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January 2019 Maintenance

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Timeline

The January 2019 Maintenance Period began Friday, January 4th at 7 am and ended Sunday, January 6th.
Recompilation of code is recommended. Please report any instability or other issues to CRCSupport@nd.edu.


System Updates / Changes

  • Various firmware updates on all compute nodes.
  • Compute nodes updated to RHEL 7.6.
  • All systems updated to use latest OpenAFS version.
  • GPU drivers on GPU nodes updated from version 390.48 to version 410.78.
  • Various security updates applied to all systems, including for latest Spectre/Meltdown-related CPU vulnerabilities.
  • All systems rebooted.


Software / Module Changes

  • UGE updated to 8.6.2.
  • Modules updated to 4.2.1.
  • Singularity updated to version 3.0.2 on all systems.
    • Note: The new version uses SIF format for images instead of SquashFS.


New Default modules

The following software titles had their default versions updated to the ones listed below.

amber/18.0
ansys/19.2
bio/bcl2fastq/2.20
bio/bwa/0.7.12
bio/cufflinks/2.2.1
cfour/1.0-p
cmake/3.13.2
comsol/5.4
cuda/9.2
gdal/gcc/2.3.1
git/2.20.1
jags/4.3
lammps/22Aug18
mathematica/11.3
matlab/2018a
namd/2.13
netcdf/intel/4.6.1
opencv/3.4
pgi/18.7
pointwise/18.2R1
quantumwise/2018.06
schrodinger/2018u3
tensorflow/1.10
valgrind/3.14


Deprecated Modules

The following modules will be removed during the May 2019 maintenance period. Note that any modules that have dependencies in this list will trigger an alert as well.

CRC_default/1.0
Rstudio/1.0.143
abaqus/2017
adina/9.3.1
ansys/18.2
bio/R/3.4.0
bio/bcl2fastq/2.19
bio/bowtie2/2.2.3
bio/bwa/0.6.2
bio/cufflinks/2.1.1
bio/cutadapt/1.6
bio/picardtools/1.119
bio/trinity/2.8.2
boost/1.63
caelus/7.04
cfour/1.0
cmake/3.9.4
comsol/5.2a
comsol/5.3
cp2k/4.0
cuda/8.0
cudnn/v6.0
espresso/5.4
gcc/6.2.0
gdal/2.1.3
git/2.8
gsl/2.3
gurobi/7.0.2
hdf5/1.8.15-gcc
intel/16.0
jags/4.2
matlab/9.2
namd/2.12
netcdf/4.4.1
openbabel/2.3.1
opencv/3.3
openface/0.2.0
openfoam/1612+
openfoam/1706
pgi/16.10
pgi/17.4
pointwise/18.0R1
python/2.7.11
quantumwise/2017.12
schrodinger/2017u3
stata/15.0
tcl/8.6.4
tensorflow/1.6
valgrind/3.13.0-intel


Previously deprecated software removed

The following modules were previously deprecated and have been removed during this maintenance period.

allinea/7.0
julia/0.5.1
erlang/18.0
rosetta/3.5
bio/python/2.7.8
bio/python/2.7.11
bio/R/3.2.3-gcc
bio/R/3.3.1-gcc
bio/qiime/1.9.1
bio/trinity/r20140717
bio/samtools/0.1.19
bio/samtools/1.1
bio/samtools/1.2
ffmpeg/2.8.3
idlutils/idl8.4
maya/2018
mpb/1.5
openfoam/2.4.0
netlogo/5.3.1
macaulay2/1.8
xmgr/4.1.2
xmgr/5.1.23
tensorflow/1.1
tensorflow/1.3
imsl/cnl8.0-gcc
imsl/fnl7.0-intel
imsl/fnl7.0-intel-old
R/3.4.0
R/3.4.0-intel-17.1
petsc/3.6.4-intel
caffe/2016-gpu
caffe2/0.8.1