A repository for setting up an installation of MaRGE on MacOS. https://github.com/josalggui/MaRGE Based on https://github.com/josalggui/MaRGE/tree/8496e873905cb16adf16a8cc1700d6a9f4ea666b
See there for more instructions.
See also https://github.com/marcos-mri/
This was setup during the ezyMRI NerdFest Portable MRI Hackathon 2024 in Singapore https://ezymri-nerdfest.sciencesconf.org/.
We will use conda for the management of python interpreter and packages
MaRGE also makes use of the timeout command which is not by default available on mac.
We will install it via the homebrew package manager.
You should be somewhat familiar with the MacOS terminal application. We will use it to run commands from the command line.
You must already have a red pitaya with a marcos-compatible image installed. These instructions do not cover this process. Check the marcos wiki here for more information: https://github.com/vnegnev/marcos_extras/wiki. During the hackathon, there were however challenges communicating with these images, at times.
With the current version of the code in this repository, the red pitaya must have IP address 192.168.1.101. What we do need to know from the red pitaya, is its IP address, the exact model and, if present, the gradient DAC board used.
install conda: see https://anaconda.org. Choose either the full anaconda or miniconda.
test that it works: you can type conda in your terminal and there is no error.
to install 'timeout' we will install the homebrew package manager:
https://brew.sh and follow the instructions. especially the last step where it asks you to copy a command to the terminal
Then, restart your terminal.
If everything worked, you can now type brew and it will not give you an error about an undefined command.
Install the timeout command with
brew install coreutils
test that it worked by typing timeout. This should print the instructions how to use timeout.
Make sure git is installed.
Type git in the terminal and make sure that there are no error messages.
The installation of homebrew (previous step) should have also installed git.
If it's not installed (git command not found) you have to install git.
The web should have instructions on how to do that.
git clone --recurse-submodules https://github.com/gabuzi/marcos-marge-macos.git
This will clone all necessary code into a subdirectory marcos-marge-macos in the current directory.
Then cd marcos-marge-macos to change into this new directory.
Run all following commands from within this folder.
You have to make sure that you have an ethernet adapter connected to your mac that is plugged in to the red pitaya's ethernet port. If you are unsure which adapter you have to configure in the preferences, you can remove it and plug it back in (it might be necessary to have the device on the other end connected via a lan cable and powered up). Then just observe which adapter changes its status to identify the right one. Alternatively, you can click through the adapters and check their 'Details -> Hardware'. Only those plugged into the computer will have a MAC address listed.
This network adapter must be configured with a static ip address (the option in the MacOS preferences is called 'manual'). The ip address must be in the same subnet as the red pitaya's IP address. If in doubt use just a neighboring address (e.g. if your red pitaya has 192.168.1.101, use 192.168.1.100 but general networking concepts are out of scope for these instructions).
create an x86-64-based conda environment (bm4d, a mandatory requirement for MaRGE requires this as it is not compiled for the new ARM based M1, M2, M3, M... MAC CPUs)
CONDA_SUBDIR=osx-64 conda create -n marcos-marge python=3.9
activate it and then persist the subdir config for any future conda commands:
conda activate marcos-marge
conda config --env --set subdir osx-64
any conda environment you create will already be x86-64, so we can just use:
conda create -n marcos-marge python=3.9
to create a conda environment with name 'marcos-marge' activate this environment
conda activate marcos-marge
we install the python requirements with pip. for mac based systems, we remove one dependency which uses cuda gpus. cuda cupy is not available on macs, so we remove this and use a modified requirements.txt file. this may make some processing features of marge fail, but the basics should still work.
run pip install -r requirements_macos.txt
Confirm that we are in the correct conda environment by confirming that your terminal prompt line now says
(marcos-marge) in the beginning.
edit the file
marge/configs/hw_config.py.copy
and set all your required hw specific options.
most importantly, is probably the rp_ip_address to point to the red pitaya (depends on the image
you have used and which way it was configured.
ADDITIONALLY: set the bash_path to /bin/bash such that the line reads
bash_path = /bin/bash
save the file as hw_config.py (i.e. remove the .copy extension)
edit the file
marge/configs/hw_config.py.copy
and check what you want to change.
then save as marge/configs/hw_config.py (i.e. remove the .copy extension)
edit the file
marge/configs/units.py.copy
and check what you want to change.
then save as marge/configs/units.py (i.e. remove the .copy extension)
edit the file
marcos_client/local_config.py.example
remove the # in front of the line #ip_address = "192.168.1.189" and set the ip address to the one corresponding to your red pitaya (same as in step above)
then also remove the # in front of the right option for the fpga_clk_freq_MHz
then also remove the # in front of the right option for the grad_board
save the file as marcos_client/local_config.py (i.e. remove the .example extension)
type ssh root@<xxx.xxx.xxx.xxx> where <xxx.xxx.xxx.xxx> is the ip address of your red pitaya.
if you have never connected to the red pitaya before, this should show a confirmation dialog to confirm the key. Confirm with yes.
If you have problems with this step, make sure that
- ethernet is connected to red pitaya and it is powered on
- red pitaya has sd card inserted with correctly configured image
- you are not also in a second network (e.g. wifi) that has addresses in the same range as the red pitaya (e.g. most home wireless routers by default would do that by giving out addresses in the 192.168.1.x range. If so, disconnect wifi to check. In the long term, you should reconfigure red pitaya to use a different ip range, otherwise you won't be able to use internet on the laptop while being connected to red pitaya.
make sure that your red pitaya is connected (step before)
then make sure that you are in the folder MaRGE of this repository.
if not, use the cd command to navigate to this directory.
you can use the pwd command to see where you are currently, and the ls command to list the files and directories in the current directory.
then make sure that you are in the right conda environment (marcos-marge) in front of your terminal if you followed these instructions.
if not, use conda activate marcos-marge to activate the environment (this makes all the required python packages that we have previously installed available).
type python -m main to launch the GUI.
You should see the session window appear.
Confirm your inputs and click on the "house" icon on the top left.
Then, the full GUI should open. You should follow MARGE instructions to figure out what to do next. You can always switch back to the terminal window that you have used to launch the GUI to check for error messages.
then click through the buttons to initialize marcos (should show a blue LED on the red pitaya), then start the marcos server and then finally launch the currently selected sequence with the clipboard icon button. Amber LEDs should flash if it's working.
Refer to the MaRGE and MaRCoS instructions for more info.