Changeset 27589


Ignore:
Timestamp:
02/17/23 13:41:46 (2 years ago)
Author:
jdquinn
Message:

CHG: Reverting to GMT 6.0.0 because executables under 6.4.0 do not link statically to libgmt; find gmtselect if it is available; removed test with restart from packaging scripts; cleanup

Location:
issm/trunk-jpl
Files:
9 edited

Legend:

Unmodified
Added
Removed

  • issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-matlab.sh

    r27502 r27589  
    3030LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself
    3131LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it
    32 MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2021,2051,2052,2053,2084,2085,2090,2101,2424,2425,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
     32MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,129,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2021,2051,2052,2053,2084,2085,2090,2101,2424,2425,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
    3333MATLAB_PATH="/usr/local/MATLAB/R2019b"
    3434

  • issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-python-3.sh

    r27502 r27589  
    3030LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself
    3131LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it
    32 PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
     32PYTHON_NROPTIONS="--benchmark all --exclude 125 126 129 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
    3333
    3434## Environment

  • issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-matlab.sh

    r27580 r27589  
    4040## Constants
    4141#
    42 MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2021,2051,2052,2053,2084,2085,2090,2101,2424,2425,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
     42MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,129,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2021,2051,2052,2053,2084,2085,2090,2101,2424,2425,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
    4343MATLAB_PATH="/Applications/MATLAB_R2022b.app"
    4444
    … …  
    113113if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then
    114114        cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt .
    115         cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect .
    116115else
    117116        echo "GMT not found"

  • issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-python-3.sh

    r27580 r27589  
    3939## Constants
    4040#
    41 PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
     41PYTHON_NROPTIONS="--benchmark all --exclude 125 126 129 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
    4242
    4343## Environment
    … …  
    105105if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then
    106106        cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt .
    107         cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect .
    108107else
    109108        echo "GMT not found"

  • issm/trunk-jpl/packagers/mac/test-issm-mac-binaries-matlab.sh

    r27569 r27589  
    1010## Constants
    1111#
    12 INSTALL_DIR=.
    13 MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2021,2051,2052,2053,2084,2085,2090,2101,2424,2425,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
     12INSTALL_DIR=${PWD}
     13MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,129,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2021,2051,2052,2053,2084,2085,2090,2101,2424,2425,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
    1414MATLAB_PATH="/Applications/MATLAB_R2022b.app"
    1515PKG="ISSM-macOS-MATLAB"

  • issm/trunk-jpl/packagers/mac/test-issm-mac-binaries-python-3.sh

    r27502 r27589  
    1010## Constants
    1111#
    12 INSTALL_DIR=.
     12INSTALL_DIR=${PWD}
    1313PKG="ISSM-macOS-Python-3"
    14 PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
     14PYTHON_NROPTIONS="--benchmark all --exclude 125 126 129 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
    1515
    1616COMPRESSED_PKG="${PKG}.zip"

  • issm/trunk-jpl/src/m/coordsystems/gmtmask.m

    r27369 r27589  
    55%      mask.ocean = gmtmask(md.mesh.lat,md.mesh.long);
    66%
     7%       TODO: Standardize discovery of GMT bin path and whether or not we have GMT
     8%       modules (i.e. `gmt select`) between this file, gmtmask.py, and
     9%       gmtmaskparallel.m
    710
    811        %are we doing a recursive call?
    … …  
    3134        %First, write our lat,long file for gmt:
    3235        nv=length(lat);
    33         filename_all = ['all_vertices-' num2str(feature('GetPid')) '.txt'];
    34         filename_oce = ['oce_vertices-' num2str(feature('GetPid')) '.txt'];
     36        filename_suffix=[num2str(feature('GetPid')) '.txt'];
     37        filename_all=['all_vertices-' filename_suffix];
     38        filename_oce=['oce_vertices-' filename_suffix];
    3539        dlmwrite(filename_all,[long lat (1:nv)'],'delimiter','\t','precision',10);
    3640
    3741        %figure out which vertices are on the ocean, which one on the continent:
    38         [status,result] = system(['gmt select ./' filename_all ' -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./' filename_oce]);
     42        gmt_select_options='-h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s';
     43        [status,result]=system(['gmt select ./' filename_all ' ' gmt_select_options ' > ./' filename_oce]);
    3944        if status~=0,
    40                 error(result);
     45                [status,result] = system(['gmtselect ./' filename_all ' ' gmt_select_options ' > ./' filename_oce]);
     46                if status~=0,
     47                        error(result);
     48                end
    4149        end
    4250

  • issm/trunk-jpl/src/m/coordsystems/gmtmask.py

    r27453 r27589  
    1010
    1111def gmtmask(lat, long, *args):
    12     """GMTMASK - figure out which lat, long points are on the ocean
     12    """gmtmask - figure out which lat, long points are on the ocean
    1313
    1414    Usage:
    … …  
    4444
    4545    # Figure out which vertices are on the ocean, which one on the continent:
    46     subprocess.call('gmt select ./all_vertices.txt -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./oce_vertices.txt', shell=True)
     46    gmt_select_options = '-h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s'
     47    subproc_cmd = 'gmt select ./all_vertices.txt ' + gmt_select_options + ' > ./oce_vertices.txt'
     48    subproc = subprocess.Popen(subproc_cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
     49    outs, errs = subproc.communicate()
     50    if errs != '':
     51        subproc_cmd = 'gmtselect ./all_vertices.txt ' + gmt_select_options + ' > ./oce_vertices.txt'
     52        subproc = subprocess.Popen(subproc_cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
     53        outs, errs = subproc.communicate()
     54        if errs != '':
     55            raise RuntimeError('gmtmask: calls to both gmt and gmtselect failed: {}'.format(errs))
    4756
    4857    # Read the con_vertices.txt file and flag our mesh vertices on the continent

  • issm/trunk-jpl/src/m/coordsystems/gmtmaskparallel.m

    r27201 r27589  
    2727
    2828        %Find path to gmt, list all possible known paths to gmt (you may need to add yours to the list)
    29    paths = {[issmdir() '/bin/gmt'],[issmdir() '/externalpackages/gmt/install/bin/gmt'],'/Applications/GMT-5.4.3.app/Contents/Resources/bin/gmt'};
    30    gmtpath = '';
    31    for i=paths
    32       if exist(i{1},'file'),
    33          gmtpath = i{1};
     29        paths = {[issmdir() '/bin'],[issmdir() '/externalpackages/gmt/install/bin'],'/Applications/GMT-5.4.3.app/Contents/Resources/bin'};
     30        gmt_path = '';
     31        for i=paths
     32                if exist([i{1} '/gmt'],'file'),
     33                        gmt_path = i{1};
    3434                        break;
    35       end
    36    end
    37    if isempty(gmtpath),
     35                end
     36        end
     37        if isempty(gmt_path),
    3838                error('gmt not found, make sure it is properly installed, or add its path to this file (line 26)');
    39    end
     39        end
     40
     41        %Figure out if we have gmtselect executable
     42        if exist([gmt_path '/gmtselect'],'file'),
     43                gmt_exec=[gmt_path '/gmtselect'];
     44        else,
     45                gmt_exec=[gmt_path '/gmtselect'];
     46        end
    4047
    4148        %Build xjobs script:
    4249        fid=fopen('xjobs.script','w');
    4350        for i=1:length(nnv)-1,
    44                 fprintf(fid,'%s gmt select ./all_vertices%i.txt -h0 -Df -R0/360/-90/90  -A0 -JQ180/200 -Nk/s/s/k/s > ./oce_vertices%i.txt\n',gmtpath,i,i);
     51                fprintf(fid,'%s ./all_vertices%i.txt -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./oce_vertices%i.txt\n',gmt_exec,i,i);
    4552        end
    4653        fclose(fid);
    … …  
    6269        mask=zeros(nv,1);
    6370        mask(flags)=1;
    64        
     71
    6572        system('rm -rf ./all_vertices*.txt ./oce_vertices*.txt vertices.txt ./gmt.history ./xjobs.script');
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