how to bind threads

Asked by 翟明星 on 2020-08-30

Dear all:

when I run the siesta binary, the output tip information says " OpenMP NOT bound". Whether binding the threads is needed? if so, how to bind the threads.Thanks!

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Siesta Version : v4.1-b4
Architecture : unknown
Compiler version: GNU Fortran (GCC) 5.4.0
Compiler flags : /PARA2/blsc558/software/openmpi/4.0.0_gcc_5.4.0/bin/mpif90 -O2 -fPIC -ftree-vvectorize -march=native -fopenmp
PP flags : -DMPI -DFC_HAVE_ABORT -DCDF -DNCDF -DNCDF_4
Libraries : libncdf.a libfdict.a /PARA2/blsc558/software/lib/scalapack/2.1.0_gcc_5.4.0/liib/libscalapack.a -L/PARA2/blsc558/software/lib/openblas/0.3.10_gcc_5.4.0/lib -lopenblas libncdf.a libfdict.a -fopenmp -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
PARALLEL version
NetCDF support
NetCDF-4 support

* Running in serial mode with MPI
* Running 24 OpenMP threads.
* Running 24 processes.
* OpenMP version 201307
* OpenMP NOT bound (please bind threads!)
* OpenMP runtime schedule DYNAMIC, chunks 1
** OpenMP runtime schedule DYNAMIC, chunks 16
>> Start of run: 30-AUG-2020 15:04:29

                           ***********************
                           * WELCOME TO SIESTA *
                           ***********************

reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.37116
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Question information

Language:
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Status:
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For:
Siesta Edit question
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Solved by:
翟明星
Solved:
2020-08-31
Last query:
2020-08-31
Last reply:
2020-08-30
Nick Papior (nickpapior) said : #1

It isn't strictly needed, but may improve performance.

I would recommend you to ask your local HPC administrator whether your
scheduler may do this for you :)

Otherwise look into OMP_PROC_BIND environment variable to see what to
choose, note that the best performing setting may be system dependent, so I
would advice you to do some benchmarks for your setup.

Den søn. 30. aug. 2020 kl. 09.25 skrev 翟明星 <
<email address hidden>>:

> New question #692666 on Siesta:
> https://answers.launchpad.net/siesta/+question/692666
>
> Dear all:
>
> when I run the siesta binary, the output tip information says " OpenMP NOT
> bound". Whether binding the threads is needed? if so, how to bind the
> threads.Thanks!
>
>
>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> Siesta Version : v4.1-b4
> Architecture : unknown
> Compiler version: GNU Fortran (GCC) 5.4.0
> Compiler flags :
> /PARA2/blsc558/software/openmpi/4.0.0_gcc_5.4.0/bin/mpif90 -O2 -fPIC
> -ftree-vvectorize -march=native -fopenmp
> PP flags : -DMPI -DFC_HAVE_ABORT -DCDF -DNCDF -DNCDF_4
> Libraries : libncdf.a libfdict.a
> /PARA2/blsc558/software/lib/scalapack/2.1.0_gcc_5.4.0/liib/libscalapack.a
> -L/PARA2/blsc558/software/lib/openblas/0.3.10_gcc_5.4.0/lib -lopenblas
> libncdf.a libfdict.a -fopenmp -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
> PARALLEL version
> NetCDF support
> NetCDF-4 support
>
> * Running in serial mode with MPI
> * Running 24 OpenMP threads.
> * Running 24 processes.
> * OpenMP version 201307
> * OpenMP NOT bound (please bind threads!)
> * OpenMP runtime schedule DYNAMIC, chunks 1
> ** OpenMP runtime schedule DYNAMIC, chunks 16
> >> Start of run: 30-AUG-2020 15:04:29
>
> ***********************
> * WELCOME TO SIESTA *
> ***********************
>
> reinit: Reading from standard input
> reinit: Dumped input in INPUT_TMP.37116
>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>
> --
> You received this question notification because you are an answer
> contact for Siesta.
>

--
Kind regards Nick

翟明星 (mxzhai) said : #2

OK,thanks!