Updated post about installation of libraries.

Author: sr-dash

_posts/2025-07-03-softwares.md

@@ -5,96 +5,53 @@ date: 2025-07-03 15:09:00
 description: instructions for setting up software packages and configuring systems for global simulations 
 tags: configuration newsystem code
 categories: research
-featured: true
+featured: false
 ---
 
-This theme implements a built-in Jekyll feature, the use of Rouge, for syntax highlighting.
-It supports more than 100 languages.
-This example is in C++.
-All you have to do is wrap your code in markdown code tags:
+Often when migrating to new systems, it can get difficult to setup all the necessary libraries and packages in the target system for 
+continuing working on the mddelling. In this post I will try to summarize the libraries required for setting up some of the simulations codes e.g., 
+SWMF, MPI-AMRVAC, SFT-1D. Some of these codes require `hdf5`, `netcdf-c/fortran`, `zlib`, `curl`, `OPENMPI` and `GCC`. 
 
-````markdown
-```c++
-code code code
-```
-````
-
-```c++
-int main(int argc, char const \*argv[])
-{
-    string myString;
-
-    cout << "input a string: ";
-    getline(cin, myString);
-    int length = myString.length();
+**GCC**
+It is quite simple to build up on the existing system libraries (on Linux/Mac systems). The bash script file [`build_gcc_13.2.0.sh`](https://github.com/darrenjs/howto/blob/master/build_scripts/build_gcc_13.2.0.sh) is the best resource for this. 
+Download the file and run it in a `bash` shell. **Add `fortran` language to the list of langiages inside the shell script.** At the end of the building, it will show the instructions to append the installed libraries to the system `$PATH`. The script downloads and installs the libraries on the system. A note of caution, the whole process may take about ~3 hrs., so be patient.
 
-    char charArray = new char * [length];
+After this, you can build the `OPENMPI` libraries. The installation version `openmpi-4.1.5` seem to work for me with the `GCC` installation versions. I prefer building the libraries with a local prefix.
 
-    charArray = myString;
-    for(int i = 0; i < length; ++i){
-        cout << charArray[i] << " ";
-    }
+Inside the openmpi-4.1.5 directory run the following,
 
-    return 0;
-}
+```
+./configure --prefix=~/opt/openmpi-4.1.5
+make -j 4
+make install
 ```
 
-For displaying code in a list item, you have to be aware of the indentation, as stated in [this FAQ](https://github.com/planetjekyll/quickrefs/blob/master/FAQ.md#q-how-can-i-get-backtick-fenced-code-blocks-eg--working-inside-lists-with-kramdown). You must indent your code by **(3 \* bullet_indent_level)** spaces. This is because kramdown (the markdown engine used by Jekyll) indentation for the code block in lists is determined by the column number of the first non-space character after the list item marker. For example: [download the bash script.](assets/pdf/build_gcc_13.2.0.sh)
-
-````markdown
-1. We can put fenced code blocks inside nested bullets, too.
-
-   1. Like this:
-
-      ```c
-      printf("Hello, World!");
-      ```
-
-   2. The key is to indent your fenced block in the same line as the first character of the line.
-````
-
-Which displays:
-
-1. We can put fenced code blocks inside nested bullets, too.
-
-   1. Like this:
-
-      ```c
-      printf("Hello, World!");
-      ```
-
-   2. The key is to indent your fenced block in the same line as the first character of the line.
-
-By default, it does not display line numbers. If you want to display line numbers for every code block, you can set `kramdown.syntax_highlighter_opts.block.line_numbers` to true in your `_config.yml` file.
-
-If you want to display line numbers for a specific code block, all you have to do is wrap your code in a liquid tag:
-
-{% raw %}
-{% highlight c++ linenos %} <br/> code code code <br/> {% endhighlight %}
-{% endraw %}
+Here are a few lines that you can add to the `~/.bashrc` or `~/.zshrc` file after the `OPENMPI` installation.
 
-The keyword `linenos` triggers display of line numbers.
-Produces something like this:
+```
+export PATH=~/openmpi-4.1.5/bin:~/opt/gcc-13.2.0/bin:$PATH
+export LD_LIBRARY_PATH=~/openmpi-4.1.5/lib:~/opt/gcc-13.2.0/lib:~/opt/gcc-13.2.0/lib64:$LD_LIBRARY_PATH
+export MANPATH=~/opt/gcc-13.2.0/share/man:$MANPATH
+export INFOPATH=~/opt/gcc-13.2.0/share/info:$INFOPATH
+```
 
-{% highlight c++ linenos %}
+After the installation you can check the version of the `gcc` by typing `gcc -v`. Similarly for `fortran` as well. At the end of this the system should have all the `mpicc, mpif90, gcc, gfortran` executables in the default `$PATH` variable.
 
-int main(int argc, char const \*argv[])
-{
-string myString;
+**netCDF**
+Installation of netcdf libraries is dependent on multiple other libraries e.g., `curl`, `zlib`, `hdf5`, `netcdf-c` and `netcdf-fortran`. Here is a shell script [install_netcdf.sh](https://github.com/sr-dash/SFT-1D/blob/main/install_netcdf.sh) for this. A few extra install flags and versions are suggested for a system-wide installation.
 
-    cout << "input a string: ";
-    getline(cin, myString);
-    int length = myString.length();
+Suggested versions 
+* `hdf5-1.14.6`, build with `--enable-fortran`, `--enable-cxx`/`--enable-parallel`.
+* `netcdf-c-4.9.3`
+* `netcdf-fortran-4.6.1`
+* `zlib-1.3.1`
+* `curl-8.14.1`
 
-    char charArray = new char * [length];
+Again the shell script downloads the required files and builds the libraries at a user location.
 
-    charArray = myString;
-    for(int i = 0; i < length; ++i){
-        cout << charArray[i] << " ";
-    }
 
-    return 0;
+**None of the scripts require admin privileges, so building these libraries should be self-sufficient.** 
 
-}
+After building these libraries, you must update the system `$PATH$` variable for future use. Individual simulation codes require independent path to the libraries.
 
-{% endhighlight %}
+Hope this helps!