ISSM Matlab error: Invalid MEX-file, undefined symbol: H5Pget_dxpl_mpio

rlaw

Hi there,

I'm trying to get a development build of ISSM set up on a Linux cluster. I managed a functional install with Python, however issues with netCDF export in Python led me to also try a Matlab build to see I could circumvent the export issue.

I can run make and make install with no errors, however running <issmversion> in Matlab (after the correct paths have been added to Matlab) produces the following error:

Invalid MEX-file '/Home/siv34/rolaw8691/ISSM/ISSM/trunk/lib/IssmConfig_matlab.mexa64':
/Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libpetsc.so.3.12:
undefined symbol: H5Pget_dxpl_mpio

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

Error in issmversion (line 13)
disp([IssmConfig('PACKAGE_NAME') ' Version ' IssmConfig('PACKAGE_VERSION')]);

because this seemed related to HDF5 I tried installing that through the externalpackages directory, listing it in my config file and doing a full new install, however this produced the same error. I also can't see any flags for h5py in the configure help documentation. I've copied in my config file below the sign off in case that's useful.

Running lld on the MEX file gives:

libhdf5.so.103 => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libhdf5.so.103 (0x00007f6e7a5cd000)

with the full output given after the config file in case that's useful.

Any help is of course very much appreciated!!

Best,
Rob

./configure \
        --prefix="$ISSM_DIR" \
        --with-matlab-dir="/usr/local/MATLAB/R2022b" \
        --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/10 -lgfortran" \
        --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
        --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
        --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
        --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \
        --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
        --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
        --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include" \
        --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich -lmpichf90 -lmpichcxx -lmpl" \
        --with-hdf5-dir="$ISSM_DIR/externalpackages/hdf5/install" \
        --enable-development \
        --with-numthreads=2

ldd lib/IssmConfig_matlab.mexa64
        linux-vdso.so.1 (0x00007ffd62fb1000)
        libISSMMatlab.so => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/lib/libISSMMatlab.so (0x00007f6e7d364000)
        libISSMCore.so => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/lib/libISSMCore.so (0x00007f6e7ccd2000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f6e7cc91000)
        libmex.so => not found
        libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f6e7caad000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6e7c8bb000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f6e7c8a0000)
        libparmetis.so => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libparmetis.so (0x00007f6e7c85e000)
        libmetis.so => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libmetis.so (0x00007f6e7c7f1000)
        libmpi.so.12 => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libmpi.so.12 (0x00007f6e7c48d000)
        libmpifort.so.12 => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libmpifort.so.12 (0x00007f6e7c411000)
        libmx.so => not found
        libmex.so => not found
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6e7c2c2000)
        libpetsc.so.3.12 => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libpetsc.so.3.12 (0x00007f6e7aca7000)
        libgfortran.so.5 => /usr/lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007f6e7a9dd000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f6e7d646000)
        librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f6e7a9d3000)
        libhdf5.so.103 => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libhdf5.so.103 (0x00007f6e7a5cd000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f6e7a5c7000)
        libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f6e7a57d000)
        libz.so.1 => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libz.so.1 (0x00007f6e7a562000)

mathieumorlighem

Hello Rob

I have never seen that one before, I looks like a conflict between HDF5 libraries. Can you do this for me:

Let's see if this symbol is in the HDF5 library provided by PETSc. Can you do:

 nm /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libhdf5.so.103 | grep H5Pget_dxpl_mpio

and tell us what you see?

MATLAB may have its own HDF5 lib that may not be compatible with PETSc's (if this is the case we can make it work by forcing MATLAB to load PETSc's first). Can you fire up MATLAB and try the same LDD command from MATLAB?

 >> !ldd $ISSM_DIR/lib/IssmConfig_matlab.mexa64

Thanks
Mathieu

rlaw

Hi Mathieu,

Thanks for the really quick reply!

running

nm /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libhdf5.so.103 | grep H5Pget_dxpl_mpio
in the Linux terminal gives

000000000033165d T H5Pget_dxpl_mpio

Running the command

!ldd $ISSM_DIR/lib/IssmConfig_matlab.mexa64

from Matlab gives

libhdf5.so.103 => /usr/local/MATLAB/R2022b/bin/glnxa64/libhdf5.so.103 (0x00007ff39c7f2000)
I just tried the pre-compiled file for Linux-MATLAB and that seems to work fine. I can at least get myself better acquainted with ISSM while I get the development install sorted.

I've copied in the whole output below.

Best,
Rob

inux-vdso.so.1 (0x00007ffff3984000)
	libISSMMatlab.so => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/lib/libISSMMatlab.so (0x00007ff3a27a5000)
	libISSMCore.so => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/lib/libISSMCore.so (0x00007ff3a2113000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007ff3a20d2000)
	libmex.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmex.so (0x00007ff3a1faa000)
	libstdc++.so.6 => /usr/local/MATLAB/R2022b/sys/os/glnxa64/libstdc++.so.6 (0x00007ff3a1dd4000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ff3a1be2000)
	libgcc_s.so.1 => /usr/local/MATLAB/R2022b/sys/os/glnxa64/libgcc_s.so.1 (0x00007ff3a1bc8000)
	libparmetis.so => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libparmetis.so (0x00007ff3a1b86000)
	libmetis.so => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libmetis.so (0x00007ff3a1b19000)
	libmpi.so.12 => /usr/local/MATLAB/R2022b/bin/glnxa64/libmpi.so.12 (0x00007ff3a17e9000)
	libmpifort.so.12 => /usr/local/MATLAB/R2022b/bin/glnxa64/libmpifort.so.12 (0x00007ff3a1767000)
	libmx.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmx.so (0x00007ff3a1449000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007ff3a12fa000)
	libpetsc.so.3.12 => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libpetsc.so.3.12 (0x00007ff39fcdf000)
	libgfortran.so.5 => /usr/local/MATLAB/R2022b/sys/os/glnxa64/libgfortran.so.5 (0x00007ff39fa23000)
	/lib64/ld-linux-x86-64.so.2 (0x00007ff3a2a87000)
	libmwfl.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfl.so (0x00007ff39f94a000)
	libut.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libut.so (0x00007ff39f89e000)
	libmwservices.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwservices.so (0x00007ff39f45a000)
	libmwfoundation_matlabdata_matlab.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_matlabdata_matlab.so (0x00007ff39f35a000)
	libmwfoundation_matlabdata.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_matlabdata.so (0x00007ff39f1fd000)
	libmwmvm.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmvm.so (0x00007ff39edf6000)
	libmwm_dispatcher_interfaces.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwm_dispatcher_interfaces.so (0x00007ff39edef000)
	libmwm_dispatcher.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwm_dispatcher.so (0x00007ff39ec32000)
	libmwi18n.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwi18n.so (0x00007ff39eac2000)
	libmwfoundation_filesystem.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_filesystem.so (0x00007ff39ea7c000)
	libmwmlutil.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmlutil.so (0x00007ff39ddf2000)
	libmwfoundation_usm.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_usm.so (0x00007ff39ddc1000)
	libmwgenerate_diag_message.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwgenerate_diag_message.so (0x00007ff39ddb8000)
	libmwmcos.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmcos.so (0x00007ff39dd2d000)
	libmwfoundation_log.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_log.so (0x00007ff39dc03000)
	libmwcpp11compat.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwcpp11compat.so (0x00007ff39dbdf000)
	libmwboost_chrono.so.1.75.0 => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwboost_chrono.so.1.75.0 (0x00007ff39d9d3000)
	libmwboost_filesystem.so.1.75.0 => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwboost_filesystem.so.1.75.0 (0x00007ff39d7b5000)
	libmwboost_log.so.1.75.0 => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwboost_log.so.1.75.0 (0x00007ff39d4e6000)
	libmwboost_thread.so.1.75.0 => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwboost_thread.so.1.75.0 (0x00007ff39d2cc000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007ff39d2c2000)
	libquadmath.so.0 => /usr/local/MATLAB/R2022b/sys/os/glnxa64/libquadmath.so.0 (0x00007ff39d277000)
	libmwmfl_permute.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmfl_permute.so (0x00007ff39d25b000)
	libmwindexingapimethods.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwindexingapimethods.so (0x00007ff39d247000)
	libicuuc.so.69 => /usr/local/MATLAB/R2022b/bin/glnxa64/libicuuc.so.69 (0x00007ff39d054000)
	libtbb.so.2 => /usr/local/MATLAB/R2022b/bin/glnxa64/libtbb.so.2 (0x00007ff39cdf0000)
	libtbbmalloc.so.2 => /usr/local/MATLAB/R2022b/bin/glnxa64/libtbbmalloc.so.2 (0x00007ff39cb96000)
	libz.so.1 => /Home/siv34/rolaw8691/ISSM/ISSM/trunk/externalpackages/petsc/install/lib/libz.so.1 (0x00007ff39cb7d000)
	libhdf5.so.103 => /usr/local/MATLAB/R2022b/bin/glnxa64/libhdf5.so.103 (0x00007ff39c7f2000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007ff39c7ec000)
	libpam.so.0 => /lib/x86_64-linux-gnu/libpam.so.0 (0x00007ff39c7da000)
	libmwboost_serialization.so.1.75.0 => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwboost_serialization.so.1.75.0 (0x00007ff39c598000)
	libunwind.so.8 => /usr/local/MATLAB/R2022b/bin/glnxa64/libunwind.so.8 (0x00007ff39c576000)
	libmwflstrings.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwflstrings.so (0x00007ff39c570000)
	libicuio.so.69 => /usr/local/MATLAB/R2022b/bin/glnxa64/libicuio.so.69 (0x00007ff39c561000)
	libmwcapabilities.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwcapabilities.so (0x00007ff39c556000)
	libmwcppmicroservices.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwcppmicroservices.so (0x00007ff39c4bf000)
	libmwcwf_interface.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwcwf_interface.so (0x00007ff39c43e000)
	libmwflstorageprovider.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwflstorageprovider.so (0x00007ff39c3dd000)
	libmwflstorageutility.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwflstorageutility.so (0x00007ff39c3d7000)
	libmwflstoragevfs.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwflstoragevfs.so (0x00007ff39c285000)
	libmwfoundation_feature.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_feature.so (0x00007ff39c225000)
	libmwlivecode.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwlivecode.so (0x00007ff39c1d7000)
	libmwmatlabstoragesystem.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmatlabstoragesystem.so (0x00007ff39c1c4000)
	libmwms.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwms.so (0x00007ff39bdd0000)
	libmwrelease_info.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwrelease_info.so (0x00007ff39bd89000)
	libmwsearch_path_utilities.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwsearch_path_utilities.so (0x00007ff39bd45000)
	libmwsettings_in_matlab.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwsettings_in_matlab.so (0x00007ff39bcfd000)
	libmwopccore.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwopccore.so (0x00007ff39bc96000)
	libmwopcmodel.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwopcmodel.so (0x00007ff39bba1000)
	libmwopczippackage.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwopczippackage.so (0x00007ff39bb85000)
	libmwsettingscore.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwsettingscore.so (0x00007ff39b791000)
	libmwstring_matrix.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwstring_matrix.so (0x00007ff39b754000)
	libmwkeybrd.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwkeybrd.so (0x00007ff39b74f000)
	libmwboost_iostreams.so.1.75.0 => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwboost_iostreams.so.1.75.0 (0x00007ff39b53e000)
	libmwboost_regex.so.1.75.0 => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwboost_regex.so.1.75.0 (0x00007ff39b267000)
	libCppMicroServices.so.3.7.0 => /usr/local/MATLAB/R2022b/bin/glnxa64/libCppMicroServices.so.3.7.0 (0x00007ff39af3f000)
	libicui18n.so.69 => /usr/local/MATLAB/R2022b/bin/glnxa64/libicui18n.so.69 (0x00007ff39ac13000)
	libmwfoundation_matlabdata_standalone.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_matlabdata_standalone.so (0x00007ff39ab4c000)
	libmwmst.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmst.so (0x00007ff39a9cb000)
	libmwthreadpool.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwthreadpool.so (0x00007ff39a9a6000)
	libmwnativedisplay.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwnativedisplay.so (0x00007ff39a993000)
	libmwstartupplugin.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwstartupplugin.so (0x00007ff39a97e000)
	libmwstartup_plugin_initializer.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwstartup_plugin_initializer.so (0x00007ff39a8ef000)
	libmvmtransportapi.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmvmtransportapi.so (0x00007ff39a8e4000)
	libmwmatlab_toolbox_events_base.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmatlab_toolbox_events_base.so (0x00007ff39a770000)
	libmwexecution_events.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwexecution_events.so (0x00007ff39a2fe000)
	libmwfoundation_tracelogger.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_tracelogger.so (0x00007ff39a2ed000)
	libmwstoragefilefolderobserver.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwstoragefilefolderobserver.so (0x00007ff39a270000)
	libmwcwf_implementation.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwcwf_implementation.so (0x00007ff39a259000)
	libmwmatlab_modules_events.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmatlab_modules_events.so (0x00007ff39a242000)
	libmwmatlab_modules_implementation.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmatlab_modules_implementation.so (0x00007ff39a1e5000)
	libmwmatlab_modules_interfaces.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmatlab_modules_interfaces.so (0x00007ff39a1da000)
	libmwmodule_descriptor_implementation.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmodule_descriptor_implementation.so (0x00007ff39a179000)
	libmwmodule_descriptor_interfaces.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmodule_descriptor_interfaces.so (0x00007ff39a0f2000)
	libmwmodule_feature.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmodule_feature.so (0x00007ff39a0d7000)
	libmwpackage_registry_interfaces.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwpackage_registry_interfaces.so (0x00007ff39a0c5000)
	libmwpackage_registry_implementation.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwpackage_registry_implementation.so (0x00007ff39a032000)
	libmwsearch_path_events.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwsearch_path_events.so (0x00007ff399ed5000)
	libmwsearch_path_impl.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwsearch_path_impl.so (0x00007ff399e09000)
	libmwsearch_path_interfaces.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwsearch_path_interfaces.so (0x00007ff399df4000)
	libmwsearch_space_implementation.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwsearch_space_implementation.so (0x00007ff399dcf000)
	libmwsearch_space_utilities.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwsearch_space_utilities.so (0x00007ff399dc9000)
	libmwddux.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwddux.so (0x00007ff399d8c000)
	libmwddux_loggingapi.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwddux_loggingapi.so (0x00007ff399c49000)
	libmwbuiltin.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwbuiltin.so (0x00007ff399505000)
	libmwresource_core.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwresource_core.so (0x00007ff3994ff000)
	libexpat.so.1 => /usr/local/MATLAB/R2022b/bin/glnxa64/libexpat.so.1 (0x00007ff3994cf000)
	libmwlocale.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwlocale.so (0x00007ff3994ca000)
	libmwfoundation_json.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_json.so (0x00007ff3994bc000)
	libmwmatlabdata_boost_serialization.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmatlabdata_boost_serialization.so (0x00007ff3994b5000)
	libmwboost_atomic.so.1.75.0 => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwboost_atomic.so.1.75.0 (0x00007ff3992ab000)
	libicudata.so.69 => /usr/local/MATLAB/R2022b/bin/glnxa64/libicudata.so.69 (0x00007ff397752000)
	libaudit.so.1 => /lib/x86_64-linux-gnu/libaudit.so.1 (0x00007ff397726000)
	libmwflcodesigning_verifier.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwflcodesigning_verifier.so (0x00007ff3976f4000)
	libmwflnetwork.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwflnetwork.so (0x00007ff397609000)
	libmwflstorageevents.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwflstorageevents.so (0x00007ff3975e9000)
	libmwfoundation_fctrl_ext.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_fctrl_ext.so (0x00007ff3975e6000)
	libmwopcmwservices.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwopcmwservices.so (0x00007ff397548000)
	libxerces-c-3.2.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libxerces-c-3.2.so (0x00007ff397165000)
	libmwmcom.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwmcom.so (0x00007ff39712a000)
	libmwfoundation_memmgr.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_memmgr.so (0x00007ff397114000)
	libmwflcrypto.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwflcrypto.so (0x00007ff3970c1000)
	libmwflcryptoutils.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwflcryptoutils.so (0x00007ff397081000)
	libmwflcryptocryptopp.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwflcryptocryptopp.so (0x00007ff396d1f000)
	libmwflcertificates.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwflcertificates.so (0x00007ff396cb4000)
	libminizip.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libminizip.so (0x00007ff396ca4000)
	libmwxmlcore.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwxmlcore.so (0x00007ff396c26000)
	libmwfoundation_matlabdata_json.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_matlabdata_json.so (0x00007ff396b00000)
	libmwopcmwpackaging.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwopcmwpackaging.so (0x00007ff396adc000)
	libmwfactory_settings_loader.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfactory_settings_loader.so (0x00007ff396ad9000)
	libmwagentspfendpointregistry.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwagentspfendpointregistry.so (0x00007ff396aa8000)
	libmwpackage_registry_events.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwpackage_registry_events.so (0x00007ff396a99000)
	libmwpackage_registry_utilities.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwpackage_registry_utilities.so (0x00007ff396a93000)
	libmwsearch_space_interfaces.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwsearch_space_interfaces.so (0x00007ff396a87000)
	libmwfoundation_paths.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_paths.so (0x00007ff396a81000)
	libmwdtoa.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwdtoa.so (0x00007ff396a68000)
	libcap-ng.so.0 => /lib/x86_64-linux-gnu/libcap-ng.so.0 (0x00007ff396a5e000)
	libcrypto-mw.so.1.1 => /usr/local/MATLAB/R2022b/bin/glnxa64/libcrypto-mw.so.1.1 (0x00007ff396791000)
	libssl-mw.so.1.1 => /usr/local/MATLAB/R2022b/bin/glnxa64/libssl-mw.so.1.1 (0x00007ff3966ff000)
	libmwfoundation_matlabjson_frontend.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwfoundation_matlabjson_frontend.so (0x00007ff3966f9000)
	libmwagentspfsharedmemory.so => /usr/local/MATLAB/R2022b/bin/glnxa64/libmwagentspfsharedmemory.so (0x00007ff3966d8000)

mathieumorlighem

ok I think this is the culprit:

 libhdf5.so.103 => /usr/local/MATLAB/R2022b/bin/glnxa64/libhdf5.so.103 (0x00007ff39c7f2000)

See how it is picking up MATLAB's HDF5 library? If you want to fix this, one way to do it is to force MATLAB to load PETSc's lib first by using LD_PRELOAD. You can for example create an alias like this:

alias ma='LD_PRELOAD=$ISSM_DIR/externalpackages/petsc/install/lib/libhdf5.so.103 matlab -nodesktop -nosplash'

otherwise you can also use the precompiled binaries too (or copy them in "libs").
All the best
Mathieu

rlaw

Hi Mathieu,

Thanks for the tips.

That seems to do the job, awesome!

I run
LD_PRELOAD="$ISSM_DIR/externalpackages/petsc/install/lib/libhdf5.so.103" matlab

and then issmversion is now producing the expected output. I'll add the alias to my .bashrc.

Best,
Rob