MD dftd4 in version 2025.1
Somayeh Ahmadkhani
Dear CP2K developers and users,
I am running CP2K for a water system containing approximately 2,600 molecules.
With CP2K version 7, I was able to save around 50 steps in a 12-hour run. However, after switching to a newer version, I now obtain data for only 2 steps in the same 12-hour period. Furthermore, when using the DFT-D4 correction, I can only obtain 1 step per 12 hours.
Could you please help me understand and resolve this performance issue?
I have attached my SBATCH script and input file for more details, in case they are useful.
Thank you in advance for your support.
Best regards,
my SBATCH script is as follows#!/bin/bash
#SBATCH --job-name=cp2k
#SBATCH --ntasks=64
#SBATCH --mem=300G
#SBATCH --nodes=4
#SBATCH --time=12:00:00
#SBATCH --error=cp2k_job.err
module load intel/
module load impi/2021.14
module load cp2k/2025.1
export OMP_NUM_THREADS=1
ulimit -s unlimited
mpirun cp2k.psmp -i PBE_water.inp -o out_put.out
Frederick Stein
Somayeh Ahmadkhani
Dear Frederick,
Thank you for your reply. Please find the details below:
Hardware: I am running on an HPC cluster with CPU model and I was shared my running script before.
System size: My system contains 2454 molecules of water around 7362 atoms in total.
Compilation details:
For CP2K version 7, as follows
CP2K version 7.1
Source code revision git:e635599
cp2kflags: omp libint fftw3 libxc elpa parallel mpi3 scalapack xsmm spglib mkl
compiler: Intel(R) Fortran Intel(R) 64 Compiler Classic for applications running on Intel(R) 64, Version 2021.13.0 Build 20240602_000000
compiler options:
-I/sw/chem/cp2k/2024.1/cpu-clx/intel_2024.2-impi_2021.13//spglib-2.5
.0/install/include -I/sw/chem/cp2k/2024.1/cpu-clx/intel_2024.2-impi_
2021.13//elpa-new_release_2023.11.001/install/include/elpa_openmp-20
23.11.001/modules -I/sw/chem/cp2k/2024.1/cpu-clx/intel_2024.2-impi_2
021.13//elpa-new_release_2023.11.001/install/include/elpa_openmp-202
3.11.001/elpa -I/sw/chem/cp2k/2024.1/cpu-clx/intel_2024.2-impi_2021.
13//libxsmm-1.17/install/include -I/sw/chem/cp2k/7.1/clx.el9/intel_2
024.2-impi_2021.13//libxc-4.3.4/install/include -I/sw/chem/cp2k/2024
.1/cpu-clx/intel_2024.2-impi_2021.13//libint-v2.6.0-cp2k-lmax-5/inst
all/include -I/sw/compiler/intel/oneapi/mkl/2024.2/include/fftw/ -I/
sw/compiler/intel/oneapi/mkl/2024.2/include -I/sw/chem/cp2k/7.1/clx.
el9/intel_2024.2-impi_2021.13/cp2k-7.1/src/start/ -I/sw/chem/cp2k/7.
1/clx.el9/intel_2024.2-impi_2021.13/cp2k-7.1/obj/local-static/psmp/e
xts/dbcsr -I/sw/comm/impi/mpi/2021.13/include/mpi -I/sw/comm/impi/mp
i/2021.13/include -I/sw/comm/impi/mpi/2021.13/include/mpi -c -O2 -fP
IC -fp-model precise -funroll-loops -qopenmp -qopenmp-simd -xCORE-AV
X512 -m64 -D__parallel -D__MPI_F08 -D__SPGLIB -D__ELPA -D__LIBXSMM -
D__LIBXC -D__LIBINT -D__FFTW3 -D__FFTW3_MKL -D__MKL -D__SCALAPACK -d
iag-disable=8291 -diag-disable=8293 -diag-disable=10448 -fpp -fpscom
p logicals -free -std08 -D__COMPILE_ARCH="local-static" "-D__COMPILE
_DATE="Fri Sep 27 15:48:17 CEST 2024"" -D__COMPILE_HOST="bcn1357" -D
__COMPILE_REVISION="git:e635599" -D__DATA_DIR="/sw/chem/cp2k/7.1/clx
.el9/intel_2024.2-impi_2021.13/cp2k-7.1/data" -D__SHORT_FILE__="star
t/cp2k.F"
For CP2K version 2025.1,
CP2K version 2025.1
Source code revision git:9635df4
cp2kflags: omp libint fftw3 fftw3_mkl libxc elpa parallel scalapack mpi_f08 cosma xsmm spglib mkl libdftd4 sirius hdf5
compiler: Intel(R) Fortran Intel(R) 64 Compiler Classic for applications running on Intel(R) 64, Version 2021.13.1 Build 20240703_000000
compiler options:
-I/home/bzfbpela/.local/easybuild/software/sirius/7.6.1-clx.el9.inte
l//include/sirius -I/home/bzfbpela/.local/easybuild/software/pugixml
/1.15-clx.el9.intel//include -I/home/bzfbpela/.local/easybuild/softw
are/spla/1.6.1-clx.el9.intel//include -I/home/bzfbpela/.local/easybu
ild/software/SpFFT/1.1.0-clx.el9.intel//include -I/sw/dataformats/hd
f5/1.14.4.3/clx.el9/intel/include -I/sw/numerics/gsl/2.8/x86_64.el9/
/include -I/home/bzfbpela/.local/easybuild/software/spglib/2.5.0-clx
.el9.intel//include -I/home/bzfbpela/.local/easybuild/software/elpa/
2024.05.001-clx.el9.intel-ifort//include/elpa_openmp-2024.05.001/mod
ules -I/home/bzfbpela/.local/easybuild/software/elpa/2024.05.001-clx
.el9.intel-ifort//include/elpa_openmp-2024.05.001/elpa -I/home/bzfbp
ela/.local/easybuild/software/libxsmm/1.17-clx.el9.intel//include -I
/home/bzfbpela/.local/easybuild/software/libxc/6.2.2-clx.el9.intel//
include -I/home/bzfbpela/.local/easybuild/software/libint-CP2K/2.6.0
-clx.el9.intel//include -I/home/bzfbpela/.local/easybuild/software/C
OSMA/2.6.6-clx.el9.intel//include/cosma -I/home/bzfbpela/.local/easy
build/software/dftd4/3.7.0-clx.el9.intel//include/ -I/home/bzfbpela/
.local/easybuild/software/dftd4/3.7.0-clx.el9.intel//include//mctc-l
ib/modules/ -I/home/bzfbpela/.local/easybuild/software/dftd4/3.7.0-c
lx.el9.intel//include//dftd4/Intel-2021.1.0.20240703/ -I/sw/compiler
/intel/oneapi/mkl/2024.2/include/fftw/ -I/sw/compiler/intel/oneapi/m
kl/2024.2/include -I/home/bzfbpela/.local/easybuild/build/CP2K/2025.
1/system-system-clx.el9.intel-ifort/cp2k-2025.1/src/start/ -I/home/b
zfbpela/.local/easybuild/build/CP2K/2025.1/system-system-clx.el9.int
el-ifort/cp2k-2025.1/obj/CP2K-2025.1-clx.el9.intel-ifort/psmp/exts/d
bcsr -I/sw/comm/impi/mpi/2021.14/include/mpi -I/sw/comm/impi/mpi/202
1.14/include -I/sw/comm/impi/mpi/2021.14/include/mpi -c -O2 -fPIC -f
p-model=precise -funroll-loops -qopenmp -qopenmp-simd -xCORE-AVX512
-m64 -traceback -D__parallel -D__MPI_F08 -D__INTEL_COMPILER -D__DATA
_DIR= -D__SIRIUS -D__SPLA -D__SPFFT -D__HDF5 -D__GSL -D__SPGLIB -D__
ELPA -D__LIBXSMM -D__LIBXC -D__LIBINT -D__COSMA -D__DFTD4 -D__FFTW3
-D__FFTW3_MKL -D__MKL -D__SCALAPACK -diag-disable=8291 -diag-disable
=8293 -diag-disable=10448 -fpp -fpscomp logicals -free -std08 -D__CO
MPILE_ARCH="CP2K-2025.1-clx.el9.intel-ifort" "-D__COMPILE_DATE="Mon
Jun 16 17:51:46 CEST 2025"" -D__COMPILE_HOST="blogin7" -D__COMPILE_R
EVISION="git:9635df4" -D__DATA_DIR="/home/bzfbpela/.local/easybuild/
build/CP2K/2025.1/system-system-clx.el9.intel-ifort/cp2k-2025.1/data
" -D__SHORT_FILE__="start/cp2k.F"
Profiles: I will prepare and share profiling results shortly. In the meantime, I will run CP2K in ENERGY_FORCEmode, as you suggested, to gather more information.
I was also shared input file earlier.
Best regards,
Somayeh Ahmadkhani
On 12 Aug 2025, at 10:34 AM, Frederick Stein <f.s...@hzdr.de> wrote:
Dear Somayeh,Generally, there a bunch of changes between versions 7 and 2025.2 making it hard to tell what the exact issue is. Can you provide more details regarding- What hardware are you running on?
- How many atoms (or molecules etc.) does you system contain? My first guess considering your box size size and your files names is ca. 4096 H2O molecules.
Frederick Stein
Que Zhu
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Johann Pototschnig
- -
- T I M I N G -
- -
-------------------------------------------------------------------------------
SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
CP2K 1 1.0 0.005 0.005 1.673 1.673
qs_energies 25 2.0 0.001 0.001 1.659 1.659
scf_env_do_scf 25 3.0 0.000 0.000 1.384 1.384
scf_env_do_scf_inner_loop 377 4.1 0.027 0.027 1.382 1.382
qs_scf_new_mos 377 5.1 0.003 0.003 1.266 1.266
...