Hi
Thanks for your help the other day(Only 1cpu is used among multicore-cpu [SOLVED]).
I could start multi-core process on abinit by writing as "enable_openmp="yes"" in the build.ac.
But then a problem has occurred.
While it's calculation, Abinit stops at the following error.
#chkpawovlp : ERROR -
PAW SPHERES ARE OVERLAPPING !
#Distance between atoms 3 and 37 is : 1.70352
PAW radius of the sphere around atom 3 is: 2.32398
PAW radius of the sphere around atom 37 is: 0.90083
This leads to a (voluminal) overlap ratio of 90.75 %
--From log file ------
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
--- !ERROR
message: |
Action: 1- decrease cutoff radius of PAW dataset
OR 2- ajust "pawovlp" input variable to allow overlap (risky)
src_file: chkpawovlp.F90
src_line: 183
...
leave_new : decision taken to exit ...
----------------------------------------------------------------------------------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode 14.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
----------------------------------------------------------------------------------------------------------------------------------------------------
Even if it's made pawovlp=-1, a strange calculation result is generated.
(Such as nuclear fusion jokingly )
For example calculation is normally running to n = about 7, and a problem occurs critically after it.
The error has occurred using this command.
$ mpirun --allow-run-as-root -n 6 abinit < $name.files > $name.log
I think that some kind of setting of OpenMPI is related to this problem.
I would appreciate it if you would give me some advice.
Best regards
Haruyuki Satou
###############################################################################################
Only 1cpu is used among multicore-cpu [SOLVED]
Postby anemonekgo » Sun Oct 11, 2015 2:34 am
Hi
I'm a beginner.
Recently I installed Abinit 7.10.4 on CentOS 6.7.
My PC is Corei7 990X_ex.(6core/12T) -RAM24G -SSD256G.
When look after a system manager when I perform Running of abinit;
I'm using only 1CPU(100%) in multicore-cpu(It is displayed 12CPU).
What setting will this have a problem with?
I'm getting good calculation results , but run time is long.
Please tell me what to do to.
Best regards,
Haruyuki Satou
======================================================================
The following configuration information
======================================================================
#build.ac file
------------------------------------------------------------
enable_mpi="yes"
enable_mpi_io="yes"
with_mpi_prefix="/usr/lib64/openmpi"
with_trio_flavor="netcdf+etsf_io"
#with_netcdf_incs="-I/usr/include"
#with_netcdf_libs="-L/usr/lib64 -lnetcdf -lnetcdff"
with_fft_flavor="fftw3"
with_fft_incs="-I/usr/include/"
with_fft_libs="-L/usr/local/lib64/gnu/fftw/3.3.4/lib -lfftw3 -lfftw3f"
with_linalg_flavor="atlas"
with_linalg_libs="-L/usr/lib64/atlas -llapack -lf77blas -lcblas -latlas"
#with_dft_flavor="atompaw+libxc"
#with_dft_flavor="atompaw+libxc+wannier90"
with_dft_flavor="atompaw+bigdft+libxc+wannier90"
enable_gw_dpc="yes"
#enable_maintainer_checks="no"
#enable_test_timeout="yes"
------------------------------------------------------------
$./configure --with-config-file=./build.ac
#no error
==============================================================================
=== Final remarks ===
==============================================================================
Summary of important options:
* C compiler : gnu version 4.9
* Fortran compiler: gnu version 4.9
* architecture : unknown unknown (64 bits)
* debugging : basic
* optimizations : standard
* OpenMP enabled : no (collapse: ignored)
* MPI enabled : yes
* MPI-IO enabled : yes
* GPU enabled : no (flavor: none)
* TRIO flavor = netcdf-fallback+etsf_io-fallback
* TIMER flavor = abinit (libs: ignored)
* LINALG flavor = atlas (libs: user-defined)
* ALGO flavor = none (libs: ignored)
* FFT flavor = fftw3 (libs: user-defined)
* MATH flavor = none (libs: ignored)
* DFT flavor = libxc-fallback+atompaw-fallback+bigdft-fallback+wannier90-fallback
Configuration complete.
You may now type "make" to build ABINIT.
(or, on a SMP machine, "make mj4", or "make multi multi_nprocs=<n>")
==============================================================================
$ make mj4
#no error
==============================================================================
$ make install
#no error
**************************************************************************************************
$cd tests
$./runtests.py -j6 fast
Test suite completed in 9.63 s (average time for test = 2.63 s, stdev = 2.63 s)
failed: 0, succeeded: 10, passed: 1, skipped: 0, disabled: 0
Suite failed passed succeeded skipped disabled run_etime tot_etime
fast 0 1 10 0 0 28.92 30.20
$./runtests.py paral -j6
Test suite completed in 86.06 s (average time for test = 4.48 s, stdev = 12.80 s)
failed: 0, succeeded: 14, passed: 7, skipped: 69, disabled: 0
[paral][t06_MPI1][np=1] has run_etime 65.40 s
[paral][t51_MPI1-t52_MPI1-t53_MPI1] has run_etime 32.28 s
[paral][t59_MPI1][np=1] has run_etime 30.34 s
[paral][t71_MPI1][np=1] has run_etime 72.22 s
[paral][t73_MPI1][np=1] has run_etime 37.03 s
[paral][t91_MPI1][np=1] has run_etime 42.28 s
Suite failed passed succeeded skipped disabled run_etime tot_etime
paral 0 7 14 69 0 403.01 406.55
**************************************************************************************************
anemonekgo
###############################################################################################
Posts: 3
Joined: Tue Sep 22, 2015 3:54 am
Top
Re: Only 1cpu is used among multicore-cpu
Postby Jordan » Mon Oct 12, 2015 7:58 am
You did not compile abinit with OpenMP support *threads" which means that if you want to use, let say 6 cores per calculation, you have to launch abinit with mpirun like
CODE: SELECT ALL
mpirun -n 6 abinit < files > log
Or for the test suite, you need to specify -n 6 instead of -j 6. For the testsuite, the -j option means launch 6 tests at the same time (parallel launch of several tests, each one runs on 1 cpus) whereas -n X means run each test on X cpus.
So for instance, runtests.py -n 6 -j 2 means do 2 tests at the same time whit 6 mpi processes for each test. So you would use 6*2=12 cores.
Cheers
Jordan
Jordan
###############################################################################################
Posts: 186
Joined: Tue May 07, 2013 9:47 am
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Re: Only 1cpu is used among multicore-cpu
Postby anemonekgo » Tue Oct 13, 2015 6:31 am
Dear Jordan
Thanks for all your help.
I could start multi-core process on abinit by writing as "enable_openmp="yes"" in the build.ac.
I failed before when it was "./configure --enable-openmp"( --> * OpenMP enabled : yes * MPI enabled : no * MPI-IO enabled : no).
Then I tried "mpirun -n 6 abinit < files > log" command with " --allow-run-as-root " option.
As a result of calculating in "BaTiO3" (ecut=15,ngkpt=8x8x8), and having tested it, I was able to shorten calculation time (90min. ---> 5min.).
What you just said really comforted me, thank you.
Sincerely.
Haruyuki Satou
anemonekgo
###############################################################################################
Posts: 3
Joined: Tue Sep 22, 2015 3:54 am
Top
Re: Only 1cpu is used among multicore-cpu
Postby anemonekgo » Fri Oct 16, 2015 11:18 am
Hi
Thanks for your help the other day.
Then a problem has happened.
While it's calculation, Abinit stops at the following error.
#chkpawovlp : ERROR -
PAW SPHERES ARE OVERLAPPING !
#Distance between atoms 3 and 37 is : 1.70352
PAW radius of the sphere around atom 3 is: 2.32398
PAW radius of the sphere around atom 37 is: 0.90083
This leads to a (voluminal) overlap ratio of 90.75 %
--from log file ------
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
--- !ERROR
message: |
Action: 1- decrease cutoff radius of PAW dataset
OR 2- ajust "pawovlp" input variable to allow overlap (risky)
src_file: chkpawovlp.F90
src_line: 183
...
leave_new : decision taken to exit ...
----------------------------------------------------------------------------------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode 14.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
----------------------------------------------------------------------------------------------------------------------------------------------------
Even if it's made pawovlp=-1, a strange calculation result is generated.
(Such as nuclear fusion jokingly )
For example calculation is normally running to n = about 7, and a problem occurs critically after it.
The error has occurred using this command.
$ mpirun --allow-run-as-root -n 6 abinit < $name.files > $name.log
I think trouble of OpenMPI.
I would appreciate it if you would give me some advice.
Best regards
Haruyuki Satou
ERROR - PAW SPHERES ARE OVERLAPPING !
Moderator: bguster