Problems when installing ISSM

wudipao88

justinquinn Okay, here's the link I shared for IssmConfig_matlab.mexw64:
[https://drive.google.com/file/d/1RK58WxjsQxYrCKkyOFFoUxIuFLDyUoxk/view?usp=drive_link]

justinquinn

wudipao88 Cool, I sent you a request for access.

wudipao88

justinquinn Ok, I got it, and I agreed.

justinquinn

wudipao88 Okay, I verified that your binary works as expected. Try adding the following to your ~/.bashrc (remove your current definition of ISSM_DIR and define yours below; also, set the MATLAB version as needed),

function change_issm_dir {
	if [[ $# -eq 1 ]]; then
		export ISSM_DIR="${1}"
	else
		export ISSM_DIR="${PWD}" # Default
	fi

	export ISSM_DIR_WIN=$(cygpath -ms "${ISSM_DIR}") # Needed by MATLAB

	if [[ "${OS}" == "mingw" ]]; then
		MATLAB_ENV_CMDS="addpath ${ISSM_DIR_WIN}/bin ${ISSM_DIR_WIN}/lib"
		MATLAB_DEV_ENV_CMDS="addpath ${ISSM_DIR_WIN}/src/m/dev; devpath"
	else
		MATLAB_DEV_ENV_CMDS="addpath ${ISSM_DIR}/src/m/dev; devpath"
	fi

	alias issm-env="source "${ISSM_DIR}"/etc/environment.sh"
	alias issm-matlab-dev-env="issm-env; matlab-cli -r '${MATLAB_DEV_ENV_CMDS}'" # Then run runme(<options>)
	alias issm-matlab-gui-dev-env="issm-env; matlab-gui -r '${MATLAB_DEV_ENV_CMDS}'" # Then run runme(<options>)
}


######################
### Path Variables ###
######################

## MATLAB
#
MATLAB_VER="R2024b" # Allows for easy resetting of MATLAB version added to PATH
export MATLAB_PATH=$(cygpath -u $(cygpath -ms "/c/Program Files/MATLAB/${MATLAB_VER}"))
export PATH="${MATLAB_PATH}/bin:${PATH}"

## ISSM
#
export ISSM_DIR="<CHANGE_TO_YOUR_ISSM_REPO>"

# Change ISSM directory and related variables
change_issm_dir	${ISSM_DIR}

From the command line, you can then run issm-matlab-gui-dev-env to start up MATLAB. If everything works, you should see a message that says, "ISSM development path correctly loaded".

NOTE: You could also simplify things by removing the change_issm_dir function and just hardcoding everything in aliases, but I shared with you what I personally use on machines where I have multiple copies of the ISSM repository.

wudipao88

justinquinn Ok, I added the following code to .bashrc and then run issm-matlab-gui-dev-env, but the reply is as follows:

-bash: matlab-gui: command not found

justinquinn

wudipao88 Oh, my bad! Add the following, start a new terminal, and run the command again,

###############
### Aliases ###
###############

## MATLAB
#
alias matlab-cli='matlab -nosplash -nodesktop'
alias matlab-gui='matlab -nosplash'

wudipao88

justinquinn Ok, I did that, but I got no feedback after running this command.

wudipao88

justinquinn Oh, after running this command MATLAB starts, but in the MATLAB command terminal it shows:

Warning: Name does not exist or is not a directory: C:\c\ISSM\src\m\dev
> Location: path (Line 109)
Location: addpath (line 86)
Function or variable 'devpath' is not recognized.

justinquinn

wudipao88 Right, sorry. I didn't notice before that you had not enabled development on ISSM and if I recall, that was your goal all along. What you have to do is modify your ISSM configuration to include,

--enable-development

You can also add the following for extended debugging of C++ code,

--enable-debugging

Then you will have to reconfigure and recompile ISSM. Then, the alias I provided you should work as expected. Sorry again for how long this journey has been, but I swear you're nearly there! 😄

wudipao88

justinquinn Ok, although MATLAB has the above error prompt (i.e. devpath is not recognized), the version information was successfully displayed after running issmversion in MATLAB. Does this mean that ISSM can be used normally and devpath errors can be ignored?

Yes, the purpose of installing ISSM from source code is to change specific settings in the model, such as the basal melt terms of the SHAKTI hydrology model. So is it feasible now?

justinquinn

wudipao88 I'm surprised issmversion works if devpath is listed as not being found. It looks like it may have something to do with the definition of ISSM_DIR? Note that it says,

C:\c\ISSM\src\m\dev

when it should really be,

C:\ISSM\src\m\dev

That said, I would go ahead and try it. Are you able to run any of the tutorials from the website? https://issm.jpl.nasa.gov/documentation/tutorials/

wudipao88

justinquinn Yes, I can run the tutorial successfully. But why does the path of dev go wrong? There is another question, is it necessary to start MATLAB from the terminal every time?

justinquinn

wudipao88 Well that's good news at least. I would suspect that down the line there might be other issues though. Can you show me how ISSM_DIR and ISSM_DIR_WIN are defined in your .bashrc? Also, what do you get from echo $ISSM_DIR and echo $ISSM_DIR_WIN in a terminal?

wudipao88

justinquinn Ok, my definition of ISSM path is as follows:

function change_issm_dir {
	if [[ $# -eq 1 ]]; then
		export ISSM_DIR="${1}"
	else
		export ISSM_DIR="${PWD}" # Default
	fi

	export ISSM_DIR_WIN=$(cygpath -ms "${ISSM_DIR}") # Needed by MATLAB

	if [[ "${OS}" == "mingw" ]]; then
		MATLAB_ENV_CMDS="addpath ${ISSM_DIR_WIN}/bin ${ISSM_DIR_WIN}/lib"
		MATLAB_DEV_ENV_CMDS="addpath ${ISSM_DIR_WIN}/src/m/dev; devpath"
	else
		MATLAB_DEV_ENV_CMDS="addpath ${ISSM_DIR}/src/m/dev; devpath"
	fi

	alias issm-env="source "${ISSM_DIR}"/etc/environment.sh"
	alias issm-matlab-dev-env="issm-env; matlab-cli -r '${MATLAB_DEV_ENV_CMDS}'" # Then run runme(<options>)
	alias issm-matlab-gui-dev-env="issm-env; matlab-gui -r '${MATLAB_DEV_ENV_CMDS}'" # Then run runme(<options>)
}


######################
### Path Variables           ###
######################

## MATLAB
#
MATLAB_VER="R2022a" # Allows for easy resetting of MATLAB version added to PATH
export MATLAB_PATH=$(cygpath -u $(cygpath -ms "/g/matlab/${MATLAB_VER}"))
export PATH="${MATLAB_PATH}/bin:${PATH}"

## ISSM
#
export ISSM_DIR="/c/ISSM"

# Change ISSM directory and related variables
change_issm_dir	${ISSM_DIR}



###############
### Aliases       ###
###############

## MATLAB
#
alias matlab-cli='matlab -nosplash -nodesktop'
alias matlab-gui='matlab -nosplash'

What I got after running echo $ISSM_DIR is:

/c/ISSM

What I got after running echo $ISSM_DIR_WIN is:

C:/ISSM

justinquinn

wudipao88 Okay, that all looks right. To be honest, I don't know why it's complaining. Let me know if you get any missing function errors while running through some of the other examples.

wudipao88

justinquinn Ok, I will inform you as soon as possible if I encounter any errors when using ISSM in the future. Now, can I change the model settings to what I want by modifying the ISSM source code? Do I need to recompile after the changes? Thanks.

justinquinn

wudipao88 If you change any of the C++ or Fortran source code, yes, you need to recompile, simply with make; make install. If you change any of the MATLAB scripts, however, those changes should be picked up if you rerun your runme in the MATLAB console.

wudipao88

justinquinn Hi justinquinn
I recently encountered a problem when using the compiled ISSM. The specific situation is that the model usually crashes after using it for a period of time (such as performing several solutions). The feedback is as follows:

Mingw-w64 runtime failure:
32 bit pseudo relocation at 00007FFB8A8123EC out of range, targeting 00007FFAE4136530, yielding the value FFFFFFFF59924140.
Mingw-w64 runtime failure:
32 bit pseudo relocation at 00007FFB8A8123EC out of range, targeting 00007FFAE4136530, yielding the value FFFFFFFF59924140.
Mingw-w64 runtime failure:
32 bit pseudo relocation at 00007FFB8A8123EC out of range, targeting 00007FFAE4136530, yielding the value FFFFFFFF59924140.

Warning
============================================================
   Binary file T_cal_test.outbin not found!

   This typically happens when the run crashed.
   Please check for error messages above or in the outlog
============================================================

Location: loadresultsfromdisk (line 16)
Location: loadresultsfromcluster (line 50)
Location: solve (line 180)

Looking forward to your help, thank you!

justinquinn

wudipao88 Hi, this is really tough to debug. Can you send me your runme and any data files via Google Drive or another file sharing service? If the files should be private I will shoot you an email from my account and you can share it just with me. Also, let me know any other conditions you're running under (i.e. np option to mpiexec, system specs).

I can't promise anything: I'll run your example, but I may not be able to even reproduce the error. Really, ISSM for Windows is experimental and we haven't had the funding/time to fully support it.

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