11. Known Issues

11.1. General

  1. python on Cray is non-functional: Could not find platform dependent libraries <exec_prefix>

    This problem and the solution to unset the environment variable CONFIG_SITE before building spack-stack environments is described in https://github.com/spack/spack/issues/40110 and https://github.com/spack/spack/issues/42132.

  2. Build errors for mapl@2.35.2 with mpich@4.1.1

    This problem is described in https://github.com/JCSDA/spack-stack/issues/608.

  3. Issues starting/finding ecflow_server due to a mismatch of hostnames

    On some systems, ecflow_server gets confused by multiple hostnames, e.g. localhost and MYORG-L-12345. The ecflow_start.sh script reports the hostname it wants to use. This name (or both) must be in /etc/hosts in the correct address line, often the loopback address (127.0.0.1).

  4. Installing/using graphical applications after switching user using sudo su

    When using a role account to install spack-stack, it is sometimes necessary to run graphical applications such as the qt online installer. The following website describes in detail how this can be done: https://www.thegeekdiary.com/how-to-set-x11-forwarding-export-remote-display-for-users-who-switch-accounts-using-sudo/

  5. ==> Error: the key "core_compilers" must be set in modules.yaml during spack module [lmod|tcl] refresh

    This error usually indicates that the wrong module type is used in the spack module ... refresh command. For example, the system is configured for lmod, but the command used is spack module tcl refresh.

  6. Runtime segmentation faults for applications with intel@2021.10.0: Relink `/opt/intel/oneapi/compiler/2024.0/lib/libirc.so' with `/lib/x86_64-linux-gnu/libc.so.6' for IFUNC symbol `memmove' - Segmentation fault (core dumped).

    This problem is caused by a bad library in the Intel oneAPI installation. The solution is to fix the library using patchelf, which requires write access to the oneAPI installation: First, verify that ldd /opt/intel/oneapi/compiler/2024.0/lib/libirc.so says it is statically linked (it isn’t). Then, run: patchelf --add-needed libc.so.6 /opt/intel/oneapi/compiler/2024.0/lib/libirc.so and your application should run rightaway (no need to recompile).

11.2. NASA Discover

  1. Timeout when fetching software during spack installs.

    Discover’s connection to the outside world can be very slow and spack sometimes aborts with fetch timeouts. Try again until it works, sometimes have to wait for a bit.

  2. configure: error: cannot guess build type; you must specify one when building freetype or other packages that use configure scripts

    This can happen if a spack install is started in a screen session, because Discover puts the temporary data in directories like /gpfsm/dnb33/tdirs/login/discover13.29716.dheinzel, which get wiped out after some time. Without screen, this problem doesn’t occur.

  3. Insufficient diskspace when building py-pytorch

    This is because py-pytorch uses directory ~/.ccache during the build, and the user’s home directories have small quotas set. This problem can be avoided by creating a symbolic link from the home directory to a different place with sufficient quota: rm -fr ~/.ccache && ln -sf /path/to/dot_ccache_pytorch/ ~/.ccache. It’s probably a good idea to revert this hack after a successful installation.

11.3. NOAA Parallel Works

  1. With the default module path, spack will detect the system as Cray, therefore one needs to remove it when building or using spack environments

  2. libxml2 won’t untar during the spack install step, because of an issue with the filesystem. This can be avoided by making libxml2 an external package

  3. The /contrib filesystem can be very, very slow

11.4. UW (Univ. of Wisconsin) S4

  1. Compiler errors when using too many threads for parallel builds

    Using more than two threads when running make (e.g. make -j4) can lead to compiler errors like the following:

[94%] Linking CXX executable test_ufo_parameters
icpc: error #10106: Fatal error in /home/opt/intel/oneapi/2022.1/compiler/2022.0.1/linux/bin/intel64/../../bin/intel64/mcpcom, terminated by kill signal
...

11.6. macOS

  1. Error invalid argument '-fgnu89-inline' not allowed with 'C++'

    This error occurs on macOS Monterey with mpich-3.4.3 installed via Homebrew when trying to build the jedi bundles that use ecbuild. The reason was that the C compiler flag -fgnu89-inline from /usr/local/Cellar/mpich/3.4.3/lib/pkgconfig/mpich.pc was added to the C++ compiler flags by ecbuild. The solution was to set CC=mpicc FC=mpif90 CXX=mpicxx when calling ecbuild for those bundles. Note that it is recommended to install mpich or openmpi with spack-stack, not with Homebrew.

  2. Installation of gdal fails with error xcode-select: error: tool 'xcodebuild' requires Xcode, but active developer directory '/Library/Developer/CommandLineTools' is a command line tools instance.

    If this happens, install the full Xcode application in addition to the Apple command line utilities, and switch xcode-select over with sudo xcode-select -s /Applications/Xcode.app/Contents/Developer (change the path if you installed Xcode somewhere else).

  3. Error AttributeError: Can't get attribute 'Mark' on <module 'ruamel.yaml.error' from ... when running spack install

    Some users are seeing this with Python 3.10 installed via Homebrew on macOS. Run export | grep SPACK_PYTHON to verify the Python version used, then run brew list to check if there are alternative Python versions available. Manually setting SPACK_PYTHON to a different version, for example via export SPACK_PYTHON=/usr/local/bin/python3.9, solves the problem.

  4. Errors handling exceptions on macOS.

    A large number of errors related to handling exceptions thrown by applications was found when using default builds or Homebrew installations of mpich or openmpi, which use flat namespaces. With our spack version, mpich and openmpi are installed with a +two_level_namespace option that fixes the problem.

  5. Errors such as Symbol not found: __cg_png_create_info_struct

    Can happen when trying to use the raster plotting scripts in fv3-jedi-tools. In that case, exporting DYLD_LIBRARY_PATH=/usr/lib/:$DYLD_LIBRARY_PATH can help. If git commands fail after this, you might need to verify where which git points to (Homebrew vs module) and unload the git module.

11.7. Ubuntu

  1. The lmod version in Ubuntu 22.04 LTS breaks spack modules.

    Ubuntu 22.04 LTS will install lmod 6.6 from official apt repositories. Module files authored by spack use the depends_on directive that was introduced in lmod 7.0. The new site config instructions in Section 6.2 circumvent the issue by using tcl/tk environment modules. If you attempt to use lmod 6.6 you will get the following error:

    $ module load stack-python
Lmod has detected the following error:  Unable to load module: python/3.10.8
/home/ubuntu/spack-stack-1.3.1/envs/skylab-4/install/modulefiles/gcc/11.3.0/python/3.10.8.lua : [string "-- -*- lua -*-..."]:16: attempt to call global 'depends_on' (a nil value)