CDO

Hi Ikmal,

CDO executes the operator steps from right to left.

That means it executes

1. '-cat $infile' then it pipes the result to
2. '-sellonlatbox,98,122,-15,15' and then it pipes the result to
3. '-monmean'

Hi Karin,

It's taking quite some time to execute those two lines of code. I tried reversing the order of the operators like so:

#!/bin/bash

infile=/Volumes/malrosie/data/satellite/chlor_a/cmems/mapped/4km/daily/*.nc
outfile=/Volumes/malrosie/data/satellite/chlor_a/cmems/mapped/4km/19970904_monthly_mean.nc

cdo -f nc -monmean -cat -sellonlatbox,98,122,-15,15 $infile $outfile

But this error showed up:

cdo(1) cat: Process started
cdo(2) sellonlatbox: Process started
cdo(1) cat:     0%cdf_create        : ncid=-1  mode=512  chunksizehint=0  file=/Volumes/malrosie/data/satellite/chlor_a/cmems/mapped/4km/daily_98125-1515/

Error (cdf_create): /Volumes/malrosie/data/satellite/chlor_a/cmems/mapped/4km/daily_98125-1515/: No such file or directory

I guess the size is not compatible, when sellonlatbox is called first. Is there any other way to speed up the process?

Thank you.

Hi again, Karin.

Wrong output! Here's the output:

cdo(1) cat: Process started
cdo(2) sellonlatbox: Process started
cdo(1) cat:     0%cdo(2) sellonlatbox: Processed 74649600 values from 2 variables over 1 timestep.

cdo(1) cat (Abort): Grid size of the input parameter CHL do not match!
[bt] Execution path:
[bt] 0   cdo                                 0x00000001007fcccc show_stackframe + 52
[bt] 1   cdo                                 0x00000001007fb960 reshGetElem + 348
[bt] 2   cdo                                 0x00000001007fb7f8 reshGetValue + 12
[bt] 3   cdo                                 0x000000010082c508 vlistInqTaxis + 68
[bt] 4   cdo                                 0x0000000100838000 streamClose + 688
[bt] 5   cdo                                 0x00000001007fb1f0 reshListDestruct + 172
[bt] 6   cdo                                 0x00000001007fa830 namespaceDelete + 88
[bt] 7   cdo                                 0x00000001007fcb40 listDestroy + 88
[bt] 8   libsystem_c.dylib                   0x00000001bfaa1dd4 __cxa_finalize_ranges + 480
[bt] 9   libsystem_c.dylib                   0x00000001bfaa1b68 exit + 44
[bt] 10  cdo                                 0x000000010056fed4 _Z15define_varnamesPKc + 0
[bt] 11  cdo                                 0x0000000100613b94 _Z9cdo_abortIJA256_cEEvRKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEEDpRKT_ + 212
[bt] 12  cdo                                 0x000000010071dd04 _Z13vlist_compareiii + 476
[bt] 13  cdo                                 0x00000001005a0ec4 _Z3CatPv + 396
[bt] 14  libsystem_pthread.dylib             0x00000001bfbb626c _pthread_start + 148
[bt] 15  libsystem_pthread.dylib             0x00000001bfbb108c thread_start + 8
ERROR, reshGetElem, resource_handle.c, line 415, called from vlist_to_pointer
errorString: "Error while trying to resolve the ID "vlistID" in `vlist_to_pointer()`: list element not found. The failed ID is 24" 

Thank you.

You can't use cat in front of another operator, it needs one or more files (see documentation https://code.mpimet.mpg.de/projects/cdo/embedded/cdo.pdf#subsection.2.2.2)

The order of the operators from your first try was ok. How fast CDO is depends on the number of files and operations you want to perform. If you only need one variable you can select it first and do the operations on only that variable.

For example do the operations only on the variable precip:

cdo -monmean \
    -sellonlatbox,98,122,-15,15 \
    -selname,precip \
    -cat '/Volumes/malrosie/data/satellite/chlor_a/cmems/mapped/4km/daily/*.nc' \
    /Volumes/malrosie/data/satellite/chlor_a/cmems/mapped/4km/19970904_monthly_mean.nc

Alright, I will do that. Thank you so much for the help.