[QE-users] How should I visualize outcomes of cp molecular dynamics
Dear All, I just tried to perform cpmd calculations which generated lots of files such as .cell, .con, .eig, .evp, .for, .hrs, .ncg, .nos, .pol, .pos, .spr, .the, .vel and .out formats. My question is which file can be used to visualize the dynamic process. Which software can be used to visualize it? Regards Dr. Jibiao Li, Department of Material Science and Engineering Yangtze Normal University Juxian Dadao 16#, Fuling, Chongqing, China Publons: https://publons.com/researcher/2283103/jibiao-li/ Email: jibia...@yznu.edu.cn, jibia...@foxmail.com, jibiao...@hotmail.com___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] [[QE-GPU]Can't find include file fftw3.f03(QE-7.0-rc1)
No matter how many places mention modifying QE make.inc on the internet, touching make.inc or Makefiles are **non-standard** practice and you are responsible and need to be capable of understanding and handling any failures. Instead, non-power users are expected to work with configure/cmake and make sure they recognize the intended libraries. In your case, configure didn't find a proper FFTW3 to use and decided to use internal FFTW and thus put __FFTW while you tried to override its decision and thus hit failure at compile time. FFTW3 is a bit unique, it is not a headless fortran library but requires files to be included like fftw3.f03. For this reason, both include path and library path need to be properly set on the compile command line. Clearly something is missing. Best, Ye === Ye Luo, Ph.D. Computational Science Division & Leadership Computing Facility Argonne National Laboratory On Tue, Dec 7, 2021 at 6:49 AM kuangll via users < users@lists.quantum-espresso.org> wrote: > Hi experts, > > I try to compile the QE - GPU version, with version qe-7.0-rc1. > > I use HPC SDK 21.9, and after successfully configuring, I modify the > DFLAGS in make.inc and use -D__FFTW3 instead of -D__FFTW. > Then error accur when compiling progress to this step: > > mpif90 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -mp -D__CUDA > -D__USE_CUSOLVER -D__FFTW3 -D__MPI -cuda -gpu=cc80,cuda11.4 > -I/qe/q-e-qe-7.0-rc1//external/devxlib/src > -I/qe/q-e-qe-7.0-rc1//external/devxlib/include -acc > -I/qe/q-e-qe-7.0-rc1//external/devxlib/src -I/qe/q-e-qe-7.0-rc1//include > -I/qe/q-e-qe-7.0-rc1//FoX/finclude -c la_types.f90 > > NVFORTRAN-F-0906-Can't find include file fftw3.f03 (fft_scalar.FFTW3.f90: > 40) > > NVFORTRAN/x86-64 Linux 21.9-0: compilation aborted > > NVFORTRAN-W-0006-Input file empty (fft_scalar.ESSL.f90) > > NVFORTRAN/x86-64 Linux 21.9-0: compilation completed with warnings > > NVFORTRAN-W-0006-Input file empty (fft_scalar.FFTW.f90) > > NVFORTRAN/x86-64 Linux 21.9-0: compilation completed with warnings > > make[1]: *** [../make.inc:16: fft_scalar.FFTW3.o] Error 2 > > make[1]: *** Waiting for unfinished jobs > > I check there's no file fftw3.f09 in LAXlib directory. Where can I get > this file? > > Thanks. > > --- > Lvlin Kuang > --- > > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] [[QE-GPU]Can't find include file fftw3.f03(QE-7.0-rc1)
On Tue, Dec 7, 2021 at 1:49 PM kuangll via users < users@lists.quantum-espresso.org> wrote: > > I check there's no file fftw3.f09 in LAXlib directory. > nor anywhere else: the name of the missing file is "fftw3.f03" Where can I get this file? > it's part of the FFTW3 distribution, not of QE Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 206, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] [[QE-GPU]Can't find include file fftw3.f03(QE-7.0-rc1)
Hi experts, I try to compile the QE - GPU version, with version qe-7.0-rc1. I use HPC SDK 21.9, and after successfully configuring, I modify the DFLAGS in make.inc and use -D__FFTW3 instead of -D__FFTW. Then error accur when compiling progress to this step: mpif90 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -mp -D__CUDA -D__USE_CUSOLVER -D__FFTW3 -D__MPI -cuda -gpu=cc80,cuda11.4 -I/qe/q-e-qe-7.0-rc1//external/devxlib/src -I/qe/q-e-qe-7.0-rc1//external/devxlib/include -acc -I/qe/q-e-qe-7.0-rc1//external/devxlib/src -I/qe/q-e-qe-7.0-rc1//include -I/qe/q-e-qe-7.0-rc1//FoX/finclude -c la_types.f90 NVFORTRAN-F-0906-Can't find include file fftw3.f03 (fft_scalar.FFTW3.f90: 40) NVFORTRAN/x86-64 Linux 21.9-0: compilation aborted NVFORTRAN-W-0006-Input file empty (fft_scalar.ESSL.f90) NVFORTRAN/x86-64 Linux 21.9-0: compilation completed with warnings NVFORTRAN-W-0006-Input file empty (fft_scalar.FFTW.f90) NVFORTRAN/x86-64 Linux 21.9-0: compilation completed with warnings make[1]: *** [../make.inc:16: fft_scalar.FFTW3.o] Error 2 make[1]: *** Waiting for unfinished jobs I check there's no file fftw3.f09 in LAXlib directory. Where can I get this file? Thanks. --- Lvlin Kuang --- ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] there are process with no planes
You are using more CPUs than there are planes of charge density in the FFT grid. Use less cpu or "-pd .true." option hth Dr. Lorenzo Paulatto IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université phone: +33 (0)1 442 79822 / skype: paulatz http://www.impmc.upmc.fr/~paulatto/ (https://link.getmailspring.com/link/39c67529-25a6-4931-be91-154856417...@getmailspring.com/0?redirect=http%3A%2F%2Fwww.impmc.upmc.fr%2F~paulatto%2F=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D) - https://anharmonic.github.io/ (https://link.getmailspring.com/link/39c67529-25a6-4931-be91-154856417...@getmailspring.com/1?redirect=https%3A%2F%2Fanharmonic.github.io%2F=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D) 23-24/423 B115, 4 place Jussieu 75252 Paris CX 05 On Dec 7 2021, at 10:49 am, Michal Husak wrote: > I am trying to run QE 6.8 on a supercomputer node with 128 cores ... > I use pure MPI parallelization > Run on 16 and 32 cores works OK ... > > Run on 64+ cores ends with following error: > Error in routine fft_type_set (6): > there are processes with no planes. Use pencil decomposition (-pd .true.) > > Can anybody explain what it means ? > Is my system to simple to it can not feed all cores ? > Where can I enter the -pd .true. option ? > > Michal Husak > UCT Prague > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] there are process with no planes
I am trying to run QE 6.8 on a supercomputer node with 128 cores ... I use pure MPI parallelization Run on 16 and 32 cores works OK ... Run on 64+ cores ends with following error: Error in routine fft_type_set (6): there are processes with no planes. Use pencil decomposition (-pd .true.) Can anybody explain what it means ? Is my system to simple to it can not feed all cores ? Where can I enter the -pd .true. option ? Michal Husak UCT Prague ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
