Software

Jupyter security issue Aug. 13, 2021

Please do not run any Jupyter applications at OSC until further notice due to a security vulnerability.

OSC will update JupyterLab and Jupyter Notebook applications to rectify this as soon as possible.

List of versions changed:

  • 0.35: removed because there is no official patch release.
  • 1.2: upgraded to 1.2.21
  • 2.1: replaced with 2.2.10 because there is no official patch release.
  • 3.0: upgraded to 3.0.17

References for more information:

OpenMPI job stopped at 'There are not enough slots available in the system to satisfy the slots'

Users would encounter a MPI job failed with openmpi/3.1.0-hpcx on Owens and Pitzer. The job would stop with the error  like "There are not enough slots available in the system to satisfy the slots". Please switch to openmpi/3.1.4-hpcx. The buggy version openmpi/3.1.0-hpcx will be removed on August 18 2020.

==========

Resolved: We removed  openmpi/3.1.0-hpcx on August 18 2020.

Error 'libim_client.so: undefined reference to uuid@' with MVAPICH2 in Conda environment

Users may encoutner an error like 'libim_client.so: undefined reference to `uuid_unparse@UUID_1.0' while compiling MPI applications with mvapich2 in some Conda enivronments. We found pre-installed libuuid package from Conda conflicting with system libuuid libraries. The affected Conda packages are python/2.7-conda5.2python/3.6-conda5.2 and python/3.7-2019.10.

Incorrect MPI launcher and compiler wrappers with Conda environments python/2.7-conda5.2 and python/3.6-conda5.2

Users may encounter under-performing MPI jobs or failures of compiling MPI applications if you are using Conda from system. We found pre-installed mpich2 package in some Conda environments overrides default MPI path. The affected Conda packages are python/2.7-conda5.2 and python/3.6-conda5.2. If users experience these issues, please re-load MPI module, e.g. module load mvapich2/2.3.2 after setting up your Conda environment.

Pages