Deepthought2

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This wiki entry is just an overview of key areas to get you started with things common to those in our department, for a more complete overview please check the DIT Deepthought Usage page. DIT Deepthought Overview Page

Overview

Running a job

Checking job status

squeue

email notification

output

Allocations

The department currently receives an annual resource allocation of ~7 million hours a year. This is provided in monthly increments of 609,920 computation hours a month. To check the current number of hours remaining for the month use the sbalance --all command. The aosc-hi account denotes the hours remaining for the current month.

Sbalance.png


debugging

Software available

There is no Portland Fortran, so you have to choose between gfrotran and Intel's ifort compilers. Software List

The following list of software and versions is confirmed to be on the Deepthought 2 compute nodes:

  • cdo
  • hdf4/4.2.10
  • hdf5/1.8.13
  • intel/2013.1.039
  • netcdf/4.3.2
  • netcdf-fortran/4.4.1
  • nco/4.4.6
  • openmpi/gnu/1.6.5 and openmpi/intel/1.8.1
  • python/2.7.8

When specifying modules to load, they should always be specified in the following order

  1. intel
  2. openmpi
  3. netcdf and/or hdf4/5
  4. netcdf-fortran
  5. other stuff

Sample gfortran environment setup script

#!/bin/bash
module load openmpi/gnu/1.6.5
module load netcdf/4.3.2
module load netcdf-fortran

export LD_LIBRARY_PATH=$NETCDF_LIBDIR:$NETCDF_FORTRAN_LIBDIR:$LD_LIBRARY_PATH
export FC=mpif90
export F77=mpif90
export CPFLAGS="$(nc-config --flibs --libs)"
export LDFLAGS="$(nc-config --fflags)"

Sample ifort environment setup script

#!/bin/bash
module load intel
module load openmpi/gnu/1.8.1
module load netcdf/4.3.2
module load netcdf-fortran

export LD_LIBRARY_PATH=$NETCDF_LIBDIR:$NETCDF_FORTRAN_LIBDIR:$LD_LIBRARY_PATH
export FC=mpif90
export F77=mpif90
export CPFLAGS="$(nc-config --flibs --libs)"
export LDFLAGS="$(nc-config --fflags)"

ulimit -s unlimited