Physics compute cluster

Introduction

The physics compute cluster is a small Linux compute cluster aimed at users who require a platform for development and the execution of small compute jobs.

Instructions on accessing the system from Linux and Windows are here Accessing the Physnodes.


Grid Engine Queues

Queue nameMaximum job timeNodes availableTotal Cores AvailableNodes Config - Cores - Memory
its-48hour48 hours69146216/20/24/28 - 64/128/256/512GB
64/128its-7day7 days1018016/20 - 64/128GB
its-14day14 days811216/20 - 64/128GB
its-nvidia-k2048 hours & 7 days23410/24 - 64GB
its-nvidia-k4048 hours & 7 days22010 - 64GB
its-nvidia-k8048 hours11010 - 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)

Installed Software

----------------------- /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







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