http://ccrm.vims.edu/w/api.php?action=feedcontributions&feedformat=atom&user=Schismguestccrmwiki - User contributions [en]2026-05-07T08:59:01ZUser contributionsMediaWiki 1.31.1http://ccrm.vims.edu/w/index.php?title=Visualization_with_VisIT&diff=1441Visualization with VisIT2020-10-12T16:05:35Z<p>Schismguest: </p>
<hr />
<div>On Windows 7 or 10:<br />
<br />
<OL><br />
<LI>First download VisIT from [https://wci.llnl.gov/simulation/computer-codes/visit/downloads LLNL site] and install. Use default dir (and record it), e.g.<br />
C:\Users\yjzhang\AppData\Local\Programs\LLNL\VisIt*<br />
<LI>Download pre-built plug-in, developed at California Dept of Water Resource [http://ccrm.vims.edu/yinglong/Courses/Hangzhou/schism_plugin_1.2_xbeta_visit2.12.3_win64_vs2012.zip here] and put the files in:<br />
C:\Users\yjzhang\AppData\Roaming\LLNL\VisIt\databases (create new dirs if necessary). This dlls location works for VisIt 2.13.2 or below. <br />
<br />
From VisIt 2.13.3, you need to put dlls on C:\Users\your_account_name\Documents\VisIt\databases. Alternatively, please email Jon Shu at Qiang.shu@water.ca.gov and let him know the version of visit you are using. Below are newer builds:<br />
<UL><br />
<LI> [http://ccrm.vims.edu/yinglong/SVN_large_files/schism_plugin_with_last_wetting_update_visit2.13.3_win64_vs2012.zip plugin build for 2.13.3]<br />
<LI> [http://ccrm.vims.edu/yinglong/SVN_large_files/schism_plugin_with_last_wetting_update_visit3.1.2_win64_vs2017.zip latest plugin build for visit 3.1.2]<br />
<br />
<!--LI> [https://cadwr.box.com/s/hkic80xg7tmjhwk94aszssrp8fh6r0fu plugin build for 2.13.3]<br />
<LI> [https://cadwr.box.com/s/4n8vn29zxxvnn69snlsc40fcmbvk54aa latest plugin build for visit 3.1.2] --><br />
</UL><br />
<LI> If the 3.1.2 plugin doesn't work on your pc, for example "SCHISM" option doesn't show up on VisIt file type menu, there are two possible causes. One cause is that your VisIt don't have netcdf_c++.dll. You can copy this file from VisIt 2.13.x to VisIt 3.1.2. Another cause is that your pc don't have MS VC++ 2017 or MS VC++ 2013 redistributable. You can download it from MS webpage. <br />
<LI>If you use SCHISM v5.6.1 (netcdf I/O), note that VisIT has issues with stack overflow with nc4, so you need to do the following work-around until LLNL fixes the issue:<br />
<UL><br />
<LI>Go to [https://www.unidata.ucar.edu/software/netcdf/docs/winbin.html UCAR] and get their installer for the latest C library, e.g. 4.5.0;<br />
<LI>Complete the installation and record the install dir.<br />
Then copy all files in bin/ of the install dir to the VisIT dir in (1) to overwrite.<br />
</UL><br />
<LI>After these steps, you'd be able to read in SCHISM outputs in ViSIT; look for 'SCHISM', 'gr3' format from the dropdown list.<br />
</OL><br />
<br />
----<br />
<br />
On Linux systems:<br />
<br />
Use svn or directly download the source code [http://columbia.vims.edu/schism/schism_visit_plugin/tags/v2.2.0 here].<br />
<br />
After compilation this can be used with VisIT version 2.12.2 to 2.13.3.<br />
<br />
Newer versions can be found at [https://github.com/schism-dev/schism_visit_plugin github].</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Visualization_with_VisIT&diff=1440Visualization with VisIT2020-09-22T22:02:58Z<p>Schismguest: </p>
<hr />
<div>On Windows 7 or 10:<br />
<br />
<OL><br />
<LI>First download VisIT from [https://wci.llnl.gov/simulation/computer-codes/visit/downloads LLNL site] and install. Use default dir (and record it), e.g.<br />
C:\Users\yjzhang\AppData\Local\Programs\LLNL\VisIt*<br />
<LI>Download pre-built plug-in, developed at California Dept of Water Resource [http://ccrm.vims.edu/yinglong/Courses/Hangzhou/schism_plugin_1.2_xbeta_visit2.12.3_win64_vs2012.zip here] and put the files in:<br />
C:\Users\yjzhang\AppData\Roaming\LLNL\VisIt\databases (create new dirs if necessary). This dlls location works for VisIt 2.13.2 or below. <br />
<br />
From VisIt 2.13.3, you need to put dlls on C:\Users\your_account_name\Documents\VisIt\databases. Alternatively, please email Jon Shu at Qiang.shu@water.ca.gov and let him know the version of visit you are using. Below are newer builds:<br />
<UL><br />
<LI> [http://ccrm.vims.edu/yinglong/SVN_large_files/schism_plugin_with_last_wetting_update_visit2.13.3_win64_vs2012.zip plugin build for 2.13.3]<br />
<LI> [http://ccrm.vims.edu/yinglong/SVN_large_files/schism_plugin_with_last_wetting_update_visit3.1.2_win64_vs2017.zip latest plugin build for visit 3.1.2]<br />
<br />
<!--LI> [https://cadwr.box.com/s/hkic80xg7tmjhwk94aszssrp8fh6r0fu plugin build for 2.13.3]<br />
<LI> [https://cadwr.box.com/s/4n8vn29zxxvnn69snlsc40fcmbvk54aa latest plugin build for visit 3.1.2] --><br />
</UL><br />
<LI> If the 3.1.2 plugin doesn't work on your pc, for example "SCHISM" option doesn't show up on VisIt file type menu, there are two possible causes. One cause is that your VisIt don't have netcdf_c++.dll. You can copy this file from VisIt 2.13.x to VisIt 3.1.2. Another cause is that your pc don't have MS VC++ 2017 redistributable. You can download it from MS webpage. <br />
<LI>If you use SCHISM v5.6.1 (netcdf I/O), note that VisIT has issues with stack overflow with nc4, so you need to do the following work-around until LLNL fixes the issue:<br />
<UL><br />
<LI>Go to [https://www.unidata.ucar.edu/software/netcdf/docs/winbin.html UCAR] and get their installer for the latest C library, e.g. 4.5.0;<br />
<LI>Complete the installation and record the install dir.<br />
Then copy all files in bin/ of the install dir to the VisIT dir in (1) to overwrite.<br />
</UL><br />
<LI>After these steps, you'd be able to read in SCHISM outputs in ViSIT; look for 'SCHISM', 'gr3' format from the dropdown list.<br />
</OL><br />
<br />
----<br />
<br />
On Linux systems:<br />
<br />
Use svn or directly download the source code [http://columbia.vims.edu/schism/schism_visit_plugin/tags/v2.2.0 here].<br />
<br />
After compilation this can be used with VisIT version 2.12.2 to 2.13.3.<br />
<br />
Newer versions can be found at [https://github.com/schism-dev/schism_visit_plugin github].</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Visualization_with_VisIT&diff=1439Visualization with VisIT2020-09-22T22:01:42Z<p>Schismguest: </p>
<hr />
<div>On Windows 7 or 10:<br />
<br />
<OL><br />
<LI>First download VisIT from [https://wci.llnl.gov/simulation/computer-codes/visit/downloads LLNL site] and install. Use default dir (and record it), e.g.<br />
C:\Users\yjzhang\AppData\Local\Programs\LLNL\VisIt*<br />
<LI>Download pre-built plug-in, developed at California Dept of Water Resource [http://ccrm.vims.edu/yinglong/Courses/Hangzhou/schism_plugin_1.2_xbeta_visit2.12.3_win64_vs2012.zip here] and put the files in:<br />
C:\Users\yjzhang\AppData\Roaming\LLNL\VisIt\databases (create new dirs if necessary). This dlls location works for VisIt 2.13.2 or below. <br />
<br />
From VisIt 2.13.3, you need to put dlls on C:\Users\your_account_name\Documents\VisIt\databases. Alternatively, please email Jon Shu at Qiang.shu@water.ca.gov and let him know the version of visit you are using. Below are newer builds:<br />
<UL><br />
<LI> [http://ccrm.vims.edu/yinglong/SVN_large_files/schism_plugin_with_last_wetting_update_visit2.13.3_win64_vs2012.zip plugin build for 2.13.3]<br />
<LI> [http://ccrm.vims.edu/yinglong/SVN_large_files/schism_plugin_with_last_wetting_update_visit3.1.2_win64_vs2017.zip latest plugin build for visit 3.1.2]<br />
<br />
<!--LI> [https://cadwr.box.com/s/hkic80xg7tmjhwk94aszssrp8fh6r0fu plugin build for 2.13.3]<br />
<LI> [https://cadwr.box.com/s/4n8vn29zxxvnn69snlsc40fcmbvk54aa latest plugin build for visit 3.1.2] --><br />
</UL><br />
<LI> If the 3.1.2 plugin doesn't work on your pc, i.e. SCHISM option doesn't show up on VisIt file type menu, there are two possible causes. One cause is that your VisIt don't have netcdf_c++.dll. You can copy this file from VisIt 2.13.x to VisIt 3.1.2. Another cause is that your pc don't have MS VC++ 2017 redistributable. You can download it from MS webpage. <br />
<LI>If you use SCHISM v5.6.1 (netcdf I/O), note that VisIT has issues with stack overflow with nc4, so you need to do the following work-around until LLNL fixes the issue:<br />
<UL><br />
<LI>Go to [https://www.unidata.ucar.edu/software/netcdf/docs/winbin.html UCAR] and get their installer for the latest C library, e.g. 4.5.0;<br />
<LI>Complete the installation and record the install dir.<br />
Then copy all files in bin/ of the install dir to the VisIT dir in (1) to overwrite.<br />
</UL><br />
<LI>After these steps, you'd be able to read in SCHISM outputs in ViSIT; look for 'SCHISM', 'gr3' format from the dropdown list.<br />
</OL><br />
<br />
----<br />
<br />
On Linux systems:<br />
<br />
Use svn or directly download the source code [http://columbia.vims.edu/schism/schism_visit_plugin/tags/v2.2.0 here].<br />
<br />
After compilation this can be used with VisIT version 2.12.2 to 2.13.3.<br />
<br />
Newer versions can be found at [https://github.com/schism-dev/schism_visit_plugin github].</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Visualization_with_VisIT&diff=1435Visualization with VisIT2020-08-19T18:26:58Z<p>Schismguest: </p>
<hr />
<div>On Windows 7 or 10:<br />
<br />
<OL><br />
<LI>First download VisIT from [https://wci.llnl.gov/simulation/computer-codes/visit/downloads LLNL site] and install. Use default dir (and record it), e.g.<br />
C:\Users\yjzhang\AppData\Local\Programs\LLNL\VisIt*<br />
<LI>Download pre-built plug-in, developed at California Dept of Water Resource [http://ccrm.vims.edu/yinglong/Courses/Hangzhou/schism_plugin_1.2_xbeta_visit2.12.3_win64_vs2012.zip here] and put the files in:<br />
C:\Users\yjzhang\AppData\Roaming\LLNL\VisIt\databases (create new dirs if necessary). This dlls location works for VisIt 2.13.2 or below. From VisIt 2.13.3, you need to put dlls on C:\Users\your_account_name\Documents\VisIt\databases. Alternatively, please email Jon Shu at Qiang.shu@water.ca.gov and let him know the version of visit you are using. Here is the link of the latest plugin build for 2.13.3 [https://cadwr.box.com/s/hkic80xg7tmjhwk94aszssrp8fh6r0fu]. Another link for the latest plugin build for visit 3.1.2 [https://cadwr.box.com/s/4n8vn29zxxvnn69snlsc40fcmbvk54aa].<br />
<LI>If you use SCHISM v5.6.1 (netcdf I/O), note that VisIT has issues with stack overflow with nc4, so you need to do the following work-around until LLNL fixes the issue:<br />
<UL><br />
<LI>Go to [https://www.unidata.ucar.edu/software/netcdf/docs/winbin.html UCAR] and get their installer for the latest C library, e.g. 4.5.0;<br />
<LI>Complete the installation and record the install dir.<br />
Then copy all files in bin/ of the install dir to the VisIT dir in (1) to overwrite.<br />
</UL><br />
<LI>After these steps, you'd be able to read in SCHISM outputs in ViSIT; look for 'SCHISM', 'gr3' format from the dropdown list.<br />
</OL><br />
<br />
----<br />
<br />
On Linux systems:<br />
<br />
Use svn or directly download the source code [http://columbia.vims.edu/schism/schism_visit_plugin/tags/v2.2.0 here].<br />
<br />
After compilation this can be used with VisIT version 2.12.2 to 2.13.3.</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Share_your_tools&diff=1406Share your tools2019-05-30T14:44:08Z<p>Schismguest: </p>
<hr />
<div>We encourage all users to share useful scripts/tools with the whole community. Please also include a short description to go with your scripts.<br />
If you cannot upload your files due to either type or size restriction, please send them to yjzhang@vims.edu.<br />
<br />
<br />
=ADCIRC tidal package for US east coast=<br />
You can download the package [http://ccrm.vims.edu/schismweb/adcirc_tide_eastcoast.tgz here].<br />
<br />
=Nicegrid: a grid post-processor=<br />
Author: André Fortunato<br/><br />
Contact: afortunato@lnec.pt<br/><br />
Purpose: Grid post-processor to automatically improve a triangular grid. NICEGRID2 automatically adds and deletes elements and nodes, and reduces the element skewness.<br/><br />
Type: FORTRAN<br/><br />
Download: [http://ccrm.vims.edu/yinglong/wiki_files/nicegrid2.zip nicegrid2.zip] <br/><br />
Reference: <br/><br />
*Fortunato, A.B., N. Bruneau; A. Azevedo; M.A.V.C. Araújo; A. Oliveira. 2011. Automatic improvement of unstructured grids for coastal simulations. Journal of Coastal Research, Special Issue 64, 1028-1032.<br />
<br />
=Matlab wrapper scripts for visualization =<br />
Author: Ben Knight <br/><br />
Contact: Ben.Knight@cawthron.org.nz<br/><br />
Purpose: wrapper for the Matlab viz tool<br/><br />
Type: matlab<br/><br />
Links: [http://ccrm.vims.edu/yinglong/wiki_files/matlab_Knight_March2014.zip].<br />
<br />
=Gambit pre-processing script=<br />
Author: Li, Jian<br/><br />
Contact:<br/><br />
Purpose: Script to convert Gambit grid format (.neu) to .gr3 <br/><br />
Type:<br/><br />
Link: [http://ccrm.vims.edu/yinglong/wiki_files/LiJian_June2011.zip]<br />
<br />
=viewgrid.py: Generate figures with grids, bathymetry, stations and vector fields=<br />
Authors: Alberto Azevedo, André Fortunato<br/><br />
Contacts: aazevedo@lnec.pt, afortunato@lnec.pt<br/><br />
Purpose: Generate figures with grids, bathymetry, stations and vector fields.<br/><br />
Type: python<br/><br />
Instructions: run as "viewgrid.py viewgrid.in". Check the file viewgrid.in.sample for instructions <br/><br />
Download: [http://ccrm.vims.edu/yinglong/wiki_files/viewgrid.zip] <br/></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Share_your_tools&diff=1405Share your tools2019-05-30T08:52:17Z<p>Schismguest: </p>
<hr />
<div>We encourage all users to share useful scripts/tools with the whole community. Please also include a short description to go with your scripts.<br />
If you cannot upload your files due to either type or size restriction, please send them to yjzhang@vims.edu.<br />
<br />
<br />
=ADCIRC tidal package for US east coast=<br />
You can download the package [http://ccrm.vims.edu/schismweb/adcirc_tide_eastcoast.tgz here].<br />
<br />
=Nicegrid: a grid post-processor=<br />
Author: André Fortunato<br/><br />
Contact: afortunato@lnec.pt<br/><br />
Purpose: Grid post-processor to automatically improve a triangular grid. NICEGRID2 automatically adds and deletes elements and nodes, and reduces the element skewness.<br/><br />
Type: FORTRAN<br/><br />
Download: [http://ccrm.vims.edu/yinglong/wiki_files/nicegrid2.zip nicegrid2.zip] <br/><br />
Reference: <br/><br />
*Fortunato, A.B., N. Bruneau; A. Azevedo; M.A.V.C. Araújo; A. Oliveira. 2011. Automatic improvement of unstructured grids for coastal simulations. Journal of Coastal Research, Special Issue 64, 1028-1032.<br />
<br />
=Matlab wrapper scripts for visualization =<br />
Author: Ben Knight <br/><br />
Contact: Ben.Knight@cawthron.org.nz<br/><br />
Purpose: wrapper for the Matlab viz tool<br/><br />
Type: matlab<br/><br />
Links: [http://ccrm.vims.edu/yinglong/wiki_files/matlab_Knight_March2014.zip].<br />
<br />
=Gambit pre-processing script=<br />
Author: Li, Jian<br/><br />
Contact:<br/><br />
Purpose: Script to convert Gambit grid format (.neu) to .gr3 <br/><br />
Type:<br/><br />
Link: [http://ccrm.vims.edu/yinglong/wiki_files/LiJian_June2011.zip]<br />
<br />
=viewgrid.py: Generate figures with grids, bathymetry, stations and vector fields=<br />
Authors: Alberto Azevedom André Fortunato<br/><br />
Contacts: aazevedo@lnec.pt, afortunato@lnec.pt<br/><br />
Purpose: Generate figures with grids, bathymetry, stations and vector fields.<br/><br />
Type: python<br/><br />
Instructions: run as "viewgrid.py viewgrid.in". Check the file viewgrid.in.sample for instructions <br/><br />
Download: [http://ccrm.vims.edu/yinglong/wiki_files/viewgrid.zip] <br/></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Share_your_tools&diff=1404Share your tools2019-05-30T08:51:32Z<p>Schismguest: </p>
<hr />
<div>We encourage all users to share useful scripts/tools with the whole community. Please also include a short description to go with your scripts.<br />
If you cannot upload your files due to either type or size restriction, please send them to yjzhang@vims.edu.<br />
<br />
<br />
=ADCIRC tidal package for US east coast=<br />
You can download the package [http://ccrm.vims.edu/schismweb/adcirc_tide_eastcoast.tgz here].<br />
<br />
=Nicegrid: a grid post-processor=<br />
Author: André Fortunato<br/><br />
Contact: afortunato@lnec.pt<br/><br />
Purpose: Grid post-processor to automatically improve a triangular grid. NICEGRID2 automatically adds and deletes elements and nodes, and reduces the element skewness.<br/><br />
Type: FORTRAN<br/><br />
Download: [http://ccrm.vims.edu/yinglong/wiki_files/nicegrid2.zip nicegrid2.zip] <br/><br />
Reference: <br/><br />
*Fortunato, A.B., N. Bruneau; A. Azevedo; M.A.V.C. Araújo; A. Oliveira. 2011. Automatic improvement of unstructured grids for coastal simulations. Journal of Coastal Research, Special Issue 64, 1028-1032.<br />
<br />
=Matlab wrapper scripts for visualization =<br />
Author: Ben Knight <br/><br />
Contact: Ben.Knight@cawthron.org.nz<br/><br />
Purpose: wrapper for the Matlab viz tool<br/><br />
Type: matlab<br/><br />
Links: [http://ccrm.vims.edu/yinglong/wiki_files/matlab_Knight_March2014.zip].<br />
<br />
=Gambit pre-processing script=<br />
Author: Li, Jian<br/><br />
Contact:<br/><br />
Purpose: Script to convert Gambit grid format (.neu) to .gr3 <br/><br />
Type:<br/><br />
Link: [http://ccrm.vims.edu/yinglong/wiki_files/LiJian_June2011.zip]<br />
<br />
=viewgrid.py: Generate figures with grids, bathymetry, stations and vector fields=<br />
Authors: Alberto Azevedom André Fortunato<br/><br />
Contacts: aazevedo@lnec.pt, afortunato@lnec.pt<br/><br />
Purpose: Generate figures with grids, bathymetry, stations and vector fields.<br/><br />
Type: python<br/><br />
Instructions: run as "viewgrid.py viewgrid.in". Check the file viewgrid.in.sample for instructions <br/><br />
Download: [File:[http://ccrm.vims.edu/yinglong/wiki_files/viewgrid.zip]] <br/></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Share_your_tools&diff=1403Share your tools2019-05-30T08:51:00Z<p>Schismguest: </p>
<hr />
<div>We encourage all users to share useful scripts/tools with the whole community. Please also include a short description to go with your scripts.<br />
If you cannot upload your files due to either type or size restriction, please send them to yjzhang@vims.edu.<br />
<br />
<br />
=ADCIRC tidal package for US east coast=<br />
You can download the package [http://ccrm.vims.edu/schismweb/adcirc_tide_eastcoast.tgz here].<br />
<br />
=Nicegrid: a grid post-processor=<br />
Author: André Fortunato<br/><br />
Contact: afortunato@lnec.pt<br/><br />
Purpose: Grid post-processor to automatically improve a triangular grid. NICEGRID2 automatically adds and deletes elements and nodes, and reduces the element skewness.<br/><br />
Type: FORTRAN<br/><br />
Download: [http://ccrm.vims.edu/yinglong/wiki_files/nicegrid2.zip nicegrid2.zip] <br/><br />
Reference: <br/><br />
*Fortunato, A.B., N. Bruneau; A. Azevedo; M.A.V.C. Araújo; A. Oliveira. 2011. Automatic improvement of unstructured grids for coastal simulations. Journal of Coastal Research, Special Issue 64, 1028-1032.<br />
<br />
=Matlab wrapper scripts for visualization =<br />
Author: Ben Knight <br/><br />
Contact: Ben.Knight@cawthron.org.nz<br/><br />
Purpose: wrapper for the Matlab viz tool<br/><br />
Type: matlab<br/><br />
Links: [http://ccrm.vims.edu/yinglong/wiki_files/matlab_Knight_March2014.zip].<br />
<br />
=Gambit pre-processing script=<br />
Author: Li, Jian<br/><br />
Contact:<br/><br />
Purpose: Script to convert Gambit grid format (.neu) to .gr3 <br/><br />
Type:<br/><br />
Link: [http://ccrm.vims.edu/yinglong/wiki_files/LiJian_June2011.zip]<br />
<br />
=viewgrid.py: Generate figures with grids, bathymetry, stations and vector fields=<br />
Authors: Alberto Azevedom André Fortunato<br/><br />
Contacts: aazevedo@lnec.pt, afortunato@lnec.pt<br/><br />
Purpose: Generate figures with grids, bathymetry, stations and vector fields.<br/><br />
Type: python<br/><br />
Instructions: run as "viewgrid.py viewgrid.in". Check the file viewgrid.in.sample for instructions <br/><br />
Download: [File:[http://ccrm.vims.edu/yinglong/wiki_files/viewgrid.zip] <br/></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Share_your_tools&diff=1402Share your tools2019-05-30T08:44:25Z<p>Schismguest: </p>
<hr />
<div>We encourage all users to share useful scripts/tools with the whole community. Please also include a short description to go with your scripts.<br />
If you cannot upload your files due to either type or size restriction, please send them to yjzhang@vims.edu.<br />
<br />
<br />
=ADCIRC tidal package for US east coast=<br />
You can download the package [http://ccrm.vims.edu/schismweb/adcirc_tide_eastcoast.tgz here].<br />
<br />
=Nicegrid: a grid post-processor=<br />
Author: André Fortunato<br/><br />
Contact: afortunato@lnec.pt<br/><br />
Purpose: Grid post-processor to automatically improve a triangular grid. NICEGRID2 automatically adds and deletes elements and nodes, and reduces the element skewness.<br/><br />
Type: FORTRAN<br/><br />
Download: [http://ccrm.vims.edu/yinglong/wiki_files/nicegrid2.zip nicegrid2.zip] <br/><br />
Reference: <br/><br />
*Fortunato, A.B., N. Bruneau; A. Azevedo; M.A.V.C. Araújo; A. Oliveira. 2011. Automatic improvement of unstructured grids for coastal simulations. Journal of Coastal Research, Special Issue 64, 1028-1032.<br />
<br />
=Matlab wrapper scripts for visualization =<br />
Author: Ben Knight <br/><br />
Contact: Ben.Knight@cawthron.org.nz<br/><br />
Purpose: wrapper for the Matlab viz tool<br/><br />
Type: matlab<br/><br />
Links: [http://ccrm.vims.edu/yinglong/wiki_files/matlab_Knight_March2014.zip].<br />
<br />
=Gambit pre-processing script=<br />
Author: Li, Jian<br/><br />
Contact:<br/><br />
Purpose: Script to convert Gambit grid format (.neu) to .gr3 <br/><br />
Type:<br/><br />
Link: [http://ccrm.vims.edu/yinglong/wiki_files/LiJian_June2011.zip]<br />
<br />
=viewgrid.py: Generate figures with grids, bathymetry, stations and vector fields=<br />
Authors: Alberto Azevedom André Fortunato<br/><br />
Contacts: aazevedo@lnec.pt, afortunato@lnec.pt<br/><br />
Purpose: Generate figures with grids, bathymetry, stations and vector fields.<br/><br />
Type: python<br/><br />
Instructions: run as "viewgrid.py viewgrid.in". Check the file viewgrid.in.sample for instructions <br/><br />
Download: [http://ccrm.vims.edu/yinglong/wiki_files/viewgrid.zip] <br/></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Share_your_tools&diff=1401Share your tools2019-05-30T08:43:32Z<p>Schismguest: </p>
<hr />
<div>We encourage all users to share useful scripts/tools with the whole community. Please also include a short description to go with your scripts.<br />
If you cannot upload your files due to either type or size restriction, please send them to yjzhang@vims.edu.<br />
<br />
<br />
=ADCIRC tidal package for US east coast=<br />
You can download the package [http://ccrm.vims.edu/schismweb/adcirc_tide_eastcoast.tgz here].<br />
<br />
=Nicegrid: a grid post-processor=<br />
Author: André Fortunato<br/><br />
Contact: afortunato@lnec.pt<br/><br />
Purpose: Grid post-processor to automatically improve a triangular grid. NICEGRID2 automatically adds and deletes elements and nodes, and reduces the element skewness.<br/><br />
Type: FORTRAN<br/><br />
Download: [http://ccrm.vims.edu/yinglong/wiki_files/nicegrid2.zip nicegrid2.zip] <br/><br />
Reference: <br/><br />
*Fortunato, A.B., N. Bruneau; A. Azevedo; M.A.V.C. Araújo; A. Oliveira. 2011. Automatic improvement of unstructured grids for coastal simulations. Journal of Coastal Research, Special Issue 64, 1028-1032.<br />
<br />
=Matlab wrapper scripts for visualization =<br />
Author: Ben Knight <br/><br />
Contact: Ben.Knight@cawthron.org.nz<br/><br />
Purpose: wrapper for the Matlab viz tool<br/><br />
Type: matlab<br/><br />
Links: [http://ccrm.vims.edu/yinglong/wiki_files/matlab_Knight_March2014.zip].<br />
<br />
=Gambit pre-processing script=<br />
Author: Li, Jian<br/><br />
Contact:<br/><br />
Purpose: Script to convert Gambit grid format (.neu) to .gr3 <br/><br />
Type:<br/><br />
Link: [http://ccrm.vims.edu/yinglong/wiki_files/LiJian_June2011.zip]<br />
<br />
=viewgrid.py: Generate figures with grids, bathymetry, stations and vector fields=<br />
Authors: Alberto Azevedom André Fortunato<br/><br />
Contacts: aazevedo@lnec.pt, afortunato@lnec.pt<br/><br />
Purpose: Generate figures with grids, bathymetry, stations and vector fields.<br/><br />
Type: python<br/><br />
Instructions: run as "viewgrid.py viewgrid.in". Check the file viewgrid.in.sample for instructions<br />
Download: [http://ccrm.vims.edu/yinglong/wiki_files/viewgrid.zip] <br/></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Visualization_with_VisIT&diff=1371Visualization with VisIT2018-12-21T00:03:31Z<p>Schismguest: </p>
<hr />
<div>On Windows 7 or 10:<br />
<br />
<OL><br />
<LI>First download VisIT from [https://wci.llnl.gov/simulation/computer-codes/visit/downloads LLNL site] and install. Use default dir (and record it), e.g.<br />
C:\Users\yjzhang\AppData\Local\Programs\LLNL\VisIt*<br />
<LI>Download pre-built plug-in, developed at California Dept of Water Resource [http://ccrm.vims.edu/yinglong/Courses/Hangzhou/schism_plugin_1.2_xbeta_visit2.12.3_win64_vs2012.zip here] and put the files in:<br />
C:\Users\yjzhang\AppData\Roaming\LLNL\VisIt\databases (create new dirs if necessary). This dlls location works for VisIt 2.13.2 or below. From VisIt 2.13.3, you need to put dlls on C:\Users\your_account_name\Documents\VisIt\databases. Alternatively, please email Jon Shu at Qiang.shu@water.ca.gov and let him know the version of visit you are using. Here is the link of plugin build for 2.13.3 [https://d3.water.ca.gov/owncloud/index.php/s/ZDCmRpZHdb7HLrz].<br />
<LI>If you use SCHISM v5.6.1 (netcdf I/O), note that VisIT has issues with stack overflow with nc4, so you need to do the following work-around until LLNL fixes the issue:<br />
<UL><br />
<LI>Go to [https://www.unidata.ucar.edu/software/netcdf/docs/winbin.html UCAR] and get their installer for the latest C library, e.g. 4.5.0;<br />
<LI>Complete the installation and record the install dir.<br />
Then copy all files in bin/ of the install dir to the VisIT dir in (1) to overwrite.<br />
</UL><br />
<LI>After these steps, you'd be able to read in SCHISM outputs in ViSIT; look for 'SCHISM', 'gr3' format from the dropdown list.<br />
</OL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=How_to_download_HYCOM&diff=1351How to download HYCOM2018-08-09T20:25:28Z<p>Schismguest: </p>
<hr />
<div>From Dr. Dan Yu (July 2018):<br />
<br />
This HYCOM download tool uses “ferret” as interface.<br><br />
Please visit [https://ferret.pmel.noaa.gov/Ferret ferret web site] to see details of the software. Also you'll need nco tool.<br><br />
Version 7.1 of ferret/pyferret or higher are tested. <br><br />
ferret/pyferret also can be installed by python conda tool. <br><br />
<br />
conda create -n FERRET -c conda-forge pyferret --yes <br><br />
source activate FERRET <br><br />
<br />
You can download our tool [http://ccrm.vims.edu/yinglong/wiki_files/hycom_dl.tgz here]. <br><br />
<br />
Once you download and untar, there’re 2 directories (9x.x_exp & 19.x_exp) that correspond to 2 different HYCOM experiment datasets; check HYCOM web site for further details about the description of the datasets.<br />
<br />
Main script is listdate.sh in each dir, edit options as you need.<br />
For example: <br />
*exp="91.1" HYCOM experiment<br />
*lon_s="120" start longitude (-180 ~ 180) <br><br />
*lon_e="125" end longitude (-180 ~ 180) <br><br />
*lat_s="20" start latitude (-90 ~ 90) <br><br />
*lat_e="25" end latitude (-90 ~ 90) <br><br />
<br />
For 19.x_exp, 1 extra var “yr” has to be defined.<br />
*yr="2012"<br />
<br />
There’re 3 optional vars you can specify, if you have large domain (and want to subsample) or encounter memory problem with ferret.<br />
*lon_i: longitudinal interval, default is 0.08, use larger if needed<br />
*lat_i: latitudinal interval , default is 0.08, use larger if needed<br />
*mem: ferret memory cache, default is 300 (MegaWords), use larger if needed<br />
<br />
Once you finish, execute listdate.sh, and it will generate listHYCOM.jnl for whole record list of experiment. <br><br />
Edit time range in listHYCOM.jnl if you wish. <br><br />
Then execute dlHYCOM.sh, and all your nc files will be in “output/”.<br />
<br />
If any error occurs, such as TMAP error or disconnection, <br><br />
please check ncfile (including size) in output directory first, <br><br />
and '''DELETE''' the lines in listHYCOM.jnl corresponding to those that have already been successfully downloaded, <br><br />
and then type: dlHYCOM.sh again! <br><br />
<br />
The download script is designed to get all variables into 3 files (SSH_*.nc, ST_*.nc, UV_*.nc) for SCHISM. <br><br />
Once you gather all you need, simply use nco command to cat your ncfiles. <br><br />
For example: ncrcat SSH_*.nc SSH_final.nc <br><br />
Then you can use "gen_hot_3Dth_from_hycom.f90" to generate your initial & open boundary conditions for SCHISM.<br><br />
<br />
Instead of downloading the whole records, the script is designed to download each record at a time to avoid too many requests to HYCOM server.<br><br />
Also using OPeNDAP protocol to only request the region you need.<br><br />
HYCOM server will reject too large a request!<br><br />
Both minimize the load of HYCOM server, and makes downloading long record possible.<br><br />
The only drawback is you will need extra disk storage to concatenate all netcdf files.<br><br />
<br />
Enjoy!</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1340Compiling SCHISM on Windows2018-07-26T02:52:33Z<p>Schismguest: /* From Associate Prof. Jian Li in CUG (Wuhan) (July 2018) */</p>
<hr />
<div>=Here are the tools and libraries Jon Shu used to build parallel SCHISM on Windows=<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To fix this issue, in the solution explorer of MS Visual Studio right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance, "TVD_SB", if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project '''pschism'''.<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase '''Stack Reserve Size''' and '''Stack Commit Size''', then rebuild pschism.<br />
<br />
</UL><br />
<br />
<br />
=From Associate Prof. Jian Li in CUG (Wuhan) (July 2018)=<br />
Some experiences can be shared about running SCHISM in Windows, I found that several executables of SCHISM_5.6.1 has been uploaded by Jon Shu in the Wiki. <br />
Now I want to share the compiling files and running case for the SCHISM5.3.1, which can be used for the developers to develop and debug the code. <br />
Besides that, I transferred part of the cohesive sediment modeling code from FVCOM model and also bundled in the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/schism_v5.3.1.zip file].<br />
I used Visual Studio 2008 and Intel Fortran 11.0 to compile SCHISM5.3.1, and the same method and softwares can be used to compile the other version of SCHISM. <br />
All the third party softwares included METIS, NetCDF, GOTM3.2 were also bundled in the software. At the same time, I also used Cygwin to compile and run the SCHISM5.3.1. <br />
Therefore, I can develop, compile and run SCHISM both in Windows and Linux alternatively.<br />
I also send the test case of the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/Sed3D_Trench_Migration.zip Sed3D_Trench_migration] to you, which can be run in Windows cmd like this: <br />
mpiexec -np 8 schism5.3.1 <br />
Wish these experiences can help the developers like the Windows OS. The different preprocessor should be used if you want to use another modules, which should be configured in the Visual Studio compiler.<br />
If you have any questions, please contact with me, my email address is lijian_cky@hotmail.com <br />
The ACE tools have also been compiled using CygWin in Windows OS, you can email me and I can send you the necessary files.</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1339Compiling SCHISM on Windows2018-07-26T02:51:59Z<p>Schismguest: </p>
<hr />
<div>=Here are the tools and libraries Jon Shu used to build parallel SCHISM on Windows=<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To fix this issue, in the solution explorer of MS Visual Studio right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance, "TVD_SB", if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project '''pschism'''.<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase '''Stack Reserve Size''' and '''Stack Commit Size''', then rebuild pschism.<br />
<br />
</UL><br />
<br />
<br />
=From Associate Prof. Jian Li in CUG (Wuhan) (July 2018)=<br />
Some experiences can be shared about running SCHISM in Windows, I found that several executables of SCHISM_5.6.1 has been uploaded by Jon Shu in the Wiki. <br />
Now I want to share the compiling files and running case for the SCHISM5.3.1, which can be used for the developers to develop and debug the code. <br />
Besides that, I transferred part of the cohesive sediment modeling code from FVCOM model and also bundled in the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/schism_v5.3.1.zip file].<br />
I used Visual Studio 2008 and Intel Fortran 11.0 to compile SCHISM5.3.1, and the same method and softwares can be used to compile the other version of SCHISM. <br />
All the third party softwares included METIS, NetCDF, GOTM3.2 were also bundled in the software. At the same time, I also used Cygwin to compile and run the SCHISM5.3.1. <br />
Therefore, I can develop, compile and run SCHISM both in Windows and Linux alternatively.<br />
I also send the test case of the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/Sed3D_Trench_Migration.zip Sed3D_Trench_migration] to you, which can be run in Windows cmd like this:<br />
<br />
mpiexec -np 8 schism5.3.1<br />
<br />
Wish these experiences can help the developers like the Windows OS. The different preprocessor should be used if you want to use another modules, which should be configured in the Visual Studio compiler. If you have any questions, please contact with me, my email address is lijian_cky@hotmail.com <br />
The ACE tools have also been compiled using CygWin in Windows OS, you can email me and I can send you the necessary files.</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1338Compiling SCHISM on Windows2018-07-26T02:51:04Z<p>Schismguest: </p>
<hr />
<div>=Here are the tools and libraries Jon Shu used to build parallel SCHISM on Windows=<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To fix this issue, in the solution explorer of MS Visual Studio right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance, "TVD_SB", if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project '''pschism'''.<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase '''Stack Reserve Size''' and '''Stack Commit Size''', then rebuild pschism.<br />
<br />
</UL><br />
<br />
<br />
=From Associate Prof. Jian Li in CUG (Wuhan) (July 2018)=<br />
Some experiences can be shared about running SCHISM in Windows, I found that several executables of SCHISM_5.6.1 has been uploaded by Jon Shu in the Wiki. <br />
<br />
Now I want to share the compiling files and running case for the SCHISM5.3.1, which can be used for the developers to develop and debug the code. Besides that, I transferred part of the cohesive sediment modeling code<br />
from FVCOM model and also bundled in the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/schism_v5.3.1.zip file].<br />
<br />
I used Visual Studio 2008 and Intel Fortran 11.0 to compile SCHISM5.3.1, and the same method and softwares can be used to compile the other version of SCHISM. All the third party softwares included METIS, NetCDF, GOTM3.2 were also bundled in the software. At the same time, I also used Cygwin to compile and run the SCHISM5.3.1. Therefore, I can develop, compile and run SCHISM both in Windows and Linux alternatively.<br />
<br />
I also send the test case of the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/Sed3D_Trench_Migration.zip Sed3D_Trench_migration] to you, which can be run in Windows cmd like this:<br />
<br />
mpiexec -np 8 schism5.3.1<br />
<br />
Wish these experiences can help the developers like the Windows OS. The different preprocessor should be used if you want to use another modules, which should be configured in the Visual Studio compiler. If you have any questions, please contact with me, my email address is lijian_cky@hotmail.com<br />
<br />
The ACE tools have also been compiled using CygWin in Windows OS, you can email me and I can send you the necessary files.</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1337Compiling SCHISM on Windows2018-07-26T02:50:18Z<p>Schismguest: /* From Associate Prof. Jian Li in CUG (Wuhan) (July 2018) */</p>
<hr />
<div>=Here are the tools and libraries Jon Shu used to build parallel SCHISM on Windows=<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To fix this issue, in the solution explorer of MS Visual Studio right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance, "TVD_SB", if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project '''pschism'''.<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase '''Stack Reserve Size''' and '''Stack Commit Size''', then rebuild pschism.<br />
<br />
</UL><br />
<br />
<br />
=From Associate Prof. Jian Li in CUG (Wuhan) (July 2018)=<br />
Some experiences can be shared about running SCHISM in Windows, I found that several executables of SCHISM_5.6.1 has been uploaded by Jon Shu in the Wiki. <br />
<br />
Now I want to share the compiling files and running case for the SCHISM5.3.1, which can be used for the developers to develop and debug the code. Besides that, I transferred part of the cohesive sediment modeling code<br />
from FVCOM model and also bundled in the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/schism_v5.3.1.zip file].<br />
<br />
I used Visual Studio 2008 and Intel Fortran 11.0 to compile SCHISM5.3.1, and the same method and softwares can be used to compile the other version of SCHISM. All the third party softwares included METIS, NetCDF, GOTM3.2 were also bundled in the software. At the same time, I also used Cygwin to compile and run the SCHISM5.3.1. Therefore, I can develop, compile and run SCHISM both in Windows and Linux alternatively.<br />
<br />
I also send the test case of the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/Sed3D_Trench_Migration.zip Sed3D_Trench_migration] to you, which can be run in Windows cmd like this:<br />
<br />
mpiexec -np 8 schism5.3.1<br />
<br />
Wish these experiences can help the developers like the Windows OS. The different preprocessor should be used if you want to use another modules, which should be configured in the Visual Studio compiler. If you have any questions, please contact with me, my email address is lijian_cky@hotmail.com<br />
<br />
The ACE tools have also been compiled using CygWin in Windows OS, you can download the file [C:\Cygwin\home\ACE\ACE.rar]and run in CygWin.</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1336Compiling SCHISM on Windows2018-07-26T02:27:21Z<p>Schismguest: </p>
<hr />
<div>=Here are the tools and libraries Jon Shu used to build parallel SCHISM on Windows=<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To fix this issue, in the solution explorer of MS Visual Studio right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance, "TVD_SB", if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project '''pschism'''.<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase '''Stack Reserve Size''' and '''Stack Commit Size''', then rebuild pschism.<br />
<br />
</UL><br />
<br />
<br />
=From Associate Prof. Jian Li in CUG (Wuhan) (July 2018)=<br />
Some experience can be shared about running SCHISM in Windows, I found that several executables of SCHISM_5.6.1 has been uploaded by Jon Shu in the Wiki. <br />
Now I want to share the compiling files and running case for the SCHISM5.3.1, which can be used for the developers to develop and debug the code. Besides that, <br />
I transferred part of the cohesive sediment modeling code<br />
from FVCOM model and also bundled in the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/schism_v5.3.1.zip file].<br />
<br />
I use Visual Studio 2008 and Intel Fortran 11.0 to compile SCHISM5.3.1, and the same method and softwares can be used to compile the other version of SCHISM. <br />
All the third party softwares included METIS, NetCDF, GOTM3.2 were also bundled in the software. At the same time, <br />
I also used Cygwin to compile and run the SCHISM5.3.1. Therefore, I can develop, compile and run SCHISM both in Windows and Linux alternatively.<br />
<br />
I also send the test case of the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/Sed3D_Trench_Migration.zip Sed3D_Trench_migration] to you, which can be run in Windows cmd like:<br />
mpiexec -np 8 schism5.3.1<br />
<br />
Wish these experiences can help the developers like the Windows OS. The different preprocessor should be used if you want to use another modules, which should be configured in the Visual Studio compiler. If you have any questions, please contact with me, my email address is lijian_cky@hotmail.com</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1335Compiling SCHISM on Windows2018-07-26T02:25:58Z<p>Schismguest: </p>
<hr />
<div>=Here are the tools and libraries Jon Shu used to build parallel SCHISM on Windows=<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To fix this issue, in the solution explorer of MS Visual Studio right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance, "TVD_SB", if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project '''pschism'''.<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase '''Stack Reserve Size''' and '''Stack Commit Size''', then rebuild pschism.<br />
<br />
</UL><br />
<br />
<br />
=From Prof. Jian Li (July 2018)=<br />
Some experience can be shared about running SCHISM in Windows, I found that several executables of SCHISM_5.6.1 has been uploaded by Jon Shu in the Wiki. <br />
Now I want to share the compiling files and running case for the SCHISM5.3.1, which can be used for the developers to develop and debug the code. Besides that, <br />
I transferred part of the cohesive sediment modeling code<br />
from FVCOM model and also bundled in the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/schism_v5.3.1.zip file].<br />
<br />
I use Visual Studio 2008 and Intel Fortran 11.0 to compile SCHISM5.3.1, and the same method and softwares can be used to compile the other version of SCHISM. <br />
All the third party softwares included METIS, NetCDF, GOTM3.2 were also bundled in the software. At the same time, <br />
I also used Cygwin to compile and run the SCHISM5.3.1. Therefore, I can develop, compile and run SCHISM both in Windows and Linux alternatively.<br />
<br />
I also send the test case of the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/Sed3D_Trench_Migration.zip Sed3D_Trench_migration] to you, which can be run in Windows cmd like:<br />
mpiexec -np 8 schism5.3.1<br />
<br />
Wish these experiences can help the developers like the Windows OS. The different preprocessor should be used if you want to use another modules, which should be configured in the Visual Studio compiler. If you have any questions, please contact with me, my email address is lijian_cky@hotmail.com</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=How_to_download_HYCOM&diff=1331How to download HYCOM2018-07-24T01:34:03Z<p>Schismguest: </p>
<hr />
<div>From Dr. Dan Yu (July 2018):<br />
<br />
This HYCOM download tool uses “ferret” as interface.<br><br />
Please visit [https://ferret.pmel.noaa.gov/Ferret ferret web site] to see details of the software. Also you'll need nco tool.<br><br />
Version 7.1 of ferret/pyferret or higher are recommended to use. <br><br />
<br />
You can download our tool [http://ccrm.vims.edu/yinglong/wiki_files/hycom_dl.tgz here].<br />
<br />
Once you download and untar, there’re 2 directories (9x.x_exp & 19.x_exp) that correspond to 2 different HYCOM experiment datasets; check HYCOM web site for further details about the description of the datasets.<br />
<br />
Main script is listdate.sh in each dir, edit options as you need.<br />
For example: <br />
*exp="91.1" HYCOM experiment<br />
*lon_s="120E" start longitude<br />
*lon_e="125E" end longitude<br />
*lat_s="20N" start latitude<br />
*lat_e="25N" end latitude<br />
<br />
For 19.x_exp, 1 extra var “yr” has to be defined.<br />
*yr="2012"<br />
<br />
There’re 3 optional vars you can specify, if you have large domain (and want to subsample) or encounter memory problem with ferret.<br />
*lon_i: longitudinal interval, default is 0.08, use larger if needed<br />
*lat_i: latitudinal interval , default is 0.08, use larger if needed<br />
*mem: ferret memory cache, default is 300 (MegaWords), use larger if needed<br />
<br />
Once you finish, execute listdate.sh, and it will generate listHYCOM.jnl for whole record list of experiment. <br><br />
Edit time range in listHYCOM.jnl if you wish. <br><br />
Then execute dlHYCOM.sh, and all your nc files will be in “output/”.<br />
<br />
If any error occurs, such as TMAP error or disconnection, <br><br />
please check ncfile (including size) in output directory first, <br><br />
and '''DELETE''' the lines in listHYCOM.jnl corresponding to those that have already been successfully downloaded, <br><br />
and then type: dlHYCOM.sh again! <br><br />
<br />
The download script is designed to get all variables into 3 files (EL_*.nc, ST_*.nc, UV_*.nc) for SCHISM. <br><br />
Once you gather all you need, simply use nco command to cat your ncfiles. <br><br />
For example: ncrcat EL_*.nc EL_final.nc <br><br />
Then you can use "gen_hot_3Dth_from_hycom.f90" to generate your initial & open boundary conditions for SCHISM.<br><br />
<br />
Instead of downloading the whole records, the script is designed to download each record at a time to avoid too many requests to HYCOM server.<br><br />
Also using OPeNDAP protocol to only request the region you need.<br><br />
HYCOM server will reject too large request!<br><br />
Both minimize the load of HYCOM server, and makes download with long record become possible.<br><br />
The only drawback is you will need extra disk storage to concatenate all netcdf files.<br><br />
<br />
Enjoy!</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1330Compiling SCHISM on Windows2018-07-23T17:07:38Z<p>Schismguest: </p>
<hr />
<div>=Here are the tools and libraries Jon Shu used to build parallel SCHISM on Windows=<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To fix this issue, in the solution explorer of MS Visual Studio right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance, "TVD_SB", if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project '''pschism'''.<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase '''Stack Reserve Size''' and '''Stack Commit Size''', then rebuild pschism.<br />
<br />
</UL><br />
<br />
<br />
=From Prof. Jian Li (July 2018)=<br />
I saw the experience sharing about running SCHISM on Windows, I found that several executables of SCHISM_5.6.1 has been uploaded in the Wiki. <br />
Now I want to share the compiling files and running case for the SCHISM5.3.1, which can be used for the developers to debug the code. Besides that, <br />
I transferred part of the cohesive sediment modeling code<br />
from FVCOM model and also bundled in the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/schism_v5.3.1.zip file].<br />
<br />
I use Visual Studio 2008 and Intel Fortran 11.0 to compile SCHISM5.3.1, and the same method and softwares can be used to compile the other version of SCHISM. <br />
All the third party softwares included METIS, NetCDF, GOTM3.2 were also bundled in the software. At the same time, <br />
I also used Cygwin to compile and run the SCHISM5.3.1. Therefore, I can develop, compile and run SCHISM both in Windows and Linux alternatively.<br />
<br />
I also send the test case of the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/Sed3D_Trench_Migration.zip Sed3D_Trench_migration] to you, which can be run in Windows cmd like:<br />
mpiexec -np 8 schism5.3.1<br />
<br />
Wish these experiences can help the developers like the Windows OS.</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1329Compiling SCHISM on Windows2018-07-20T22:05:30Z<p>Schismguest: </p>
<hr />
<div>=Here are the tools and libraries Jon Shu used to build parallel SCHISM on Windows=<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To fix this issue, in the solution explorer of MS Visual Studio right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance, "TVD_SB", if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project '''pschism'''.<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase '''Stack Reserve Size''' and '''Stack Commit Size'''. <br />
<br />
</UL><br />
<br />
<br />
=From Prof. Jian Li (July 2018)=<br />
I saw the experience sharing about running SCHISM on Windows, I found that several executables of SCHISM_5.6.1 has been uploaded in the Wiki. <br />
Now I want to share the compiling files and running case for the SCHISM5.3.1, which can be used for the developers to debug the code. Besides that, <br />
I transferred part of the cohesive sediment modeling code<br />
from FVCOM model and also bundled in the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/schism_v5.3.1.zip file].<br />
<br />
I use Visual Studio 2008 and Intel Fortran 11.0 to compile SCHISM5.3.1, and the same method and softwares can be used to compile the other version of SCHISM. <br />
All the third party softwares included METIS, NetCDF, GOTM3.2 were also bundled in the software. At the same time, <br />
I also used Cygwin to compile and run the SCHISM5.3.1. Therefore, I can develop, compile and run SCHISM both in Windows and Linux alternatively.<br />
<br />
I also send the test case of the [http://ccrm.vims.edu/yinglong/wiki_files/LiJian/Sed3D_Trench_Migration.zip Sed3D_Trench_migration] to you, which can be run in Windows cmd like:<br />
mpiexec -np 8 schism5.3.1<br />
<br />
Wish these experiences can help the developers like the Windows OS.</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1308Compiling SCHISM on Windows2018-07-19T19:02:30Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To fix this issue, in the solution explorer of MS Visual Studio right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance, "TVD_SB", if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project '''pschism'''.<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase '''Stack Reserve Size''' and '''Stack Commit Size'''. <br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1307Compiling SCHISM on Windows2018-07-19T19:01:41Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To fix this issue, in the solution explorer of MS Visual Studio, right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance "TVD_SB" if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project '''pschism'''.<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase '''Stack Reserve Size''' and '''Stack Commit Size'''. <br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1306Compiling SCHISM on Windows2018-07-19T19:00:42Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To make the project compiled, in the solution explorer of MS Visual Studio, right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance "TVD_SB" if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project '''pschism'''.<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase '''Stack Reserve Size''' and '''Stack Commit Size'''. <br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1305Compiling SCHISM on Windows2018-07-19T19:00:00Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To make the project compiled, in the solution explorer of MS Visual Studio, right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance "TVD_SB" if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project """pschism""".<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase """Stack Reserve Size""" and """Stack Commit Size"". <br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1304Compiling SCHISM on Windows2018-07-19T18:59:45Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To make the project compiled, in the solution explorer of MS Visual Studio, right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance "TVD_SB" if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<LI> Build the project """pschism"".<br />
<LI> If your pschism executable throw error of stack overflow when running, it means the reserved stack size is not enough for the executable. You can either run it with more threads in parallel or change the reserved stack size via Visual Studio. To change stack size, Right click project '''pschism''' to show property pages, go to '''Linker->System''', and increase """Stack Reserve Size""" and """Stack Commit Size"". <br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1303Compiling SCHISM on Windows2018-07-19T18:52:42Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To make the project compiled, in the solution explorer of MS Visual Studio, right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance "TVD_SB" if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1302Compiling SCHISM on Windows2018-07-19T18:52:03Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To make the project compiled, in the solution explorer of MS Visual Studio, right click project '''hydro''' to show property pages, go to '''Fortran->Preprocessor->Preprocessor Definitions''' to make sure you have the correct TVD_LIM defined, For instance "TVD_SB" if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project '''pschsim''' has to be adjust manually in Visual Studio. Right click project '''pschism''' to show property pages, go to '''Linker->Input->Additional Dependencies''' and check if you have the correct and complete third party libs. I usually just add all the paths of third party libs manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1301Compiling SCHISM on Windows2018-07-19T18:49:48Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To make the project compiled, in the solution explorer of MS Visual Studio, right click project 'hydro' to show property pages, go to 'Fortran'->'Preprocessor'->'Preprocessor Definitions' to make sure you have the correct TVD_LIM defined, For instance "TVD_SB" if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project 'pschsim' has to be adjust manually in Visual Studio. Right click project 'pschism' to show property pages, go to 'Linker'->'Input'->'Additional Dependencies' and check if you have the correct and complete third party libs. I usually just add all the paths of third party libs manually, here is the list of my input.<br />
<br />
<UL><br />
Z:\schism\third_party\netCDF432\netCDF_c\lib\netcdf.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\netcdf_f90.lib Z:\schism\third_party\netCDF432\netCDF_fortran\lib\ncfortran.lib Z:\schism\third_party\hdf5\lib\hdf5_hl.lib Z:\schism\third_party\hdf5\lib\hdf5.lib Z:\schism\third_party\hdf5\lib\zlib.lib Z:\schism\third_party\parmetis-4.0.3\lib\parmetis.lib Z:\schism\third_party\parmetis-4.0.3\metis\lib\metis.lib "C:\Program Files\Microsoft HPC Pack 2008 R2\lib\amd64\msmpi.lib" "C:\Program Files\Microsoft HPC Pack 2008 R2\Lib\amd64\msmpifec.lib" <br />
</UL><br />
<br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1300Compiling SCHISM on Windows2018-07-19T18:44:51Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To make the project compiled, in the solution explorer of MS Visual Studio, right click project ''hydro to show property pages, go to ''Fortran->''Preprocessor->''Preprocessor Definitions to make sure you have the correct TVD_LIM defined, For instance "TVD_SB" if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project 'pschsim' has to be adjust manually in Visual Studio. <br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1299Compiling SCHISM on Windows2018-07-19T18:44:19Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS Visual Studio 2010 project. <br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<LI> Current SCHSIM cmake system doesn't work very well on Windows, I have seen TVD_LIM preprocessor was not set correctly in the resulting project. To make the project compiled, in the solution explorer of MS Visual Studio, right click project ''hydro to show property pages, go to ''Fortran->''Preprocessor->''Preprocessor Definitions to make sure you have the correct TVD_LIM defined, For instance "TVD_SB" if you choose SB option for TVD_LIM. <br />
<br />
Also,I found third party lib path for the project ''pschsim has to be adjust manually in Visual Studio. <br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1298Compiling SCHISM on Windows2018-07-19T18:30:52Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS visual studio 2010 project.<br />
<br />
<UL><br />
"cmake -C ..\v5.6.1\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1\src"</UL><br />
<br />
<br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1297Compiling SCHISM on Windows2018-07-19T18:30:04Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS visual studio 2010 project.<br />
<br />
<UL><br />
"cmake -C ..\v5.6.1_clean\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1_clean\src"</UL><br />
<br />
<br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1296Compiling SCHISM on Windows2018-07-19T18:29:04Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE Windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<LI> Create a directory for SCHSIM build, say v5.6.1_build. Start Windows cmd from this folder, type the command line below to generate<br />
MS visual studio 2010 project.<br />
<br />
"cmake -C ..\v5.6.1_clean\cmake\SCHISM.local.cmake.win -DCMAKE_BUILD_TYPE:STRING=Release -G"Visual Studio 10 Win64" --build . Z:\schism\v5.6.1_clean\src"<br />
<br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1295Compiling SCHISM on Windows2018-07-19T16:59:08Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1294Compiling SCHISM on Windows2018-07-19T16:57:40Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [[Media:Example.ogg]]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1293Compiling SCHISM on Windows2018-07-19T16:54:32Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which are here [[File:third_party.zip]]<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win.txt]]<br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=File:SCHSIM.local.cmake.win.txt&diff=1292File:SCHSIM.local.cmake.win.txt2018-07-19T16:51:39Z<p>Schismguest: </p>
<hr />
<div></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1291Compiling SCHISM on Windows2018-07-19T16:50:19Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which can be downloaded at [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here].<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE windows cache file in SCHSIM source code\cmake\SCHSIM.local.cmake.win. <br />
You may turn on/off extra modules in this file, and you must set TVD_LIM option to build hydro. You also need to<br />
edit the location of third party libs. Here is a example [[File:SCHSIM.local.cmake.win]]<br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1290Compiling SCHISM on Windows2018-07-19T16:45:09Z<p>Schismguest: </p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which can be downloaded at [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here].<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL><br />
<br />
Here are the steps to build it<br />
<UL><br />
<LI> Edit the CMAKE windows cache file in SCHSIM source code<br />
<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Compiling_SCHISM_on_Windows&diff=1289Compiling SCHISM on Windows2018-07-19T16:43:42Z<p>Schismguest: Created page with "Here are the tools and libraries I used to build parallel SCHSIM on Windows <UL> <LI> MS Visual Studio 2010 <LI> MS HPC package 2008, which can be downloaded at [https:/..."</p>
<hr />
<div>Here are the tools and libraries I used to build parallel SCHSIM on Windows<br />
<br />
<UL><br />
<LI> MS Visual Studio 2010<br />
<LI> MS HPC package 2008, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<LI> Intel Compiler<br />
<LI> SVN 1.6.16<br />
<LI> CMAKE 3.02<br />
<LI> Prebuild third party libs, which can be downloaded at [https://d3.water.ca.gov/owncloud/index.php/s/uGOYtAHVteLDJSb here].<br />
This zip file contains HDF5,netCDF4 and parmetis.<br />
</UL></div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Main_Page&diff=1288Main Page2018-07-19T16:04:15Z<p>Schismguest: /* Part I: Formal documentation pages */</p>
<hr />
<div><br />
<!-- The map below indicates the location of visitors to this site. Click on the map to see a larger view.<br />
{|<br />
|[http://www.revolvermaps.com/?target=enlarge&amp;i=3r854vj4vdn&amp;color=ff0000&amp;m=0 http://rd.revolvermaps.com/h/m/a/0/ff0000/139/0/3r854vj4vdn.png]<br />
|-<br />
|}<br />
<br/><br />
<br /><br /--><br />
<br />
= SCHISM WIKI & Forum =<br />
<br />
<OL><br />
<LI> The information on this wiki site under 'User contribution' is contributed by users and developers alike, and therefore the developers cannot guarantee all info is correct and up to date, although they are committed to patrolling the site regularly. Verify if necessary by sending a message to the SCHISM mailing-list: schism_list@vims.edu<br />
<LI>Click the logo on the left anytime to get back to this main wiki page. 'SCHISM web' below is a link to the main SCHISM web site <br />
<LI> Some info may be version sensitive, and so consult the files in your source code bundle for up-to-date info<br />
<LI> Please consider contributing to any topic and suggest new topics of your interest. You first need to have an account created for you (we do not allow people to create accounts themselves to prevent spams). If you would like to contribute to the page please send an e-mail to [mailto:yjzhang@vims.edu Joseph Zhang], with some basic info: your ''real'' name and email address. <br />
<LI> The links below that have content are in blue.<br />
</OL><br />
<br />
----<br />
{|<br />
|The map below indicates the location of visitors to this site. <br>Click on the map to see a larger view || || || || || || || || || || || || [http://ccrm.vims.edu/schismweb/ '''SCHISM web'''] <br />
<br />
|- <br />
| [http://www.revolvermaps.com/?target=enlarge&amp;i=3r854vj4vdn&amp;color=ff0000&amp;m=0 http://rd.revolvermaps.com/h/m/a/0/ff0000/139/0/3r854vj4vdn.png] || || || || || || <br />
|- <br />
|}<br />
<br />
<br />
----<br />
<br />
== Part I: Formal documentation pages ==<br />
<br />
----<br />
* [http://ccrm.vims.edu/schismweb/ SCHISM web]<br />
<br />
<br />
* [[Getting Started]]<br />
** [[Downloading and compiling SCHISM and utilities]]<br />
** [[Installation on Mac]]<br />
** [[Running SCHISM on Windows]]<br />
** [[Compiling SCHISM on Windows]]<br />
<br />
* [[Online tutorials]]<br />
<br />
<br />
* [[Extra model documentation]]<br />
<!-- ** [http://ccrm.vims.edu/schismweb/combined_theory_manual.pdf Theory Manual]<br />
** [http://ccrm.vims.edu/schismweb/manual.html Description of some input files]<br />
** [[For developers]] <br />
**[http://ccrm.vims.edu/yinglong/wiki_files/MPI_developers_notes.pdf Developer's notes on the code] <br />
<br />
** [[Windwave module]] <br />
** [[Sediment Transport Module (3D)]]<br />
** [[Sediment Transport Module (2D)]] <br />
** [[Water quality module]]--><br />
** [[Ecosystem modules]]<br />
** [[Oil spill module]]<br />
<br />
<br />
<!--*[[User manual]]<br />
** [http://ccrm.vims.edu/schism/manual.html Hydrodynamics]<br />
** [[Scalar Transport]]<br />
** [[Sediment Transport]]<br />
** [[Windwave]]<br />
** [[Ecology]] <br />
** [[Hydraulic module]]--><br />
<br />
<br />
----<br />
<br />
== Part II: User contributions ==<br />
* [[Jobs and positions available]]<br />
<!-- * [[SCHISM FAQ]] --><br />
* [[Special topics]]<br />
** [[Convergence study with SCHISM]]<br />
** [[Conservation]]<br />
** [[ACE tools]]<br />
<!-- ** [[Mesh generation]] <br />
** [[Simulating wetting and drying with SCHISM]]<br />
** [[Salt intrusion study with SCHISM]]<br />
** [[2D vs. 3D mode]] <br />
**[[Debugging after a run crashes]]<br />
** [[Hydrostatic vs. non-hydrostatic calculation]]<br />
** [[Explicit vs. implicit calculation]]<br />
** [[Spatial and temporal discretization]]--><br />
** [[Updating a simulation after changing an existing mesh]]<br />
** [[Tides]]<br />
** [[Salinity and temperature nudging]]<br />
** [[Harmonic analysis]]<br />
** [http://ccrm.vims.edu/yinglong/wiki_files/Report-ChezyFlow-Sept2011.pdf Bottom boundary layer formulation in SCHISM]<br />
** [[Baroclinic vs. barotropic mode]]<br />
** [[Atmospheric forcing]]<br />
** [[Tsunami simulation]]<br />
** [[How to download HYCOM]]<br />
<br />
<!-- * [[Output formats and postprocessing]]<br />
** [[Harmonic analysis]]<br />
** [[Visualization]]<br />
** [[Parallel output: time and processor blocks]]<br />
** [[One way nesting]] --><br />
<br />
* [[FAQ]]<br />
* [[Sharing your tools]]<br />
<br />
== Getting started ==<br />
* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.<br />
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]<br />
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]<br />
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Running_SCHISM_on_Windows&diff=1287Running SCHISM on Windows2018-07-19T16:00:19Z<p>Schismguest: </p>
<hr />
<div>The instruction below is from Jon Shu (Cal-DWR) (July 2018)<br />
<br />
* First download the compiled schism 5.6.1 windows with the necessary dlls at [http://ccrm.vims.edu/yinglong/wiki_files/pschism_5.6.1_ms_2010_x64.zip here] and decompress.<br />
<br />
* To run it parallel in windows, you need to install MS HPC 2008 package, which can be downloaded at [https://www.microsoft.com/en-us/download/details.aspx?id=14737 here]<br />
<br />
* To run it in parallel on windows, make sure the Microsoft mpiexec is in your path and before other mpiexec (for instance intel mpiexec if you have intel compiler installed before). You can check it by typing “where mpiexec ” under windows command console (or which mpiexec if you have cygwin installed)<br />
<br />
* Copy all input files and the executable and dlls from above into a directory, and then execute the program inside:<br />
mpiexec -np 8 pschism</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=How_to_download_HYCOM&diff=1269How to download HYCOM2018-07-14T00:43:42Z<p>Schismguest: </p>
<hr />
<div>From Dr. Dan Yu (July 2018):<br />
<br />
This HYCOM download tool is using “ferret” as interface.<br />
Please visit [https://ferret.pmel.noaa.gov/Ferret ferret web site] to see details.<br />
<br />
You can download this tool [http://ccrm.vims.edu/yinglong/wiki_files/hycom_dl.tgz here].<br />
<br />
Once you download and untar, there’re 2 directories (9x.x_exp & 19.x_exp) represent different HYCOM experiment data, check HYCOM web site for further details.<br />
<br />
Main script is listdate.sh, edit options as you needed.<br />
For example: <br />
*exp="91.1" HYCOM experiment<br />
*lon_s="120E" start longitude<br />
*lon_e="125E" end longitude<br />
*lat_s="20N" start latitude<br />
*lat_e="25N" end latitude<br />
<br />
For 19.x_exp, 1 extra var “yr” has to be defined.<br />
*yr="2012"<br />
<br />
There’re 3 optional vars you can add, if you have large domain or encounter memory problem of ferret.<br />
*lon_i : longitude interval, default is 0.08, has to be larger if needed<br />
*lat_i : latitude interval , default is 0.08, has to be larger if needed<br />
*mem : ferret memory cache, default is 300 (MegaWords), change larger if needed<br />
<br />
Once you finish, execute listdate.sh, it will give you listHYCOM.jnl for whole record list of experiment. <br><br />
Edit time range in listHYCOM.jnl as you needed. <br><br />
Execute dlHYCOM.sh, all your nc files will be in “output”.<br />
<br />
If any bad situation happened, such as TMAP error or disconnection, <br><br />
please check ncfile (including size) in output directory first, <br><br />
and '''DO DELETE''' the line which already successfully download in listHYCOM.jnl! <br><br />
Then type: dlHYCOM.sh again! <br><br />
<br />
The download script is designed to get all variables into 3 files (EL_*.nc, ST_*.nc, UV_*.nc) for SCHISM. <br><br />
Once you gather all you need, simply use nco command to cat your ncfiles. <br><br />
For example: ncrcat EL_*.nc EL_final.nc <br><br />
Then you can use "gen_hot_3Dth_from_hycom.f90" to generate your initial & open boundary conditions for SCHISM.<br />
<br />
Enjoy!</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=How_to_download_HYCOM&diff=1268How to download HYCOM2018-07-14T00:41:13Z<p>Schismguest: </p>
<hr />
<div>From Dr. Dan Yu (July 2018):<br />
<br />
This HYCOM download tool is using “ferret” as interface.<br />
Please visit [https://ferret.pmel.noaa.gov/Ferret ferret web site] to see details.<br />
<br />
You can download this tool [http://ccrm.vims.edu/yinglong/wiki_files/hycom_dl.tgz here].<br />
<br />
Once you download and untar, there’re 2 directories (9x.x_exp & 19.x_exp) represent different HYCOM experiment data, check HYCOM web site for further details.<br />
<br />
Main script is listdate.sh, edit options as you needed.<br />
For example: <br />
*exp="91.1" HYCOM experiment<br />
*lon_s="120E" start longitude<br />
*lon_e="125E" end longitude<br />
*lat_s="20N" start latitude<br />
*lat_e="25N" end latitude<br />
<br />
For 19.x_exp, 1 extra var “yr” has to be defined.<br />
*yr="2012"<br />
<br />
There’re 3 optional vars you can add, if you have large domain or encounter memory problem of ferret.<br />
*lon_i : longitude interval, default is 0.08, has to be larger if needed<br />
*lat_i : latitude interval , default is 0.08, has to be larger if needed<br />
*mem : ferret memory cache, default is 300 (M), change larger if needed<br />
<br />
Once you finish, execute listdate.sh, it will give you listHYCOM.jnl for whole record list of experiment. <br><br />
Edit time range in listHYCOM.jnl as you needed. <br><br />
Execute dlHYCOM.sh, all your nc files will be in “output”.<br />
<br />
If any bad situation happened, such as TMAP error or disconnection, <br><br />
please check ncfile (including size) in output directory first, <br><br />
and '''DO DELETE''' the line which already successfully download in listHYCOM.jnl! <br><br />
Then type: dlHYCOM.sh again! <br><br />
<br />
The download script is designed to get all variables into 3 files (EL_*.nc, ST_*.nc, UV_*.nc) for SCHISM. <br><br />
Once you gather all you need, simply use nco command to cat your ncfiles. <br><br />
For example: ncrcat EL_*.nc EL_final.nc <br><br />
Then you can use "gen_hot_3Dth_from_hycom.f90" to generate your initial & open boundary conditions for SCHISM.<br />
<br />
Enjoy!</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=How_to_download_HYCOM&diff=1267How to download HYCOM2018-07-14T00:33:27Z<p>Schismguest: </p>
<hr />
<div>From Dr. Dan Yu (July 2018):<br />
<br />
This HYCOM download tool is using “ferret” as interface.<br />
Please visit [https://ferret.pmel.noaa.gov/Ferret ferret web site] to see details.<br />
<br />
You can download this tool [http://ccrm.vims.edu/yinglong/wiki_files/hycom_dl.tgz here].<br />
<br />
Once you download and untar, there’re 2 directories (9x.x_exp & 19.x_exp) represent different HYCOM experiment data, check HYCOM web site for further details.<br />
<br />
Main script is listdate.sh, edit options as you needed.<br />
For example: <br />
*exp="91.1" HYCOM experiment<br />
*lon_s="120E" start longitude<br />
*lon_e="125E" end longitude<br />
*lat_s="20N" start latitude<br />
*lat_e="25N" end latitude<br />
<br />
For 19.x_exp, 1 extra var “yr” has to be defined.<br />
*yr="2012"<br />
<br />
There’re 3 optional vars you can add, if you have large domain or encounter memory problem of ferret.<br />
*lon_i : longitude interval, default is 0.08, has to be larger if needed<br />
*lat_i : latitude interval , default is 0.08, has to be larger if needed<br />
*mem : ferret memory cache, default is 300M, change larger if needed<br />
<br />
Once you finish, execute listdate.sh, it will give you listHYCOM.jnl for whole record list of experiment.<br />
Edit time range in listHYCOM.jnl as you needed. Execute dlHYCOM.sh, all your nc files will be in “output”.<br />
<br />
If any bad situation happened, such as TMAP error or disconnection, please check ncfile (including size) in output directory first, <br />
and '''DO DELETE''' the line which already successfully download in listHYCOM.jnl! Then type: dlHYCOM.sh again!<br />
<br />
The download script is designed to get all variables into 3 files (EL_*.nc, ST_*.nc, UV_*.nc) for SCHISM. Once you gather all you need, simply use nco command to cat your ncfiles.<br />
For example: ncrcat EL_*.nc EL_final.nc<br />
Then you can use "gen_hot_3Dth_from_hycom.f90" to generate your initial & open boundary conditions for SCHISM.<br />
<br />
Enjoy!</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=How_to_download_HYCOM&diff=1260How to download HYCOM2018-07-13T20:56:22Z<p>Schismguest: Created page with "This HYCOM download tool is using “ferret” as interface. Please visit ferret web site (https://ferret.pmel.noaa.gov/Ferret ) to see details. You can download this tool fr..."</p>
<hr />
<div>This HYCOM download tool is using “ferret” as interface.<br />
Please visit ferret web site (https://ferret.pmel.noaa.gov/Ferret ) to see details.<br />
<br />
You can download this tool from …<br />
Once you download and untar, there’re 2 directories (9x.x_exp & 19.x_exp) represent different HYCOM experiment data, check HYCOM web site for further details.<br />
<br />
Main script is listdate.sh, edit options as you needed.<br />
For example: <br />
exp="91.1" HYCOM experiment<br />
lon_s="120E" start longitude<br />
lon_e="125E" end longitude<br />
lat_s="20N" start latitude<br />
lat_e="25N" end latitude<br />
<br />
For 19.x_exp, 1 extra var “yr” has to be defined.<br />
yr="2012"<br />
<br />
There’re 3 optional vars you can add, if you have large domain or encounter memory problem of ferret.<br />
lon_i : longitude interval, default is 0.08, has to be larger if needed<br />
lat_i : latitude interval , default is 0.08, has to be larger if needed<br />
mem : ferret memory cache, default is 300M, change larger if needed<br />
<br />
Once you finish, execute listdate.sh, it will give you listHYCOM.jnl for whole record list of experiment.<br />
Edit time range in listHYCOM.jnl as you needed. Execute dlHYCOM.sh, all your nc files will be in “output”.<br />
<br />
If any bad situation happened, such as TMAP error or disconnection, please check ncfile (including size) in output directory first, and DO DELETE the line which already successfully download in listHYCOM.jnl! Then type: dlHYCOM.sh again!<br />
<br />
The download script is designed to get all variables into 3 files (EL_*.nc, ST_*.nc, UV_*.nc) for SCHISM. Once you gather all you need, simply use nco command to cat your ncfiles.<br />
For example: ncrcat EL_*.nc EL_final.nc<br />
Then you can use "gen_hot_3Dth_from_hycom.f90" to generate your init & OB for SCHISM.<br />
<br />
Enjoy!</div>Schismguesthttp://ccrm.vims.edu/w/index.php?title=Installation_on_Mac&diff=1258Installation on Mac2018-06-29T01:30:16Z<p>Schismguest: </p>
<hr />
<div>Below is a recipe provided by Dr. Carsten Lemmen.<br />
<br />
From a clean macOS (currently High Sierra), first you need to have a compiler (a clang comes with Xcode)<br />
<br />
<UL><br />
<LI>Install XCode from AppStore<br />
<LI>Install XCode Command Line Tools from within XCode <br />
<LI>run xcodebuild -license and type "agree"<br />
<br />
<LI>Install MacPorts, i.e. install a toolchain with open source developer tools; there are at least three prominent systems that help you do this (1) fink (2) home-brew (3) macports. Either of them is probably fine and the choice is a matter of taste. I have been using macports. <br />
<br />
<LI>By default, all your programs installed through ports will end up in the prefix /opt/local, so add to your path<br />
<br />
<UL><br />
<LI> export PATH=$PATH:/opt/local/bin<br />
</UL><br />
<br />
<LI>Install the packages needed for SCHISM, i.e. deal with netcdf/openmpi/compiler. I have chosen clang5 as my c++, gfortran7 as fortran, and openmpi as MPI for this example<br />
<br />
<UL><br />
<LI>port selfupdate<br />
<LI>port install openmpi-clang50 +gcc7<br />
<LI>port install netcdf-fortran +gcc7 +openmpi<br />
</UL><br />
<LI>Install cmake<br />
<UL><br />
<LI>port install cmake<br />
</UL><br />
</UL><br />
<br />
That should give you a build system very similar to Linux, i.e. continue with creating a build directory, running cmake with path to SCHISM/src, e.g.:<br />
<br />
<p></p><br />
cd <nowiki>$BUILD_DIR</nowiki>; cmake <nowiki>$SCHISM_DIR/trunk/src</nowiki> -DNetCDF_FORTRAN_DIR=/opt/local -DCMAKE_Fortran_COMPILER=mpifort -DCMAKE_CXX_COMPILER=mpicc -DNetCDF_C_DIR=/opt/local -DTVD_LIM=SB; make pschism</div>Schismguest