Due to the current gap in continued funding from the U.S. National Science Foundation (NSF), the NSF Unidata Program Center has temporarily paused most operations. See NSF Unidata Pause in Most Operations for details.
Due to the current gap in continued funding from the U.S. National Science Foundation (NSF), the NSF Unidata Program Center has temporarily paused most operations. See NSF Unidata Pause in Most Operations for details.
On 02/24/2017 01:19 PM, Zhiyu (Drew) Li wrote:
Thanks Rob. I have another question. How much of performance gain would we get from using parallel-netcdf-c (or say MPI-IO) on a mainstream desktop PC (one multi-core cpu with one hdd or ssd)? Currently we dont have a parallel file system environment (software/hardware) at out lab.
If your goal is peak performance on one node, then I doubt MPI-IO approaches (either directly or through a library like Unidata NetCDF or Northwestern/Argonne Parallel-NetCDF) will outperform the serial version.
performance should be pretty close, though! Perhaps its worth a small serial cost so that you have code you can develop, debug, and test locally, then pick up and put on a supercomputer some day.
When it comes to I/O, there's not much gain to be had by having more cores. If you only have one HDD or SSD, then there's no benefit to having multiple writers/readers, aside from whatever benefit there is to having multiple operations in flight (serial libraries would benefit from that too, though).
==rob
Thanks Drew On Fri, Feb 24, 2017 at 11:50 AM, Rob Latham <robl@xxxxxxxxxxx <mailto:robl@xxxxxxxxxxx>> wrote: 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> <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> <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 <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 _______________________________________________ NOTE: All exchanges posted to Unidata maintained email lists are recorded in the Unidata inquiry tracking system and made publicly available through the web. Users who post to any of the lists we maintain are reminded to remove any personal information that they do not want to be made public. netcdfgroup mailing list netcdfgroup@xxxxxxxxxxxxxxxx <mailto:netcdfgroup@xxxxxxxxxxxxxxxx> For list information or to unsubscribe, visit: http://www.unidata.ucar.edu/mailing_lists/ <http://www.unidata.ucar.edu/mailing_lists/>
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