Create an executable

In the tutorial below you will have to replace everything that is in cursive red with your own personal names. The rest is just copy-paste.

Execute the following in the same terminal/window!

1) Create directory

First you should come up with a name for your executable. To make the rest of this tutorial easier set the variable 'My_Abs' to the name of your choice:

             My_Abs=name_of_my_executable

Then create yourself a directory under your home(!) (so it gets backup up) in which you want to create the executable.

For example:

           mkdir -p ~/gem/v_5.1.1/Abs/${My_Abs}

2) Populate directory

Go into the executable directory you just created above. For example:

            cd ~/gem/v_5.1.1/Abs/${My_Abs}

a) Clone the Git repository you want

Before cloning anything make sure the owner of the code you want to clone has commited all modifications! Otherwise you will not get them. Then you can clone the source code with:

             git clone full_Abs_directory_of_sourcecode_to_clone/gem

Or you can clone my latest verison with:

             git clone ~winger/gem/v_5.1.1/Abs/UQAM_latest/gem

If you get something like the following your cloning was successful:

b) Uncommited changes

Only if there were uncommited changes to the code you would like to get as well you will have to copy the modified files by hand. This is not elegant at all, but if you want to make sure you got all modifications you can also remove your source code and then copy the source code you want by hand. For example:

             cd ~/gem/v_5.1.1/Abs/${My_Abs}/gem/src
             rm -rf gemdyn modelutils rpnphy
             cd full_Abs_directory_of_sourcecode_to_clone/gem/src
             rsync -ruvt gemdyn modelutils rpnphy ~/gem/v_5.1.1/Abs/${My_Abs}/gem/src

c) Create working directories

Change into 'gem' directory that came with the clone:

             cd ~/gem/v_5.1.1/Abs/${My_Abs}/gem

So the object files, libraries and executables will not be under your home, create links for the directories 'build' and 'work'. Pick a place under which you want to keep the object files, libraries and executables. Preferably under the default(!) space of you professors, for example:

            work_space=/project/def-professor/${USER}/GEM_WORK_DIR     # Set 'professor' to the CC name of your professor. You can find all of them under ~/projects.

Create the directories and the links (using ${My_Abs} from above) :

            mkdir -p ${work_space}/${My_Abs}/build
            mkdir -p ${work_space}/${My_Abs}/work
            ln -s ${work_space}/${My_Abs}/build
            ln -s ${work_space}/${My_Abs}/work

d) Check directory content

Execute a simple 'ls' command to check if your directory content looks okay:

            ls -al

If the list you are getting looks like the following your initial setup looks fine:

drwxr-xr-x.  ...  25600 Jul 17 14:20 .
drwxr-xr-x.  ...  25600 Jul 17 14:09 ..
drwxr-xr-x.  ...  25600 Jul 17 14:09 .git
-rw-r--r--.  ...    145 Jul 17 14:09 .gitignore
-rw-r--r--.  ... 109127 Jul 17 14:09 Doxyfile
-rw-r--r--.  ..   8903 Jul 17 14:09 README.md
-rw-r--r--.  ...      6 Jul 17 14:09 VERSION
lrwxrwxrwx.  ...     68 Jul 17 14:20 build -> /project/def-jtheriau/pnf000/GEM_WORK_DIR/UQAM_P3_Margaux_2024/build
drwxr-xr-x.  ...  25600 Jul 17 14:09 configurations
drwxr-xr-x.  ...  25600 Jul 17 14:09 doc
-rwxr-xr-x.  ...   1421 Jul 17 14:09 download-dbase.sh
-rw-r--r--.  ...    558 Jul 17 14:09 goas-devel.code-workspace
drwxr-xr-x.  ...  25600 Jul 17 14:09 project
drwxr-xr-x.  ...  25600 Jul 17 14:09 scripts
drwxr-xr-x. ...  25600 Jul 17 14:14 src
-rwxr-xr-x.  ...     89 Jul 17 14:09 vstudio
lrwxrwxrwx.  ...     67 Jul 17 14:20 work -> /project/def-jtheriau/pnf000/GEM_WORK_DIR/UQAM_P3_Margaux_2024/work

3) Create the executable

a) Acquire compiler

Only needed once per window/terminal!
You can used the same alias used to acquire the compiler to run GEM:

            511

b) If you are not already in it, go into the 'gem' directory of your abs-directory:

            cd ~/gem/v_5.1.1/Abs/${My_Abs}/gem

c) Set the variable 'abs_dir' to the name of your executable directory, including the 'gem' directory (needed under e))

            abs_dir=$(pwd)

d) Change into 'build' directory:

            cd build

e) Create make files and dependencies

(Only needed once and whenever you add any new routines or add include files or module "use" lines to an existing routine.)

            cmake   -DCOMPILER=intel   -DCMAKE_VERBOSE_MAKEFILE=ON    -DWORK_PREFIX=${abs_dir}/work    ${abs_dir}/project

f) Compile and create executable

            make -j4 maingemdm

If the executable got created, you will find it under:

            ls -lh src/maingem/maingemdm

It should have close to 50 MB.

4) Modify source code (optional)

a) You can find the main GEM routines under .../gem/src/*/*, for example :

Most dynamic routines are under:

            .../gem/src/gemdyn/base

Most physics routines are under:

            .../gem/src/rpnphy/base

Most surface routines are under:

            .../gem/src/rpnphy/surface

Find and edit the routines you want to modify.

b) Recreate the executable

Once you modified the routine(s) you want you need to recreate the executable.

To do this you need to go back in the 'build' directory!

Only if you add any new routines or add include files or module "use" lines to an existing routine you first need to recreate the dependencies and make files by re-executing the full cmake command under point 3d) again - see above.

Otherwise, it is enough to just re-execute:

            make -j4 maingemdm

If you just want to compile one routine without creating the executable (to save time) you can just compile a routine, for example utils/sfclayer_mod.F90 with:

            cd .../build/src/rpnphy
            make utils/sfclayer_mod.F90.o

5) Use your executable

To use your own executable set 'GEM_ovbin' in your 'configexp.cfg' to the path of your executable directory, up until but excluding the 'gem' directory. For example:

            GEM_ovbin=~/gem/v_5.1.1/Abs/${My_Abs}

Modify compiler flags (optional)

Compile one routine without optimization, '-O0'

• edit the file named CMakeLists.txt in the main directory where the subroutine is situated (for example, src/rpnphy/CMakeLists.txt if the subroutine is situated in the physics directory)
• copy the following example before the last line (add_library...) and modify it according to your needs:

set_source_files_properties(utils/sfclayer_mod.F90 PROPERTIES COMPILE_OPTIONS "-O0")

• make sure you use a recent version of cmake (at least 3.11) - on Narval we do
  
• you can verify the option was passed by looking at the file flags.make situated in the corresponding directory in the build directory, for example build/src/rpnphy/CMakeFiles/phy.dir/flags.make:

# Custom options: src/rpnphy/CMakeFiles/phy.dir/utils/sfclayer_mod.F90.o_OPTIONS = -O0

Then go back into your 'build' directory and compile with the usual:

    make maingemdm
or
    make -j4 maingemdm

When compiling this routine now you should see something like the following:
Building Fortran object src/rpnphy/CMakeFiles/phy.dir/utils/sfclayer_mod.F90.o
...  -O2 -g   -O0 -c ...

The second '-O0' should overwrite the first '-O2'.

Set 'fp-model' to 'precise' or 'strict'

In project/Linux-x86_64-intel.cmake change in line 24 '-fp-model source' to '-fp-model precise' (Vivian) resp. '-fp-model strict' (Ron).