Index: /issm/trunk-jpl/externalpackages/gsl/install-android.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/gsl/install-android.sh	(revision 14287)
+++ /issm/trunk-jpl/externalpackages/gsl/install-android.sh	(revision 14288)
@@ -28,11 +28,10 @@
     patch Makefile.am < Makefile.am.patch
 
-    autoreconf -iv --force -I $ISSM_DIR/externalpackages/autotools/install/share/aclocal
+    autoreconf -i
 
     ./configure \
         --build="i386-apple-darwin10.8.0" \
         --host=$host_triplet \
-	    --prefix="$ISSM_DIR/externalpackages/gsl/install/" \
-        --disable-static
+	    --prefix="$ISSM_DIR/externalpackages/gsl/install"
 fi
 
Index: /issm/trunk-jpl/externalpackages/howatmask/enviread.m
===================================================================
--- /issm/trunk-jpl/externalpackages/howatmask/enviread.m	(revision 14288)
+++ /issm/trunk-jpl/externalpackages/howatmask/enviread.m	(revision 14288)
@@ -0,0 +1,323 @@
+function I=enviread(varargin)
+%enviread: Read binary image files using ENVI header information
+%
+%I=enviread('filename') where the header file is named filename.hdr
+%and exists in the same directory. Otherwise use 
+%
+%I=enviread('filename','hdrfilename')
+%
+%The output structure I contains fields I.x, I.y, I.z and I.info
+%containing the x-coordinate vector, y-coordinate vector,
+%images data and header info, respectively. I.z will be in whatever
+%number format (double, int, etc.) as in the envi file.
+%
+%Original version by Ian Howat, Ohio State Universtiy, ihowat@gmail.com
+%Thanks to Yushin Ahn and Ray Jung
+%
+%% Current version 3 - adding subsetting feature to read only parts of
+%% files.
+
+file=varargin{1};
+hdrfile=[deblank(file),'.hdr'];
+info=read_envihdr(hdrfile);
+sub = [1, info.samples, 1, info.lines];
+if nargin==2
+    if varargin{2}=='date'
+        [pathstr, name, ext, versn] = fileparts(file);
+        info.hdrname=hdrfile;
+        info.ipath=pathstr;
+        info.iname=name;
+        info.ipname=file;
+        info.year =name(1:4);
+        info.month=name(5:6);
+        info.day  =name(7:8);
+        info.date =name(1:8);
+        info.sfname=name(1:14);
+        info.datenum=datenum(str2double(info.year),...
+            str2double(info.month),str2double(info.day));
+    end
+end
+
+% subset
+if nargin == 3;
+    if strcmp(varargin{2},'pixel_subset');
+        sub = varargin{3};
+    elseif strcmp(varargin{2},'map_subset');
+        sub = varargin{3};
+        subx = (sub(1:2)-info.map_info.mapx)./info.map_info.dx;
+        suby = (info.map_info.mapy - sub(3:4))./info.map_info.dy;
+        subx = round(subx);
+        suby = round(suby);
+        
+        subx(subx < 1) = 1;
+        suby(suby < 1) = 1;
+        subx(subx > info.samples) = info.samples;
+        suby(suby > info.lines)   = info.lines;
+      
+        sub  = [subx,suby];
+    end
+end
+
+sub(1:2) = sort(sub(1:2));
+sub(3:4) = sort(sub(3:4));
+
+
+%% Make geo-location vectors
+if isfield(info.map_info,'mapx') && isfield(info.map_info,'mapy')
+    xi = info.map_info.image_coords(1);
+    yi = info.map_info.image_coords(2);
+    xm = info.map_info.mapx;
+    ym = info.map_info.mapy;
+    %adjust points to corner (1.5,1.5)
+    if yi > 1.5
+        ym =  ym + ((yi*info.map_info.dy)-info.map_info.dy);
+    end
+    if xi > 1.5
+        xm = xm - ((xi*info.map_info.dy)-info.map_info.dx);
+    end
+
+    I.x = xm + ((0:info.samples-1).*info.map_info.dx);
+    I.y = ym - ((0:info.lines-1).*  info.map_info.dy);
+    %I.x = xm + (subE(1):subE(2)-1).*info.map_info.dx;
+    %I.y = ym - (subE(3):subE(4)-1).*info.map_info.dy;
+end
+
+
+I.x = I.x(sub(1):sub(2));
+I.y = I.y(sub(3):sub(4));
+
+
+%% Set binary format parameters
+switch info.byte_order
+    case {0}
+        machine = 'ieee-le';
+    case {1}
+        machine = 'ieee-be';
+    otherwise
+        machine = 'n';
+end
+switch info.data_type
+    case {1}
+        format = 'uint8';
+    case {2}
+        format= 'int16';
+    case{3}
+        format= 'int32';
+    case {4}
+        format= 'single';
+    case {5}
+        format= 'double';
+    case {6}
+        disp('>> Sorry, Complex (2x32 bits)data currently not supported');
+        disp('>> Importing as double-precision instead');
+        format= 'double';
+    case {9}
+        error('Sorry, double-precision complex (2x64 bits) data currently not supported');
+    case {12}
+        format= 'uint16';
+    case {13}
+        format= 'uint32';
+    case {14}
+        format= 'int64';
+    case {15}
+        format= 'uint64';
+    otherwise
+        error(['File type number: ',num2str(dtype),' not supported']);
+end
+
+%% file read
+% Version 2 code by Yushin Ahn - replaces resize calls with loops (except
+% for BIP formats) to work on big arrays.
+
+        %tmp=zeros(info.lines, info.samples,info.bands,format);
+        tmp=zeros(sub(4)-sub(3)+1,sub(2)-sub(1)+1,info.bands,format);
+        fid=fopen(file,'r');
+
+switch lower(info.interleave)
+
+    case {'bsq'}
+        % Format:
+        % [Band 1]       
+        % R1: C1, C2, C3, ...
+        % R2: C1, C2, C3, ...
+        %  ...
+        % RN: C1, C2, C3, ...
+        %
+        % [Band 2]
+        %  ...
+        % [Band N]
+
+%% Old Script w/out subsetting
+%         for b=1:info.bands
+%             for i=1:info.lines
+%                 t=fread(fid,info.samples,format);
+%                 tmp(i,:,b)=t;    
+%             end
+%         end
+        
+%% New Subsetting script - IMH
+        offset1=(sub(3)-1)*info.samples;
+        fseek(fid,offset1,'bof');
+        for b=1:info.bands
+            for i=sub(3):sub(4)
+                t=fread(fid,info.samples,format);
+                %if i >=  sub(3) && i <= sub(4)
+                    tmp(i-sub(3)+1,:,b)=t(sub(1):sub(2));
+                %end
+            end
+            offset2 = info.samples*info.lines*b+offset1;
+            fseek(fid,offset2,'bof');
+        end
+
+    case {'bil'}
+        % Format:        
+        % [Row 1]      
+        % B1: C1, C2, C3, ...
+        % B2: C1, C2, C3, ...
+        %
+        %  ...
+        % [Row N]
+
+%         for i=1:info.lines
+%             for b=1:info.bands
+%                  t=fread(fid,info.samples,format);
+%                 tmp(i,:,b)=t;       
+%             end
+%         end
+      
+%% New Subsetting script - IMH
+        for i=1:sub(4) 
+            for b=1:info.bands
+                t=fread(fid,info.samples,format);
+                if i >=  sub(3) && i <= sub(4) 
+                    tmp(i-sub(3)+1,:,b)=t(sub(1):sub(2));    
+                end
+            end
+        end
+
+
+
+    case {'bip'}
+    
+        % Row 1
+        % C1: B1 B2 B3, ...
+        % C2: B1 B2 B3, ...
+        % ...
+        % Row N
+        %This section authored by Ray Jung, APL-Johns Hopkins
+        Z = fread(fid,info.samples*info.lines*info.bands,format,0,machine);  
+        Z = reshape(Z, [info.bands, info.samples, info.lines]);
+
+        for k=1:info.bands
+            tmp(:,:,k) = squeeze(Z(k,:,:))';
+        end     
+end
+fclose(fid);
+
+% tmp2=zeros(subE(4)-subE(3)+1,subE(2)-subE(1)+1,info.bands,format);
+% [a,b]=size(tmp);
+% for i=1:info.bands
+%     tmp2(xoff+1:a,yoff+1:b,1)=tmp(1:a,1:b,1);
+% end
+I.z=tmp;
+I.info =info;
+
+
+
+%% sub function
+function info = read_envihdr(hdrfile)
+% READ_ENVIHDR read and return ENVI image file header information.
+%   INFO = READ_ENVIHDR('HDR_FILE') reads the ASCII ENVI-generated image
+%   header file and returns all the information in a structure of
+%   parameters.
+%
+%   Example:
+%   >> info = read_envihdr('my_envi_image.hdr')
+%   info =
+%          description: [1x101 char]
+%              samples: 658
+%                lines: 749
+%                bands: 3
+%        header_offset: 0
+%            file_type: 'ENVI Standard'
+%            data_type: 4
+%           interleave: 'bsq'
+%          sensor_type: 'Unknown'
+%           byte_order: 0
+%             map_info: [1x1 struct]
+%      projection_info: [1x102 char]
+%     wavelength_units: 'Unknown'
+%           pixel_size: [1x1 struct]
+%           band_names: [1x154 char]
+%
+%   NOTE: This function is used by ENVIREAD to import data.
+% Ian M. Howat, Applied Physics Lab, University of Washington
+% ihowat@apl.washington.edu
+% Version 1: 19-Jul-2007 00:50:57
+fid = fopen(hdrfile);
+while fid;
+    line = fgetl(fid);
+    if line == -1
+        break
+    else
+        eqsn = findstr(line,'=');
+        if ~isempty(eqsn)
+            param = strtrim(line(1:eqsn-1));
+            param(findstr(param,' ')) = '_';
+            value = strtrim(line(eqsn+1:end));
+            if isempty(str2num(value))
+                if ~isempty(findstr(value,'{')) && isempty(findstr(value,'}'))
+                    while isempty(findstr(value,'}'))
+                        line = fgetl(fid);
+                        value = [value,strtrim(line)];
+                    end
+                end
+                eval(['info.',param,' = ''',value,''';'])
+            else
+                eval(['info.',param,' = ',value,';'])
+            end
+        end
+    end
+end
+fclose(fid);
+
+if isfield(info,'map_info')
+    line = info.map_info;
+    line(line == '{' | line == '}') = [];
+    line = strtrim(split(line,','));
+    info.map_info = [];
+    info.map_info.projection = line{1};
+    info.map_info.image_coords = [str2num(line{2}),str2num(line{3})];
+    info.map_info.mapx = str2num(line{4});
+    info.map_info.mapy = str2num(line{5});
+    info.map_info.dx  = str2num(line{6});
+    info.map_info.dy  = str2num(line{7});
+    if length(line) == 9
+        info.map_info.datum  = line{8};
+        info.map_info.units  = line{9}(7:end);
+    elseif length(line) == 11
+        info.map_info.zone  = str2num(line{8});
+        info.map_info.hemi  = line{9};
+        info.map_info.datum  = line{10};
+        info.map_info.units  = line{11}(7:end);
+    end
+end
+
+if isfield(info,'pixel_size')
+    line = info.pixel_size;
+    line(line == '{' | line == '}') = [];
+    line = strtrim(split(line,','));
+    info.pixel_size = [];
+    info.pixel_size.x = str2num(line{1});
+    info.pixel_size.y = str2num(line{2});
+    info.pixel_size.units = line{3}(7:end);
+end
+
+%%
+function A = split(s,d)
+%This function by Gerald Dalley (dalleyg@mit.edu), 2004
+A = {};
+while (length(s) > 0)
+    [t,s] = strtok(s,d);
+    A = {A{:}, t};
+end
Index: /issm/trunk-jpl/externalpackages/howatmask/subsetGimpIceMask.m
===================================================================
--- /issm/trunk-jpl/externalpackages/howatmask/subsetGimpIceMask.m	(revision 14288)
+++ /issm/trunk-jpl/externalpackages/howatmask/subsetGimpIceMask.m	(revision 14288)
@@ -0,0 +1,282 @@
+function [M,Mx,My] = subsetGimpIceMask(x0,x1,y0,y1)
+% subsetGimpIceMask samples mask tiles for a given coordinate range
+%
+%   [M,Mx,My] = subsetGimpIceMask(x0,x1,y0,y1) returns the mask in array M
+%   with map vectors Mx and My within the bounding box specified by
+%   coordinate ranges x0 < x1 and y0 < y1. The function finds tiles
+%   overlappimg the box, samples the tiles and mosaics the samples into one
+%   array.
+%
+% 	Example: Specify the following coordinate range and map the result.
+%   >> x0 = 260000; x1 = 377900;  y0 = -2609400; y1 = -2543000;
+%   >> [M,Mx,My] = subsetGimpIceMask(x0,x1,y0,y1);
+%   >> imagesc(Mx,My,M); axis equal xy; colormap gray;
+%
+%   Ian Howat, Ohio State University, ihowat@gmail.com
+%   The Greenland Ice Mapping Project is funded by NASA.
+%   $Revision: 0 $  $Date: 09-Nov-2011 14:48:24$
+%
+
+%make coordinate index
+nt = 6;
+ps = 15;
+xn0 = -640000 ; %xn1 = 857550;
+yn0 =  -3313350; %yn1 = -665450;
+
+c = 16640;
+r = 29420;
+
+x = xn0:ps:xn0 + c.*ps.*nt;
+y = yn0:ps:yn0 + r.*ps.*nt;
+
+X = cell(1,nt);
+Y = cell(nt,1);
+i=1;
+for i=1:nt;
+    
+    X{i} = [x((i-1)*c+1),x(i*c)];
+    Y{i} = [y((i-1)*r+1),y(i*r)];
+    
+end
+
+X = repmat(X,[nt,1]);
+Y = repmat(Y,[1,nt]);
+N = cell(size(X));
+
+
+i=1;
+for i=1:numel(X)
+    N{i} = [[X{i}(1),Y{i}(2)];...
+        [X{i}(2),Y{i}(2)];...
+        [X{i}(2),Y{i}(1)];...
+        [X{i}(1),Y{i}(1)]];
+end
+
+
+%% find overlapping tiles
+p = [[x0,y1];[x1,y1];[x1,y0];[x0,y0]];
+
+n = zeros(size(N));
+
+i=1;
+for i=1:numel(N)
+    n(i) = any(inpolygon(p(:,1),p(:,2),N{i}(:,1),N{i}(:,2)));
+end
+i=1;
+for i=1:size(n,1)
+    n(i,find(n(i,:),1,'first'):find(n(i,:),1,'last')) = 1;
+end
+i=1;
+for i=1:size(n,2)
+    n(find(n(:,i),1,'first'):find(n(:,i),1,'last'),i) = 1;
+end
+
+[i,j] = find(n);
+row = (min(i):max(i))';
+col = min(j):max(j);
+col = repmat(col,[length(row),1])-1;
+row = repmat(row,[1,size(col,2)])-1;
+
+% make output cells
+M = cell(size(row));
+Mx = M;
+My = M;
+
+% read each overlapping file and populate output cell
+j=1;
+for j=1:size(col,2)
+    i=1;
+    for i=1:size(row,1);
+        m = enviread(['GimpIceMask_15m_tile',num2str(col(i,j)),'_',...
+            num2str(row(i,j))],'map_subset',[x0 x1 y0 y1]);
+        M{end-i+1,j} = m.z;
+        Mx{end-i+1,j} = m.x;
+        My{end-i+1,j} = m.y';
+        
+        
+    end
+end
+
+% put together cells
+M = cell2mat(M);
+Mx =cell2mat(Mx(1,:));
+My =cell2mat(My(:,1));
+
+
+function I=enviread(varargin)
+
+file=varargin{1};
+hdrfile=[deblank(file),'.hdr'];
+info=read_envihdr(hdrfile);
+sub = [1, info.samples, 1, info.lines];
+
+sub = varargin{3};
+subx = (sub(1:2)-info.map_info.mapx)./info.map_info.dx;
+suby = (info.map_info.mapy - sub(3:4))./info.map_info.dy;
+subx = round(subx);
+suby = round(suby);
+
+subx(subx < 1) = 1;
+suby(suby < 1) = 1;
+subx(subx > info.samples) = info.samples;
+suby(suby > info.lines)   = info.lines;
+
+sub  = [subx,suby];
+
+sub(1:2) = sort(sub(1:2));
+sub(3:4) = sort(sub(3:4));
+
+%% Make geo-location vectors
+if isfield(info.map_info,'mapx') && isfield(info.map_info,'mapy')
+    xi = info.map_info.image_coords(1);
+    yi = info.map_info.image_coords(2);
+    xm = info.map_info.mapx;
+    ym = info.map_info.mapy;
+    %adjust points to corner (1.5,1.5)
+    if yi > 1.5
+        ym =  ym + ((yi*info.map_info.dy)-info.map_info.dy);
+    end
+    if xi > 1.5
+        xm = xm - ((xi*info.map_info.dy)-info.map_info.dx);
+    end
+    
+    I.x = xm + ((0:info.samples-1).*info.map_info.dx);
+    I.y = ym - ((0:info.lines-1).*  info.map_info.dy);
+    
+end
+
+I.x = I.x(sub(1):sub(2));
+I.y = I.y(sub(3):sub(4));
+
+%% Set binary format parameters
+switch info.byte_order
+    case {0}
+        machine = 'ieee-le';
+    case {1}
+        machine = 'ieee-be';
+    otherwise
+        machine = 'n';
+end
+
+format = 'uint8';
+
+tmp=zeros(sub(4)-sub(3)+1,sub(2)-sub(1)+1,info.bands,format);
+fid=fopen(file,'r');
+
+offset1=(sub(3)-1)*info.samples;
+fseek(fid,offset1,'bof');
+for b=1:info.bands
+    for i=sub(3):sub(4)
+        t=fread(fid,info.samples,format);
+        tmp(i-sub(3)+1,:,b)=t(sub(1):sub(2));
+    end
+    offset2 = info.samples*info.lines*b+offset1;
+    fseek(fid,offset2,'bof');
+end
+
+fclose(fid);
+
+I.z=tmp;
+I.info =info;
+
+%% sub function
+function info = read_envihdr(hdrfile)
+% READ_ENVIHDR read and return ENVI image file header information.
+%   INFO = READ_ENVIHDR('HDR_FILE') reads the ASCII ENVI-generated image
+%   header file and returns all the information in a structure of
+%   parameters.
+%
+%   Example:
+%   >> info = read_envihdr('my_envi_image.hdr')
+%   info =
+%          description: [1x101 char]
+%              samples: 658
+%                lines: 749
+%                bands: 3
+%        header_offset: 0
+%            file_type: 'ENVI Standard'
+%            data_type: 4
+%           interleave: 'bsq'
+%          sensor_type: 'Unknown'
+%           byte_order: 0
+%             map_info: [1x1 struct]
+%      projection_info: [1x102 char]
+%     wavelength_units: 'Unknown'
+%           pixel_size: [1x1 struct]
+%           band_names: [1x154 char]
+%
+%   NOTE: This function is used by ENVIREAD to import data.
+% Ian M. Howat, Applied Physics Lab, University of Washington
+% ihowat@apl.washington.edu
+% Version 1: 19-Jul-2007 00:50:57
+fid = fopen(hdrfile);
+while fid;
+    line = fgetl(fid);
+    if line == -1
+        break
+    else
+        eqsn = findstr(line,'=');
+        if ~isempty(eqsn)
+            param = strtrim(line(1:eqsn-1));
+            param(findstr(param,' ')) = '_';
+            value = strtrim(line(eqsn+1:end));
+            if isempty(str2num(value))
+                if ~isempty(findstr(value,'{')) && isempty(findstr(value,'}'))
+                    while isempty(findstr(value,'}'))
+                        line = fgetl(fid);
+                        value = [value,strtrim(line)];
+                    end
+                end
+                eval(['info.',param,' = ''',value,''';'])
+            else
+                eval(['info.',param,' = ',value,';'])
+            end
+        end
+    end
+end
+fclose(fid);
+
+if isfield(info,'map_info')
+    line = info.map_info;
+    line(line == '{' | line == '}') = [];
+    line = strtrim(split(line,','));
+    info.map_info = [];
+    info.map_info.projection = line{1};
+    info.map_info.image_coords = [str2num(line{2}),str2num(line{3})];
+    info.map_info.mapx = str2num(line{4});
+    info.map_info.mapy = str2num(line{5});
+    info.map_info.dx  = str2num(line{6});
+    info.map_info.dy  = str2num(line{7});
+    if length(line) == 9
+        info.map_info.datum  = line{8};
+        info.map_info.units  = line{9}(7:end);
+    elseif length(line) == 11
+        info.map_info.zone  = str2num(line{8});
+        info.map_info.hemi  = line{9};
+        info.map_info.datum  = line{10};
+        info.map_info.units  = line{11}(7:end);
+    end
+end
+
+if isfield(info,'pixel_size')
+    line = info.pixel_size;
+    line(line == '{' | line == '}') = [];
+    line = strtrim(split(line,','));
+    info.pixel_size = [];
+    info.pixel_size.x = str2num(line{1});
+    info.pixel_size.y = str2num(line{2});
+    info.pixel_size.units = line{3}(7:end);
+end
+
+%%
+function A = split(s,d)
+%This function by Gerald Dalley (dalleyg@mit.edu), 2004
+A = {};
+while (length(s) > 0)
+    [t,s] = strtok(s,d);
+    A = {A{:}, t};
+end
+
+
+
+
Index: /issm/trunk-jpl/externalpackages/metis/install-4.0-hoffman2.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/metis/install-4.0-hoffman2.sh	(revision 14288)
+++ /issm/trunk-jpl/externalpackages/metis/install-4.0-hoffman2.sh	(revision 14288)
@@ -0,0 +1,24 @@
+#!/bin/bash
+set -eu
+
+#Some cleanup
+rm -rf install metis-4.0
+mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz'
+
+#Untar 
+tar -zxvf  metis-4.0.tar.gz
+
+#Move metis into install directory
+mv metis-4.0/* install
+rm -rf metis-4.0
+
+#Apply patches
+cd install 
+patch -p1 < ../metis-4.0.patch
+patch Makefile.in ../configs/4.0/pleiades/Makefile.in.patch
+
+#Compile
+make
Index: /issm/trunk-jpl/externalpackages/petsc/install-3.2-hoffman2.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-3.2-hoffman2.sh	(revision 14288)
+++ /issm/trunk-jpl/externalpackages/petsc/install-3.2-hoffman2.sh	(revision 14288)
@@ -0,0 +1,35 @@
+#!/bin/bash
+set -eu
+
+#Some cleanup
+rm -rf install petsc-3.2-p3 src
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz'
+
+#Untar and move petsc to install directory
+tar -zxvf  petsc-3.2-p3.tar.gz
+mv petsc-3.2-p3/* src/
+rm -rf petsc-3.2-p3
+
+#configure
+cd src
+./config/configure.py \
+	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
+	--with-mpi=1 \
+	--PETSC_ARCH=linux-gnu-amd64 \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+	--with-debugging=0 \
+	--download-mumps=yes \
+	--download-scalapack=yes \
+	--download-blacs=yes \
+	--download-blas=yes \
+	--download-f-blas-lapack=yes \
+	--download-plapack=yes \
+	--download-parmetis=yes \
+	--with-pic=1
+
+#Compile petsc and install it
+make
+make install