ assert(sendcount==recvcount || sendtype==recvtype); // we handle only identical representations #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=AMPI_Allgather(sendbuf, sendcount, @@ -60,5 +60,5 @@ # endif #else -# ifdef _HAVE_ADOLC_ +# ifdef _HAVE_AD_ if (sendtype==ISSM_MPI_DOUBLE) { IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; @@ -76,5 +76,5 @@ assert(sendtype==recvtype); // we handle only identical representations #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=AMPI_Allgatherv(sendbuf, sendcount, @@ -97,5 +97,5 @@ #else assert(sendcount==recvcounts[0]); // we handle only identical representations -# ifdef _HAVE_ADOLC_ +# ifdef _HAVE_AD_ if (sendtype==ISSM_MPI_DOUBLE) { IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; @@ -113,5 +113,5 @@ int rc=0; #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=AMPI_Allreduce(sendbuf, recvbuf, @@ -129,5 +129,5 @@ # endif #else -# ifdef _HAVE_ADOLC_ +#ifdef _HAVE_AD_ if (datatype==ISSM_MPI_DOUBLE) { IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; @@ -145,5 +145,5 @@ int rc=0; #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=AMPI_Barrier(comm); # else @@ -159,5 +159,5 @@ int rc=0; #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=AMPI_Bcast(buffer, count, @@ -181,5 +181,5 @@ int rc=0; #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) assert(0); // to be implemented # else @@ -215,12 +215,19 @@ int ISSM_MPI_Finalize(void){ /*{{{*/ - int rc=0; -#ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ - rc=AMPI_Finalize_NT(); -# else - rc=MPI_Finalize(); -# endif -#endif + int rc=0; + #ifdef _HAVE_MPI_ + #if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + #if defined(_HAVE_ADJOINTMPI_) + rc=AMPI_Finalize(); + #elif defined(_HAVE_MEDIPACK_) + TOOL::finalize(); + rc=AMPI_Finalize(); + #else + rc=AMPI_Finalize_NT(); + #endif + #else + rc=MPI_Finalize(); + #endif + #endif return rc; }/*}}}*/ @@ -230,5 +237,5 @@ assert(sendtype==recvtype && sendcnt==recvcnt); // we handle only identical representations #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=AMPI_Gather(sendbuf, sendcnt, @@ -250,5 +257,5 @@ # endif #else -# ifdef _HAVE_ADOLC_ +# ifdef _HAVE_AD_ if (sendtype==ISSM_MPI_DOUBLE) { IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; @@ -267,5 +274,5 @@ assert(sendtype==recvtype); // we handle only identical representations #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=AMPI_Gatherv(sendbuf, sendcnt, @@ -290,5 +297,5 @@ #else assert(sendcnt==recvcnts[0]); // we handle only identical representations -# ifdef _HAVE_ADOLC_ +#ifdef _HAVE_AD_ if (sendtype==ISSM_MPI_DOUBLE) { IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; @@ -304,12 +311,19 @@ int ISSM_MPI_Init(int *argc, char ***argv){ /*{{{*/ - int rc=0; -#ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ - rc=AMPI_Init_NT(argc,argv); -# else - rc=MPI_Init(argc,argv); -# endif -#endif + int rc=0; + #ifdef _HAVE_MPI_ + #if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + #if defined(_HAVE_ADJOINTMPI_) + rc=AMPI_Init(argc,argv); + #elif defined(_HAVE_MEDIPACK_) + rc=AMPI_Init(argc,argv); + TOOL::init(); + #else + rc=AMPI_Init_NT(argc,argv); + #endif + #else + rc=MPI_Init(argc,argv); + #endif + #endif return rc; }/*}}}*/ @@ -318,5 +332,5 @@ int rc=0; #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=AMPI_Recv(buf, count, @@ -324,5 +338,7 @@ source, tag, + #if !defined(_HAVE_ADJOINTMPI_) && !defined(_HAVE_MEDIPACK_) AMPI_FROM_SEND, // as long as there are no other variants + #endif comm, status); @@ -347,5 +363,5 @@ int rc=0; #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=AMPI_Reduce(sendbuf, recvbuf, @@ -365,5 +381,5 @@ # endif #else -# ifdef _HAVE_ADOLC_ +# ifdef _HAVE_AD_ if (datatype==ISSM_MPI_DOUBLE) { IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; @@ -382,5 +398,5 @@ assert(sendtype==recvtype && sendcnt==recvcnt); // we handle only identical representations #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=AMPI_Scatter(sendbuf, sendcnt, @@ -402,5 +418,5 @@ # endif #else -# ifdef _HAVE_ADOLC_ +# ifdef _HAVE_AD_ if (sendtype==ISSM_MPI_DOUBLE) { IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; @@ -419,5 +435,5 @@ assert(sendtype==recvtype); // we handle only identical representations #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=AMPI_Scatterv(sendbuf, sendcnts, @@ -442,5 +458,5 @@ #else assert(sendcnts[0]==recvcnt); // we handle only identical representations -# ifdef _HAVE_ADOLC_ +# ifdef _HAVE_AD_ if (sendtype==ISSM_MPI_DOUBLE) { IssmDouble* activeSendBuf=(IssmDouble*)(sendbuf)+displs[0]; @@ -458,5 +474,5 @@ int rc=0; #ifdef _HAVE_MPI_ -# ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=AMPI_Send(buf, count, @@ -464,5 +480,7 @@ dest, tag, + #if !defined(_HAVE_ADJOINTMPI_) && !defined(_HAVE_MEDIPACK_) AMPI_TO_RECV, // as long as there are no other variants + #endif comm); # else @@ -492,4 +510,6 @@ #ifdef _HAVE_ADOLC_ ensureContiguousLocations(aSize); +#else + fprintf(stderr, "*** Codipack ISSM_MPI_ContiguousInAdolc()\n"); #endif }/*}}}*/ @@ -498,5 +518,5 @@ int rc=0; #ifdef _HAVE_MPI_ -#ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=MPI_Comm_split(comm, color, key, newcomm); #else @@ -512,5 +532,5 @@ int rc=0; #ifdef _HAVE_MPI_ -#ifdef _HAVE_AMPI_ +#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) rc=MPI_Intercomm_create(comm,local_leader,peer_comm,remote_leader,tag,newintercomm); #else Index: /issm/trunk/src/c/toolkits/mpi/issmmpi.h =================================================================== --- /issm/trunk/src/c/toolkits/mpi/issmmpi.h (revision 23393) +++ /issm/trunk/src/c/toolkits/mpi/issmmpi.h (revision 23394) @@ -16,8 +16,27 @@ #include "../../shared/Numerics/types.h" -#ifdef _HAVE_MPI_ +#if defined(_HAVE_MPI_) /*Include header files: {{{*/ - #ifdef _HAVE_AMPI_ - #include + #if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + #if defined(_HAVE_ADJOINTMPI_) + #include + + #elif defined(_HAVE_MEDIPACK_) + #include "medi/medi.hpp" + using namespace medi; + #include "medi/codiMediPackTypes.hpp" + #if defined(_HAVE_CODIPACK_) + #define TOOL CoDiPackTool + #define AMPI_ADOUBLE TOOL::MPI_TYPE + #elif defined(_HAVE_ADOLC_) + #include "adolc/medipacksupport.h" + #define TOOL AdolcTool + #else + #error "don't know about AD tool" + #endif + + #else + #include + #endif #elif _HAVE_PETSC_MPI_ // Petsc now hides there MPI header. It can be reached through Petsc. #include @@ -27,31 +46,58 @@ /*}}}*/ /*MPI defines: *{{{*/ + // types + #if defined(_HAVE_MEDIPACK_) && !defined(_WRAPPERS_) + typedef AMPI_Comm ISSM_MPI_Comm; + typedef AMPI_Datatype ISSM_MPI_Datatype; + typedef AMPI_Op ISSM_MPI_Op; + typedef AMPI_Status ISSM_MPI_Status; + #else typedef MPI_Comm ISSM_MPI_Comm; typedef MPI_Datatype ISSM_MPI_Datatype; typedef MPI_Op ISSM_MPI_Op; typedef MPI_Status ISSM_MPI_Status; + #endif - // data types - #define ISSM_MPI_CHAR MPI_CHAR - #ifdef _HAVE_AMPI_ - #define ISSM_MPI_DOUBLE AMPI_ADOUBLE // corresponds to IssmDouble - #else - #define ISSM_MPI_DOUBLE MPI_DOUBLE // corresponds to IssmDouble + #if defined(_HAVE_MEDIPACK_) && !defined(_WRAPPERS_) + #define ISSM_MPI_CHAR AMPI_CHAR + #define ISSM_MPI_DOUBLE AMPI_ADOUBLE // corresponds to IssmDouble + #define ISSM_MPI_PDOUBLE AMPI_DOUBLE // corresponds to IssmPDouble + #define ISSM_MPI_INT AMPI_INT + + // operations + #define ISSM_MPI_MAX AMPI_MAX + #define ISSM_MPI_MIN AMPI_MIN + #define ISSM_MPI_PROD AMPI_PROD + #define ISSM_MPI_SUM AMPI_SUM + + // others + #define ISSM_MPI_COMM_WORLD AMPI_COMM_WORLD + #define ISSM_MPI_STATUS_IGNORE AMPI_STATUS_IGNORE + #define ISSM_MPI_ANY_TAG AMPI_ANY_TAG + #define ISSM_MPI_ANY_SOURCE AMPI_ANY_SOURCE + + #else + #if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + #define ISSM_MPI_DOUBLE AMPI_ADOUBLE + #else + #define ISSM_MPI_DOUBLE MPI_DOUBLE + #endif + #define ISSM_MPI_PDOUBLE MPI_DOUBLE + #define ISSM_MPI_INT MPI_INT + #define ISSM_MPI_CHAR MPI_CHAR + + // operations + #define ISSM_MPI_MAX MPI_MAX + #define ISSM_MPI_MIN MPI_MIN + #define ISSM_MPI_PROD MPI_PROD + #define ISSM_MPI_SUM MPI_SUM + + // others + #define ISSM_MPI_COMM_WORLD MPI_COMM_WORLD + #define ISSM_MPI_STATUS_IGNORE MPI_STATUS_IGNORE + #define ISSM_MPI_ANY_TAG MPI_ANY_TAG + #define ISSM_MPI_ANY_SOURCE MPI_ANY_SOURCE #endif - #define ISSM_MPI_PDOUBLE MPI_DOUBLE // corresponds to IssmPDouble - #define ISSM_MPI_INT MPI_INT - - // operations - #define ISSM_MPI_MAX MPI_MAX - #define ISSM_MPI_MIN MPI_MIN - #define ISSM_MPI_PROD MPI_PROD - #define ISSM_MPI_SUM MPI_SUM - - // others - #define ISSM_MPI_COMM_WORLD MPI_COMM_WORLD - #define ISSM_MPI_STATUS_IGNORE MPI_STATUS_IGNORE - #define ISSM_MPI_ANY_TAG MPI_ANY_TAG - #define ISSM_MPI_ANY_SOURCE MPI_ANY_SOURCE /*other include files: */ @@ -90,5 +136,5 @@ template ISSM_MPI_Datatype TypeToMPIType(){assert(false);}; template <> inline ISSM_MPI_Datatype TypeToMPIType(){return ISSM_MPI_DOUBLE;}; -#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) +#if defined(_HAVE_AD_) && !defined(_WRAPPERS_) template <> inline ISSM_MPI_Datatype TypeToMPIType(){return ISSM_MPI_PDOUBLE;}; #endif Index: /issm/trunk/src/c/toolkits/mumps/MumpsSolve.cpp =================================================================== --- /issm/trunk/src/c/toolkits/mumps/MumpsSolve.cpp (revision 23393) +++ /issm/trunk/src/c/toolkits/mumps/MumpsSolve.cpp (revision 23394) @@ -18,4 +18,5 @@ #include "../mpi/issmmpi.h" #include "../adolc/adolcincludes.h" +#include "../codipack/codipackincludes.h" #include "../issm/SparseRow.h" #include "./mumpsincludes.h" @@ -25,4 +26,9 @@ void MumpsInit(DMUMPS_STRUC_C &theMumpsStruc){ + theMumpsStruc.n = 0; + theMumpsStruc.nz = 0; + theMumpsStruc.a = NULL; + theMumpsStruc.jcn = NULL; + theMumpsStruc.irn = NULL; theMumpsStruc.par = 1; theMumpsStruc.sym = 0; @@ -98,5 +104,5 @@ } -#ifdef _HAVE_ADOLC_ +#ifdef _HAVE_AD_ // prototype for active variant void MumpsSolve(int n, @@ -354,6 +360,5 @@ #ifdef _HAVE_ADOLC_ - -int mumpsSolveEDF(int iArrLength, int* iArr, int /* ignored */, IssmPDouble* dp_x, int /* ignored */, IssmPDouble* dp_y) { +int mumpsSolveEDF(int iArrLength, int* iArr, int /* ignored */, IssmPDouble* dp_x, int /* ignored */, IssmPDouble* dp_y){/*{{{*/ // unpack parameters int n=iArr[0]; @@ -381,7 +386,6 @@ xDelete(local_irn); return 0; -} - -void MumpsSolve(int n,int nnz,int local_nnz,int* irn_loc,int* jcn_loc,IssmDouble *a_loc,IssmDouble *rhs,Parameters* parameters){ +}/*}}}*/ +void MumpsSolve(int n,int nnz,int local_nnz,int* irn_loc,int* jcn_loc,IssmDouble *a_loc,IssmDouble *rhs,Parameters* parameters){/*{{{*/ int packedDimsSparseArrLength=1+1+1+local_nnz+local_nnz; int *packedDimsSparseArr=xNew(packedDimsSparseArrLength); @@ -425,10 +429,6 @@ xDelete(pack_A_rhs); xDelete(packedDimsSparseArr); -} - -int fos_reverse_mumpsSolveEDF(int iArrLength, int* iArr, - int m, IssmPDouble *dp_U, - int nPlusNz, IssmPDouble *dp_Z, - IssmPDouble *dp_x, IssmPDouble *dp_y) { +}/*}}}*/ +int fos_reverse_mumpsSolveEDF(int iArrLength, int* iArr, int m, IssmPDouble *dp_U, int nPlusNz, IssmPDouble *dp_Z, IssmPDouble *dp_x, IssmPDouble *dp_y) {/*{{{*/ // unpack parameters int n=iArr[0]; @@ -481,5 +481,168 @@ xDelete(local_irn); return 3; -} - -#endif +}/*}}}*/ +#endif + +#ifdef _HAVE_CODIPACK_ +void MumpsSolve_codi_b(void* tape_in,void* data_in,void* ra) {/*{{{*/ + + /*recast data_in and tape*/ + codi::DataStore* data = (codi::DataStore*)data_in; + //IssmDouble::TapeType& tape = (IssmDouble::TapeType&)tape_in; + IssmDouble::TapeType& tape = IssmDouble::getGlobalTape(); + + + IssmDouble::Real* valueATrans; + IssmDouble::GradientData* indexATrans; + int* irnATrans; + int* jcnATrans; + IssmDouble::GradientData* indexB; + IssmDouble::Real* valueX; + IssmDouble::GradientData* indexX; + int n; + int nnz; + int local_nnz; + Parameters* parameters; + + data->getData(valueATrans); + data->getData(indexATrans); + data->getData(irnATrans); + data->getData(jcnATrans); + data->getData(indexB); + data->getData(valueX); + data->getData(indexX); + data->getData(n); + data->getData(nnz); + data->getData(local_nnz); + data->getData(parameters); + + // create the adjoint vector for x and reset the adjoint values on the tape + IssmDouble::GradientValue* adjX = xNew(n); + getVectorAdjoint(tape, indexX, adjX, n); + + MumpsSolve(n, nnz, local_nnz, irnATrans, jcnATrans, valueATrans, adjX, parameters); + // adjX contains now the solution + + updateVectorAdjoint(tape, indexB, adjX, n); + + // bcast dp_y (the solution of the forward system) + ISSM_MPI_Bcast(valueX,n,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + // bcast the adjoint of the right-hand-side, i.e. this solution + ISSM_MPI_Bcast(adjX,n,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + + for(int i=0; igetData(valueATrans); + data->getData(indexATrans); + data->getData(irnATrans); + data->getData(jcnATrans); + data->getData(indexB); + data->getData(valueX); + data->getData(indexX); + data->getData(n); + data->getData(nnz); + data->getData(local_nnz); + data->getData(parameters); + + xDelete(valueATrans); + xDelete(indexATrans); + xDelete(irnATrans); + xDelete(jcnATrans); + xDelete(indexB); + xDelete(valueX); + xDelete(indexX); +} +/*}}}*/ +void MumpsSolve(int n,int nnz,int local_nnz,int* irn_loc,int* jcn_loc,IssmDouble *a_loc,IssmDouble *rhs,Parameters* parameters){/*{{{*/ + IssmDouble::TapeType& tape = IssmDouble::getGlobalTape(); + codi::DataStore* dataHandler = NULL; + + if(tape.isActive()) { + dataHandler = new codi::DataStore(); + + // create the index and double vector for the matrix + IssmDouble::Real* valueATrans = xNew(local_nnz); + IssmDouble::GradientData* indexATrans = xNew(local_nnz); + int* irnATrans = xNew(local_nnz); + int* jcnATrans = xNew(local_nnz); + + // read the data for the matrix A in a transposed fashion + for (int i=0; i(n); + getVectorGradData(rhs, indexB, n); + + dataHandler->addData(valueATrans); + dataHandler->addData(indexATrans); + dataHandler->addData(irnATrans); + dataHandler->addData(jcnATrans); + dataHandler->addData(indexB); + } + + // unpack the primal values from the matrix and the vector + IssmDouble::Real* valueA = xNew(local_nnz); + IssmDouble::Real* valueB = xNew(n); + // read the data from A and B + getVectorPrimal(a_loc, valueA, local_nnz); + getVectorPrimal(rhs, valueB, n); + + MumpsSolve(n, nnz, local_nnz, irn_loc, jcn_loc, valueA, valueB, parameters); + // valueB contains now the solution + + // pack the values into rhs + setVectorPrimal(rhs, valueB, n); + + if(tape.isActive()) { + // create the index vector X and register x as active variables + IssmDouble::GradientData* indexX = xNew(n); + registerVector(rhs, indexX, n); + + dataHandler->addData(valueB); // contains the values from x + dataHandler->addData(indexX); + + // store other arguments + dataHandler->addData(n); + dataHandler->addData(nnz); + dataHandler->addData(local_nnz); + dataHandler->addData(parameters); // we assume here that parameters is still intact when the reverse run is called + + //tape.pushExternalFunction(&MumpsSolve_codi_b, dataHandler, &MumpsSolve_codi_delete); + tape.pushExternalFunctionHandle(&MumpsSolve_codi_b,(void*)dataHandler, &MumpsSolve_codi_delete); + } else { + // if the tape is active valueB is stored in the dataHandler and deleted in the reverse sweep + xDelete(valueB); + } + + xDelete(valueA); +} +/*}}}*/ +#endif Index: /issm/trunk/src/c/toolkits/petsc/objects/PetscMat.cpp =================================================================== --- /issm/trunk/src/c/toolkits/petsc/objects/PetscMat.cpp (revision 23393) +++ /issm/trunk/src/c/toolkits/petsc/objects/PetscMat.cpp (revision 23394) @@ -21,5 +21,5 @@ PetscMat::PetscMat(){/*{{{*/ this->matrix=NULL; - #ifdef _HAVE_ADOLC_ + #ifdef _HAVE_AD_ this->amatrix=NULL; #endif Index: /issm/trunk/src/c/toolkits/petsc/objects/PetscMat.h =================================================================== --- /issm/trunk/src/c/toolkits/petsc/objects/PetscMat.h (revision 23393) +++ /issm/trunk/src/c/toolkits/petsc/objects/PetscMat.h (revision 23394) @@ -27,5 +27,5 @@ Mat matrix; - #ifdef _HAVE_ADOLC_ + #ifdef _HAVE_AD_ IssmDouble* amatrix; #endif Index: /issm/trunk/src/c/toolkits/petsc/objects/PetscSolver.cpp =================================================================== --- /issm/trunk/src/c/toolkits/petsc/objects/PetscSolver.cpp (revision 23393) +++ /issm/trunk/src/c/toolkits/petsc/objects/PetscSolver.cpp (revision 23394) @@ -15,4 +15,5 @@ #include "../../../shared/io/Comm/IssmComm.h" #include "../../../shared/Enum/Enum.h" +#include "../../../shared/io/Print/Print.h" void PetscSolve(PetscVec** puf, PetscMat* Kff, PetscVec* pf, PetscVec* uf0,PetscVec* df, Parameters* parameters){ /*{{{*/ @@ -156,4 +157,5 @@ KSPGetIterationNumber(ksp,&iteration_number); if (iteration_number<0) _error_("Solver diverged at iteration number: " << -iteration_number); + if (VerboseSolver()) _printf0_("Petsc: "<< iteration_number << " KSP iterations\n"); /*Free resources:*/ Index: /issm/trunk/src/c/toolkits/petsc/objects/PetscVec.cpp =================================================================== --- /issm/trunk/src/c/toolkits/petsc/objects/PetscVec.cpp (revision 23393) +++ /issm/trunk/src/c/toolkits/petsc/objects/PetscVec.cpp (revision 23394) @@ -21,5 +21,5 @@ PetscVec::PetscVec(){/*{{{*/ this->vector=NULL; - #ifdef _HAVE_ADOLC_ + #ifdef _HAVE_AD_ this->avector=NULL; #endif Index: /issm/trunk/src/c/toolkits/petsc/objects/PetscVec.h =================================================================== --- /issm/trunk/src/c/toolkits/petsc/objects/PetscVec.h (revision 23393) +++ /issm/trunk/src/c/toolkits/petsc/objects/PetscVec.h (revision 23394) @@ -25,5 +25,5 @@ Vec vector; - #ifdef _HAVE_ADOLC_ + #ifdef _HAVE_AD_ IssmDouble* avector; #endif Index: /issm/trunk/src/c/toolkits/toolkits.h =================================================================== --- /issm/trunk/src/c/toolkits/toolkits.h (revision 23393) +++ /issm/trunk/src/c/toolkits/toolkits.h (revision 23394) @@ -30,4 +30,8 @@ #endif +#ifdef _HAVE_CODIPACK_ +#include "./codipack/codipackincludes.h" +#endif + #ifdef _HAVE_TRIANGLE_ #include "./triangle/triangleincludes.h" Index: /issm/trunk/src/m/classes/SMBgradientscomponents.m =================================================================== --- /issm/trunk/src/m/classes/SMBgradientscomponents.m (revision 23394) +++ /issm/trunk/src/m/classes/SMBgradientscomponents.m (revision 23394) @@ -0,0 +1,90 @@ +%SMBgradientscomponents Class definition +% +% Usage: +% SMBgradientscomponents=SMBgradientscomponents(); + +classdef SMBgradientscomponents + properties (SetAccess=public) + accuref = NaN; + accualti = NaN; + accugrad = NaN; + runoffref = NaN; + runoffalti = NaN; + runoffgrad = NaN; + requested_outputs = {}; + end + methods + function self=SMBgradientscomponents(varargin) % {{{ + switch nargin + case 0 + self=setdefaultparameters(self); + otherwise + error('constructor not supported'); + end + end % }}} + + function self = extrude(self,md) % {{{ + + %Nothing for now + + end % }}} + function list = defaultoutputs(self,md) % {{{ + list = {'runoff'}; + end % }}} + function self = initialize(self,md) % {{{ + + %Nothing done for now + + end % }}} + function self = setdefaultparameters(self) % {{{ + + %Nothing for now + + end % }}} + function md=checkconsistency(self,md,solution,analyses) % {{{ + if ismember('MasstransportAnalysis',analyses), + md = checkfield(md,'fieldname','smb.accuref','timeseries',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.accualti','numel',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.accugrad','numel',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.runoffref','timeseries',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.runoffalti','numel',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.runoffgrad','numel',1,'NaN',1,'Inf',1); + end + md = checkfield(md,'fieldname','masstransport.requested_outputs','stringrow',1); + end % }}} + + function disp(self) % {{{ + disp(sprintf(' surface forcings parameters:')); + disp(sprintf('\n SMB gradients components parameters:')); + fielddisplay(self,'accuref',' reference value of the accumulation'); + fielddisplay(self,'accualti',' Altitude at which the accumulation is equal to the reference value'); + fielddisplay(self,'accugrad',' Gradient of the variation of the accumulation (0 for uniform accumulation)'); + fielddisplay(self,'runoffref',' reference value of the runoff m w.e. y-1 (temperature times ddf)'); + fielddisplay(self,'runoffalti',' Altitude at which the runoff is equal to the reference value'); + fielddisplay(self,'runoffgrad',' Gradient of the variation of the runoff (0 for uniform runoff) m w.e. m-1 y-1 (lpase rate times ddf)'); + fielddisplay(self,'requested_outputs','additional outputs requested'); + + end % }}} + function marshall(self,prefix,md,fid) % {{{ + + WriteData(fid,prefix,'name','md.smb.model','data',11,'format','Integer'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accuref','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts,'scale',1./md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accualti','format','Double'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accugrad','format','Double','scale',1./md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoffref','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts,'scale',1./md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoffalti','format','Double'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoffgrad', ... + 'format','Double','scale',1./md.constants.yts); + + %process requested outputs + outputs = self.requested_outputs; + pos = find(ismember(outputs,'default')); + if ~isempty(pos), + outputs(pos) = []; %remove 'default' from outputs + outputs = [outputs defaultoutputs(self,md)]; %add defaults + end + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray'); + + end % }}} + end +end Index: /issm/trunk/src/m/classes/SMBgradientscomponents.py =================================================================== --- /issm/trunk/src/m/classes/SMBgradientscomponents.py (revision 23394) +++ /issm/trunk/src/m/classes/SMBgradientscomponents.py (revision 23394) @@ -0,0 +1,78 @@ +from fielddisplay import fielddisplay +from checkfield import checkfield +from WriteData import WriteData +from project3d import project3d + +class SMBgradientscomponents(object): + """ + SMBgradients Class definition + + Usage: + SMBgradients=SMBgradientscomponents(); + For now it has accumulation, runoff ans retention which could be aither refreezing and/or evaporation + """ + + def __init__(self): # {{{ + self.accuref = float('NaN') + self.accualti = float('NaN') + self.accugrad = float('NaN') + self.runoffref = float('NaN') + self.runoffalti = float('NaN') + self.runoffgrad = float('NaN') + self.requested_outputs = ['default'] + #}}} + def __repr__(self): # {{{ + string=" surface forcings parameters:" + string="%s\n%s"%(string,fielddisplay(self,'accuref',' reference value of the accumulation')) + string="%s\n%s"%(string,fielddisplay(self,'accualti',' Altitude at which the accumulation is equal to the reference value')) + string="%s\n%s"%(string,fielddisplay(self,'accugrad',' Gradient of the variation of the accumulation (0 for uniform accumulation)')) + string="%s\n%s"%(string,fielddisplay(self,'runoffref',' reference value of the runoff m w.e. y-1 (temperature times ddf)')) + string="%s\n%s"%(string,fielddisplay(self,'runoffalti',' Altitude at which the runoff is equal to the reference value')) + string="%s\n%s"%(string,fielddisplay(self,'runoffgrad',' Gradient of the variation of the runoff (0 for uniform runoff) m w.e. m-1 y-1 (lpase rate times ddf)')) + string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','additional outputs requested')) + + return string + #}}} + def extrude(self,md): # {{{ + #Nothing for now + return self + #}}} + def defaultoutputs(self,md): # {{{ + return ['SmbMassBalance','SmbRunoff'] + #}}} + def initialize(self,md): # {{{ + #Nothing for now + return self + #}}} + def checkconsistency(self,md,solution,analyses): # {{{ + if 'MasstransportAnalysis' in analyses: + md = checkfield(md,'fieldname','smb.accuref','singletimeseries',1,'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.accualti','numel',[1],'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.accugrad','numel',[1],'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.runoffref','singletimeseries',1,'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.runoffalti','numel',[1],'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.runoffgrad','numel',[1],'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','masstransport.requested_outputs','stringrow',1) + return md + # }}} + def marshall(self,prefix,md,fid): # {{{ + + yts=md.constants.yts + + WriteData(fid,prefix,'name','md.smb.model','data',11,'format','Integer') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accuref','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts,'scale',1./md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accualti','format','Double') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accugrad','format','Double','scale',1./md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoffref','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts,'scale',1./md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoffalti','format','Double') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoffgrad','format','Double','scale',1./md.constants.yts) + + #process requested outputs + outputs = self.requested_outputs + indices = [i for i, x in enumerate(outputs) if x == 'default'] + if len(indices) > 0: + outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] + outputs =outputscopy + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray') + + # }}} Index: /issm/trunk/src/m/classes/SMBpddSicopolis.m =================================================================== --- /issm/trunk/src/m/classes/SMBpddSicopolis.m (revision 23394) +++ /issm/trunk/src/m/classes/SMBpddSicopolis.m (revision 23394) @@ -0,0 +1,133 @@ +%SMBpddSicopolis Class definition +% +% Usage: +% SMBpddSicopolis=SMBpddSicopolis(); + +classdef SMBpddSicopolis + properties (SetAccess=public) + precipitation = NaN; + monthlytemperatures = NaN; + temperature_anomaly = NaN; + precipitation_anomaly = NaN; + smb_corr = NaN; + desfac = 0; + s0p = NaN; + s0t = NaN; + rlaps = 0; + isfirnwarming = 0; + requested_outputs = {}; + end + methods + function self = SMBpddSicopolis(varargin) % {{{ + switch nargin + case 0 + self=setdefaultparameters(self); + otherwise + error('constructor not supported'); + end + end % }}} + function self = extrude(self,md) % {{{ + self.precipitation=project3d(md,'vector',self.precipitation,'type','node'); + self.monthlytemperatures=project3d(md,'vector',self.monthlytemperatures,'type','node'); + self.temperature_anomaly=project3d(md,'vector',self.temperature_anomaly,'type','node'); + self.precipitation_anomaly=project3d(md,'vector',self.precipitation_anomaly,'type','node'); + self.smb_corr=project3d(md,'vector',self.smb_corr,'type','node'); + self.s0p=project3d(md,'vector',self.s0p,'type','node'); + self.s0t=project3d(md,'vector',self.s0t,'type','node'); + + end % }}} + function list = defaultoutputs(self,md) % {{{ + list = {''}; + end % }}} + function self = initialize(self,md) % {{{ + + if isnan(self.s0p), + self.s0p=zeros(md.mesh.numberofvertices,1); + disp(' no SMBpddSicopolis.s0p specified: values set as zero'); + end + if isnan(self.s0t), + self.s0t=zeros(md.mesh.numberofvertices,1); + disp(' no SMBpddSicopolis.s0t specified: values set as zero'); + end + if isnan(self.temperature_anomaly), + self.temperature_anomaly=zeros(md.mesh.numberofvertices,1); + disp(' no SMBpddSicopolis.temperature_anomaly specified: values set as zero'); + end + if isnan(self.precipitation_anomaly), + self.precipitation_anomaly=ones(md.mesh.numberofvertices,1); + disp(' no SMBpddSicopolis.precipitation_anomaly specified: values set as ones'); + end + if isnan(self.smb_corr), + self.smb_corr=zeros(md.mesh.numberofvertices,1); + disp(' no SMBpddSicopolis.smb_corr specified: values set as zero'); + end + + end % }}} + function self = setdefaultparameters(self) % {{{ + + self.isfirnwarming = 1; + self.desfac = -log(2.0)/1000; + self.rlaps = 7.4; + + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + + if (strcmp(solution,'TransientSolution') & md.transient.issmb == 0), return; end + + if ismember('MasstransportAnalysis',analyses), + md = checkfield(md,'fieldname','smb.desfac','<=',1,'numel',1); + md = checkfield(md,'fieldname','smb.s0p','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1]); + md = checkfield(md,'fieldname','smb.s0t','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1]); + md = checkfield(md,'fieldname','smb.rlaps','>=',0,'numel',1); + md = checkfield(md,'fieldname','smb.monthlytemperatures','timeseries',1,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices+1 12]); + md = checkfield(md,'fieldname','smb.precipitation','timeseries',1,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices+1 12]); + end + md = checkfield(md,'fieldname','smb.requested_outputs','stringrow',1); + + end % }}} + function disp(self) % {{{ + disp(sprintf(' surface forcings parameters:')); + + disp(sprintf('\n SICOPOLIS PDD scheme (Calov & Greve, 2005) :')); + fielddisplay(self,'monthlytemperatures','monthly surface temperatures [K]'); + fielddisplay(self,'precipitation','monthly surface precipitation [m/yr water eq]'); + fielddisplay(self,'temperature_anomaly','anomaly to monthly reference temperature (additive; [K])'); + fielddisplay(self,'precipitation_anomaly','anomaly to monthly precipitation (multiplicative, e.g. q=q0*exp(0.070458*DeltaT) after Huybrechts (2002)); [no unit])'); + fielddisplay(self,'smb_corr','correction of smb after PDD call [m/a]'); + fielddisplay(self,'s0p','should be set to elevation from precip source (between 0 and a few 1000s m, default is 0) [m]'); + fielddisplay(self,'s0t','should be set to elevation from temperature source (between 0 and a few 1000s m, default is 0) [m]'); + fielddisplay(self,'rlaps','present day lapse rate (default is 7.4 degree/km)'); + fielddisplay(self,'desfac','desertification elevation factor (default is -log(2.0)/1000)'); + fielddisplay(self,'isfirnwarming','is firnwarming (Reeh 1991) activated (0 or 1, default is 1)'); + fielddisplay(self,'requested_outputs','additional outputs requested (TemperaturePDD, SmbAccumulation, SmbMelt)'); + end % }}} + function marshall(self,prefix,md,fid) % {{{ + + yts=md.constants.yts; + + WriteData(fid,prefix,'name','md.smb.model','data',10,'format','Integer'); + + WriteData(fid,prefix,'object',self,'class','smb','fieldname','isfirnwarming','format','Boolean'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','desfac','format','Double'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','s0p','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','s0t','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','rlaps','format','Double'); + + WriteData(fid,prefix,'object',self,'class','smb','fieldname','monthlytemperatures','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','temperature_anomaly','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitation_anomaly','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','smb_corr','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + + %process requested outputs + outputs = self.requested_outputs; + pos = find(ismember(outputs,'default')); + if ~isempty(pos), + outputs(pos) = []; %remove 'default' from outputs + outputs = [outputs defaultoutputs(self,md)]; %add defaults + end + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray'); + + end % }}} + end +end Index: /issm/trunk/src/m/classes/SMBpddSicopolis.py =================================================================== --- /issm/trunk/src/m/classes/SMBpddSicopolis.py (revision 23394) +++ /issm/trunk/src/m/classes/SMBpddSicopolis.py (revision 23394) @@ -0,0 +1,153 @@ +import numpy as np +from fielddisplay import fielddisplay +from checkfield import checkfield +from WriteData import WriteData +from project3d import project3d +from MatlabFuncs import * +from helpers import * + +class SMBpddSicopolis(object): + """ + SMBpddSicopolis Class definition + + Usage: + SMBpddSicopolis=SMBpddSicopolis() +""" + + def __init__(self): # {{{ + self.precipitation = float('NaN') + self.monthlytemperatures = float('NaN') + self.temperature_anomaly = float('NaN') + self.precipitation_anomaly = float('NaN') + self.smb_corr = float('NaN') + self.desfac = 0 + self.s0p = float('NaN') + self.s0t = float('NaN') + self.rlaps = 0 + self.isfirnwarming = 0 + self.requested_outputs = [] + + self.setdefaultparameters() + # }}} + + @staticmethod + def SMBpddSicopolis(*args): # {{{ + nargin = len(args) + + if nargin == 0: + return SMBpddSicopolis() + else: + raise RuntimeError('SMBpddSicopolis: constructor not supported') + # }}} + + def extrude(self,md): # {{{ + self.precipitation = project3d(md,'vector',self.precipitation,'type','node') + self.monthlytemperatures = project3d(md,'vector',self.monthlytemperatures,'type','node') + self.temperature_anomaly = project3d(md,'vector',self.temperature_anomaly,'type','node') + self.precipitation_anomaly = project3d(md,'vector',self.precipitation_anomaly,'type','node') + self.smb_corr = project3d(md,'vector',self.smb_corr,'type','node') + self.s0p = project3d(md,'vector',self.s0p,'type','node') + self.s0t = project3d(md,'vector',self.s0t,'type','node') + # }}} + + def defaultoutputs(self,md): # {{{ + l = [''] + return l + # }}} + + def initialize(self,md): # {{{ + + if np.isnan(self.s0p): + self.s0p = np.zeros((md.mesh.numberofvertices,)) + print ' no SMBpddSicopolis.s0p specified: values set as zero' + + if np.isnan(self.s0t): + self.s0t = np.zeros((md.mesh.numberofvertices,)) + print ' no SMBpddSicopolis.s0t specified: values set as zero' + + if np.isnan(self.temperature_anomaly): + self.temperature_anomaly = np.zeros((md.mesh.numberofvertices,)) + print ' no SMBpddSicopolis.temperature_anomaly specified: values set as zero' + + if np.isnan(self.precipitation_anomaly): + self.precipitation_anomaly = np.ones((md.mesh.numberofvertices,)) + print ' no SMBpddSicopolis.precipitation_anomaly specified: values set as ones' + + if np.isnan(self.smb_corr): + self.smb_corr = np.zeros((md.mesh.numberofvertices,)) + print ' no SMBpddSicopolis.smb_corr specified: values set as zero' + # }}} + + def setdefaultparameters(self): # {{{ + + self.isfirnwarming = 1 + self.desfac = -np.log(2.0)/1000 + self.rlaps = 7.4 + + # }}} + + def checkconsistency(self,md,solution,analyses): # {{{ + + if (strcmp(solution,'TransientSolution') and md.transient.issmb == 0): + return + + if 'MasstransportAnalysis' in analyses: + md = checkfield(md,'fieldname','smb.desfac','<=',1,'numel',1) + md = checkfield(md,'fieldname','smb.s0p','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1]) + md = checkfield(md,'fieldname','smb.s0t','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1]) + md = checkfield(md,'fieldname','smb.rlaps','>=',0,'numel',1) + md = checkfield(md,'fieldname','smb.monthlytemperatures','timeseries',1,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices+1,12]) + md = checkfield(md,'fieldname','smb.precipitation','timeseries',1,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices+1,12]) + + md = checkfield(md,'fieldname','smb.requested_outputs','stringrow',1) + + return md + # }}} + + def __repr__(self): # {{{ + string = ' surface forcings parameters:' + string += '\n SICOPOLIS PDD scheme (Calov & Greve, 2005) :' + + string = "%s\n%s"%(string,fielddisplay(self,'monthlytemperatures','monthly surface temperatures [K]')) + string = "%s\n%s"%(string,fielddisplay(self,'precipitation','monthly surface precipitation [m/yr water eq]')) + string = "%s\n%s"%(string,fielddisplay(self,'temperature_anomaly','anomaly to monthly reference temperature (additive [K])')) + string = "%s\n%s"%(string,fielddisplay(self,'precipitation_anomaly','anomaly to monthly precipitation (multiplicative, e.g. q=q0*exp(0.070458*DeltaT) after Huybrechts (2002)) [no unit])')) + string = "%s\n%s"%(string,fielddisplay(self,'smb_corr','correction of smb after PDD call [m/a]')) + string = "%s\n%s"%(string,fielddisplay(self,'s0p','should be set to elevation from precip source (between 0 and a few 1000s m, default is 0) [m]')) + string = "%s\n%s"%(string,fielddisplay(self,'s0t','should be set to elevation from temperature source (between 0 and a few 1000s m, default is 0) [m]')) + string = "%s\n%s"%(string,fielddisplay(self,'rlaps','present day lapse rate (default is 7.4 degree/km)')) + string = "%s\n%s"%(string,fielddisplay(self,'desfac','desertification elevation factor (default is -log(2.0)/1000)')) + string = "%s\n%s"%(string,fielddisplay(self,'isfirnwarming','is firnwarming (Reeh 1991) activated (0 or 1, default is 1)')) + string = "%s\n%s"%(string,fielddisplay(self,'requested_outputs','additional outputs requested (TemperaturePDD, SmbAccumulation, SmbMelt)')) + # }}} + + def marshall(self,prefix,md,fid): # {{{ + + yts=md.constants.yts + + WriteData(fid,prefix,'name','md.smb.model','data',10,'format','Integer') + + WriteData(fid,prefix,'object',self,'class','smb','fieldname','isfirnwarming','format','Boolean') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','desfac','format','Double') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','s0p','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','s0t','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','rlaps','format','Double') + + WriteData(fid,prefix,'object',self,'class','smb','fieldname','monthlytemperatures','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','temperature_anomaly','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitation_anomaly','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','smb_corr','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + + #process requested outputs + outputs = self.requested_outputs + pos = np.where('default' in outputs) + if not isempty(pos): + outputs[pos] = [] #remove 'default' from outputs + outputs = [outputs,defaultoutputs(self,md)] #add defaults + + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray') + + # }}} + + Index: /issm/trunk/src/m/classes/autodiff.js =================================================================== --- /issm/trunk/src/m/classes/autodiff.js (revision 23393) +++ /issm/trunk/src/m/classes/autodiff.js (revision 23394) @@ -14,4 +14,5 @@ this.gcTriggerRatio=2.0; this.gcTriggerMaxSize=65536; + this.tapeAlloc = 15000000; }// }}} @@ -29,4 +30,5 @@ fielddisplay(this,'gcTriggerRatio','free location block sorting/consolidation triggered if the ratio between allocated and used locations exceeds gcTriggerRatio'); fielddisplay(this,'gcTriggerMaxSize','free location block sorting/consolidation triggered if the allocated locations exceed gcTriggerMaxSize'); + fielddisplay(this,'tapeAlloc','Iteration count of a priori memory allocation of the AD tape'); }// }}} @@ -49,4 +51,5 @@ checkfield(md,'fieldname','autodiff.gcTriggerRatio','>=',0); checkfield(md,'fieldname','autodiff.gcTriggerMaxSize','>=',65536); + checkfield(md,'fieldname','autodiff.tapeAlloc','>=',0); //go through our dependents and independents and check consistency: @@ -79,4 +82,5 @@ WriteData(fid,prefix,'object',this,'fieldname','gcTriggerRatio','format','Double'); WriteData(fid,prefix,'object',this,'fieldname','gcTriggerMaxSize','format','Double'); + WriteData(fid,prefix,'object',this,'fieldname','tapeAlloc','format','Integer'); //}}} //process dependent variables {{{ @@ -216,4 +220,5 @@ this.gcTriggerRatio=NullFix(this.gcTriggerRatio,NaN); this.gcTriggerMaxSize=NullFix(this.gcTriggerMaxSize,NaN); + this.tapeAlloc=NullFix(this.tapeAlloc,NaN); }//}}} //properties @@ -229,4 +234,5 @@ this.gcTriggerRatio = NaN; this.gcTriggerMaxSize = NaN; + this.tapeAlloc = NaN; this.setdefaultparameters(); Index: /issm/trunk/src/m/classes/autodiff.m =================================================================== --- /issm/trunk/src/m/classes/autodiff.m (revision 23393) +++ /issm/trunk/src/m/classes/autodiff.m (revision 23394) @@ -17,4 +17,5 @@ gcTriggerRatio = NaN; gcTriggerMaxSize = NaN; + tapeAlloc = NaN; end %}}} @@ -35,4 +36,5 @@ self.gcTriggerRatio=2.0; self.gcTriggerMaxSize=65536; + self.tapeAlloc = 15000000; end % }}} function md = checkconsistency(self,md,solution,analyses) % {{{ @@ -51,4 +53,5 @@ md = checkfield(md,'fieldname','autodiff.gcTriggerRatio','>=',0); md = checkfield(md,'fieldname','autodiff.gcTriggerMaxSize','>=',65536); + md = checkfield(md,'fieldname','autodiff.tapeAlloc','>=',0); %go through our dependents and independents and check consistency: @@ -75,4 +78,5 @@ fielddisplay(self,'gcTriggerRatio','free location block sorting/consolidation triggered if the ratio between allocated and used locations exceeds gcTriggerRatio'); fielddisplay(self,'gcTriggerMaxSize','free location block sorting/consolidation triggered if the allocated locations exceed gcTriggerMaxSize'); + fielddisplay(self,'tapeAlloc','Iteration count of a priori memory allocation of the AD tape'); end % }}} function marshall(self,prefix,md,fid) % {{{ @@ -95,4 +99,5 @@ WriteData(fid,prefix,'object',self,'fieldname','gcTriggerRatio','format','Double'); WriteData(fid,prefix,'object',self,'fieldname','gcTriggerMaxSize','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','tapeAlloc','format','Integer'); %}}} %process dependent variables {{{ Index: /issm/trunk/src/m/classes/autodiff.py =================================================================== --- /issm/trunk/src/m/classes/autodiff.py (revision 23393) +++ /issm/trunk/src/m/classes/autodiff.py (revision 23394) @@ -25,4 +25,5 @@ self.gcTriggerMaxSize = float('NaN') self.gcTriggerRatio = float('NaN') + self.tapeAlloc = float('NaN') if not len(args): self.setdefaultparameters() @@ -43,4 +44,5 @@ s+="%s\n" % fielddisplay(self,'gcTriggerRatio',"free location block sorting/consolidation triggered if the ratio between allocated and used locations exceeds gcTriggerRatio") s+="%s\n" % fielddisplay(self,'gcTriggerMaxSize',"free location block sorting/consolidation triggered if the allocated locations exceed gcTriggerMaxSize)") + s+="%s\n" % fielddisplay(self,'tapeAlloc','Iteration count of a priori memory allocation of the AD tape'); return s @@ -54,4 +56,5 @@ self.gcTriggerRatio=2.0 self.gcTriggerMaxSize=65536 + self.tapeAlloc = 15000000; return self # }}} @@ -68,4 +71,5 @@ md = checkfield(md,'fieldname','autodiff.gcTriggerRatio','>=',2.0) md = checkfield(md,'fieldname','autodiff.gcTriggerMaxSize','>=',65536) + md = checkfield(md,'fieldname','autodiff.tapeAlloc','>=',0); #Driver value: @@ -97,5 +101,6 @@ WriteData(fid,prefix,'object',self,'fieldname','gcTriggerRatio','format','Double'); WriteData(fid,prefix,'object',self,'fieldname','gcTriggerMaxSize','format','Double'); - #}}} + WriteData(fid,prefix,'object',self,'fieldname','tapeAlloc','format','Integer'); + #}}} #process dependent variables {{{ num_dependent_objects=len(self.dependents) Index: /issm/trunk/src/m/classes/cfdragcoeffabsgrad.m =================================================================== --- /issm/trunk/src/m/classes/cfdragcoeffabsgrad.m (revision 23394) +++ /issm/trunk/src/m/classes/cfdragcoeffabsgrad.m (revision 23394) @@ -0,0 +1,78 @@ +%CFDRAGCOEFFABSGRAD class definition +% +% Usage: +% cfdragcoeffabsgrad=cfdragcoeffabsgrad(); +% cfdragcoeffabsgrad=cfdragcoeffabsgrad('name','SurfaceAltimetry',... +% 'definitionstring','Outputdefinition1',... +% 'model_string','Surface',... +% 'weights',ones(md.mesh.numberofvertices,1),... +% 'weights_string','WeightsSurfaceObservations'); +% +% + +classdef cfdragcoeffabsgrad + properties (SetAccess=public) + %cfdragcoeffabsgrad + name = ''; + definitionstring = ''; %string that identifies this output definition uniquely, from 'Outputdefinition[1-100]' + weights = NaN; %weight coefficients for every vertex + weights_string = ''; %string to identify this particular set of weights + cumulated = NaN; %do we cumulate cfdragcoeffabsgrad through time? + end + + methods + function self = extrude(self,md) % {{{ + if ~isnan(self.weights) + self.weights=project3d(md,'vector',self.weights,'type','node'); + end + end % }}} + function self = cfdragcoeffabsgrad(varargin) % {{{ + if nargin==0, + self=setdefaultparameters(self); + else + %use provided options to change fields + options=pairoptions(varargin{:}); + + %get name + self.name=getfieldvalue(options,'name',''); + self.definitionstring=getfieldvalue(options,'definitionstring'); + self.weights=getfieldvalue(options,'weights',NaN); + self.weights_string=getfieldvalue(options,'weights_string',''); + + end + end % }}} + function self = setdefaultparameters(self) % {{{ + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + + if ~ischar(self.name), + error('cfdragcoeffabsgrad error message: ''name'' field should be a string!'); + end + OutputdefinitionStringArray={}; + for i=1:100 + OutputdefinitionStringArray{i}=strcat('Outputdefinition',num2str(i)); + end + md = checkfield(md,'fieldname','self.definitionstring','field',self.definitionstring,'values',OutputdefinitionStringArray); + + md = checkfield(md,'fieldname','self.weights','field',self.weights,'timeseries',1,'NaN',1,'Inf',1); + + end % }}} + function md = disp(self) % {{{ + + disp(sprintf(' TimeMisfit:\n')); + + fielddisplay(self,'name','identifier for this cfdragcoeffabsgrad response'); + fielddisplay(self,'definitionstring','string that identifies this output definition uniquely, from ''Outputdefinition[1-10]'''); + fielddisplay(self,'weights','weights (at vertices) to apply to the cfdragcoeffabsgrad'); + fielddisplay(self,'weights_string','string for weights for identification purposes'); + + end % }}} + function md = marshall(self,prefix,md,fid) % {{{ + + WriteData(fid,prefix,'data',self.name,'name','md.cfdragcoeffabsgrad.name','format','String'); + WriteData(fid,prefix,'data',self.definitionstring,'name','md.cfdragcoeffabsgrad.definitionstring','format','String'); + WriteData(fid,prefix,'data',self.weights,'name','md.cfdragcoeffabsgrad.weights','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'data',self.weights_string,'name','md.cfdragcoeffabsgrad.weights_string','format','String'); + end % }}} + end +end Index: /issm/trunk/src/m/classes/clusters/stallo.m =================================================================== --- /issm/trunk/src/m/classes/clusters/stallo.m (revision 23394) +++ /issm/trunk/src/m/classes/clusters/stallo.m (revision 23394) @@ -0,0 +1,218 @@ +% Stallo cluster class definition +% This is a SLURM queue +% The priorities are given to: +% - Large jobs +% - Short jobs +% - small number of job per user +% +% There are some 20cpu nodes and 16cpu nodes, with 32GB (a few with 128GB) mem per node, you can ask for part of a node if you need more memory.(1 node, 2 CPUS and 10GB per cpu for example) + +% Usage: +% cluster=stallo(); +% cluster=stallo('np',3); +% cluster=stallo('np',3,'login','username'); + +%node task and cpu must be defined, ask andreas for his stallo.py? + +classdef stallo + properties (SetAccess=public) + % {{{ + name = 'stallo'; + login = ''; + numnodes = 2; + cpuspernode = 10; + mem = 1.5; + queue = 'normal'; + time = 2*60; + codepath = ''; + executionpath = ''; + interactive = 0; + port = []; + accountname = ''; + profiling = 0; + bbftp = 0; + % }}} + end + methods + function cluster=stallo(varargin) % {{{ + + %initialize cluster using default settings if provided + if (exist('stallo_settings')==2), stallo_settings; end + + %use provided options to change fields + cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); + end + %}}} + function disp(cluster) % {{{ + % 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(' accountname: %s',cluster.accountname)); + disp(sprintf(' numnodes: %i',cluster.numnodes)); + disp(sprintf(' cpuspernode: %i, cpu per nodes',cluster.cpuspernode)); + disp(sprintf(' queue: %s, name of the queue (normal (D), short,singlenode,multinode,devel)',cluster.queue)); + disp(sprintf(' codepath: %s',cluster.codepath)); + disp(sprintf(' executionpath: %s',cluster.executionpath)); + disp(sprintf(' interactive: %i',cluster.interactive)); + disp(sprintf(' time: %i, walltime requested in minutes',cluster.time)); + disp(sprintf(' memory: %i, memory per CPU',cluster.mem)); + disp(sprintf(' profiling: %i, enable profiling if 1 default is 0',cluster.profiling)); + end + %}}} + function md = checkconsistency(cluster,md,solution,analyses) % {{{ + + available_queues={'short','normal','singlenode','multinode','devel'}; + queue_requirements_time=[60 2*24*60 28*24*60 28*24*60 4*60]; + queue_requirements_np=[2048 2048 20 2048 2048]; + + QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,1) + + %Miscelaneous + if isempty(cluster.login), md = checkmessage(md,'login empty'); end + if isempty(cluster.accountname), md = checkmessage(md,'accountname empty'); end + if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end + if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end + + end + %}}} + function numprocs=np(cluster) % {{{ + %compute number of processors + numprocs=cluster.numnodes*cluster.cpuspernode; + end + %}}} + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ + + if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end + if(isgprof), disp('gprof not supported by cluster, ignoring...'); end + + executable='issm.exe'; + if isdakota, + version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3)); + if (version>=6), + executable='issm_dakota.exe'; + end + end + if isoceancoupling, + executable='issm_ocean.exe'; + end + + days=floor(cluster.time/(60*24)); + hours=floor((cluster.time-(days*60*24))/60); + minutes=floor(mod((cluster.time-(days*60*24)-(hours*60)),60)); + + %write queuing script + fid=fopen([modelname '.queue'],'w'); + fprintf(fid,'#!/bin/bash -l\n'); + fprintf(fid,'#SBATCH --job-name=%s \n',modelname); + fprintf(fid,'#SBATCH --qos=%s \n',cluster.queue); + fprintf(fid,'#SBATCH --nodes=%i \n',cluster.numnodes); + fprintf(fid,'#SBATCH --ntasks-per-node=%i \n',cluster.cpuspernode); + fprintf(fid,'#SBATCH --time=%02i-%02i:%02i:00 \n',days,hours,minutes); + fprintf(fid,'#SBATCH --mem-per-cpu=%iMB\n',1000*cluster.mem); % mem in MB + if (mod(cluster.np,16)+mod(cluster.np,20))==0, + fprintf(fid,'#SBATCH --ntask=%i\n',cluster.np); + end + fprintf(fid,'#SBATCH --account=%s\n',cluster.accountname); + fprintf(fid,'#SBATCH --output %s/%s/%s.outlog \n',cluster.executionpath,dirname,modelname); + fprintf(fid,'#SBATCH --error %s/%s/%s.errlog \n\n',cluster.executionpath,dirname,modelname); + + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath);%FIXME + fprintf(fid,'module purge\n'); + fprintf(fid,'module load CMake/3.8.0-GCCcore-6.3.0\n'); + fprintf(fid,'module load Automake/1.15.1-GCCcore-6.3.0\n'); + fprintf(fid,'module load libtool/2.4.6\n'); + fprintf(fid,'module load OpenSSL/1.1.0e-intel-2017a\n'); + fprintf(fid,'module load PETSc/3.7.5-intel-2017a-downloaded-deps\n'); + + fprintf(fid,'cd %s/%s/\n\n',cluster.executionpath,dirname); + if cluster.profiling==1, + fprintf(fid,'module load perf-report\n'); + fprintf(fid,'perf-report mpirun -np %i %s/%s %s %s/%s %s\n',cluster.np,cluster.codepath,executable,solution,cluster.executionpath,dirname,modelname); + else + fprintf(fid,'mpirun -np %i %s/%s %s %s/%s %s\n',cluster.np,cluster.codepath,executable,solution,cluster.executionpath,dirname,modelname); + end + %}}} + if ~io_gather, %concatenate the output files: + fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); + end + fclose(fid); + + %in interactive mode, create a run file, and errlog and outlog file + if cluster.interactive, + fid=fopen([modelname '.run'],'w'); + fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); + if ~io_gather, %concatenate the output files: + fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); + end + fclose(fid); + fid=fopen([modelname '.errlog'],'w'); + fclose(fid); + fid=fopen([modelname '.outlog'],'w'); + fclose(fid); + end + end + + + function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{ + + %compress the files into one zip. + compressstring=['tar -zcf ' dirname '.tar.gz ']; + for i=1:numel(filelist), + compressstring = [compressstring ' ' filelist{i}]; + end + if cluster.interactive, + compressstring = [compressstring ' ' modelname '.run ' modelname '.errlog ' modelname '.outlog ']; + end + system(compressstring); + disp('uploading input file and queueing script'); + if cluster.interactive==10, + directory=[pwd() '/run/']; + elseif cluster.interactive, + directory=[cluster.executionpath '/Interactive' num2str(cluster.interactive)]; + else + directory=cluster.executionpath; + end + + if ~cluster.bbftp, + issmscpout(cluster.name,directory,cluster.login,cluster.port,{[dirname '.tar.gz']}); + else + issmbbftpout(cluster.name,directory,cluster.login,cluster.port,cluster.numstreams,{[dirname '.tar.gz']}); + + end + end %}}} + function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{ + + %lauch command, to be executed via ssh + if ~cluster.interactive, + if ~isempty(restart) + launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && qsub ' modelname '.queue ']; + else + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ... + ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && qsub ' modelname '.queue ']; + end + else + if ~isempty(restart) + launchcommand=['cd ' cluster.executionpath '/Interactive' num2str(cluster.interactive)]; + else + if cluster.interactive==10, + launchcommand=['cd ' pwd() '/run && tar -zxf ' dirname '.tar.gz']; + else + launchcommand=['cd ' cluster.executionpath '/Interactive' num2str(cluster.interactive) ' && tar -zxf ' dirname '.tar.gz']; + end + end + end + + disp('launching solution sequence on remote cluster'); + issmssh(cluster.name,cluster.login,cluster.port,launchcommand); + end + %}}} + function Download(cluster,dirname,filelist)% {{{ + + %copy files from cluster to current directory + directory=[cluster.executionpath '/' dirname '/']; + issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist); + + end %}}} + end +end Index: /issm/trunk/src/m/classes/clusters/stallo.py =================================================================== --- /issm/trunk/src/m/classes/clusters/stallo.py (revision 23393) +++ /issm/trunk/src/m/classes/clusters/stallo.py (revision 23394) @@ -12,10 +12,10 @@ except ImportError: print 'You need stallo_settings.py to proceed, check presence and sys.path' - + class stallo(object): """ Stallo cluster class definition This is a SLURM queue - The priorities are given to: + The priorities are given to: - Large jobs - Short jobs @@ -23,5 +23,5 @@ There are some 20cpu nodes and 16cpu nodes, with 32GB (a few with 128GB) mem per node, you can ask for part of a node if you need more memory.(1 node, 2 CPUS and 10GB per cpu for example) - + Usage: @@ -51,7 +51,7 @@ #OK get other fields self=options.AssignObjectFields(self) - self.np=self.numnodes*self.cpuspernode + self.np=self.numnodes*self.cpuspernode # }}} - + def __repr__(self): # {{{ @@ -61,5 +61,5 @@ s = "%s\n%s"%(s,fielddisplay(self,'login','login')) s = "%s\n%s"%(s,fielddisplay(self,'numnodes','number of nodes')) - s = "%s\n%s"%(s,fielddisplay(self,'cpuspernode','number of nodes per CPUs')) + s = "%s\n%s"%(s,fielddisplay(self,'cpuspernode','number of CPUs per nodes')) s = "%s\n%s"%(s,fielddisplay(self,'mem','memory per CPU')) s = "%s\n%s"%(s,fielddisplay(self,'queue','name of the queue (normal (D), short,singlenode,multinode,devel)')) @@ -104,18 +104,23 @@ if isoceancoupling: executable='issm_ocean.exe' - #write queuing script + #write queuing script shortname=modelname[0:min(12,len(modelname))] + timeobj=datetime.timedelta(minutes=self.time) + m,s=divmod(timeobj.total_seconds(), 60) + h,m=divmod(m, 60) + d,h=divmod(h, 60) + timestring="%02d-%02d:%02d:%02d" % (d, h, m, s) + fid=open(modelname+'.queue','w') - fid.write('#!/bin/bash -l\n') fid.write('#SBATCH --job-name=%s \n' % shortname) - fid.write('#SBATCH --partition %s \n' % self.queue) - fid.write('#SBATCH --nodes=%i' % self.numnodes) - fid.write('#SBATCH --ntasks-per-nodes==%i \n' % self.cpuspernode) - fid.write('#SBATCH --time=%s\n' % self.time) #walltime is minutes - fid.write('#SBATCH --mem-per-cpu=%iGB\n' % self.mem)# mem is in GB + fid.write('#SBATCH --qos=%s \n' % self.queue) + fid.write('#SBATCH --nodes=%i \n' % self.numnodes) + fid.write('#SBATCH --ntasks-per-node=%i \n' % self.cpuspernode) + fid.write('#SBATCH --time={}\n'.format(timestring)) #walltime is minutes + fid.write('#SBATCH --mem-per-cpu={}MB\n'.format(int(1000*self.mem)))# mem is in MB if (np.mod(self.np,16)+np.mod(self.np,20))==0: fid.write('#SBATCH --ntask=%i\n' % self.np) - fid.write('#SBATCH --account=%s\n' % self.accountname) + fid.write('#SBATCH --account=%s\n' % self.accountname) fid.write('#SBATCH --output %s/%s/%s.outlog \n' % (self.executionpath,dirname,modelname)) fid.write('#SBATCH --error %s/%s/%s.errlog \n\n' % (self.executionpath,dirname,modelname)) Index: /issm/trunk/src/m/classes/clusters/tetralith.m =================================================================== --- /issm/trunk/src/m/classes/clusters/tetralith.m (revision 23394) +++ /issm/trunk/src/m/classes/clusters/tetralith.m (revision 23394) @@ -0,0 +1,216 @@ +%teralith class definition +% +% Usage: +% cluster=tetralith(); +% cluster=tetralith('np',3); +% cluster=tetralith('np',3,'login','username'); + +classdef tetralith + properties (SetAccess=public) + % {{{ + name = 'tetralith'; + login = ''; + numnodes = 2; + cpuspernode = 32; + mem = 2000; %MB + queue = 'normal'; + time = 2*60; %[minutes] + codepath = ''; + executionpath = ''; + interactive = 0; + port = []; + accountname = ''; + % }}} + end + methods + function cluster=tetralith(varargin) % {{{ + + %initialize cluster using default settings if provided + if (exist('tetralith_settings')==2), tetralith_settings; end + + %use provided options to change fields + cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); + end + %}}} + function disp(cluster) % {{{ + % 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(' accountname: %s',cluster.accountname)); + disp(sprintf(' numnodes: %i',cluster.numnodes)); + disp(sprintf(' cpuspernode: %i',cluster.cpuspernode)); + disp(sprintf(' np: %i', cluster.cpuspernode*cluster.numnodes)); + disp(sprintf(' queue: %s',cluster.queue)); + disp(sprintf(' codepath: %s',cluster.codepath)); + disp(sprintf(' executionpath: %s',cluster.executionpath)); + disp(sprintf(' interactive: %i',cluster.interactive)); + disp(sprintf(' time: %i',cluster.time)); + disp(sprintf(' memory: %i',cluster.mem)); + end + %}}} + function md = checkconsistency(cluster,md,solution,analyses) % {{{ + + available_queues={'normal','devel'}; + queue_requirements_time=[7*24*60 60]; + queue_requirements_np=[1024 2*32]; + + QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,1) + + %Miscelaneous + if isempty(cluster.login), md = checkmessage(md,'login empty'); end + if isempty(cluster.accountname), md = checkmessage(md,'accountname empty'); end + if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end + if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end + + end + %}}} + function numprocs=np(self) % {{{ + %compute number of processors + numprocs=self.numnodes*self.cpuspernode; + end + %}}} + function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{ + + if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end + if(isgprof), disp('gprof not supported by cluster, ignoring...'); end + + %compute number of processors +% cluster.np=cluster.numnodes*cluster.cpuspernode; + np(cluster);%=cluster.numnodes*cluster.cpuspernode; + + %write queuing script + fid=fopen([modelname '.queue'],'w'); + fprintf(fid,'#!/bin/bash\n'); + fprintf(fid,'#\n'); + fprintf(fid,'#SBATCH --job-name=%s\n',modelname); +% fprintf(fid,'#SBATCH -p %s \n',cluster.partition); + fprintf(fid,'#SBATCH -A %s \n',cluster.accountname); +% fprintf(fid,'#SBATCH --mail-type=ALL\n'); + fprintf(fid,'#SBATCH -N %i -n %i\n',cluster.numnodes,cluster.cpuspernode); + %calculate walltime in hh:mm:ss format + walltime=datestr(cluster.time/(60*24),'HH:MM:SS') + fprintf(fid,'#SBATCH -t %s\n',walltime); %walltime should be in hh:mm:ss + fprintf(fid,'#SBATCH --mem=%i\n',cluster.mem); + fprintf(fid,'#SBATCH -o %s.outlog \n',modelname); + fprintf(fid,'#SBATCH -e %s.errlog \n\n',modelname); +% fprintf(fid,'module load intelcomp/17.0.0\n') %module load not recommended within job script at Tetralith +% fprintf(fid,'module load mpt/2.14\n') +% fprintf(fid,'module load petsc/3.7.4d\n') +% fprintf(fid,'module load parmetis/4.0.3\n') +% fprintf(fid,'module load mumps/5.0.2\n') +% fprintf(fid,'export ISSM_DIR="%s"\n',cluster.codepath); %FIXME + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME + fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME + fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname); +% fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); +% fprintf(fid,'mpiexec_mpt -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); + fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); +% fprintf(fid,'mpirun -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); + if ~io_gather, %concatenate the output files: + fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); + end + fclose(fid); + end + %}}} + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ + + if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end + if(isgprof), disp('gprof not supported by cluster, ignoring...'); end + + executable='issm.exe'; + if isdakota, + version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3)); + if (version>=6), + executable='issm_dakota.exe'; + end + end + if isoceancoupling, + executable='issm_ocean.exe'; + end + + %compute number of processors +% cluster.np=cluster.numnodes*cluster.cpuspernode; + np(cluster);%=cluster.numnodes*cluster.cpuspernode; +% shortname = substring(modelname,1,min(12,length(modelname))); + + %write queuing script + fid=fopen([modelname '.queue'],'w'); + fprintf(fid,'#!/bin/bash\n'); + fprintf(fid,'#\n'); + fprintf(fid,'#SBATCH --job-name=%s\n',modelname); +% fprintf(fid,'#SBATCH -p %s \n',cluster.partition); + fprintf(fid,'#SBATCH -A %s \n',cluster.accountname); +% fprintf(fid,'#SBATCH --mail-type=ALL\n'); + fprintf(fid,'#SBATCH -N %i -n %i\n',cluster.numnodes,cluster.cpuspernode); + %calculate walltime in hh:mm:ss format + walltime=datestr(cluster.time/(60*24),'HH:MM:SS'); + fprintf(fid,'#SBATCH -t %s\n',walltime); %walltime should be in hh:mm:ss + fprintf(fid,'#SBATCH --mem=%i\n',cluster.mem); + fprintf(fid,'#SBATCH -o %s.outlog \n',modelname); + fprintf(fid,'#SBATCH -e %s.errlog \n\n',modelname); +% fprintf(fid,'module load intelcomp/17.0.0\n') %module load not recommended within job script at Tetralith +% fprintf(fid,'module load mpt/2.14\n') +% fprintf(fid,'module load petsc/3.7.4d\n') +% fprintf(fid,'module load parmetis/4.0.3\n') +% fprintf(fid,'module load mumps/5.0.2\n') + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME +% fprintf(fid,'export ISSM_DIR="%s"\n',cluster.codepath); %FIXME + fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME + fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname); +% fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); + fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); +% fprintf(fid,'mpirun -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); +% fprintf(fid,'mpiexec_mpt -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); + + if ~io_gather, %concatenate the output files: + fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); + end + fclose(fid); + + %in interactive mode, create a run file, and errlog and outlog file + if cluster.interactive, + fid=fopen([modelname '.run'],'w'); + fprintf(fid,'mpiexec_mpt -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); + if ~io_gather, %concatenate the output files: + fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); + end + fclose(fid); + fid=fopen([modelname '.errlog'],'w'); + fclose(fid); + fid=fopen([modelname '.outlog'],'w'); + fclose(fid); + end + end %}}} + function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{ + + %compress the files into one zip. + compressstring=['tar -zcf ' dirname '.tar.gz ']; + for i=1:numel(filelist), + compressstring = [compressstring ' ' filelist{i}]; + end + system(compressstring); + disp('uploading input file and queueing script'); + directory=cluster.executionpath; +% issmbbftpout(cluster.name,directory,cluster.login,cluster.port,cluster.numstreams,{[dirname '.tar.gz']}); + issmscpout(cluster.name,directory,cluster.login,cluster.port,{[dirname '.tar.gz']}); + + end + %}}} + function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{ + + disp('launching solution sequence on remote cluster'); + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ... + ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && hostname && sbatch ' modelname '.queue ']; + + issmssh(cluster.name,cluster.login,cluster.port,launchcommand); + end %}}} + function Download(cluster,dirname,filelist)% {{{ + + %copy files from cluster to current directory + directory=[cluster.executionpath '/' dirname '/']; + issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist); + + end %}}} + end +end Index: /issm/trunk/src/m/classes/geometry.py =================================================================== --- /issm/trunk/src/m/classes/geometry.py (revision 23393) +++ /issm/trunk/src/m/classes/geometry.py (revision 23394) @@ -13,9 +13,9 @@ def __init__(self): # {{{ - self.surface = float('NaN') - self.thickness = float('NaN') + self.surface = float('NaN') + self.thickness = float('NaN') self.base = float('NaN') - self.bed = float('NaN') - self.hydrostatic_ratio = float('NaN') + self.bed = float('NaN') + self.hydrostatic_ratio = float('NaN') #set defaults Index: /issm/trunk/src/m/classes/groundingline.js =================================================================== --- /issm/trunk/src/m/classes/groundingline.js (revision 23393) +++ /issm/trunk/src/m/classes/groundingline.js (revision 23394) @@ -29,5 +29,5 @@ checkfield(md,'fieldname','groundingline.melt_interpolation','values',['NoMeltOnPartiallyFloating', 'SubelementMelt1', 'SubelementMelt2', 'FullMeltOnPartiallyFloating']); - if (this.migration !='None'){ + if(this.migration !='None' & md.trans.isgroundingline==1 & solution == 'TransientSolution'){ if (isNaN(md.geometry.bed)){ md.checkmessage('requesting grounding line migration, but bathymetry is absent!'); Index: /issm/trunk/src/m/classes/groundingline.m =================================================================== --- /issm/trunk/src/m/classes/groundingline.m (revision 23393) +++ /issm/trunk/src/m/classes/groundingline.m (revision 23394) @@ -33,5 +33,5 @@ md = checkfield(md,'fieldname','groundingline.melt_interpolation','values',{'NoMeltOnPartiallyFloating' 'SubelementMelt1' 'SubelementMelt2' 'FullMeltOnPartiallyFloating'}); - if ~strcmp(self.migration,'None'), + if ~strcmp(self.migration,'None') & strcmp(solution,'TransientSolution') & md.transient.isgroundingline==1, if isnan(md.geometry.bed), md = checkmessage(md,['requesting grounding line migration, but bathymetry is absent!']); Index: /issm/trunk/src/m/classes/groundingline.py =================================================================== --- /issm/trunk/src/m/classes/groundingline.py (revision 23393) +++ /issm/trunk/src/m/classes/groundingline.py (revision 23394) @@ -45,5 +45,5 @@ md = checkfield(md,'fieldname','groundingline.melt_interpolation','values',['SubelementMelt1','SubelementMelt2','NoMeltOnPartiallyFloating','FullMeltOnPartiallyFloating']) - if not m.strcmp(self.migration,'None'): + if(not m.strcmp(self.migration,'None') and md.transient.isgroundingline and solution=='TransientSolution'): if np.any(np.isnan(md.geometry.bed)): md.checkmessage("requesting grounding line migration, but bathymetry is absent!") Index: /issm/trunk/src/m/classes/numberedcostfunction.m =================================================================== --- /issm/trunk/src/m/classes/numberedcostfunction.m (revision 23393) +++ /issm/trunk/src/m/classes/numberedcostfunction.m (revision 23394) @@ -1,3 +1,3 @@ -%M1QN3INVERSION class definition +%NUMBEREDCOSTFUNCTION class definition % % Usage: @@ -44,18 +44,18 @@ function md = checkconsistency(self,md,solution,analyses) % {{{ - num_costfunc=size(md.inversion.cost_functions,2); + num_costfunc=size(self.cost_functions,2); - md = checkfield(md,'fieldname','inversion.cost_functions','size',[1 num_costfunc],'values',supportedcostfunctions()); - md = checkfield(md,'fieldname','inversion.cost_functions_coefficients','size',[md.mesh.numberofvertices num_costfunc],'>=',0); - + md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.dependent{X}.cost_functions','field',self.cost_functions,'size',[1 num_costfunc],'values',supportedcostfunctions()); + md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.cost_functions_coefficients','field',self.cost_functions_coefficients,'size',[md.mesh.numberofvertices numel(self.cost_functions)],'>=',0); + if strcmp(solution,'BalancethicknessSolution') - md = checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); - md = checkfield(md,'fieldname','inversion.surface_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.thickness_obs','field',self.thickness_obs,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.surface_obs','field',self.surface_obs,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); elseif strcmp(solution,'BalancethicknessSoftSolution') - md = checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.thickness_obs','field',self.thickness_obs,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); else - md = checkfield(md,'fieldname','inversion.vx_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.vx_obs','field',self.vx_obs,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); if ~strcmp(domaintype(md.mesh),'2Dvertical'), - md = checkfield(md,'fieldname','inversion.vy_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.vy_obs','field',self.vy_obs,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); end end Index: /issm/trunk/src/m/classes/taoinversion.py =================================================================== --- /issm/trunk/src/m/classes/taoinversion.py (revision 23393) +++ /issm/trunk/src/m/classes/taoinversion.py (revision 23394) @@ -97,5 +97,5 @@ else: self.algorithm = 'tao_blmvm'; - + #several responses can be used: self.cost_functions=101; @@ -110,8 +110,8 @@ if numel(self.cost_functions_coefficients) > 1: self.cost_functions_coefficients=project3d(md,'vector',self.cost_functions_coefficients,'type','node') - + if numel(self.min_parameters) > 1: self.min_parameters=project3d(md,'vector',self.min_parameters,'type','node') - + if numel(self.max_parameters)>1: self.max_parameters=project3d(md,'vector',self.max_parameters,'type','node') @@ -123,5 +123,5 @@ return md if not IssmConfig('_HAVE_TAO_')[0]: - md = checkmessage(md,['TAO has not been installed, ISSM needs to be reconfigured and recompiled with TAO']) + md = md.checkmessage('TAO has not been installed, ISSM needs to be reconfigured and recompiled with TAO') Index: /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.py =================================================================== --- /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.py (revision 23393) +++ /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.py (revision 23394) @@ -18,5 +18,5 @@ print ('New file name is {}'.format(newname)) filename=newname - + NCData=Dataset(filename, 'w', format='NETCDF4') NCData.description = 'Results for run' + md.miscellaneous.name @@ -100,10 +100,10 @@ Subgroup.__setattr__('classtype',md.__dict__[group].__class__.__name__) subfields=dict.keys(md.__dict__[group].__dict__[field].__dict__) - + for subfield in subfields: if str(subfield)!='outlog': Var=md.__dict__[group].__dict__[field].__dict__[subfield] DimDict=CreateVar(NCData,Var,subfield,Subgroup,DimDict) - + NCData.close() @@ -130,9 +130,10 @@ str:str, dict:str} - + val_dim=np.shape(val_shape)[0] + #Now define and fill up variable #treating scalar string or bool as atribute - if val_type==str or val_type==unicode or val_type==bool: + if val_type in [str,unicode,bool]: Group.__setattr__(str(field).swapcase(), str(var)) #treating list as string table @@ -147,5 +148,5 @@ if val_shape==0: ncvar= [] - else: + else: for elt in range(0,val_shape[0]): ncvar[elt] = var[elt] @@ -164,5 +165,5 @@ ncvar[elt,1]=str(dict.values(var)[elt]) #converting to str to avoid potential problems #Now dealing with numeric variables - else: + elif val_type in [float,'float64',np.float64,int,'int64']: dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim) ncvar = Group.createVariable(str(field),TypeDict[val_type],dimensions,zlib=True) @@ -175,4 +176,6 @@ except TypeError: #type does not accept nan, get vallue of the variable ncvar[:] = var + else: + print('WARNING type "{}" is unknown for "{}.{}"'.format(val_type,Group.name,field)) return DimDict Index: /issm/trunk/src/m/contrib/defleurian/paraview/enveloppeVTK.py =================================================================== --- /issm/trunk/src/m/contrib/defleurian/paraview/enveloppeVTK.py (revision 23393) +++ /issm/trunk/src/m/contrib/defleurian/paraview/enveloppeVTK.py (revision 23394) @@ -9,11 +9,11 @@ creates a directory with the vtk files for displays in paraview (only work for triangle and wedges based on their number of nodes) - - Give only the results for nw but could be extended to geometry, mask... - - input: filename destination + + Give only the results for nw but could be extended to geometry, mask... + + input: filename destination (string) ------------------------------------------------------------------ -model this is md +model this is md ------------------------------------------------------------------ By default only the results are exported, you can add whichever @@ -40,22 +40,38 @@ os.mkdir(filename) - IsEnveloppe=np.where(model.mesh.vertexonbase | model.mesh.vertexonsurface) - #get the element related variables + # {{{get the element related variables if 'z' in dict.keys(model.mesh.__dict__): - points=np.column_stack((model.mesh.x,model.mesh.y,model.mesh.z)) - num_of_elt=np.size(np.isnan(model.mesh.lowerelements))+np.size(np.isnan(model.mesh.upperelements)) - low_elt_num=np.size(np.isnan(model.mesh.lowerelements)) - top_elt_num=np.size(np.isnan(model.mesh.upperelements)) + is_enveloppe=np.logical_or(model.mesh.vertexonbase,model.mesh.vertexonsurface) + enveloppe_index=np.where(is_enveloppe)[0] + convert_index=np.nan*np.ones(np.shape(model.mesh.x)) + convert_index=np.asarray([[i,np.where(enveloppe_index==i)[0][0]] for i,val in enumerate(convert_index) if any(enveloppe_index==i)]) + points=np.column_stack((model.mesh.x[enveloppe_index], + model.mesh.y[enveloppe_index], + model.mesh.z[enveloppe_index])) + low_elt_num=np.size(np.where(np.isnan(model.mesh.lowerelements))) + top_elt_num=np.size(np.where(np.isnan(model.mesh.upperelements))) + num_of_elt=low_elt_num+top_elt_num + connect=model.mesh.elements[np.where(is_enveloppe[model.mesh.elements-1])].reshape(int(num_of_elt),3)-1 + for elt in range(0, num_of_elt): + connect[elt,0]=convert_index[np.where(convert_index==connect[elt,0])[0],1][0] + connect[elt,1]=convert_index[np.where(convert_index==connect[elt,1])[0],1][0] + connect[elt,2]=convert_index[np.where(convert_index==connect[elt,2])[0],1][0] + else: - points=np.column_stack((model.mesh.x,model.mesh.y,np.zeros(np.shape(model.mesh.x)))) + points=np.column_stack((model.mesh.x, + model.mesh.y, + np.zeros(np.shape(model.mesh.x)))) num_of_elt=np.shape(model.mesh.elements)[0] - - num_of_points=np.size(points)[0] - dim=np.size(points)[1] - point_per_elt=np.shape(model.mesh.elements)[1] - + connect=model.mesh.elements-1 + enveloppe_index=np.arange(0,np.size(model.mesh.x)) + + every_nodes=np.size(model.mesh.x) + num_of_points=np.size(enveloppe_index) + dim=3 + point_per_elt=3 celltype=5 #triangles - - #this is the result structure + + # }}} + # {{{this is the result structure res_struct=model.results if (len(res_struct.__dict__)>0): @@ -64,13 +80,14 @@ num_of_sols=len(solnames) num_of_timesteps=1 - #%building solutionstructure + #%building solutionstructure for solution in solnames: #looking for multiple time steps if (np.size(res_struct.__dict__[solution])>num_of_timesteps): num_of_timesteps=np.size(res_struct.__dict__[solution]) - num_of_timesteps=int(num_of_timesteps)+1 + num_of_timesteps=int(num_of_timesteps) else: num_of_timesteps=1 - + # }}} + # {{{write header and mesh for step in range(0,num_of_timesteps): timestep=step @@ -83,17 +100,12 @@ for point in points: fid.write('%f %f %f \n'%(point[0], point[1], point[2])) - + fid.write('CELLS %d %d\n' %(num_of_elt, num_of_elt*(point_per_elt+1))) - # if exist('low_elt_num') - # triaconnect=zeros(num_of_elt,3); - # triaconnect(1:low_elt_num,:)=model.mesh.elements(find(isnan(model.mesh.lowerelements)),1:3); - # upshift=-min(min(model.mesh.elements(find(isnan(model.mesh.upperelements)),4:6)))+1+max(max(model.mesh.elements(find(isnan(model.mesh.lowerelements)),1:3))); - # triaconnect(1+low_elt_num:num_of_elt,:)=model.mesh.elements(find(isnan(model.mesh.upperelements)),4:6)+upshift; - # fprintf(fid,s,[(3)*ones(num_of_elt,1) triaconnect-1]'); for elt in range(0, num_of_elt): - - fid.write('3 %d %d %d\n' %(model.mesh.elements[elt,0]-1,model.mesh.elements[elt,1]-1,model.mesh.elements[elt,2]-1)) - + fid.write('3 %d %d %d\n' %(connect[elt,0], + connect[elt,1], + connect[elt,2])) + fid.write('CELL_TYPES %d\n' %num_of_elt) for elt in range(0, num_of_elt): @@ -101,6 +113,6 @@ fid.write('POINT_DATA %s \n' %str(num_of_points)) - - #loop over the different solution structures + # }}} + # {{{loop over the different solution structures if 'solnames' in locals(): for sol in solnames: @@ -110,8 +122,8 @@ else: timestep = np.size(res_struct.__dict__[sol]) - + #getting the fields in the solution if(np.size(res_struct.__dict__[sol])>1): - fieldnames=dict.keys(res_struct.__dict__[sol].__getitem__(timestep-1).__dict__) + fieldnames=dict.keys(res_struct.__dict__[sol].__getitem__(timestep).__dict__) else: fieldnames=dict.keys(res_struct.__dict__[sol].__dict__) @@ -119,39 +131,40 @@ for field in fieldnames: if(np.size(res_struct.__dict__[sol])>1): - fieldstruct=res_struct.__dict__[sol].__getitem__(timestep-1).__dict__[field] + fieldstruct=res_struct.__dict__[sol].__getitem__(timestep).__dict__[field] else: fieldstruct=res_struct.__dict__[sol].__dict__[field] - if ((np.size(fieldstruct))==num_of_points): + if ((np.size(fieldstruct))==every_nodes): fid.write('SCALARS %s float 1 \n' % field) fid.write('LOOKUP_TABLE default\n') for node in range(0,num_of_points): #paraview does not like NaN, replacing - if np.isnan(fieldstruct[node]): + if np.isnan(fieldstruct[enveloppe_index[node]]): fid.write('%e\n' % -9999.9999) #also checking for verry small value that mess up - elif (abs(fieldstruct[node])<1.0e-20): + elif (abs(fieldstruct[enveloppe_index[node]])<1.0e-20): fid.write('%e\n' % 0.0) else: - fid.write('%e\n' % fieldstruct[node]) - - #loop on arguments, if something other than result is asked, do - #it now + fid.write('%e\n' % fieldstruct[enveloppe_index[node]]) + # }}} + # {{{loop on arguments, if something other than result is asked, do it now + for other in args: other_struct=model.__dict__[other] othernames=(dict.keys(other_struct.__dict__)) for field in othernames: -# fprintf(fid,s,res_struct.(fieldnames{k})(IsEnveloppe)); - if ((np.size(other_struct.__dict__[field]))==num_of_points): + if ((np.size(other_struct.__dict__[field]))==every_nodes): fid.write('SCALARS %s float 1 \n' % field) fid.write('LOOKUP_TABLE default\n') for node in range(0,num_of_points): #paraview does not like NaN, replacing - if np.isnan(other_struct.__dict__[field][node]): + if np.isnan(other_struct.__dict__[field][enveloppe_index[node]]): fid.write('%e\n' % -9999.9999) #also checking for verry small value that mess up - elif (abs(other_struct.__dict__[field][node])<1.0e-20): + elif (abs(other_struct.__dict__[field][enveloppe_index[node]])<1.0e-20): fid.write('%e\n' % 0.0) else: - fid.write('%e\n' % other_struct.__dict__[field][node]) + fid.write('%e\n' % other_struct.__dict__[field][enveloppe_index[node]]) + + # }}} fid.close(); Index: /issm/trunk/src/m/contrib/defleurian/paraview/exportVTK.py =================================================================== --- /issm/trunk/src/m/contrib/defleurian/paraview/exportVTK.py (revision 23393) +++ /issm/trunk/src/m/contrib/defleurian/paraview/exportVTK.py (revision 23394) @@ -9,11 +9,11 @@ creates a directory with the vtk files for displays in paraview (only work for triangle and wedges based on their number of nodes) - - Give only the results for nw but could be extended to geometry, mask... - - input: filename destination + + Give only the results for nw but could be extended to geometry, mask... + + input: filename destination (string) ------------------------------------------------------------------ -model this is md +model this is md ------------------------------------------------------------------ By default only the results are exported, you can add whichever @@ -67,5 +67,5 @@ num_of_sols=len(solnames) num_of_timesteps=1 - #%building solutionstructure + #%building solutionstructure for solution in solnames: #looking for multiple time steps @@ -91,7 +91,7 @@ for point in points: fid.write('%f %f %f \n'%(point[0], point[1], point[2])) - + fid.write('CELLS %d %d\n' %(num_of_elt, num_of_elt*(point_per_elt+1))) - + if point_per_elt==3: for elt in range(0, num_of_elt): @@ -117,5 +117,5 @@ else: timestep = np.size(res_struct.__dict__[sol]) - + #getting the fields in the solution if(np.size(res_struct.__dict__[sol])>1): @@ -187,11 +187,14 @@ # reloaded variable are generally of dim 2 elif np.shape(other_struct.__dict__[field])[0]==num_of_points: + # we want only vector + if np.shape(other_struct.__dict__[field])[1]==1: fid.write('SCALARS %s float 1 \n' % field) fid.write('LOOKUP_TABLE default\n') for node in range(0,num_of_points): #paraview does not like NaN, replacing + print other_struct.__dict__[field][node] if np.isnan(other_struct.__dict__[field][node]): fid.write('%e\n' % -9999.9999) - #also checking for verry small value that mess up + #also checking for verry small value that mess up elif (abs(other_struct.__dict__[field][node])<1.0e-20): fid.write('%e\n' % 0.0) Index: /issm/trunk/src/m/mesh/planet/gmsh/gmshplanet.m =================================================================== --- /issm/trunk/src/m/mesh/planet/gmsh/gmshplanet.m (revision 23393) +++ /issm/trunk/src/m/mesh/planet/gmsh/gmshplanet.m (revision 23394) @@ -23,5 +23,5 @@ resolution=getfieldvalue(options,'resolution')*1000; - %initialize mesh: + %initialize mesh: mesh=mesh3dsurface; @@ -97,5 +97,5 @@ end fprintf(fid,'};\n'); - + fclose(fid); % }}} @@ -111,5 +111,5 @@ end if isempty(gmshpath), - error('gmt not found, make sure it is properly installed'); + error('gmsh not found, make sure it is properly installed'); end @@ -160,20 +160,20 @@ mesh.numberofelements=fscanf(fid,'%i',1); A=fscanf(fid,'%i %i %i %i %i %i %i %i',[8 mesh.numberofelements]); - mesh.elements=A(6:8,:)'; + mesh.elements=A(6:8,:)'; A=fscanf(fid,'%s',1); if ~strcmp(A,'$EndElements'), error(['Expecting $EndElements (' A ')']); end - fclose(fid); + fclose(fid); %}}} - %figure out other fields in mesh3dsurface: + %figure out other fields in mesh3dsurface: mesh.r=sqrt(mesh.x.^2+mesh.y.^2+mesh.z.^2); mesh.lat = asin(mesh.z./mesh.r)/pi*180; mesh.long = atan2(mesh.y,mesh.x)/pi*180; - %erase files: + %erase files: system('rm -rf sphere.geo sphere.msh sphere.pos'); - %return mesh: + %return mesh: return; Index: /issm/trunk/src/m/mesh/triangle.py =================================================================== --- /issm/trunk/src/m/mesh/triangle.py (revision 23393) +++ /issm/trunk/src/m/mesh/triangle.py (revision 23394) @@ -2,7 +2,7 @@ import numpy as np from mesh2d import mesh2d -from Triangle import Triangle from NodeConnectivity import NodeConnectivity from ElementConnectivity import ElementConnectivity +from Triangle_python import Triangle_python import MatlabFuncs as m @@ -50,5 +50,5 @@ #Mesh using Triangle md.mesh=mesh2d() - md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers=Triangle(domainname,riftname,area) + md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers=Triangle_python(domainname,riftname,area) md.mesh.elements=md.mesh.elements.astype(int) md.mesh.segments=md.mesh.segments.astype(int) Index: /issm/trunk/src/m/mesh/triangle2dvertical.m =================================================================== --- /issm/trunk/src/m/mesh/triangle2dvertical.m (revision 23393) +++ /issm/trunk/src/m/mesh/triangle2dvertical.m (revision 23394) @@ -25,5 +25,5 @@ %Mesh using Triangle -[elements,x,z,segments,segmentmarkers]=Triangle(domainname,'',area); +[elements,x,z,segments,segmentmarkers]=Triangle_matlab(domainname,'',area); %check that all the created nodes belong to at least one element Index: /issm/trunk/src/m/modules/Chaco.py =================================================================== --- /issm/trunk/src/m/modules/Chaco.py (revision 23393) +++ /issm/trunk/src/m/modules/Chaco.py (revision 23394) @@ -5,5 +5,5 @@ Usage: - [assgn] = Chaco(A,vwgts,ewgts,x,y,z,options,nparts,goal); + assgn = Chaco(A,vwgts,ewgts,x,y,z,options,nparts,goal); A: Input adjacency matrix Index: /issm/trunk/src/m/modules/MeshPartition.m =================================================================== --- /issm/trunk/src/m/modules/MeshPartition.m (revision 23393) +++ /issm/trunk/src/m/modules/MeshPartition.m (revision 23394) @@ -3,5 +3,5 @@ % % Usage: -% [element_partitioning,node_partitioning]=MeshPartition(md,numpartitions)"); +% [element_partitioning,node_partitioning]=MeshPartition(md,numpartitions); % % element_partitioning: Vector of partitioning area numbers, for every element. @@ -35,3 +35,3 @@ % Call mex module -[element_partitioning, node_partitioning] = MeshPartition_matlab(numberofvertices,elements,numberofvertices2d,elements2d,numberoflayers,meshelementtype,numpartitions); +[element_partitioning, node_partitioning] = MeshPartition_matlab(numberofvertices,elements,numberofvertices2d,elements2d,numberoflayers,elementtype,numpartitions); Index: /issm/trunk/src/m/modules/MeshPartition.py =================================================================== --- /issm/trunk/src/m/modules/MeshPartition.py (revision 23393) +++ /issm/trunk/src/m/modules/MeshPartition.py (revision 23394) @@ -9,5 +9,5 @@ Usage: - [element_partitioning,node_partitioning]=MeshPartition(md.mesh,numpartitions)") + [element_partitioning,node_partitioning]=MeshPartition(md.mesh,numpartitions) element_partitioning: Vector of partitioning area numbers, for every element. @@ -38,5 +38,5 @@ #Call module - [element_partitioning, node_partitioning] = MeshPartition_python(numberofvertices, elements, numberofvertices2d, elements2d, numberoflayers, meshelementtype, numpartitions) + [element_partitioning, node_partitioning] = MeshPartition_python(numberofvertices, elements, numberofvertices2d, elements2d, numberoflayers,elementtype, numpartitions) return [element_partitioning, node_partitioning] Index: /issm/trunk/src/m/modules/Scotch.py =================================================================== --- /issm/trunk/src/m/modules/Scotch.py (revision 23393) +++ /issm/trunk/src/m/modules/Scotch.py (revision 23394) @@ -2,5 +2,5 @@ def Scotch(*varargin): -'''SCOTCH - Scotch partitioner + '''SCOTCH - Scotch partitioner Usage: Index: sm/trunk/src/m/modules/Triangle.py =================================================================== --- /issm/trunk/src/m/modules/Triangle.py (revision 23393) +++ (revision ) @@ -1,21 +1,0 @@ -from Triangle_python import Triangle_python - -def Triangle(domainoutlinefilename,rifts,mesh_area): - """ - TRIMESH - Mesh a domain using an .exp file - - Usage: - [index,x,y,segments,segmentmarkers]=Triangle(domainoutlinefilename,rifts,mesh_area); - - index,x,y: defines a triangulation - segments: An array made of exterior segments to the mesh domain outline - segmentmarkers: An array flagging each segment - - domainoutlinefilename: an Argus domain outline file - mesh_area: The maximum area desired for any element of the resulting mesh - """ - # Call mex module - index,x,y,segments,segmentmarkers=Triangle_python(domainoutlinefilename,rifts,mesh_area) - # Return - return index,x,y,segments,segmentmarkers - Index: /issm/trunk/src/m/partition/AreaAverageOntoPartition.py =================================================================== --- /issm/trunk/src/m/partition/AreaAverageOntoPartition.py (revision 23394) +++ /issm/trunk/src/m/partition/AreaAverageOntoPartition.py (revision 23394) @@ -0,0 +1,59 @@ +import numpy as np + +def AreaAverageOntoPartition(md,vector,layer=None): + '''AREAAVERAGEONTOPARTITION + compute partition values for a certain vector expressed on the vertices of the mesh. + Use area weighted average. + + Usage: + average=AreaAverageOntoPartition(md,vector) + average=AreaAverageOntoPartition(md,vector,layer) #if in 3D, chose which layer is partitioned +''' + #some checks + if len(np.shape(md.mesh)) == 3: + if layer == None: + raise RuntimeError('AreaAverageOntoPartition: layer should be provided onto which Area Averaging occurs') + + #save 3D model + md3d = md + + md.mesh.elements = md.mesh.elements2d + md.mesh.x = md.mesh.x2d + md.mesh.y = md.mesh.y2d + md.mesh.numberofvertices = md.mesh.numberofvertices2d + md.mesh.numberofelements = md.mesh.numberofelements2d + md.qmu.vertex_weight = [] + md.mesh.vertexconnectivity = [] + + #run connectivity routine + md = adjacency(md) + + #finally, project vector: + vector = project2d(md3d,vector,layer) + md.qmu.partition = project2d(md3d,md3d.qmu.partition,layer) + + + #ok, first check that part is Matlab indexed + #part = md.qmu.partition + + #some check: + if md.qmu.numberofpartitions != max(md.qmu.partition): + raise RuntimeError('AreaAverageOntoPartition error message: ''npart'' should be equal to max(md.qmu.partition)') + + + #initialize output + partvector = np.zeros((max(md.qmu.partition),)) + + #start weight average + weightedvector = vector*md.qmu.vertex_weight + for i in range(max(md.qmu.partition)): + pos=np.where(md.qmu.partition==i) + partvector[i]=sum(weightedvector[pos])/sum(md.qmu.vertex_weight[pos]) + + + #in 3D, restore 3D model: + if len(np.shape(md.mesh)) == 3: + md = md3d + + return partvector + Index: /issm/trunk/src/m/partition/partitioner.py =================================================================== --- /issm/trunk/src/m/partition/partitioner.py (revision 23393) +++ /issm/trunk/src/m/partition/partitioner.py (revision 23394) @@ -3,8 +3,9 @@ import MatlabFuncs as m from adjacency import * -#from Chaco import * +from Chaco import * #from Scotch import * -#from MeshPartition import * +from MeshPartition import * from project3d import * +from mesh2d import * def partitioner(md,*varargin): @@ -60,27 +61,28 @@ if m.strcmpi(package,'chaco'): - raise RuntimeError('Chaco is not currently supported for this function') + #raise RuntimeError('Chaco is not currently supported for this function') # default method (from chaco.m) - #method=np.array([1,1,0,0,1,1,50,0,.001,7654321]).reshape(-1,1) - #method[0]=3 # global method (3=inertial (geometric)) - #method[2]=0 # vertex weights (0=off, 1=on) + method=np.array([1,1,0,0,1,1,50,0,.001,7654321]) + method[0]=3 # global method (3=inertial (geometric)) + method[2]=0 # vertex weights (0=off, 1=on) #specify bisection - #method[5]=options.getfieldvalue('section')# ndims (1=bisection, 2=quadrisection, 3=octasection) + method[5]=options.getfieldvalue('section')# ndims (1=bisection, 2=quadrisection, 3=octasection) #are we using weights? - #if m.strcmpi(options.getfieldvalue('weighting'),'on'): - #weights=np.floor(md.qmu.vertex_weight/min(md.qmu.vertex_weight)) - #method[2]=1 - #else: - #weights=[] + if m.strcmpi(options.getfieldvalue('weighting'),'on'): + weights=np.floor(md.qmu.vertex_weight/min(md.qmu.vertex_weight)) + method[2]=1 + else: + weights=[] + method = method.reshape(-1,1) # transpose to 1x10 instead of 10 + # partition into nparts - #if isinstance(md.mesh,mesh2d): - #part=Chaco(md.qmu.adjacency,weights,[],md.mesh.x, md.mesh.y,np.zeros((md.mesh.numberofvertices,)),method,npart,[]).T+1 #index partitions from 1 up. like metis. - #else: - #part=Chaco(md.qmu.adjacency,weights,[],md.mesh.x, md.mesh.y,md.mesh.z,method,npart,[]).T+1 #index partitions from 1 up. like metis. - + if isinstance(md.mesh,mesh2d): + part=np.array(Chaco(md.qmu.adjacency,weights,np.array([]),md.mesh.x, md.mesh.y,np.zeros((md.mesh.numberofvertices,)),method,npart,np.array([]))).T+1 #index partitions from 1 up. like metis. + else: + part=np.array(Chaco(md.qmu.adjacency,weights,np.array([]),md.mesh.x, md.mesh.y,md.mesh.z,method,npart,np.array([]))).T+1 #index partitions from 1 up. like metis. elif m.strcmpi(package,'scotch'): Index: /issm/trunk/src/m/plot/applyoptions.m =================================================================== --- /issm/trunk/src/m/plot/applyoptions.m (revision 23393) +++ /issm/trunk/src/m/plot/applyoptions.m (revision 23394) @@ -142,4 +142,6 @@ if exist(options,'colorbarcornerposition'), c=colorbar(getfieldvalue(options,'colorbarcornerposition'),'peer',gca); + elseif exist(options,'colorbarpos') & ischar(getfieldvalue(options,'colorbarpos')), + c=colorbar(getfieldvalue(options,'colorbarpos')); else c=colorbar('peer',gca); @@ -151,5 +153,5 @@ set(c,'Ylim',lim); end - if exist(options,'colorbarpos'), + if exist(options,'colorbarpos') & isnumeric(getfieldvalue(options,'colorbarpos')), set(c,'Position',getfieldvalue(options,'colorbarpos')); end Index: /issm/trunk/src/m/plot/googlemaps.m =================================================================== --- /issm/trunk/src/m/plot/googlemaps.m (revision 23393) +++ /issm/trunk/src/m/plot/googlemaps.m (revision 23394) @@ -123,5 +123,20 @@ '&scale=' num2str(scale)]; url = ['http://maps.google.com/maps/api/staticmap?' params]; - [X, map]=imread(url,'png'); + count = 0; + countmax = 10; + while(true) + try, + [X, map]=imread(url,'png'); + break; + catch me, + count = count+1; + disp(['Failed, trying again... (' num2str(countmax-count) ' more attempts)']); + pause(.3); + if count>countmax, + disp('Giving up...'); + rethrow(me); + end + end + end X=ind2rgb(X,map); indx1 = floor(x*width)+1; Index: /issm/trunk/src/m/qmu/dakota_in_write.py =================================================================== --- /issm/trunk/src/m/qmu/dakota_in_write.py (revision 23393) +++ /issm/trunk/src/m/qmu/dakota_in_write.py (revision 23394) @@ -62,5 +62,5 @@ filei2=fullfile(pathstr,name+ext) - print 'Opening Dakota input file \''+filei2 + '\'' + print 'Opening Dakota input file \''+filei2 + '\'.' try: with open(filei2,'w+') as fidi: Index: /issm/trunk/src/m/qmu/dakota_out_parse.py =================================================================== --- /issm/trunk/src/m/qmu/dakota_out_parse.py (revision 23393) +++ /issm/trunk/src/m/qmu/dakota_out_parse.py (revision 23394) @@ -241,4 +241,15 @@ dmax95 =prctile_issm(data,95,0) + # Note: the following line may cause the following warning + # (should not crash or invalidate results) when one of + # the inputs does not change with respect to the + # other/s causing an internal divide-by-zero error + + #/usr/local/lib/python2.7/dist-packages/numpy/lib/function_base.py:3163: + # RuntimeWarning: invalid value encountered in true_divide + # c /= stddev[:,None] + + # (and/or the same but with "c /= stddev[None, :]") + dcorrel=np.corrcoef(data.T) Index: /issm/trunk/src/m/qmu/helpers.py =================================================================== --- /issm/trunk/src/m/qmu/helpers.py (revision 23393) +++ /issm/trunk/src/m/qmu/helpers.py (revision 23394) @@ -250,5 +250,5 @@ pass - # if all of that fails, then if is not empty + # if all of that fails, then it is not empty return False Index: /issm/trunk/src/m/qmu/preqmu.py =================================================================== --- /issm/trunk/src/m/qmu/preqmu.py (revision 23393) +++ /issm/trunk/src/m/qmu/preqmu.py (revision 23394) @@ -45,6 +45,7 @@ raise RuntimeError('Existing '+str(options.qmudir)+' directory, cannot overwrite. Specify "overwrite","y" option in solve arguments.') - - os.makedirs(qmudir) + # os.makedirs() raises error when dir exists, matlab's mkdir() does not + if not os.path.isdir(qmudir): + os.makedirs(qmudir) os.chdir(qmudir) Index: /issm/trunk/src/m/qmu/process_qmu_response_data.m =================================================================== --- /issm/trunk/src/m/qmu/process_qmu_response_data.m (revision 23393) +++ /issm/trunk/src/m/qmu/process_qmu_response_data.m (revision 23394) @@ -43,8 +43,6 @@ %ok, process the domains named in qmu_mass_flux_profiles, to build a list of segments (MatArray) md.qmu.mass_flux_segments=cell(num_mass_flux,1); - md.qmu.mass_flux_segments for i=1:num_mass_flux, md.qmu.mass_flux_segments{i}=MeshProfileIntersection(md.mesh.elements,md.mesh.x,md.mesh.y,[md.qmu.mass_flux_profile_directory '/' md.qmu.mass_flux_profiles{i}]); end - md.qmu.mass_flux_segments end Index: /issm/trunk/src/m/solve/WriteData.py =================================================================== --- /issm/trunk/src/m/solve/WriteData.py (revision 23393) +++ /issm/trunk/src/m/solve/WriteData.py (revision 23394) @@ -7,5 +7,5 @@ """ WRITEDATA - write model field in binary file - + Usage: WriteData(fid,varargin) @@ -57,5 +57,5 @@ #Step 1: write the enum to identify this record uniquely fid.write(struct.pack('i',len(name))) - fid.write(struct.pack('%ds' % len(name),name)) + fid.write(struct.pack('%ds' % len(name),name)) #Step 2: write the data itself. @@ -67,6 +67,6 @@ fid.write(struct.pack('i',4+4)) #1 bool (disguised as an int)+code - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write integer @@ -81,9 +81,9 @@ fid.write(struct.pack('i',4+4)) #1 integer + code - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write integer - fid.write(struct.pack('i',data)) + fid.write(struct.pack('i',data)) # }}} @@ -95,9 +95,9 @@ fid.write(struct.pack('i',8+4)) #1 double+code - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write double - fid.write(struct.pack('d',data)) + fid.write(struct.pack('d',data)) # }}} @@ -106,10 +106,10 @@ fid.write(struct.pack('i',len(data)+4+4)) #string + string size + code - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write string - fid.write(struct.pack('i',len(data))) - fid.write(struct.pack('%ds' % len(data),data)) + fid.write(struct.pack('i',len(data))) + fid.write(struct.pack('%ds' % len(data),data)) # }}} @@ -135,17 +135,17 @@ fid.write(struct.pack('i',4+4+8*np.product(s)+4+4)) #2 integers (32 bits) + the double matrix + code + matrix type - #write data code and matrix type: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) fid.write(struct.pack('i',mattype)) #now write matrix if np.ndim(data)==1: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',1)) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) for i in xrange(s[0]): fid.write(struct.pack('d',float(data[i]))) #get to the "c" convention, hence the transpose else: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) for i in xrange(s[0]): for j in xrange(s[1]): @@ -174,17 +174,17 @@ fid.write(struct.pack('i',4+4+8*np.product(s)+4+4)) #2 integers (32 bits) + the double matrix + code + matrix type - #write data code and matrix type: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) fid.write(struct.pack('i',mattype)) #now write matrix if np.ndim(data) == 1: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',1)) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) for i in xrange(s[0]): fid.write(struct.pack('d',float(data[i]))) #get to the "c" convention, hence the transpose else: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) for i in xrange(s[0]): for j in xrange(s[1]): @@ -217,17 +217,17 @@ fid.write(struct.pack('i',recordlength)) #2 integers (32 bits) + the double matrix + code + matrix type - #write data code and matrix type: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) fid.write(struct.pack('i',mattype)) #now write matrix if np.ndim(data) == 1: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',1)) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) for i in xrange(s[0]): fid.write(struct.pack('d',float(data[i]))) #get to the "c" convention, hence the transpose else: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) for i in xrange(s[0]): for j in xrange(s[1]): @@ -266,6 +266,6 @@ fid.write(struct.pack('i',recordlength)) #2 integers (32 bits) + the matrix + code + matrix type - #write data code and matrix type: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) fid.write(struct.pack('i',mattype)) @@ -276,12 +276,12 @@ if rangeA == 0: - A = A*0 - else: - A = (A-offsetA)/rangeA*255. - + A = A*0 + else: + A = (A-offsetA)/rangeA*255. + #now write matrix if np.ndim(data) == 1: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',1)) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) fid.write(struct.pack('d',float(offsetA))) fid.write(struct.pack('d',float(rangeA))) @@ -292,6 +292,6 @@ elif np.product(s) > 0: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) fid.write(struct.pack('d',float(offsetA))) fid.write(struct.pack('d',float(rangeA))) @@ -324,11 +324,11 @@ #write length of record - fid.write(struct.pack('i',recordlength)) - - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + fid.write(struct.pack('i',recordlength)) + + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #write data, first number of records - fid.write(struct.pack('i',len(data))) + fid.write(struct.pack('i',len(data))) for matrix in data: @@ -343,11 +343,11 @@ if np.ndim(matrix) == 1: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',1)) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) for i in xrange(s[0]): fid.write(struct.pack('d',float(matrix[i]))) #get to the "c" convention, hence the transpose else: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) for i in xrange(s[0]): for j in xrange(s[1]): @@ -363,16 +363,16 @@ #write length of record - fid.write(struct.pack('i',recordlength)) - - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + fid.write(struct.pack('i',recordlength)) + + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write length of string array - fid.write(struct.pack('i',len(data))) + fid.write(struct.pack('i',len(data))) #now write the strings for string in data: - fid.write(struct.pack('i',len(string))) - fid.write(struct.pack('%ds' % len(string),string)) + fid.write(struct.pack('i',len(string))) + fid.write(struct.pack('%ds' % len(string),string)) # }}} @@ -383,6 +383,6 @@ def FormatToCode(format): # {{{ """ - This routine takes the format string, and hardcodes it into an integer, which - is passed along the record, in order to identify the nature of the dataset being + This routine takes the format string, and hardcodes it into an integer, which + is passed along the record, in order to identify the nature of the dataset being sent. """ Index: /issm/trunk/src/wrappers/Chaco/Chaco.cpp =================================================================== --- /issm/trunk/src/wrappers/Chaco/Chaco.cpp (revision 23393) +++ /issm/trunk/src/wrappers/Chaco/Chaco.cpp (revision 23394) @@ -47,13 +47,13 @@ /*Fetch Data*/ FetchChacoData(&nvtxs,&adjacency,&start,&ewgts,A_IN,EWGTS_IN); - FetchData(&vwgts,&nterms,VWGTS_IN); - FetchData(&x,&nterms,X_IN); - FetchData(&y,&nterms,Y_IN); - FetchData(&z,&nterms,Z_IN); - FetchData(&in_options,&nterms,OPTNS_IN); + FetchData(&vwgts,&nterms,VWGTS_IN); + FetchData(&x,&nterms,X_IN); + FetchData(&y,&nterms,Y_IN); + FetchData(&z,&nterms,Z_IN); + FetchData(&in_options,&nterms,OPTNS_IN); for (i=0;i<(nterms<10?nterms:10);i++) options[i]=in_options[i]; //copy in_options into default options - FetchData(&npart,NPARTS_IN); + FetchData(&npart,NPARTS_IN); //int * nparts=xNew(1); nparts[0]=npart; //weird Chacox interface ain't it? - FetchData(&goal,&nterms,GOAL_IN); + FetchData(&goal,&nterms,GOAL_IN); /*Allocate output: */ Index: /issm/trunk/src/wrappers/DistanceToMaskBoundary/DistanceToMaskBoundary.cpp =================================================================== --- /issm/trunk/src/wrappers/DistanceToMaskBoundary/DistanceToMaskBoundary.cpp (revision 23393) +++ /issm/trunk/src/wrappers/DistanceToMaskBoundary/DistanceToMaskBoundary.cpp (revision 23394) @@ -43,5 +43,6 @@ /*Call core of computation: */ - DistanceToMaskBoundaryx(&distance,x,y,mask,nods); + _error_("messing up with AD, is this fonction really used??"); + //DistanceToMaskBoundaryx(&distance,x,y,mask,nods); /*Write results: */ Index: /issm/trunk/src/wrappers/IssmConfig/IssmConfig.cpp =================================================================== --- /issm/trunk/src/wrappers/IssmConfig/IssmConfig.cpp (revision 23393) +++ /issm/trunk/src/wrappers/IssmConfig/IssmConfig.cpp (revision 23394) @@ -66,4 +66,14 @@ else if(strcmp(name,"_HAVE_M1QN3_")==0){ #ifdef _HAVE_M1QN3_ + value = 1.; + #endif + } + else if(strcmp(name,"_HAVE_ADOLC_")==0){ + #ifdef _HAVE_ADOLC_ + value = 1.; + #endif + } + else if(strcmp(name,"_HAVE_CODIPACK_")==0){ + #ifdef _HAVE_CODIPACK_ value = 1.; #endif Index: /issm/trunk/src/wrappers/javascript/Makefile.am =================================================================== --- /issm/trunk/src/wrappers/javascript/Makefile.am (revision 23393) +++ /issm/trunk/src/wrappers/javascript/Makefile.am (revision 23394) @@ -1,3 +1,3 @@ -AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ +AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @CODIPACKINCL@ AUTOMAKE_OPTIONS = subdir-objects Index: /issm/trunk/src/wrappers/matlab/Makefile.am =================================================================== --- /issm/trunk/src/wrappers/matlab/Makefile.am (revision 23393) +++ /issm/trunk/src/wrappers/matlab/Makefile.am (revision 23394) @@ -1,3 +1,3 @@ -AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ +AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@ AUTOMAKE_OPTIONS = subdir-objects Index: /issm/trunk/src/wrappers/python/Makefile.am =================================================================== --- /issm/trunk/src/wrappers/python/Makefile.am (revision 23393) +++ /issm/trunk/src/wrappers/python/Makefile.am (revision 23394) @@ -1,3 +1,3 @@ -AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ @AMPIINCL@ +AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@ AUTOMAKE_OPTIONS = subdir-objects Index: /issm/trunk/src/wrappers/python/io/FetchPythonData.cpp =================================================================== --- /issm/trunk/src/wrappers/python/io/FetchPythonData.cpp (revision 23393) +++ /issm/trunk/src/wrappers/python/io/FetchPythonData.cpp (revision 23394) @@ -32,5 +32,5 @@ } else if (PyInt_Check(py_float)) - dscalar=(double)PyInt_AsLong(py_float); + dscalar=(double)PyInt_AsLong(py_float); else if (PyBool_Check(py_float)) dscalar=(double)PyLong_AsLong(py_float); @@ -132,5 +132,6 @@ double* dmatrix=NULL; double* matrix=NULL; - int M,N; + int M=0; + int N=0; int ndim; npy_intp* dims=NULL; @@ -236,5 +237,6 @@ /*output: */ int* matrix=NULL; - int M,N; + int M=0; + int N=0; int ndim; npy_intp* dims=NULL; @@ -325,5 +327,6 @@ bool* bmatrix=NULL; bool* matrix=NULL; - int M,N; + int M=0; + int N=0; int ndim; npy_intp* dims=NULL; @@ -411,5 +414,5 @@ double* dvector=NULL; double* vector=NULL; - int M; + int M=0; int ndim; npy_intp* dims=NULL; @@ -499,5 +502,5 @@ /*output: */ float* vector=NULL; - int M; + int M=0; int ndim; npy_intp* dims=NULL; @@ -539,5 +542,5 @@ /*transform into int vector: */ vector=xNew(M); - for(i=0;i(M); - for(i=0;i(nvtxs+1); + pyGetJc(a,nvtxs,mwstart); + + int* mwadjacency = xNewZeroInit(nzmax); + pyGetIr(a,nvtxs,nzmax,mwadjacency); + + int* start = xNew(nvtxs+1); + for(int i=0;i(nzmax); + for(int i=0; i(nedges); + for(int i = 0; i> runme(id=[101,102]) etc... - + Available options: 'id' followed by the list of ids or (parts of) test names requested @@ -37,8 +37,8 @@ 'procedure' 'check' : run the test (default) 'update': update the archive - + Usage: runme(varargin) - + Examples: runme() @@ -49,5 +49,4 @@ runme(id=[[101,102],['Dakota','Slr']]) """ - from parallelrange import parallelrange from IdToName import IdToName @@ -82,17 +81,14 @@ flist=glob('test*.py') #File name must start with 'test' and must end by '.py' and must be different than 'test.py' list_ids=[int(file[4:-3]) for file in flist if not file == 'test.py'] #Keep test id only (skip 'test' and '.py') - #print 'list_ids =',list_ids i1,i2=parallelrange(rank,numprocs,len(list_ids)) #Get tests for this cpu only list_ids=list_ids[i1:i2+1] - #print 'list_ids after parallelrange =',list_ids - - if id: + + if np.size(id) > 0 and not id==None: test_ids = set(GetIds(id)).intersection(set(list_ids)) else: # if no tests are specifically provided, do them all test_ids = set(list_ids) - - #print 'test_ids after list =',test_ids + # }}} #GET exclude {{{ @@ -100,6 +96,4 @@ test_ids=test_ids.difference(exclude_ids) - #print 'test_ids after exclude =',sorted(test_ids) - #return # }}} #Process Ids according to benchmarks {{{ @@ -124,8 +118,6 @@ elif benchmark=='adolc': test_ids=test_ids.intersection(set(range(3001,3200))) - #print 'test_ids after benchmark =',test_ids test_ids=list(test_ids) test_ids.sort() - #print 'test_ids after sort =',test_ids # }}} @@ -190,5 +182,5 @@ if np.shape(field) != np.shape(archive): raise RuntimeError("Field '"+archive_name+"' from test is malformed; shape is "+str(np.shape(field.T))+", should be "+str(np.shape(archive))+" (or "+str(np.shape(archive.T))+").") - + error_diff=np.amax(np.abs(archive-field),axis=0)/(np.amax(np.abs(archive),axis=0)+float_info.epsilon) Index: /issm/trunk/test/NightlyRun/test2084.m =================================================================== --- /issm/trunk/test/NightlyRun/test2084.m (revision 23393) +++ /issm/trunk/test/NightlyRun/test2084.m (revision 23394) @@ -1,4 +1,3 @@ - -%Test Name: GiaCaron. +%Test Name: GiaCaron %Forward Love number solution for a viscoelastic earth, model M3-L70-V01 from %Spada, G., Barletta, V. R., Klemann, V., Riva, R. E. M., Martinec, Z., @@ -39,5 +38,5 @@ %loading love numbers field_names ={'LoveH_loading_elastic','LoveK_loading_elastic','LoveL_loading_elastic'}; -field_tolerances={7.0e-10,7.0e-10,7.0e-10}; +field_tolerances={4.3e-9,4.3e-9,4.3e-9}; field_values={... (md.results.LoveSolution.LoveHr(:,1)),... @@ -57,5 +56,5 @@ %Fields and tolerances to track changes field_names ={field_names{:},'LoveH_loading_realpart','LoveK_loading_realpart','LoveL_loading_realpart','LoveH_loading_imagpart','LoveK_loading_imagpart','LoveL_loading_imagpart'}; -field_tolerances={field_tolerances{:},7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10}; +field_tolerances={field_tolerances{:},5e-7,5e-7,5e-7,5e-7,5e-7,5e-7}; field_values={field_values{:},... (md.results.LoveSolution.LoveHr(:,:)),... @@ -75,5 +74,5 @@ %tidal love numbers field_names ={field_names{:},'LoveH_tidal_elastic','LoveK_tidal_elastic','LoveL_tidal_elastic','LoveH_tidal_realpart','LoveK_tidal_realpart','LoveL_tidal_realpart','LoveH_tidal_imagpart','LoveK_tidal_imagpart','LoveL_tidal_imagpart'}; -field_tolerances={field_tolerances{:},7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10}; +field_tolerances={field_tolerances{:},8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6}; field_values={field_values{:},... (md.results.LoveSolution.LoveHr(:,1)),... @@ -115,5 +114,5 @@ % %field_names ={field_names{:},'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'}; -%field_tolerances={field_tolerances{:},7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10}; +%field_tolerances={field_tolerances{:},2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6}; %field_values={field_values{:},... % (md.results.LoveSolution.LoveHr(:,1)),... @@ -147,5 +146,5 @@ field_names ={field_names{:},'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'}; -field_tolerances={field_tolerances{:},7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10}; +field_tolerances={field_tolerances{:},2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6}; field_values={field_values{:},... (md.results.LoveSolution.LoveHr(:,1)),... Index: /issm/trunk/test/NightlyRun/test2084.py =================================================================== --- /issm/trunk/test/NightlyRun/test2084.py (revision 23393) +++ /issm/trunk/test/NightlyRun/test2084.py (revision 23394) @@ -1,8 +1,9 @@ -#Test Name: GiaCaron. Forward Love number solution for a viscoelastic earth, -# model M3-L70-V01 from Spada, G., Barletta, V. R., Klemann, V., Riva, R. E. M., -# Martinec, Z., Gasperini, P., Lund, B., Wolf, D., Vermeersen, L. L. A. -# and King, M. A. (2011), A benchmark study for glacial isostatic -# adjustment codes. Geophysical Journal International, -# 185: 106-132. doi:10.1111/j.1365-246X.2011.04952.x +#Test Name: GiaCaron +#Forward Love number solution for a viscoelastic earth, +#model M3-L70-V01 from Spada, G., Barletta, V. R., Klemann, V., Riva, R. E. M., +#Martinec, Z., Gasperini, P., Lund, B., Wolf, D., Vermeersen, L. L. A. +#and King, M. A. (2011), A benchmark study for glacial isostatic +#adjustment codes. Geophysical Journal International, +#185: 106-132. doi:10.1111/j.1365-246X.2011.04952.x from model import * @@ -48,6 +49,6 @@ #Fields and tolerances to track changes #loading love numbers -field_names=['LoveHe','LoveKe','LoveLe'] -field_tolerances=[3.7e-9,3.7e-9,3.7e-9] +field_names=['LoveH_loading_elastic','LoveK_loading_elastic','LoveL_loading_elastic'] +field_tolerances=[4.3e-9,4.3e-9,4.3e-9] field_values=[ np.array(md.results.LoveSolution.LoveHr)[:,0], @@ -67,6 +68,6 @@ #Fields and tolerances to track changes #loading love numbers -field_names+=['LoveHlr','LoveKlr','LoveLlr','LoveHli','LoveKli','LoveLli'] -field_tolerances+=[3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9] +field_names+=['LoveH_loading_realpart','LoveK_loading_realpart','LoveL_loading_realpart','LoveH_loading_imagpart','LoveK_loading_imagpart','LoveL_loading_imagpart'] +field_tolerances+=[5e-7,5e-7,5e-7,5e-7,5e-7,5e-7] field_values+=[ np.array(md.results.LoveSolution.LoveHr), @@ -87,6 +88,6 @@ #tidal love numbers, check -field_names+=['LoveHtr','LoveKtr','LoveLtr','LoveHti','LoveKti','LoveLti'] -field_tolerances+=[3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9] +field_names+=['LoveH_tidal_elastic','LoveK_tidal_elastic','LoveL_tidal_elastic','LoveH_tidal_realpart','LoveK_tidal_realpart','LoveL_tidal_realpart','LoveH_tidal_imagpart','LoveK_tidal_imagpart','LoveL_tidal_imagpart'] +field_tolerances+=[8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6] field_values+=[ np.array(md.results.LoveSolution.LoveHr)[:,0], @@ -127,6 +128,6 @@ #md=solve(md,'lv') # -#field_names=[field_names,'LoveHmr','LoveKmr','LoveLmr','LoveHmi','LoveKmi','LoveLmi'] -#field_tolerances=[field_tolerances,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] +#field_names=[field_names,'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'] +#field_tolerances=[field_tolerances,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9] #field_values=[field_values,\ # (md.results.LoveSolution.LoveHr[:][0]),\ @@ -186,6 +187,6 @@ md.love.nfreq=len(md.love.frequencies) -field_names+=['LoveHmr','LoveKmr','LoveLmr','LoveHmi','LoveKmi','LoveLmi'] -field_tolerances+=[3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9] +field_names+=['LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'] +field_tolerances+=[2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6] field_values+=[ np.array(md.results.LoveSolution.LoveHr)[:,0], Index: /issm/trunk/test/NightlyRun/test211.js =================================================================== --- /issm/trunk/test/NightlyRun/test211.js (revision 23393) +++ /issm/trunk/test/NightlyRun/test211.js (revision 23394) @@ -12,10 +12,10 @@ //Fields and tolerances to track changes field_names=[ - 'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsGroundediceMeltingRate1', - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2', + 'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsGroundediceMeltingRate1', + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2', 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3']; field_tolerances=[ 2e-08,2e-08,5e-05,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08, - 5e-06,5e-06,8e-05,5e-06,1e-07,5e-07,5e-07,5e-07,3e-06,5e-05, + 5e-06,5e-06,8e-05,5e-06,5e-07,5e-07,5e-07,5e-07,3e-06,5e-05, 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05]; field_values=[ Index: /issm/trunk/test/NightlyRun/test211.m =================================================================== --- /issm/trunk/test/NightlyRun/test211.m (revision 23393) +++ /issm/trunk/test/NightlyRun/test211.m (revision 23394) @@ -16,5 +16,5 @@ field_tolerances={... 2e-08,2e-08,5e-05,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,... - 5e-06,5e-06,8e-05,5e-06,1e-07,5e-07,5e-07,5e-07,3e-06,5e-05,... + 5e-06,5e-06,8e-05,5e-06,5e-07,5e-07,5e-07,5e-07,3e-06,5e-05,... 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05}; field_values={... Index: /issm/trunk/test/NightlyRun/test211.py =================================================================== --- /issm/trunk/test/NightlyRun/test211.py (revision 23393) +++ /issm/trunk/test/NightlyRun/test211.py (revision 23394) @@ -26,6 +26,6 @@ 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'] field_tolerances=[2e-08,2e-08,5e-05,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08, - 5e-06,5e-06,8e-05,5e-06,1e-07,5e-07,5e-07,5e-07,3e-06,5e-05, - 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05] + 5e-06,5e-06,8e-05,5e-06,5e-07,5e-07,5e-07,5e-07,3e-06,5e-05, + 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05] field_values=[md.results.TransientSolution[0].Vx, md.results.TransientSolution[0].Vy, Index: /issm/trunk/test/NightlyRun/test215.m =================================================================== --- /issm/trunk/test/NightlyRun/test215.m (revision 23393) +++ /issm/trunk/test/NightlyRun/test215.m (revision 23394) @@ -24,5 +24,5 @@ %Fields and tolerances to track changes field_names ={'Gradient','Misfits','MaterialsRheologyBbar','Pressure','Vel','Vx','Vy'}; -field_tolerances={4.6e-08,1e-08,2e-08,1e-09,2e-09,2e-08,2e-08}; +field_tolerances={4.6e-08,1e-08,2e-08,2e-09,3e-09,2e-08,2e-08}; field_values={... (md.results.StressbalanceSolution.Gradient1),... Index: /issm/trunk/test/NightlyRun/test215.py =================================================================== --- /issm/trunk/test/NightlyRun/test215.py (revision 23393) +++ /issm/trunk/test/NightlyRun/test215.py (revision 23394) @@ -37,5 +37,5 @@ # Fields and tolerances to track changes field_names =['Gradient','Misfits','MaterialsRheologyBbar','Pressure','Vel','Vx','Vy'] -field_tolerances=[4.6e-08,1e-08,2e-09,1e-08,2e-09,2e-08,2e-08] +field_tolerances=[4.6e-08,1e-08,2e-08,2e-09,3e-09,2e-08,2e-08] field_values=[md.results.StressbalanceSolution.Gradient1, md.results.StressbalanceSolution.J, Index: /issm/trunk/test/NightlyRun/test234.py =================================================================== --- /issm/trunk/test/NightlyRun/test234.py (revision 23394) +++ /issm/trunk/test/NightlyRun/test234.py (revision 23394) @@ -0,0 +1,101 @@ +#Test Name: SquareShelfTranForceNeg2dDakotaSamp +import numpy as np +import scipy.io as spio +from os import getcwd +from model import * +from socket import gethostname +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from solve import * +from SMBgemb import * +from partitioner import * +from dmeth_params_set import * + +md = triangle(model(),'../Exp/Square.exp',180000.) +md = setmask(md,'all','') +md = parameterize(md,'../Par/SquareShelf.py') +md = setflowequation(md,'SSA','all') +md.cluster = generic('name',gethostname(),'np',3) + +md.timestepping.time_step = 1 +md.settings.output_frequency = 1 +md.timestepping.final_time = 4 + +smb = np.ones((md.mesh.numberofvertices,))*3.6 +smb = np.array([smb,smb*-1]).T + +md.smb.mass_balance = smb +md.smb.mass_balance = np.concatenate((md.smb.mass_balance,[[1.5,3]])) +md.transient.isthermal = 0 + +#Dakota options + +#dakota version +version = IssmConfig('_DAKOTA_VERSION_') +version = float(version[0]) + +#partitioning +md.qmu.numberofpartitions = 20 +md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') +md.qmu.partition = md.qmu.partition - 1 + +#variables +md.qmu.variables.surface_mass_balance = normal_uncertain.normal_uncertain('scaled_SmbMassBalance',1,0.1) + +#responses +md.qmu.responses.MaxVel = response_function.response_function('MaxVel',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.IceVolume = response_function.response_function('IceVolume',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux1 = response_function.response_function('indexed_MassFlux_1',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux2 = response_function.response_function('indexed_MassFlux_2',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux3 = response_function.response_function('indexed_MassFlux_3',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux4 = response_function.response_function('indexed_MassFlux_4',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux5 = response_function.response_function('indexed_MassFlux_5',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.massFlux6 = response_function.response_function('indexed_MassFlux_6',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) + +#mass flux profiles +md.qmu.mass_flux_profiles = ['../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp'] +md.qmu.mass_flux_profile_directory = getcwd() + +## nond_sampling study +md.qmu.method = dakota_method.dakota_method('nond_samp') +md.qmu.method = dmeth_params_set(md.qmu.method,'seed',1234,'samples',20,'sample_type','lhs') +dver = str(version) +if ((int(dver[0]) == 4 and int(dver[2])>2) or int(dver[0])>4): + md.qmu.method = dmeth_params_set(md.qmu.method,'rng','rnum2') + +#parameters +md.qmu.params.direct = True +md.qmu.params.analysis_components = '' +md.qmu.params.interval_type = 'forward' +md.qmu.params.tabular_graphics_data = True +md.qmu.isdakota = 1 + +if version >= 6: + md.qmu.params.analysis_driver = 'matlab' + md.qmu.params.evaluation_scheduling = 'master' + md.qmu.params.processors_per_evaluation = 2 +else: + md.qmu.params.analysis_driver = 'stressbalance' + md.qmu.params.evaluation_concurrency = 1 + +md.stressbalance.reltol = 10**-5 #tighten for qmu analyses +md.transient.requested_outputs = ['IceVolume'] + +#solve +md.verbose = verbose('000000000') # this line is recommended +md = solve(md,'Transient','overwrite','y') +md.qmu.results = md.results.dakota + +#Fields and tolerances to track changes +md.results.dakota.moments = [] +for i in range(8): + md.results.dakota.moments.append(md.results.dakota.dresp_out[i].mean) + +for i in range(8): + md.results.dakota.moments.append(md.results.dakota.dresp_out[i].stddev) + +field_names = ['moments'] +field_tolerances = [1e-11] +field_values = [md.results.dakota.moments] Index: /issm/trunk/test/NightlyRun/test235.py =================================================================== --- /issm/trunk/test/NightlyRun/test235.py (revision 23394) +++ /issm/trunk/test/NightlyRun/test235.py (revision 23394) @@ -0,0 +1,97 @@ +#Test Name: SquareShelfTranForceNeg2dDakotaLocal +import numpy as np +import scipy.io as spio +from os import getcwd +from model import * +from socket import gethostname +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from solve import * +from SMBgemb import * +from partitioner import * +from dmeth_params_set import * + +md = triangle(model(),'../Exp/Square.exp',180000.) +md = setmask(md,'all','') +md = parameterize(md,'../Par/SquareShelf.py') +md = setflowequation(md,'SSA','all') +md.cluster = generic('name',gethostname(),'np',3) + +md.timestepping.time_step = 1 +md.settings.output_frequency = 1 +md.timestepping.final_time = 4 + +smb = np.ones((md.mesh.numberofvertices,))*3.6 +smb = np.array([smb,smb*-1]).T + +md.smb.mass_balance = smb +md.smb.mass_balance = np.concatenate((md.smb.mass_balance,[[1.5,3]])) +md.transient.isthermal = 0 + +#Dakota options + +#dakota version +version = IssmConfig('_DAKOTA_VERSION_') +version = float(version[0]) + +#partitioning +md.qmu.numberofpartitions = 20 +md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') +md.qmu.partition = md.qmu.partition - 1 + +#variables +md.qmu.variables.surface_mass_balance = normal_uncertain.normal_uncertain('scaled_SmbMassBalance',1,100) + +#responses +md.qmu.responses.MaxVel = response_function.response_function('MaxVel',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.IceVolume = response_function.response_function('IceVolume',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux1 = response_function.response_function('indexed_MassFlux_1',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux2 = response_function.response_function('indexed_MassFlux_2',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux3 = response_function.response_function('indexed_MassFlux_3',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux4 = response_function.response_function('indexed_MassFlux_4',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux5 = response_function.response_function('indexed_MassFlux_5',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.massFlux6 = response_function.response_function('indexed_MassFlux_6',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) + +#mass flux profiles +md.qmu.mass_flux_profiles = ['../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp'] +md.qmu.mass_flux_profile_directory = getcwd() + +#method +md.qmu.method = dakota_method.dakota_method('nond_l') + +#parameters +md.qmu.params.direct = True +md.qmu.params.analysis_components = '' +md.qmu.params.interval_type = 'forward' +md.qmu.params.fd_gradient_step_size = '0.1' +md.qmu.isdakota = 1 + +if version >= 6: + md.qmu.params.analysis_driver = 'matlab' + md.qmu.params.evaluation_scheduling = 'master' + md.qmu.params.processors_per_evaluation = 2 +else: + md.qmu.params.analysis_driver = 'stressbalance' + md.qmu.params.evaluation_concurrency = 1 + +md.stressbalance.reltol = 10**-5 #tighten for qmu analyses +md.transient.requested_outputs = ['IceVolume'] + +#solve +md.verbose = verbose('000000000') # this line is recommended +md = solve(md,'Transient','overwrite','y') +md.qmu.results = md.results.dakota + +#Fields and tolerances to track changes +md.results.dakota.moments = [] +for i in range(8): + md.results.dakota.moments.append(md.results.dakota.dresp_out[i].mean) + +for i in range(8): + md.results.dakota.moments.append(md.results.dakota.dresp_out[i].stddev) + +field_names = ['moments'] +field_tolerances = [1e-11] +field_values = [md.results.dakota.moments] Index: /issm/trunk/test/NightlyRun/test245.m =================================================================== --- /issm/trunk/test/NightlyRun/test245.m (revision 23394) +++ /issm/trunk/test/NightlyRun/test245.m (revision 23394) @@ -0,0 +1,47 @@ +%Test Name: SquareShelfTranIspddSicopolisSSA2d +md=triangle(model(),'../Exp/Square.exp',150000.); +md=setmask(md,'all',''); +md=parameterize(md,'../Par/SquareShelf.par'); + +% Use of SMBpddSicopolis +md.smb = SMBpddSicopolis(); +% initalize pdd fields +md.smb=initialize(md.smb,md); +md.smb.s0p=md.geometry.surface; +md.smb.s0t=md.geometry.surface; + +% +md.smb.monthlytemperatures=[]; md.smb.precipitation=[]; md.smb.precipitation=[]; +temp_ma_present=-10*ones(md.mesh.numberofvertices,1)-md.smb.rlaps*md.geometry.surface/1000; +temp_mj_present=10*ones(md.mesh.numberofvertices,1)-md.smb.rlaps*md.geometry.surface/1000; +precipitation=5*ones(md.mesh.numberofvertices,1); +for imonth=0:11 + md.smb.monthlytemperatures(1:md.mesh.numberofvertices,imonth+1)=md.materials.meltingpoint+temp_ma_present+(temp_mj_present-temp_ma_present)*sin(double(imonth+1-4)*pi/6.0); + md.smb.monthlytemperatures(md.mesh.numberofvertices+1,imonth+1)=((imonth+1)/12); + md.smb.precipitation(1:md.mesh.numberofvertices,imonth+1)=precipitation; + md.smb.precipitation(md.mesh.numberofvertices+1,imonth+1)=((imonth+1)/12); +end + +% time steps and resolution +md.timestepping.time_step=1; +md.settings.output_frequency=1; +md.timestepping.final_time=2; + +md.transient.issmb=1; +md.transient.ismasstransport=1; +md.transient.isstressbalance=0; +md.transient.isthermal=0; + +md.transient.requested_outputs={'default','TemperaturePDD'}; +md.cluster=generic('name',oshostname(),'np',1); % 3 for the cluster +md=solve(md,'Transient'); + +%Fields and tolerances to track changes +field_names ={'TemperaturePDD1','SmbMassBalance1','TemperaturePDD2','SmbMassBalance2'}; +field_tolerances={1e-13,1e-13,1e-13,1e-13}; +field_values={... + (md.results.TransientSolution(1).TemperaturePDD),... + (md.results.TransientSolution(1).SmbMassBalance),... + (md.results.TransientSolution(2).TemperaturePDD),... + (md.results.TransientSolution(2).SmbMassBalance),... + }; Index: /issm/trunk/test/NightlyRun/test245.py =================================================================== --- /issm/trunk/test/NightlyRun/test245.py (revision 23394) +++ /issm/trunk/test/NightlyRun/test245.py (revision 23394) @@ -0,0 +1,59 @@ +#Test Name: SquareShelfTranIspddSicopolisSSA2d +import numpy as np +from model import * +from socket import gethostname +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from solve import * + +from SMBpddSicopolis import * + +md = triangle(model(),'../Exp/Square.exp',150000.) +md = setmask(md,'all','') +md = parameterize(md,'../Par/SquareShelf.py') + +# Use of SMBpddSicopolis +md.smb = SMBpddSicopolis() +# initalize pdd fields +md.smb.initialize(md) +md.smb.s0p = md.geometry.surface +md.smb.s0t = md.geometry.surface + +# +md.smb.monthlytemperatures = np.empty((md.mesh.numberofvertices+1,12)) +md.smb.precipitation = np.empty((md.mesh.numberofvertices+1,12)) +temp_ma_present = -10. * np.ones((md.mesh.numberofvertices,)) - md.smb.rlaps * md.geometry.surface / 1000. +temp_mj_present = 10. * np.ones((md.mesh.numberofvertices,)) - md.smb.rlaps * md.geometry.surface / 1000. +precipitation = 5. * np.ones((md.mesh.numberofvertices,)) +for imonth in range(12): + md.smb.monthlytemperatures[0:md.mesh.numberofvertices,imonth] = md.materials.meltingpoint + temp_ma_present + (temp_mj_present - temp_ma_present) * np.sin((imonth + 1. - 4.) * np.pi / 6.0) + md.smb.monthlytemperatures[md.mesh.numberofvertices,imonth] = ((imonth+1)/12.) + md.smb.precipitation[0:md.mesh.numberofvertices,imonth] = precipitation + md.smb.precipitation[md.mesh.numberofvertices,imonth] = ((imonth+1)/12.) + +# time steps and resolution +md.timestepping.time_step = 1 +md.settings.output_frequency = 1 +md.timestepping.final_time = 2 + +md.transient.issmb = 1 +md.transient.ismasstransport = 1 +md.transient.isstressbalance = 0 +md.transient.isthermal = 0 + +md.transient.requested_outputs = ['default','TemperaturePDD'] +md.cluster = generic('name',gethostname(),'np',1) # 3 for the cluster +md = solve(md,'Transient') + +#Fields and tolerances to track changes +field_names = ['TemperaturePDD1','SmbMassBalance1','TemperaturePDD2','SmbMassBalance2'] +field_tolerances = [1e-13,1e-13,1e-13,1e-13] +field_values = [ + md.results.TransientSolution[0].TemperaturePDD, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[1].TemperaturePDD, + md.results.TransientSolution[1].SmbMassBalance, + ] + Index: /issm/trunk/test/NightlyRun/test290.m =================================================================== --- /issm/trunk/test/NightlyRun/test290.m (revision 23393) +++ /issm/trunk/test/NightlyRun/test290.m (revision 23394) @@ -11,5 +11,5 @@ %Fields and tolerances to track changes field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={5e-5,5e-5,8e-5,5e-5,1e-7}; +field_tolerances={5e-5,5e-5,8e-4,5e-4,2e-7}; field_values={... (md.results.StressbalanceSolution.Vx),... Index: /issm/trunk/test/NightlyRun/test290.py =================================================================== --- /issm/trunk/test/NightlyRun/test290.py (revision 23393) +++ /issm/trunk/test/NightlyRun/test290.py (revision 23394) @@ -21,5 +21,5 @@ #Fields and tolerances to track changes field_names =['Vx', 'Vy', 'Vz', 'Vel','Pressure'] -field_tolerances=[5e-5,5e-5,8e-5,5e-5,1e-7] +field_tolerances=[5e-5,5e-5,8e-4,5e-4,2e-7] field_values=[\ md.results.StressbalanceSolution.Vx,\ Index: /issm/trunk/test/NightlyRun/test3015.m =================================================================== --- /issm/trunk/test/NightlyRun/test3015.m (revision 23393) +++ /issm/trunk/test/NightlyRun/test3015.m (revision 23394) @@ -15,12 +15,23 @@ %setup autodiff parameters index=1; %this is the scalar component we are checking against -md.autodiff.independents={... - independent('name','md.geometry.thickness','type','vertex','nods',md.mesh.numberofvertices,'fos_forward_index',index) + +if IssmConfig('_HAVE_CODIPACK_') + md.autodiff.independents={... + independent('name','md.geometry.thickness','type','vertex','nods',md.mesh.numberofvertices) + }; + md.autodiff.dependents={... + dependent('name','IceVolume','type','scalar','fos_reverse_index',index)... + }; + md.autodiff.driver='fos_reverse'; +else + md.autodiff.independents={... + independent('name','md.geometry.thickness','type','vertex','nods',md.mesh.numberofvertices,'fos_forward_index',index) }; -md.autodiff.dependents={... - dependent('name','IceVolume','type','scalar')... - }; -md.autodiff.driver='fos_forward'; + md.autodiff.dependents={... + dependent('name','IceVolume','type','scalar')... + }; + md.autodiff.driver='fos_forward'; +end %parameters for the step-wise derivative @@ -70,7 +81,11 @@ md=solve(md,'Masstransport'); %retrieve directly -dVdh_ad=md.results.MasstransportSolution.AutodiffJacobian; +if IssmConfig('_HAVE_CODIPACK_') + dVdh_ad=md.results.MasstransportSolution.AutodiffJacobian(index); +else + dVdh_ad=md.results.MasstransportSolution.AutodiffJacobian; +end -disp(sprintf('dV/dh: analytical: %16.16g\n using adolc: %16.16g\n',dVdh_an,dVdh_ad)); +disp(sprintf('dV/dh: analytical: %16.16g\n using ad: %16.16g\n',dVdh_an,dVdh_ad)); %Fields and tolerances to track changes Index: /issm/trunk/test/NightlyRun/test3480.m =================================================================== --- /issm/trunk/test/NightlyRun/test3480.m (revision 23393) +++ /issm/trunk/test/NightlyRun/test3480.m (revision 23394) @@ -18,4 +18,5 @@ md.inversion.iscontrol=1; md.autodiff.isautodiff=1; +md.autodiff.driver='fos_reverse'; md.friction.coefficient(1:md.mesh.numberofvertices,1)=50; Index: /issm/trunk/test/NightlyRun/test3481.m =================================================================== --- /issm/trunk/test/NightlyRun/test3481.m (revision 23393) +++ /issm/trunk/test/NightlyRun/test3481.m (revision 23394) @@ -18,4 +18,5 @@ md.inversion.iscontrol=1; md.autodiff.isautodiff=1; +md.autodiff.driver='fos_reverse'; md.friction.coefficient(1:md.mesh.numberofvertices,1)=50; Index: /issm/trunk/test/NightlyRun/test413.py =================================================================== --- /issm/trunk/test/NightlyRun/test413.py (revision 23394) +++ /issm/trunk/test/NightlyRun/test413.py (revision 23394) @@ -0,0 +1,66 @@ +#Test Name: SquareSheetShelfDiadSSA3dDakotaPart +import numpy as np +from model import * +from socket import gethostname +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from solve import * +from partitioner import * +from importancefactors import * + +md = triangle(model(),'../Exp/Square.exp',150000.) +md = setmask(md,'../Exp/SquareShelf.exp','') +md = parameterize(md,'../Par/SquareSheetShelf.py') +md = setflowequation(md,'SSA','all') +md.cluster = generic('name',gethostname(),'np',3) + +#Dakota options + +#dakota version +version = IssmConfig('_DAKOTA_VERSION_') +version = float(version[0]) + +#partitioning +md.qmu.numberofpartitions = 20 +md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') +md.qmu.partition = md.qmu.partition-1 + +#variables +md.qmu.variables.rho_ice = normal_uncertain.normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01) +md.qmu.variables.drag_coefficient = normal_uncertain.normal_uncertain('scaled_FrictionCoefficient',1,0.01) + +#responses +md.qmu.responses.MaxVel = response_function.response_function('MaxVel',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) + +#method +md.qmu.method = dakota_method.dakota_method('nond_l') + +#parameters +md.qmu.params.direct = True +md.qmu.params.interval_type = 'forward' + +if version >= 6: + md.qmu.params.analysis_driver = 'matlab' + md.qmu.params.evaluation_scheduling = 'master' + md.qmu.params.processors_per_evaluation = 2 +else: + md.qmu.params.analysis_driver = 'stressbalance' + md.qmu.params.evaluation_concurrency = 1 + + +#imperative! +md.stressbalance.reltol = 10**-5 #tighten for qmu analyses +md.qmu.isdakota = 1 + +#solve +md.verbose = verbose('000000000') # this line is recommended +md = solve(md,'Stressbalance','overwrite','y') + +#Fields and tolerances to track changes +md.qmu.results = md.results.dakota +md.results.dakota.importancefactors = importancefactors(md,'scaled_FrictionCoefficient','MaxVel').T +field_names = ['importancefactors'] +field_tolerances = [1e-10] +field_values = [md.results.dakota.importancefactors] Index: /issm/trunk/test/NightlyRun/test414.py =================================================================== --- /issm/trunk/test/NightlyRun/test414.py (revision 23394) +++ /issm/trunk/test/NightlyRun/test414.py (revision 23394) @@ -0,0 +1,92 @@ +#Test Name: SquareSheetShelfDiadSSA3dDakotaMassFlux +import numpy as np +from os import getcwd +from model import * +from socket import gethostname +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from solve import * +from partitioner import * + +md = triangle(model(),'../Exp/Square.exp',150000.) +md = setmask(md,'../Exp/SquareShelf.exp','') +md = parameterize(md,'../Par/SquareSheetShelf.py') +md = setflowequation(md,'SSA','all') +md.cluster = generic('name',gethostname(),'np',3) +md.materials.rho_ice = 10**7 #involved in the mass flux, make it easy +md.geometry.thickness[:] = 1 #make it easy +md.geometry.surface = md.geometry.base+md.geometry.thickness + +#constrain all velocities to 1 m/yr, in the y-direction +md.stressbalance.spcvx = np.zeros((md.mesh.numberofvertices,)) +md.stressbalance.spcvy = np.ones((md.mesh.numberofvertices,)) +md.stressbalance.spcvz = np.zeros((md.mesh.numberofvertices,)) + +#Dakota options + +#dakota version +version = IssmConfig('_DAKOTA_VERSION_') +version = float(version[0]) + +#partitioning +md.qmu.numberofpartitions = 20 +md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') +md.qmu.partition = md.qmu.partition-1 + +#variables +md.qmu.variables.drag_coefficient = normal_uncertain.normal_uncertain('scaled_FrictionCoefficient',1,0.01) + +#responses +md.qmu.responses.MaxVel = response_function.response_function('MaxVel',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux1 = response_function.response_function('indexed_MassFlux_1',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux2 = response_function.response_function('indexed_MassFlux_2',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux3 = response_function.response_function('indexed_MassFlux_3',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux4 = response_function.response_function('indexed_MassFlux_4',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux5 = response_function.response_function('indexed_MassFlux_5',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux6 = response_function.response_function('indexed_MassFlux_6',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux7 = response_function.response_function('indexed_MassFlux_7',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) + +#mass flux profiles +md.qmu.mass_flux_profiles = ['../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp','../Exp/Square.exp'] +md.qmu.mass_flux_profile_directory = getcwd() + +#method +md.qmu.method = dakota_method.dakota_method('nond_l') + +#parameters +md.qmu.params.direct = True +md.qmu.params.interval_type = 'forward' +md.qmu.isdakota = 1 +md.stressbalance.reltol = 10**-5 #tighten for qmu analyses + +if version >= 6: + md.qmu.params.analysis_driver = 'matlab' + md.qmu.params.evaluation_scheduling = 'master' + md.qmu.params.processors_per_evaluation = 2 +else: + md.qmu.params.analysis_driver = 'stressbalance' + md.qmu.params.evaluation_concurrency = 1 + +#solve +md.verbose = verbose('000000000') # this line is recommended +md = solve(md,'Stressbalance','overwrite','y') +md.qmu.results = md.results.dakota + +#Fields and tolerances to track changes +#ok, mass flux of 3 profiles should be -3 Gt/yr -3 Gt/yr and the sum, which is -6 Gt/yr +#we recover those mass fluxes through the mean of the response. +#also, we recover the max velo, which should be 1m/yr. +#we put all that data in the moments, which we will use to test for success. +#also, check that the stddev are 0. +md.results.dakota.moments = [] +for i in range(8): + md.results.dakota.moments.append(md.results.dakota.dresp_out[i].mean) + +for i in range(8): + md.results.dakota.moments.append(md.results.dakota.dresp_out[i].stddev) + +field_names = ['moments'] +field_tolerances = [1e-11] +field_values = [md.results.dakota.moments] Index: /issm/trunk/test/NightlyRun/test417.py =================================================================== --- /issm/trunk/test/NightlyRun/test417.py (revision 23394) +++ /issm/trunk/test/NightlyRun/test417.py (revision 23394) @@ -0,0 +1,106 @@ +#Test Name: SquareSheetShelfDiadSSA3dDakotaSamp +import numpy as np +from os import getcwd +from model import * +from socket import gethostname +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from solve import * +from partitioner import * +from dmeth_params_set import * + +md = triangle(model(),'../Exp/Square.exp',150000.) +md = setmask(md,'../Exp/SquareShelf.exp','') +md = parameterize(md,'../Par/SquareSheetShelf.py') +md = setflowequation(md,'SSA','all') +md.cluster = generic('name',gethostname(),'np',3) +md.materials.rho_ice = 10**7 #involved in the mass flux, make it easy +md.geometry.thickness[:] = 1 #make it easy +md.geometry.surface = md.geometry.base+md.geometry.thickness + +#constrain all velocities to 1 m/yr, in the y-direction +md.stressbalance.spcvx[:] = 0 +md.stressbalance.spcvy[:] = 1 +md.stressbalance.spcvz[:] = 0 + +#Dakota options + +#dakota version +version = IssmConfig('_DAKOTA_VERSION_') +version = float(version[0]) + +#partitioning +md.qmu.numberofpartitions = 20 +md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') +md.qmu.partition = md.qmu.partition-1 + +#variables +md.qmu.variables.drag_coefficient = normal_uncertain.normal_uncertain('scaled_FrictionCoefficient',1,0.01) + +#responses +md.qmu.responses.MaxVel = response_function.response_function('MaxVel',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux1 = response_function.response_function('indexed_MassFlux_1',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux2 = response_function.response_function('indexed_MassFlux_2',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux3 = response_function.response_function('indexed_MassFlux_3',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux4 = response_function.response_function('indexed_MassFlux_4',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux5 = response_function.response_function('indexed_MassFlux_5',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux6 = response_function.response_function('indexed_MassFlux_6',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.MassFlux7 = response_function.response_function('indexed_MassFlux_7',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) + +#mass flux profiles +md.qmu.mass_flux_profiles = ['../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp','../Exp/Square.exp'] +md.qmu.mass_flux_profile_directory = getcwd() + +#method +md.qmu.method = dakota_method.dakota_method('nond_samp') +md.qmu.method = dmeth_params_set(md.qmu.method,'seed',1234,'samples',20,'sample_type','lhs') + +#parameters +md.qmu.params.direct = True +md.qmu.params.analysis_components = '' +md.qmu.params.tabular_graphics_data = True; + +if version >= 6: + md.qmu.params.analysis_driver = 'matlab' + md.qmu.params.evaluation_scheduling = 'master' + md.qmu.params.processors_per_evaluation = 2 +else: + md.qmu.params.analysis_driver = 'stressbalance' + md.qmu.params.evaluation_concurrency = 1 + +#partitioning +md.qmu.numberofpartitions = 20 +md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') +md.qmu.partition = md.qmu.partition-1 +md.qmu.isdakota = 1 + +md.stressbalance.reltol = 10**-5 #tighten for qmu analyses + +#solve +md.verbose = verbose('000000000') # this line is recommended + +# There may be a pair of numpy warnings in the function true_divide, +# this is normal and will not affect the results +# See src/m/qmu/dakota_out_parse.py, function "dak_tab_out" for details +md = solve(md,'Stressbalance','overwrite','y') + +#Fields and tolerances to track changes +md.qmu.results = md.results.dakota + +#ok, mass flux of 3 profiles should be -3 Gt/yr -3 Gt/yr and the sum, which is -6 Gt/yr +#we recover those mass fluxes through the mean of the response. +#also, we recover the max velo, which should be 1m/yr. +#we put all that data in the montecarlo field, which we will use to test for success. +#also, check that the stddev are 0. +md.results.dakota.montecarlo = [] +for i in range(8): + md.results.dakota.montecarlo.append(md.results.dakota.dresp_out[i].mean) + +for i in range(8): + md.results.dakota.montecarlo.append(md.results.dakota.dresp_out[i].stddev) + +field_names = ['moments'] +field_tolerances = [1e-11] +field_values = [md.results.dakota.montecarlo] Index: /issm/trunk/test/NightlyRun/test418.py =================================================================== --- /issm/trunk/test/NightlyRun/test418.py (revision 23394) +++ /issm/trunk/test/NightlyRun/test418.py (revision 23394) @@ -0,0 +1,43 @@ +#Test Name: SquareSheetShelfDiadSSA3dDakotaAreaAverage + +# this test may crash + +import numpy as np +from model import * +from socket import gethostname +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from solve import * +from partitioner import * +from AreaAverageOntoPartition import * + +#test partitioning, and partition averaging +# python cannot handle resolutions greater than 30010 +md = triangle(model(),'../Exp/Square.exp',30000.) +#print md.mesh.numberofvertices +md = setmask(md,'../Exp/SquareShelf.exp','') +md = parameterize(md,'../Par/SquareSheetShelf.py') +md = setflowequation(md,'SSA','all') +md.cluster = generic('name',gethostname(),'np',3) + +#partitioning +md.qmu.numberofpartitions = 100 + +#corrupted size vs. prev_size +#Aborted (core dumped) +md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions) + + +md.qmu.partition=md.qmu.partition-1 + +vector = np.arange(1,1+md.mesh.numberofvertices,1).reshape(-1,1) +# double check this before committing: +#print 'before AreaAverageOntoPartition' +vector_on_partition = AreaAverageOntoPartition(md,vector) +vector_on_nodes = vector_on_partition[md.qmu.partition+1] + +field_names = ['vector_on_nodes'] +field_tolerances = [1e-11] +field_values = [vector_on_nodes] Index: /issm/trunk/test/NightlyRun/test420.py =================================================================== --- /issm/trunk/test/NightlyRun/test420.py (revision 23394) +++ /issm/trunk/test/NightlyRun/test420.py (revision 23394) @@ -0,0 +1,71 @@ +#Test Name: SquareSheetShelfDakotaScaledResponse + +import numpy as np +from model import * +from socket import gethostname +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from solve import * +from partitioner import * + +md = triangle(model(),'../Exp/Square.exp',200000.) +md = setmask(md,'../Exp/SquareShelf.exp','') +md = parameterize(md,'../Par/SquareSheetShelf.py') +md = setflowequation(md,'SSA','all') +md.cluster = generic('name',gethostname(),'np',3) + +#partitioning +md.qmu.numberofpartitions = 10 +md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions) +md.qmu.partition = md.qmu.partition-1 +md.qmu.isdakota = 1 + +#Dakota options + +#dakota version +version = IssmConfig('_DAKOTA_VERSION_') +version = float(version[0]) + +#variables +md.qmu.variables.rho_ice = normal_uncertain.normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01) + +#responses +md.qmu.responses.MaxVel = response_function.response_function('scaled_Thickness',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) + +#method +md.qmu.method = dakota_method.dakota_method('nond_l') + +#parameters +md.qmu.params.direct = True +md.qmu.params.interval_type = 'forward' + +if version >= 6: + md.qmu.params.analysis_driver = 'matlab' + md.qmu.params.evaluation_scheduling = 'master' + md.qmu.params.processors_per_evaluation = 2 +else: + md.qmu.params.analysis_driver = 'stressbalance' + md.qmu.params.evaluation_concurrency = 1 + +#imperative! +md.stressbalance.reltol = 10**-5 #tighten for qmu analysese + +#solve +md.verbose = verbose('000000000') # this line is recommended +md = solve(md,'Stressbalance','overwrite','y') +md.qmu.results = md.results.dakota + +#test on thickness +h = np.zeros((md.qmu.numberofpartitions,)) +for i in range(md.qmu.numberofpartitions): + h[i] = md.qmu.results.dresp_out[i].mean + +#project onto grid +thickness = h[(md.qmu.partition).flatten()] + +#Fields and tolerances to track changes +field_names = ['Thickness'] +field_tolerances = [1e-10] +field_values = [thickness] Index: /issm/trunk/test/NightlyRun/test421.m =================================================================== --- /issm/trunk/test/NightlyRun/test421.m (revision 23393) +++ /issm/trunk/test/NightlyRun/test421.m (revision 23394) @@ -10,5 +10,5 @@ %Fields and tolerances to track changes field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-06,9e-07,2e-05,2e-06,2e-06}; +field_tolerances={2e-06,9e-07,2e-05,2e-06,2e-06}; field_values={... (md.results.StressbalanceSolution.Vx),... Index: /issm/trunk/test/NightlyRun/test421.py =================================================================== --- /issm/trunk/test/NightlyRun/test421.py (revision 23393) +++ /issm/trunk/test/NightlyRun/test421.py (revision 23394) @@ -20,5 +20,5 @@ #Fields and tolerances to track changes field_names =['Vx','Vy','Vz','Vel','Pressure'] -field_tolerances=[1e-06,9e-07,2e-05,2e-06,2e-06] +field_tolerances=[2e-06,9e-07,2e-05,2e-06,2e-06] field_values=[\ md.results.StressbalanceSolution.Vx,\ Index: /issm/trunk/test/NightlyRun/test444.py =================================================================== --- /issm/trunk/test/NightlyRun/test444.py (revision 23394) +++ /issm/trunk/test/NightlyRun/test444.py (revision 23394) @@ -0,0 +1,127 @@ +#Test Name: SquareShelfTranForceNeg2dDakotaLocal +import numpy as np +from os import getcwd +from model import * +from socket import gethostname +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from solve import * +from SMBgemb import * +from partitioner import * +from dmeth_params_set import * +from ContourToMesh import * +from regionaloutput import * + +#model not consistent: equality thickness=surface-base violated + +md = triangle(model(),'../Exp/Square.exp',150000.) +md = setmask(md,'../Exp/SquareShelf.exp','') +md = parameterize(md,'../Par/SquareSheetShelf.py') +md.geometry.bed = md.geometry.base.copy() +pos = np.where(md.mask.groundedice_levelset < 0) +md.geometry.bed[pos] = md.geometry.base[pos]-10 +md.friction.coefficient = 20. * np.ones((md.mesh.numberofvertices,)) +md.friction.p = np.ones((md.mesh.numberofelements,)) +md.friction.q = np.ones((md.mesh.numberofelements,)) +md.transient.isthermal = 0 +md.transient.isgroundingline = 1 +md.groundingline.migration = 'AggressiveMigration' + +md.settings.output_frequency = 3 +md = setflowequation(md,'SSA','all') +md.cluster = generic('name',oshostname(),'np',3) + +regionalmask = np.zeros((md.mesh.numberofvertices,)) +c_in = ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,'../Exp/SquareHalfRight.exp','node',1) +regionalmask[np.where(c_in)] = 1 +md.transient.requested_outputs = ['default','GroundedArea','FloatingArea','IceVolumeAboveFloatation','GroundedArea1','FloatingArea1','TotalFloatingBmb1','TotalGroundedBmb1','TotalSmb1', + 'IceMass1','IceVolume1','IceVolumeAboveFloatation1','IceVolumeAboveFloatation'] +md.outputdefinition.definitions.append(regionaloutput('name','GroundedArea1','outputnamestring','GroundedArea','mask',regionalmask, + 'definitionstring','Outputdefinition1')) +md.outputdefinition.definitions.append(regionaloutput('name','FloatingArea1','outputnamestring','FloatingArea','mask',regionalmask, + 'definitionstring','Outputdefinition2')) +md.outputdefinition.definitions.append(regionaloutput('name','TotalFloatingBmb1','outputnamestring','TotalFloatingBmb','mask',regionalmask, + 'definitionstring','Outputdefinition3')) +md.outputdefinition.definitions.append(regionaloutput('name','TotalGroundedBmb1','outputnamestring','TotalGroundedBmb','mask',regionalmask, + 'definitionstring','Outputdefinition4')) +md.outputdefinition.definitions.append(regionaloutput('name','IceMass1','outputnamestring','IceMass','mask',regionalmask, + 'definitionstring','Outputdefinition5')) +md.outputdefinition.definitions.append(regionaloutput('name','IceVolume1','outputnamestring','IceVolume','mask',regionalmask, + 'definitionstring','Outputdefinition6')) +md.outputdefinition.definitions.append(regionaloutput('name','IceVolumeAboveFloatation1','outputnamestring','IceVolumeAboveFloatation','mask',regionalmask, + 'definitionstring','Outputdefinition7')) +md.outputdefinition.definitions.append(regionaloutput('name','TotalSmb1','outputnamestring','TotalSmb','mask',regionalmask, + 'definitionstring','Outputdefinition8')) +md.outputdefinition.definitions.append(regionaloutput('name','TotalSmb2','outputnamestring','TotalSmb','mask',regionalmask, + 'definitionstring','Outputdefinition9')) + +md.extrude(3,1.) +md.collapse() + +#Dakota options + +#dakota version +version = IssmConfig('_DAKOTA_VERSION_') +version = float(version[0]) + +#variables +md.qmu.variables.drag_coefficient = normal_uncertain.normal_uncertain('scaled_BasalforcingsFloatingiceMeltingRate',1,0.1) + +#responses +md.qmu.responses.IceMass1 = response_function.response_function('Outputdefinition5',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.IceVolume1 = response_function.response_function('Outputdefinition6',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.IceVolumeAboveFloatation1 = response_function.response_function('Outputdefinition7',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.IceVolumeAboveFloatation = response_function.response_function('IceVolumeAboveFloatation',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.GroundedArea1 = response_function.response_function('Outputdefinition1',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.FloatingArea1 = response_function.response_function('Outputdefinition2',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.TotalFloatingBmb1 = response_function.response_function('Outputdefinition3',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.TotalGroundedBmb1 = response_function.response_function('Outputdefinition4',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.TotalSmb1 = response_function.response_function('Outputdefinition8',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.TotalSmb2 = response_function.response_function('Outputdefinition9',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) +md.qmu.responses.FloatingArea = response_function.response_function('FloatingArea',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) + +#method +md.qmu.method = dakota_method.dakota_method('nond_samp') +md.qmu.method = dmeth_params_set(md.qmu.method,'seed',1234,'samples',20,'sample_type','random') + +#parameters +md.qmu.params.direct = True +md.qmu.params.analysis_components = '' +md.qmu.params.tabular_graphics_data = True + +if version >= 6: + md.qmu.params.analysis_driver = 'matlab' + md.qmu.params.evaluation_scheduling = 'master' + md.qmu.params.processors_per_evaluation = 2 +else: + md.qmu.params.analysis_driver = 'stressbalance' + md.qmu.params.evaluation_concurrency = 1 + +#partitioning +md.qmu.numberofpartitions = 10 +md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') +md.qmu.partition = md.qmu.partition-1 +md.qmu.isdakota = 1 + +md.stressbalance.reltol = 10**-5 #tighten for qmu analyses + +#solve +md.verbose = verbose('000000000') # this line is recommended +md = solve(md,'Transient','overwrite','y') + +#Fields and tolerances to track changes +md.qmu.results = md.results.dakota + +#we put all the mean and stdev data in the montecarlo field, which we will use to test for success. +md.results.dakota.montecarlo = [] +for i in range(11): + md.results.dakota.montecarlo.append(md.results.dakota.dresp_out[i].mean) + +for i in range(11): + md.results.dakota.montecarlo.append(md.results.dakota.dresp_out[i].stddev) + +field_names = ['montecarlo'] +field_tolerances = [1e-11] +field_values = [md.results.dakota.montecarlo] Index: /issm/trunk/test/NightlyRun/test455.m =================================================================== --- /issm/trunk/test/NightlyRun/test455.m (revision 23393) +++ /issm/trunk/test/NightlyRun/test455.m (revision 23394) @@ -14,5 +14,5 @@ md=solve(md,'Stressbalance'); field_names ={field_names{:},['Vx' i{1}],['Vy' i{1}],['Vz' i{1}],['Vel' i{1}],['Pressure' i{1}]}; - field_tolerances={field_tolerances{:},6e-08,6e-08,6e-08,6e-08,3e-13}; + field_tolerances={field_tolerances{:},7e-08,6e-08,6e-08,6e-08,3e-13}; field_values={field_values{:},... (md.results.StressbalanceSolution.Vx),... Index: /issm/trunk/test/NightlyRun/test455.py =================================================================== --- /issm/trunk/test/NightlyRun/test455.py (revision 23393) +++ /issm/trunk/test/NightlyRun/test455.py (revision 23394) @@ -24,5 +24,5 @@ md=solve(md,'Stressbalance') field_names =field_names+['Vx'+i,'Vy'+i,'Vz'+i,'Vel'+i,'Pressure'+i] - field_tolerances=field_tolerances+[6e-08,6e-08,6e-08,6e-08,3e-13] + field_tolerances=field_tolerances+[7e-08,6e-08,6e-08,6e-08,3e-13] field_values=field_values+[\ md.results.StressbalanceSolution.Vx,\ Index: /issm/trunk/test/NightlyRun/test701.m =================================================================== --- /issm/trunk/test/NightlyRun/test701.m (revision 23393) +++ /issm/trunk/test/NightlyRun/test701.m (revision 23394) @@ -35,4 +35,5 @@ md.stressbalance.spcvx(find(vertexflags(md.mesh,4)))=0; md.stressbalance.spcvy(find(vertexflags(md.mesh,4)))=0; +md.basalforcings.floatingice_melting_rate=zeros(md.mesh.numberofvertices,1); %Misc Index: /issm/trunk/test/NightlyRun/test701.py =================================================================== --- /issm/trunk/test/NightlyRun/test701.py (revision 23393) +++ /issm/trunk/test/NightlyRun/test701.py (revision 23394) @@ -42,4 +42,5 @@ md.stressbalance.spcvx[np.where(md.mesh.vertexflags(4))] = 0. md.stressbalance.spcvy[np.where(md.mesh.vertexflags(4))] = 0. +md.basalforcings.floatingice_melting_rate=np.zeros((md.mesh.numberofvertices,)) #Misc Index: /issm/trunk/test/NightlyRun/test702.m =================================================================== --- /issm/trunk/test/NightlyRun/test702.m (revision 23393) +++ /issm/trunk/test/NightlyRun/test702.m (revision 23394) @@ -34,4 +34,5 @@ md.stressbalance.spcvx(find(vertexflags(md.mesh,4)))=800; md.stressbalance.spcvy(find(vertexflags(md.mesh,4)))=0; +md.basalforcings.floatingice_melting_rate=zeros(md.mesh.numberofvertices,1); %Misc Index: /issm/trunk/test/NightlyRun/test702.py =================================================================== --- /issm/trunk/test/NightlyRun/test702.py (revision 23394) +++ /issm/trunk/test/NightlyRun/test702.py (revision 23394) @@ -0,0 +1,85 @@ +#Test Name: FlowbandFSsheetshelf +import numpy as np +#from scipy.interpolate import interp1d +from model import * +from setflowequation import * +from solve import * +from NowickiProfile import * +from bamgflowband import * +from paterson import * + +#mesh parameters +x = np.arange(-5,5.5,.5).T +[b,h,sea] = NowickiProfile(x) +x = x * 10**3 +h = h * 10**3 +b = (b-sea) * 10**3 + +#mesh domain +md = bamgflowband(model(),x,b+h,b,'hmax',150.) + +#parameterize +md.geometry.surface = np.interp(md.mesh.x,x,b+h) +md.geometry.base = np.interp(md.mesh.x,x,b) +md.geometry.thickness = md.geometry.surface - md.geometry.base + +#mask +md.mask.ice_levelset = -np.ones((md.mesh.numberofvertices,)) +md.mask.ice_levelset[np.where(md.mesh.vertexflags(2))] = 0 +md.mask.groundedice_levelset = -0.5*np.ones((md.mesh.numberofvertices)) +md.mask.groundedice_levelset[np.where(md.mesh.x<0)]=0.5 + +#materials +md.initialization.temperature = (273. - 20.) * np.ones((md.mesh.numberofvertices,)) +md.materials.rheology_B = paterson(md.initialization.temperature) +md.materials.rheology_n = 3 * np.ones((md.mesh.numberofelements,)) + +#damage +md.damage.D = np.zeros((md.mesh.numberofvertices,)) +md.damage.spcdamage = float('NaN') * np.ones((md.mesh.numberofvertices,)) + +#friciton +md.friction.coefficient = np.zeros((md.mesh.numberofvertices,)) +md.friction.coefficient[np.where(md.mesh.vertexflags(1))] = 20 +md.friction.p = np.ones((md.mesh.numberofelements,)) +md.friction.q = np.ones((md.mesh.numberofelements,)) + +#boundary conditions +md.stressbalance.spcvx = float('NaN') * np.ones((md.mesh.numberofvertices,)) +md.stressbalance.spcvy = float('NaN') * np.ones((md.mesh.numberofvertices,)) +md.stressbalance.spcvz = float('NaN') * np.ones((md.mesh.numberofvertices,)) +md.stressbalance.referential = float('NaN') * np.ones((md.mesh.numberofvertices,6)) +md.stressbalance.loadingforce = np.zeros((md.mesh.numberofvertices,3)) +md.stressbalance.spcvx[np.where(md.mesh.vertexflags(4))] = 800. +md.stressbalance.spcvy[np.where(md.mesh.vertexflags(4))] = 0. +md.basalforcings.floatingice_melting_rate=np.zeros((md.mesh.numberofvertices,)) + +#misc +md = setflowequation(md,'FS','all') +md.stressbalance.abstol = float('NaN') +md.stressbalance.FSreconditioning = 1 +md.stressbalance.maxiter = 20 +md.flowequation.augmented_lagrangian_r = 10000. +md.flowequation.augmented_lagrangian_rhop = 10000. +md.initialization.pressure = md.constants.g * md.materials.rho_ice * (md.geometry.surface - md.mesh.y) +md.miscellaneous.name = 'test702' +md.groundingline.migration = 'None' +md.cluster = generic('np',2) + +#Fields and tolerances to track changes +field_names = [] +field_tolerances = [] +field_values = [] +for i in ['MINI','MINIcondensed','TaylorHood','XTaylorHood','LATaylorHood']: + print ' ' + print '======Testing ' +i+ ' Full-Stokes Finite element=====' + md.flowequation.fe_FS = i + md = solve(md,'Stressbalance') + field_names.extend(['Vx'+i,'Vy'+i,'Vel'+i,'Pressure'+i]) + field_tolerances.extend([8e-5,8e-5,8e-5,1e-08]) + field_values.extend([ + md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Pressure + ])