MATLAB not finding directory after pointing to it

kmosley

Hello,

I'm trying to use ISSM on a local x86_64 linux machine. After sourcing to $ISSM_DIR and then starting matlab, I add the following paths to bin and lib in my ISSM directory:

addpath /home/dell/issm-files/ISSM/bin /home/dell/issm-files/ISSM/lib

I then attempt issmversion, which gives the following error:

Invalid MEX-file '/home/dell/issm-files/ISSM/lib/IssmConfig_matlab.mexa64':
/usr/local/MATLAB/R2024a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by
/home/dell/issm-files/ISSM/lib/libISSMCore.so)

Error in IssmConfig (line 14)
value = IssmConfig_matlab(string);

Error in issmversion (line 19)
disp([IssmConfig('PACKAGE_NAME') ' Version ' IssmConfig('PACKAGE_VERSION')]);

I try the following fix, from the website, starting with the library path preloaded:

LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/libsstdc++.so.6 matlab

But I get the same error. Anyone know what the issue is here? Thanks

justinquinn

kmosley See https://issm.jpl.nasa.gov/documentation/faq/matlab/, section 'MATLAB complains about GLIBCXX libraries'.

kmosley

justinquinn I did look this up and did the following to point to the library:

LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6 matlab

I now do not get the missing libstdc++.so.6 error. I do however get this:

Invalid MEX-file
'/home/dell/issm-files/ISSM/lib/IssmConfig_matlab.mexa64':
/home/dell/issm-files/ISSM/externalpackages/petsc/install/lib/libparmetis.so:
undefined symbol: MPI_Comm_f2c

Error in IssmConfig (line 14)
value = IssmConfig_matlab(string);

Error in issmversion (line 19)
disp([IssmConfig('PACKAGE_NAME') ' Version ' IssmConfig('PACKAGE_VERSION')]);

I looked around at the forum and saw someone had a similar issue with library, so I ran:

!ldd $ISSM_DIR/lib/IssmConfig_matlab.mexa64

In this output, I see libparmetis.so => /home/dell/issm-files/ISSM/externalpackages/petsc/install/lib/libparmetis.so (0x00007440024e1000), which should be the right place?

justinquinn

kmosley Nice! Glad to hear that worked.

Regarding libparmetis, yes, it's finding the correct library but that symbol is undefined. Which PETSc install script did you use on this machine? _f2c implies a Fortran to C conversion wrapper function in the MPI implementation. If you used PETSc to all compile and install mpich, this should all be handled. What does your ISSM configuration look like for this machine?

kmosley

justinquinn I used install-linux-3.21.sh.

I will attach the configure file.

configure.sh

744B

kmosley

justinquinn Looking around, I'm seeing that it may also be an mpi issue? Let me know if you want me to just delete and reinstall everything

justinquinn

kmosley That all looks good. My only recommendation here is to try to reinstall PETSc. I haven't see this error elsewhere and I am not able to reproduce it, unfortunately.

justinquinn

kmosley Try just reinstalling PETSc first, which will reinstall MPICH.

kmosley

justinquinn I tried reinstalling petsc, which didn't work. I then deleted and reinstalled. Now I am getting this error:

make[3]: *** No rule to make target '/home/dell/issm-files/ISSM/src/m/mesh/planet/gmsh/*.m', needed by 'all-am'. Stop.
make[3]: Leaving directory '/home/dell/issm-files/ISSM/src/m'
make[2]: *** [Makefile:470: all-recursive] Error 1
make[2]: Leaving directory '/home/dell/issm-files/ISSM/src'
make[1]: *** [Makefile:525: all-recursive] Error 1
make[1]: Leaving directory '/home/dell/issm-files/ISSM'
make: *** [Makefile:457: all] Error 2

This is after doing distclean, then reconfiguring and making again

justinquinn

kmosley There shouldn't be anything to make in that directory anyhow. Are you up to date with the repo? You could try also autoreconf -ivf; make; make install from $ISSM_DIR.

kmosley

justinquinn I just did the reinstall today, cloned from github.

Also, /home/dell/issm-files/ISSM is what my $ISSM_DIR points to

justinquinn

kmosley No, I mean try cd $ISSM_DIR; autoreconf -ivf; make; make install

kmosley

justinquinn I just tried that. Got the same exact error.

I am on an Ubuntu 22.04 linux if that means anything

kmosley

justinquinn Hello, as an update, I have tried downloading the precompiled binary for matlab instead. Upon starting matlab and pointing the paths, I got this error:

Invalid MEX-file '/home/dell/ISSM-Linux-MATLAB/lib/IssmConfig_matlab.mexa64': /usr/local/MATLAB/R2024a/bin/glnxa64/../../sys/os/glnxa64/libgcc_s.so.1:
version `GCC_12.0.0' not found (required by /home/dell/ISSM-Linux-MATLAB/lib/IssmConfig_matlab.mexa64)

Error in IssmConfig (line 14)
value = IssmConfig_matlab(string);

Error in issmversion (line 19)
disp([IssmConfig('PACKAGE_NAME') ' Version ' IssmConfig('PACKAGE_VERSION')]);

I then installed gcc 12:

sudo apt install gcc-12

And got the same error

justinquinn

kmosley Okay, this is good to know about the binaries. We build them on Debian 12, and I'd like to extend support to Ubuntu 22.04.

Regarding the No rule to make target '/home/dell/issm-files/ISSM/src/m/mesh/planet/gmsh/*.m', Mathieu has addressed that and responded to your other post.

kmosley

justinquinn Ok. After doing git pull, should I reconfigure, configure, then try make and make install again?

justinquinn

kmosley Yep, that should do it.

kmosley

Doing the git pull, autoreconf, configure, make, then make install worked.

For the libstdc++.so.6 and MPI errors, I had to point to both of them in LD_PRELOAD. This is what worked for me:

LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6:"${ISSM_DIR}/externalpackages/petsc/install/lib/libmpi.so:${ISSM_DIR}/externalpackages/petsc/install/lib/libmpifort.so" matlab -softwareopengl

I had to add the -softwareopengl to deal with the "Low Level Graphics" error.

Thanks!

justinquinn

kmosley Perfect! Glad to hear it's all sorted now. Let us know if you have any other issues.