Introduction
YARCC is a small Linux compute cluster aimed at users who require a platform for development and the execution of small compute jobs. The configuration of YARCC is aimed to be a mirror of the regional N8 facility. This will enable users to move their code to a larger resource with ease.
Instructions on accessing the system from Linux and Windows are here /wiki/spaces/RHPC/pages/25107532.
Hardware Infrastructure (January 2017)
Cluster Configuration
- 70 nodes, 138 processors, 1462 cores, 10.2TB RAM
There are six nodes containing GPU cards:
- 2 nodes with a nVidia K20 GPGPU card
- 2 nodes with a nVidia K40 GPGPU card
- 1 node with a nVidia K80 GPGPU card
- 1 node with 2 Intel XEON-phi cards
A detailed list of the hardware can be found here: qhost.pdf
Node specification:
| Number of nodes | Cores | Memory (GB) |
|---|---|---|
| 2 | 10 | 64 |
| 1 | 10 | 128 |
| 4 | 16 | 64 |
| 2 | 16 | 128 |
| 3 | 20 | 64 |
| 10 | 20 | 128 |
| 8 | 20 | 256 |
| 30 | 24 | 128 |
| 4 | 24 | 256 |
| 2 | 28 | 512 |
Grid Engine Queues
| Queue name | Maximum job time | Nodes available | Total Cores Available | Nodes Config - Cores - Memory |
|---|---|---|---|---|
| its-48hour | 48 hours | 69 | 1462 | 16/20/24/28 - 64/128/256/512GB |
| 64/128its-7day | 7 days | 10 | 180 | 16/20 - 64/128GB |
| its-14day | 14 days | 8 | 112 | 16/20 - 64/128GB |
| its-nvidia-k20 | 48 hours & 7 days | 2 | 34 | 10/24 - 64GB |
| its-nvidia-k40 | 48 hours & 7 days | 2 | 20 | 10 - 64GB |
| its-nvidia-k80 | 48 hours | 1 | 10 | 10 - 128GB |
Ina addition to the above there are a number of departmental queues that have a range of job times some up to 80 days in length.
Please note: you should not specify the queue in your job script, the gird engine will select the most appropriate queue for your job.
Please contact andrew.smith@york.ac.uk if you have any comments, or suggestions, on the configuration of the queues.
Software Infrastructure
Operating System - Centos Linux 7.3 (http://www.centos.org/)
Grid Engine - Sun Grid Engine (https://arc.liv.ac.uk/trac/SGE)
----------------------- /opt/yarcc/Modules/applications ------------------------
amber/14 genesis/2.4beta phenix/1.9.1692
argos3/3.0.0 genometools/1.5.8 phyml/20140223
atlas/3.10.2 git/2.8.3 Platanus/1.2.1
bcftools/1.2 grace/5.1.25 praat/6.0.05
BEAST/1.8.3 gromacs/2016.1 R/2.15.3
BEAST/2.3.2 gromacs/5.0 R/3.1.0
blast/2.2.29 gurobi/6.0.4 R/3.1.2
blast/2.2.31 h5utils/1.12.1 R/3.2.2
Blast2GO/2.5 Harminv/1.4 R/3.3.1
Blast2GO/3.1 HTK/3.4.1 R/3.3.1.centos6
Blast2GO/3.1.research0 I-TASSER/4.0 rosetta/2014.35.57232
Blast2GO/4.0.7 JAGS/3.4.0 Sage/6.2
bowtie2/2.2.5 LAMMPS/28Jun14 samtools/1.2
bwa/0.7.10 LibSBMLSim/1.1.0 sickle/1.33
castep/7.03 lua/5.2.4 SPSS/22
CEM_Solutions/2014.2 lua/5.3.1 SPSS/23
CEM_Solutions/2015.0 Maple/18 Stata/13
Code_Saturne/3.0.5 Mathematica/10.0.0 swig/3.0.8
Columbus/7.0 Matlab/R2014a tau/2.23.1
Columbus/7.0_2016-07-26 Matlab/R2015a TensorFlow/0.12.1
concept/12.0 maven/3.3.9 TensorFlow/0.9.0
concept/12.0.25 Meep/1.3 texinfo/5.2
cplex/12.6.0.0 MPB/1.5 theano/0.8.2
CST_MWS/2015 MrBayes/3.2.2 tophat/2.0.14
cufflinks/2.2.1 nco/4.4.4 tophat/2.1.1
embree/2.8.0 ncview/2.1.2 vasp/4.6
FDR3/3.2 Newton-X/1.4.0-2 vasp/5.3.3
FDR3/3.3.0 OpenBLAS/0.2.9 vasp/5.3.3-gamma
FDR3/3.4.0 OpenBUGS/3.2.3 vasp/5.3.3-opt
ferret/6.9 OpenFOAM/2.3.0 vasp/5.3.3-vtst
ffmpeg/2.2.4 ORCA/3.0.3 vasp/5.4.1p3
ffmpeg/3.1 PAFEC/8824b visit/2.7.3
gaussian/G03 parafem/2.0.819 Visual_Environment/10.0
gaussian/G09 ParaView/4.1.0 vraystd/33004
gaussian/G09d01 Pari-GP/2.7.1 vraystd/demo_32003
genesis/2.3 pdt/3.20 wkhtmltox/0.12.3
------------------------- /opt/yarcc/Modules/compilers -------------------------
Anaconda/2.3.0
Anaconda3/2.3.0
ant/1.9.4
cuda/6.5.14
cuda/7.0.28
cuda/7.5.18
cuda/8.0.44
ghc/7.8.2
ghc/7.8.3
gnu/4.7.4
gnu/4.8.3
gnu/4.9.0
go/1.3
icc/2013_sp1.3.174
ics/2013_sp1.2.144
ifort/2013_sp1.3.174
JaMPCuda/2015.01.16
jruby/3.2.2
maven/3.2.2
mono/3.8.0
ncl/6.2.0
opencl-intel-sdk/2016_6.0.0.1904
parallel_studio_xe/2016_composer_edition
prolog/6.6.6
python/2.7.11
python/2.7.6
python/3.4.0
python/3.5.1
python/3.5.3
python/3.6.0
ruby/2.1.2
ruby/2.3.1
Tcl/8.6.1
yasm/1.2.0
yasm/1.3.0
------------------------- /opt/yarcc/Modules/libraries -------------------------
armadillo/4.600.4 mpc/1.0.2
armadillo/6.200.4 mpe2/1.3.0
beagle-lib/2.1.2 mpfr/3.1.2
beagle-lib/r1260 MPICH/3.1.2
boost/1.55.0 MPICH/3.1.4
bzip2/1.0.6 MPICH/3.2
cppunit/1.13.2 mpich2/1.4.1
eigen/3.4.2 mvapich2/2.0
FANN/2.2.0 mvapich2/2.1
FANN/2.2.0.AVX mysql-connector-java/5.1.40
FANN/2.2.0.CORE-AVX-I NetCDF/4.1.3
fftw/2.1.5 NetCDF/4.3.2
fftw/3.3.3 NetCDF/4.4.1
fftw/3.3.4 NetCDF-fortran/4.4.2
GAlib/2.4.7 OpenCV/2.4.13
GDAL/1.11.2 OpenCV/2.4.9
gmp/6.0.0 OpenCV/3.1.0
gphoto2/2.5.10 openmpi/1.8.1
gsl/1.9 openmpi/1.8.3
h4toh5tools/2.2.2 openmpi/1.8.8
hdf4/4.2.11 petsc/3.5.0
hdf5/1.8.13 pgplot/5.2
hdf5/1.8.17 Qt/4.8.6
hdf-java/1.8.13 Qt/5.3.1
htslib/1.2.1 rasqal/0.9.32
hypre/2.9.0b redland/1.0.17
lapack/3.5.0 redland-bindings/1.0.17.1
lapacke/3.5.0 snack/2.2.10
libibverbs/1.1.4 SuiteSparse/4.2.1
libmatheval/1.1.11 szip/2.1
libraptor2/2.0.14 Tk/8.6.1
libsbml/5.12.0 voro/2.2.4
MatlabCompilerRuntime/R2014a vtk/6.1.0
MatlabCompilerRuntime/R2015a zlib/1.2.8
---------------------- /opt/yarcc/Modules/infrastructure -----------------------
autoconf/2.69 cpu/E5-2680v3 java/1.7.0_60
automake/1.15 eclipse/java.luna.SR1 java/1.8.0_05
bit/64 eclipse/parallel.juno.SR2 java/1.8.0_73
cmake/3.0.0 eclipse/parallel.luna.SR1 PyCharm/2.0.4
cpu/AVX hwloc/1.11.2 sge/8.1.6
cpu/AVX2 iggi/1 SGE/8.1.6
------------------------ /opt/yarcc/Modules/electronics ------------------------
Xilinx_ISE/14.7 Xilinx_Vivado/2014.2
--------------------------- /opt/yarcc/Modules/arch ----------------------------
centos/7
------------------------- /opt/yarcc/Modules/chemistry -------------------------
Newton-X/1.4.0-3
Infrastructure Topology
How the Grid Engine Works
