DOF with holes does not read correctly with mpi-serial

[gold2718]

I'm currently running into this on Hobart with a current (very close to master) version of CIME. I'm not sure how to get the PIO or NetCDF version in this situation.
The issue is doing a read_darray in serial mode seems to leave out the zero DOF entries so that the destination array has packed values.
With 1 task using MPI, things work fine and get the same answer as 48 tasks. The DOF arrays being passed to pio_initdecomp are the same but the read-in arrays are different.

As an example:

I have an array initially set to -1
The DOF is 1, 2, 3, 0, 4, 5, 0, 6, 7
The values on file are `1, 2, 3, 4, 5, 6, 7'

With holes, the correct read is:

array = 1, 2, 3, -1, 4, 5, -1, 6, 7

that is, the positive numbers were read into the correct places. In serial mode, I get:

array = 1, 2, 3, 4, 5, 6, 7, -1, -1

I see this behavior with both PIO1 (Nag) and PIO2 (PGI) on Hobart.

[jedwards4b]

@edhartnett is there a test of read with holes in the repo? So far unable to reproduce this problem and think it may be netcdf version. @gold2718 the netcdf version is listed in env_mach_specific

[jedwards4b]

@gold2718 I am not able to reproduce the problem as you describe it above, although I can reproduce the original cam-se problem.

[jedwards4b]

I figured out a test case, the problem is in mpi-serial and I will report it there.

[jedwards4b]

Moved to MCSclimate/MCT#53

[gold2718]

Moved to ESMCI/mpi-serial#11