Ubuntu/MATLAB2023 error: Invalid MEX-file undefined symbol H5Pget_dxpl_mpio

eschwans

Hello,

I'm attempting to get ISSM working on Ubuntu (with MATLAB 2023a) and have been receiving the same error / feedback from MATLAB and my terminal as the user in this post: [https://issm.ess.uci.edu/forum/d/381-issm-matlab-error-invalid-mex-file-undefined-symbol-h5pget-dxpl-mpio]

libhdf5.so.103 => /usr/local/MATLAB/R2023a/bin/glnxa64/libhdf5.so.103 (0x00007ff39c7f2000)

However, while implementing the suggested quick fix of pre-loading libraries removes the issue with "issmversion" output in MATLAB any subsequent attempts to run ISSM scripts result in a MATLAB crash and the below terminal output. Attempts to preload the libraries both in the MATLAB-launching alias in my bash profile or in command-line prior to launching MATLAB result in the same crash report.

Warning! HDF5 library version mismatched error
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.10.8, library is 1.10.5
(Rest of output below)

The PETSC install script used in this build was the linux 3.12 version–I haven't yet tried rebuilding using a newer version as I'm not sure if this would upgrade the hdf library versions (from 1.10.5 to 1.10.8) or not.

I also tried to install the HDF5 external package, but the install script doesn't finish running / creating the install directory as the the tarball downloaded from the repository is throwing an "unexpected end of file" error, and can't be opened.

Short of setting a flag to ignore the error and possibly encountering segmentation faults in the future, how can I go about rectifying the version difference between what MATLAB2023a expects and what I have installed via PETSC?

It should be noted that I don't actually need the HDF5-associated NetCDF functionality in my model build--I just need it to run!

Thanks in advance for any help or insight!

-Emily

SUMMARY OF THE HDF5 CONFIGURATION
=================================

General Information:

HDF5 Version: 1.10.5
Configured on: Wed Jun 5 14:13:38 EDT 2024
Configured by: eps5217@ingrid.geosc.psu.edu
Host system: x86_64-unknown-linux-gnu
Uname information: Linux ingrid.geosc.psu.edu 5.15.0-107-generic #117₂₀.04.1-Ubuntu SMP Tue Apr 30 10:35:57 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: /ingrid/s0/eps5217/issm/trunk-jpl/externalpackages/petsc/install

Compiling Options:

Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high

Linking Options:

Libraries: static, shared
Statically Linked Executables:
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -ldl -lm -Wl,-rpath,/ingrid/s0/eps5217/issm/trunk-jpl/externalpackages/petsc/install/lib -L/ingrid/s0/eps5217/issm/trunk-jpl/externalpackages/petsc/install/lib -lz -lm
Archiver: /bin/ar
AR_FLAGS: cr
Ranlib: ranlib

Languages:

C: yes
C Compiler: /ingrid/s0/eps5217/issm/trunk-jpl/externalpackages/petsc/install/bin/mpicc ( MPICH version 3.3.1 Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.4.0-1ubuntu1₂₀.04.2' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-9QDOt0/gcc-9-9.4.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu built with gcc version 9.4.0 (Ubuntu 9.4.0-1ubuntu1₂₀.04.2))
CPPFLAGS: -I/ingrid/s0/eps5217/issm/trunk-jpl/externalpackages/petsc/install/include
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
C Flags: -fstack-protector -g -O
H5 C Flags: -std=c99 -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -finline-functions -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -O
AM C Flags:
Shared C Library: yes
Static C Library: yes
Fortran: yes
Fortran Compiler: /ingrid/s0/eps5217/issm/trunk-jpl/externalpackages/petsc/install/bin/mpif90 ( MPICH version 3.3.1 Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.4.0-1ubuntu1₂₀.04.2' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-9QDOt0/gcc-9-9.4.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu built with gcc version 9.4.0 (Ubuntu 9.4.0-1ubuntu1₂₀.04.2))
Fortran Flags: -ffree-line-length-0 -g -O
H5 Fortran Flags: -pedantic -Wall -Wextra -Wunderflow -Wimplicit-interface -Wsurprising -Wno-c-binding-type -s -O2
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes
C++: no
Java: no

Features:

Parallel HDF5: yes
Parallel Filtered Dataset Writes: yes
Large Parallel I/O: yes
High-level library: yes
Threadsafety: no
Default API mapping: v18
With deprecated public symbols: yes
I/O filters (external): deflate(zlib)
MPE:
Direct VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: no
Memory allocation sanity checks: no
Function stack tracing: no
Strict file format checks: no
Optimization instrumentation: no
Bye...
QXcbGlxIntegration::initialize

Xcb GLX gl-integration successfully initialized
Killed

justinquinn

eschwans Hi, that install script for PETSc is very outdated, so I would recommend using install-3.20-linux anyhow. I also recommend compiling HDF as a standalone external package. You can consult jenkins/ross-debian_linux-full for our configuration that includes for Dakota and SE capabilites. (I'm not suggesting you install all of these packages, but it does list the external package install scripts we use for our own nightly runs, and the order in which you should install some of them to handle dependencies. Note in your case, the only dependency for HDF5 is zlib, which will be installed by PETSc.)

eschwans

justinquinn
Thanks! I figured as much, and, as is usual right after I finally post on this forum, I did fix the issue by rebuilding using the latest PETSC version...seems the HDF5 libraries for MATLAB2023a and those installed using the install-3.17-linux.sh script now agree (or are at least compatible), and the crash report has gone away without having to pre-load libraries in either command-line or the bash profile.

I still don't have the HDF5 external package installed--the install scripts get hung up on checkout for the tarball, but that might be because it's (my own) older version of trunk-jpl that I'm working with.

If this thread isn't helpful since it was just a version mismatch, feel free to delete!

mathieumorlighem

Hi Emily! Do you really need HDF5 for your installation of ISSM? we really rarely need it (I never install it)

justinquinn

mathieumorlighem Also, now that you have a sane build, you might want to consider moving to the GitHub repo as we have migrated now and will not be updating the svn repo further: https://github.com/ISSMteam/ISSM

eschwans

mathieumorlighem No, I don't! I didn't try to install it until I got stuck on that error and rebuilt ISSM, and ultimately, I didn't need the HDF external package installed to get rid of the PETSc/MATLAB built-in library incompatibility.