NOCSCOMBINE is old and slow. Use REBUILD_NEMO instead.
NOCSCOMBINE is a tool to combine the per-processor NetCDF results files that are generated when NEMO is run in parallel using MPI. One description of its use can be found at http://www.hector.ac.uk/cse/distributedcse/reports/nemo/nemo_notes/node18.html. The NOCSCOMBINE code was downloaded from ftp://ftp.soc.soton.ac.uk/omfftp/NEMO/.
nocscombine.F90 file contains this notice regarding distribution and use of the package:
Unless otherwise indicated, all other software has been authored by an employee or employees of the National Oceanography Centre, Southampton, UK (NOCS). NOCS operates as a collaboration between the Natural Environment Research Council (NERC) and the University of Southampton. The public may copy and use this software without charge, provided that this Notice and any statement of authorship are reproduced on all copies. Neither NERC nor the University makes any warranty, express or implied, or assumes any liability or responsibility for the use of this software.
NOCSCOMBINE FORTRAN program that assembles a global NetCDF archive from a series of NEMO output files. USAGE :: nocscombine -f inputfile [-o outfile] [-v] [-s] [-d list of variables] [-ts tstart] [-te tend] -f inputfile Mandatory argument. inputfile is the filename of one of the NEMO restart or diagnostic files. This should be the whole filename of one of the individual processor files (i.e. include the node number, eg. ORCA1_00010101_restart_0012.nc). This program works on NetCDF NEMO output files. The program will create a NetCDF archive covering the entire global domain. [-o outputfile ] Optional argument. outputfilename is the required name of the outputfile. By default this name will be constructed from the inputfilename by stripping off the processor number. I.e.: inputfile : ORCA1_00010101_restart_0012.nc outputfile: ORCA1_00010101_restart.nc The -o option permits the user to override this behaviour. [-c coordinatefile ] Optional argument. coordinatefile is the name of the global coordinate file relevant to the NEMO model which produced the individual processor files. This file is required to ensure complete nav_lon and nav_lat fields in cases where wholly land areas have been omitted from a parallel run (i.e. jpnij .ne. jpni*jpnj). The corrections are applied after the collation phase. If this argument is supplied and the output file exists then the collation phase is not performed but the coordinate corrections are still applied. In the latter scenario the (otherwise) mandatory inputfile argument is not required. [-n processor_offset ] Optional argument. Start collating from this processor number and process domains in order, cycling back through 0 if necessary. This is useful to prevent multiple simulataneous accesses when running nocscombine in a task-farming environment [-v] Optional argument. Switches on verbose reporting for debugging [-s] Optional argument. Normal behaviour is to show a limited amount of progress information. This option runs the utility without any output to stdout. [-showhaloes] Optional argument. Early versions of nocscombine erroneously copied across the halo rows and columns too. Potentially producing lines of unset values if the halo points were not set in the individual restart files (as could happen for some purely diagnostic fields). Use -showhaloes to reproduce this feature if required. [-d] comma-separated list of variables Collate only the named datasets [-ts] time-slice (integer) to begin extraction at [-te] time-slice (integer) to end extraction at. If the -te option is not used then only one time-instance is extracted (as set by the -ts option) Examples: --------- nocscombine -f ORCA025-N10_1m_19670913_19680410_grid_T_0220.nc \ -o N10_1967_Tvars.nc \ -d "sosstsst,sosaline,sossheig,sowaflep,sowaflup,sorunoff,sowaflcd, sosalflx,sohefldo,soshfldo,somxl010,somixhgt,soicecov,sohefldp, sowafldp,sosafldp,sobowlin" \ -ts 1 -te 4 On Hector the Lustre filesystem can be used to speed up i/o by "striping" the named output file: lfs setstripe N10_nov1967_pt.nc 0 -1 3 nocscombine -f ORCA025-N10_1m_19670913_19680410_grid_T_0220.nc \ -o N10_nov1967_pt.nc -d votemper -ts 2 N10_nov1967_pt.nc [ 0] [ 1] [ 2] .......... Completed in 148.805 seconds lfs setstripe N10_nov1967_s.nc 0 -1 3 nocscombine -f ORCA025-N10_1m_19670913_19680410_grid_T_0220.nc \ -o N10_nov1967_s.nc -d vosaline -ts 2 N10_nov1967_s.nc [ 0] [ 1] [ 2] .......... Completed in 147.961 seconds
NOCSCOMBINE.tar tarball includes several
Makefiles but it is almost certainly necessary to create your own
Makefile to set the
and LIBS variables appropriately.
This repository contains
Makefile.jasper to build nocscombine on
jasper.westgrid.ca using the values:
FC = ifort -fixed -80 -O3 -DLARGE_FILE -c LDR = ifort -O3 -fixed -o nocscombine NCHOME = /lustre/jasper/software/netcdf/netcdf-4.1.3 LIBS = -L$(NCHOME)/lib -I$(NCHOME)/include -lnetcdf -lnetcdff -lhdf5_hl -lhdf5 -lz -lsz