Update: We think this is fixed. Please submit a ticket if you encounter further problems.
As a result of updates made during yesterday's downtime, software built with mvapich2/1.7 is failing with the error:
libibumad.so.2: cannot open shared object file: No such file or directory
We're working on fixing the problem.
LAMMPS 14May16 was built with the USER-OMP package on Oakley, Ruby, and Owens. Its default behavior is to spawn too many OpenMP threads. lammps/14May16 batch scripts that do not use the USER-OMP package should set the OMP_NUM_THREADS environment variable to 1 as a workaround, e.g.:export OMP_NUM_THREADS=1
for Bourne type shells andsetenv OMP_NUM_THREADS 1
for C type shells.
Some MVAPICH2 MPI installations on Oakley, Ruby, and Owens, such as the default module mvapich2/2.2 as well as mvapich2/2.1, appear to have a bug that is triggered by certain programs. The symptoms are 1) the program hangs or 2) the program fails with an error related to Allreduce or Bcast.
Intel compiler versions 11 and later on Glenn do not support the -mkl compiler options. Contact oschelp@osc.edu for workarounds.
Typical symptoms are
../fft3d.h(184): catastrophic error: cannot open source file "mkl_dfti.h" ld: cannot find -lmkl_intel_lp64
NAMD 2.11 precompiled binaries do not work. Please use NAMD 2.11 installed from the source and available via module namd/2.11.
The NAMD 2.11 issue involves changes to the command charmrun in Charmm++.
A typical symtom is:
Batch scripts loading module lammps-7Dec15 should use the user's login shell or
the Korn shell, e.g. #PBS -S /bin/ksh
There is a bug that causes the module load to fail if the job script specifies the Bash shell, i.e.:
#PBS -S /bin/bash
Alternatiely you can unload mpi and intel-10.x before loading the lammps module.
An example failure is:
OSC has acquired its new ABAQUS license with new license terms. Use is now limited by both institution and for use in educational, institutional, instructional, and/or research purposes. Results arising from use of OSC’s license must be made freely available to anyone without reasonable delay.
Due to the way our Fluent and ANSYS modules are configured, simultaneously loading multiple of either module will cause a cryptic error. The most common case of this happening is when multiple of a users jobs are started at the same time and all load the module at once. In order for this error to manifest, the modules have to be loaded at precisely the same time; a rare occurrence, but a probable occurrence over the long term.
If you encounter this error you are not at fault. Please resubmit the failed job(s).
Certain modules are not working for all clusters since the downtime. We have reports specifically that Amber, Gaussian, and Turbomole are not working. We are working to resolve the issue, but until then jobs using Amber, Gaussian, Turbomole, or other software with permissions restrictions will not work.