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On 02/22/2017 10:46 AM, Zhiyu (Drew) Li wrote:
Hi there, I am playing with the parallel-netcdf-c examples to learn if I could apply this technology to improve netcdf i/o in my project. I got some questions about this example tst_parallel4.c found at https://github.com/Unidata/netcdf-c/blob/master/nc_test4/tst_parallel4.c <https://github.com/Unidata/netcdf-c/blob/master/nc_test4/tst_parallel4.c>. I saw the statements "nc_var_par_access(ncid, varid, NC_COLLECTIVE)" and "nc_var_par_access(ncid, varid, NC_INDEPENDENT)" are commented out on lines 133 and 134 (https://github.com/Unidata/netcdf-c/blob/master/nc_test4/tst_parallel4.c#L133 <https://github.com/Unidata/netcdf-c/blob/master/nc_test4/tst_parallel4.c#L133>). Q1: Is this nc_var_par_access() statement optional?
It's optional. I like to add it to make explicit if I am requesting indepnedent i/o or collective i/o. Long ago the docs and the implementation differed on what was the default. I make it explicit and don't have to worry.
Q2: I enabled each of the two lines one at a time to test NC_COLLECTIVE
mode and NC_INDEPENDENT mode separately. Each test was ran with 4
processes (mpiexec -np 4 ./tst_parallel4). Then I used jumpshot to
visualize the clog2 files they produced. The snapshots are attached
below. The green bars represent "Write to netcdf file" events (I turn
off other bars (other mpi events) in visualization).
Inline image 1
NC_INDEPENDENT mode
In NC_INDEPENDENT mode, the Write events occurred at different time
steps in the 4 processes (the x-axis is time step). If I understood it
correctly, although we had 4 processes running in parallel, the Write
events still happened in sequence, not in parallel, because p0 wrote
first, then p1 wrote, and then p2, and then p3 wrote last. Is it
supposed to be like this???
It is. Look a few lines above where the test inserts some sleep calls if USE_MPE is defined (I guess to make it more visually interesting?)
https://github.com/Unidata/netcdf-c/blob/master/nc_test4/tst_parallel4.c#L130
NC_COLLECTIVE mode
In NC_COLLECTIVE mode, p0 started writing first but its Write event
lasted until the fourth process p3 finished writing. I thought all the
four process should start and stop writing at the same time in
NC_COLLECTIVE mode???
If there are sleep calls in the test, then some processes will reach the collective call later. The test does demonstrate the one big drawback of collective calls: if there is skew, then a "pseudo-synchronization" occurs as the first process cannot make progress until the last process enters the collective.
(note: in this case all processes leave the collective at about the same time. that's not necessarily guaranteed by a collective operation, not even MPI_BARRIER).
The MPE traces you have shown are consistent with the test.I'm so pleased you are using MPE. We haven't had funding to work on it for a few years, but it still comes in handy!
==rob
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