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Installing on Mac Studio

Instructions for installing the SCHISM plugins for VisIt 3.1.4 on a Mac Studio that has an M1 chip.

We are using VisIt 3.1.4 to use client-server mode from Expanse. The local VisIt(client) must use the same VisIt as the HPC(server). Older versions of VisIt(pre-M1) are only available as x86, so an extra CMAKE flag is needed to compile for x86 instead of the default arm(M1) processor.

Install VisIt 3.1.4

First, install VisIt 3.1.4 in the usual Mac way: download, click, drag to applications. Test it by clicking on the application icon to open VisIt, then close VisIt.

To follow the instructions below, VisIt must be in the path. If you open a terminal and type visit, it will probably say command not found: visit. The VisIt executable is usually here: /Applications/VisIt.app/Contents/Resources/bin. Confirm the following opens VisIt.

/Applications/VisIt.app/Contents/Resources/bin/visit

To avoid typing the whole filepath, add VisIt to your PATH by doing:

export PATH="/Applications/VisIt.app/Contents/Resources/bin:$PATH"
visit

That PATH will only be valid while that terminal is open. To add an additional executable path to your environment, add it to the 'dot' file for your shell, which (unless you changed your default shell), is the file ~/.zshrc. Open ~/.zshrc and add the following,

export PATH="/Applications/VisIt.app/Contents/Resources/bin:$PATH"

Exit the terminal and open a new one. Now, visit should be in your path. The command xml2plugin used below is a VisIt command. To confirm that both are in your path, do:

which visit
which xml2plugin

If that was successful, you're ready to move on.

Get CMake

Download CMake for Mac, drag it into the applications bin. Open CMake, in the top menu bar, click Tools, choose How to Install For Command Line Use. I chose this way:

sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install

Install the plugins

Install the unstructure_data plugin:

cd unstructure_data

Save a copy of the main VisIt plugin class files to your home directory. These files will be overwritten in the next step by VisIt's code skeleton generating tool.

cp avtSCHISMFileFormat.C ~
cp avtSCHISMFileFormat.h ~

The command xml2plugin is a VisIt command.

xml2plugin -clobber SCHISMOutput.xml

SCHISMOutput.xml is the file used by VisIt code generating tool to create code skeleton and makelist file.

Use two backup plugin class file to overwrite the files avtSCHISMFileFormat.C and avtSCHISMFileFormat.h.

cp ~/avtSCHISMFileFormat.C .
cp ~/avtSCHISMFileFormat.h .

Make a build directory:

mkdir build
cd build

Use cmake to create the make system. My mac is arm but the executable for VisIt 3.1.4 is x86_64, so the next command tells it to target x86.

cmake -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_OSX_ARCHITECTURES=x86_64 ..

Run make to build plugins binary.

make

Check

ls ~/.visit/3.1.4/darwin-x86_64/plugins/databases

There should be four new files in ~/.visit/3.1.4/darwin-x86_64/plugins/databases:

libESCHISMDatabase_par.so
libESCHISMDatabase_ser.so
libISCHISMDatabase_par.so
libMSCHISMDatabase_par.so

Repeat the steps for the other plugins:

cd ~/schism_visit_plugin/prop
cp avtpropFileFormat.C ~
cp avtpropFileFormat.h ~
xml2plugin -clobber prop.xml
cp ~/avtpropFileFormat.C .
cp ~/avtpropFileFormat.h .
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_OSX_ARCHITECTURES=x86_64 ..
make
ls ~/.visit/3.1.4/darwin-x86_64/plugins/databases

Works.

And

cd ~/schism_visit_plugin/gr3
cp avtgr3FileFormat.C ~
cp avtgr3FileFormat.h ~
xml2plugin -clobber gr3.xml
cp ~/avtgr3FileFormat.C .
cp ~/avtgr3FileFormat.h .
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_OSX_ARCHITECTURES=x86_64 ..
make
ls ~/.visit/3.1.4/darwin-x86_64/plugins/databases

Works.

And

cd ~/schism_visit_plugin/mdschism
cp avtMDSCHISMFileFormat.C ~
cp avtMDSCHISMFileFormat.h ~
xml2plugin -clobber mdschism.xml
cp ~/avtMDSCHISMFileFormat.C .
cp ~/avtMDSCHISMFileFormat.h .
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_OSX_ARCHITECTURES=x86_64 ..
make

Error.

So, this is where we hack the makefiles, as per Eric's email,

vi CMakeFiles/EMDSCHISMDatabase_par.dir/flags.make
vi CMakeFiles/MMDSCHISMDatabase.dir/flags.make
vi CMakeFiles/EMDSCHISMDatabase_ser.dir/flags.make
vi CMakeFiles/IMDSCHISMDatabase.dir/flags.make

remove all the

libnetcdf_c++.dylib libnetcdf.dylib libhdf5_hl.dylib libhdf5.dylib libsz.dylib libz.dylib

Then make

make

Check

ls ~/.visit/3.1.4/darwin-x86_64/plugins/databases

And here you go:

(base) lllowe@LisasMacStudio build % ls ~/.visit/3.1.4/darwin-x86_64/plugins/databases
libEMDSCHISMDatabase_par.dylib libEgr3Database_par.dylib      libIMDSCHISMDatabase.dylib     libMMDSCHISMDatabase.dylib
libEMDSCHISMDatabase_ser.dylib libEgr3Database_ser.dylib      libISCHISMDatabase.dylib       libMSCHISMDatabase.dylib
libESCHISMDatabase_par.dylib   libEpropDatabase_par.dylib     libIgr3Database.dylib          libMgr3Database.dylib
libESCHISMDatabase_ser.dylib   libEpropDatabase_ser.dylib     libIpropDatabase.dylib         libMpropDatabase.dylib

Now try it out. Links to data are on the SCHISM visualization page

wget -r -nH --cut-dirs=2 -np -R "index.html*" http://ccrm.vims.edu/yinglong/SVN_large_files/Scribe_IO_outputs/
wget -r -nH --cut-dirs=2 -np -R "index.html*" http://ccrm.vims.edu/yinglong/SVN_large_files/SCHISM_v5.6.1_sample_outputs/