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First pass adding basic prerequisites #296

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merged 12 commits into from
Jun 13, 2023
117 changes: 88 additions & 29 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -17,52 +17,111 @@ For further details about the method, please refer to the [PDF documentation](ht

## Getting started

To use TDMS, it needs to be built against [FFTW](https://www.fftw.org/) and [MATLAB](https://www.mathworks.com/products/matlab.html), which must be downloaded and installed first.
To install, follow these steps:

```bash
$ git clone [email protected]:UCL/TDMS.git
$ cd TDMS
$ git checkout v1.0.0 # the stable version
$ mkdir build; cd build
$ cmake ../tdms \
# -DMatlab_ROOT_DIR=/usr/local/MATLAB/R2019b/ \
# -DFFTW_ROOT=/usr/local/fftw3/ \
# -DCMAKE_INSTALL_PREFIX=$HOME/.local/
$ make install
```

If CMake cannot find MATLAB, FFTW, or install to the default installation prefix, uncomment the relevant line(s) and modify the path(s) accordingly.
We don't ship binaries at the moment, so to use TDMS, it has to be compiled.
It needs to be built against [FFTW](https://www.fftw.org/) and [MATLAB](https://www.mathworks.com/products/matlab.html), which must be downloaded and installed first.

<details>
<summary>Mac-specific instructions</summary>
<summary><img src="https://github.com/EgoistDeveloper/operating-system-logos/blob/master/src/24x24/UBT.png"/> Linux prerequisite setup</summary>

To compile TDMS on a Mac, you will need an x86 compiler with libraries for OpenMP.
You can install these using [Homebrew](https://brew.sh) with the command:
Assuming you don't already have them, you'll need a C++ compiler, CMake, OpenMP and FFTW.

For Debian-based distributions this should be as simple as
```{sh}
$ brew install llvm
$ sudo apt install git gcc cmake libfftw3-dev libgomp1
```

After installing with Homebrew, you may need to set the following CMake arguments:
</details>

<details>
<summary><img src="https://github.com/EgoistDeveloper/operating-system-logos/blob/master/src/24x24/MAC.png"/> MacOS prerequisite setup</summary>

On MacOS you will need an x86 compiler with libraries for OpenMP.
You'll need to download the latest [Xcode tools](https://apps.apple.com/app/xcode).

Everything else can be installed using [Homebrew](https://brew.sh):

```{sh}
-DCMAKE_CXX_COMPILER=/Users/username/.local/homebrew/opt/llvm/bin/clang++
-DOMP_ROOT=/Users/username/.local/homebrew/opt/llvm/
-DCXX_ROOT=/Users/username/.local/homebrew/opt/llvm
-DHDF5_ROOT=/Users/username/.local/homebrew/opt/hdf5
$ brew install cmake fftw llvm
```

On an ARM Mac, you will need to install the x86 version of Homebrew.
To do so, use the following commands:
On an ARM Mac, you will need to install the x86 version of Homebrew:

```{sh}
$ arch -x86_64 zsh
$ arch -x86_64 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
$ arch -x86_64 /usr/local/bin/brew install llvm hdf5
$ arch -x86_64 /usr/local/bin/brew install cmake fftw llvm
```

</details>

<details>
<summary><img src="https://github.com/EgoistDeveloper/operating-system-logos/blob/master/src/24x24/WIN.png"/> Windows prerequisite setup</summary>
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Tagging @edggjames FYI... 👇


TDMS was developed on, and has been extensively tested on linux.
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TDMS was developed on, and has been extensively tested on linux.
TDMS was developed - and extensively tested - on linux.

Support for Windows is quite new and experimental (please [report](https://github.com/UCL/TDMS/issues/new/choose) any issues you encounter!).

It might be more straightforward to use the [Windows subsystem for Linux (WSL2)](https://learn.microsoft.com/en-gb/windows/wsl/install), or set up an linux virtual machine.

However, TDMS _can_ be compiled natively on Windows.
This has been tested Windows 10 with PowerShell.

Assuming you don't already have them, you'll need to download and install:

* [MATLAB](https://www.mathworks.com/products/matlab.html),
* [Visual Studio](https://visualstudio.microsoft.com/vs/community/) and **be sure to select the C++ kit**,
* [CMake](https://cmake.org/download/),
* and [FFTW](https://www.fftw.org/install/windows.html).

Potentially the simplest way to get FFTW is via [conda](https://anaconda.org/conda-forge/fftw):

```{pwsh}
PS> conda install -c conda-forge fftw --yes
```

You'll need to ensure the paths to FFTW and MATLAB (the locations of `fftw3.dll` and `libmex.dll` respectively) are in the `env:Path`.

These can be found, e.g. by
```{pwsh}
PS> conda list fftw # assuming you installed via conda
PS> which.exe MATLAB
```
Which should return something like `C:\Program Files (x86)\MATLAB\R20XXx\bin\matlab` and maybe `C:\ProgramData\envs\base\bin`.
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Which should return something like `C:\Program Files (x86)\MATLAB\R20XXx\bin\matlab` and maybe `C:\ProgramData\envs\base\bin`.
Which should return something like `C:\Program Files (x86)\MATLAB\R20XXx\bin\` for MATLAB, and `C:\ProgramData\anaconda\envs\base\Library\lib` or `C:\Users\<your username>\anaconda\Library\lib\cmake\fftw3`.

If you downloaded FFTW and created `fftw3.dll` with `lib.exe`, you just need to know where you saved it.

You can append the paths:

```{pwsh}
PS> $env:Path += ";C:\Program Files (x86)\MATLAB\R20XXx\bin\;C:\ < wherever fftw3.dll is >"
```

Which will help Windows locate `.dll` files later.
For all following instructions, you'll have to substitute our mentions of `tdms` with `tdms.exe` and `$` is used to denote a command prompt which, in PowerShell would look like `PS>`

</details>

------

You'll need to download and install [MATLAB](https://www.mathworks.com/products/matlab.html), and take note where the headers are installed.
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</details>

## Installation

To compile and install, follow these steps:

```{sh}
$ git clone [email protected]:UCL/TDMS.git
$ cd TDMS
$ git checkout v1.0.0 # the stable version
$ mkdir build; cd build
$ cmake ../tdms \
# -DMatlab_ROOT_DIR=/usr/local/MATLAB/R20XXx/ \
# -DFFTW_ROOT=/usr/local/fftw3/ \
# -DCMAKE_INSTALL_PREFIX=$HOME/.local/
$ cmake --build . --target install --config Release
```

If CMake cannot find MATLAB, FFTW, or install to the default installation prefix, uncomment the relevant line(s) and modify the path(s) accordingly.

You can check that `tdms` was installed correctly and is in your `PATH` by running:
```{sh}
$ tdms --help
Expand Down Expand Up @@ -102,7 +161,7 @@ In a terminal run
$ which tdms
```

Copy the full path (something like `/usr/local/bin/tdms`) into [`run_pstd_bscan.m`](https://github.com/UCL/TDMS/blob/main/examples/arc_01/run_pstd_bscan.m), replacing the `'tdms'` text in the calls to the `system()` function.
Copy the full path (something like `/usr/local/bin/tdms`) into [`run_pstd_bscan.m`](https://github.com/UCL/TDMS/blob/main/examples/arc_01/run_pstd_bscan.m), replacing the ` 'tdms' ` text in the calls to the ``system()`` function.
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</details>

Expand Down