The vpic_reconnection_tutorial from xiaocanli

vpic_reconnection_tutorial's Introduction

Hi there, this is Xiaocan Li (李晓璨) 👋

I am a research scientist working at the Department of Physics and Astronomy of Dartmouth College now.
I am studying particle acceleration processes in magnetic reconnection and plasma turbulence through numerical simulations. I aim to explain the origin of the energetic particles in solar flares and other explosive astrophysical events.
🌱 I’m currently working on
- stochastic-parker: a code solving particle transport equations using the stochastic method.
📫 How to reach me:
- Email: [email protected]
- Website: https://xiaocanli.github.io/
- My Github: xiaocanli

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vpic_reconnection_tutorial's Issues

Error during deck compilation

Hi,

I was trying to follow the HDF5 VPIC guide for installing VPIC on perlmutter. I cloned VPIC from https://github.com/xiaocanli/vpic, as suggested in the manual.

However, I got error during the compilation of the reconnection deck. I modified Makefile_permutter_cpu to correctly identify the build/bin directory, but then

> make -f Makefile_perlmutter_cpu
/global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/build/bin/vpic reconnection.cc
/opt/cray/pe/craype/2.7.20/bin/CC  -DDISABLE_DYNAMIC_RESIZING -DMIN_NP=128 -DVPIC_USE_LEGACY_SORT -DVPIC_USE_OPENMP -DUSE_V4_AVX2 -DUSE_V8_AVX2 -DVPIC_ENABLE_HDF5 -g -O2 -ffast-math -fno-unsafe-math-optimizations -fomit-frame-pointer -fno-strict-aliasing -Winline -rdynamic -dynamic -fopenmp -I -std=c++11  -DVPIC_USE_LEGACY_SORT -fopenmp -DVPIC_USE_OPENMP -DUSE_V4_AVX2 -DUSE_V8_AVX2 -I. -I/global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/src -I -std=c++11  -DVPIC_USE_LEGACY_SORT -fopenmp -DVPIC_USE_OPENMP -DUSE_V4_AVX2 -DUSE_V8_AVX2 -DINPUT_DECK=reconnection.cc /global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/deck/main.cc /global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/deck/wrapper.cc -o reconnection.Linux -Wl,-rpath,/global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/build -L/global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/build -lvpic     -lpthread -ldl
In file included from ./test_particle/tracer.hh:87,
                 from ./reconnection.cc:14,
                 from /global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/deck/wrapper.cc:4:
./test_particle/test_particle.h:8:10: fatal error: Kokkos_DualView.hpp: No such file or directory
    8 | #include "Kokkos_DualView.hpp"
      |          ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [Makefile_perlmutter_cpu:6: all] Error 1

The same thing occurred when running compile_deck.sh:

./compile_deck.sh perlmutter_cpu

Note: the module "craype-hugepages2M" cannot be unloaded because it was not loaded.


Currently Loaded Modules:
  1) craype-x86-milan                        9) craype/2.7.20            17) craype-accel-nvidia80
  2) libfabric/1.15.2.0                     10) gcc/11.2.0               18) gpu/1.0
  3) craype-network-ofi                     11) perftools-base/23.03.0   19) conda/Miniconda3-py311_23.5.2-0
  4) xpmem/2.6.2-2.5_2.27__gd067c3f.shasta  12) cpe/23.03                20) evp-patch
  5) PrgEnv-gnu/8.3.3                       13) xalt/2.10.2              21) python/3.11                     (dev)
  6) cray-dsmml/0.2.2                       14) Nsight-Compute/2022.1.1  22) cray-hdf5-parallel/1.12.2.3     (io)
  7) cray-libsci/23.02.1.1                  15) Nsight-Systems/2022.2.1
  8) cray-mpich/8.1.25                      16) cudatoolkit/11.7

  Where:
   dev:  Development Tools and Programming Languages
   io:   Input/output software



lfs setstripe: setstripe error for 'spectrum': Inappropriate ioctl for device
lfs setstripe: setstripe error for 'particle': Inappropriate ioctl for device
lfs setstripe: setstripe error for 'tracer': Inappropriate ioctl for device
lfs setstripe: setstripe error for 'field_hdf5': Inappropriate ioctl for device
lfs setstripe: setstripe error for 'hydro_hdf5': Inappropriate ioctl for device
/global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/build/bin/vpic reconnection.cc
/opt/cray/pe/craype/2.7.20/bin/CC  -DDISABLE_DYNAMIC_RESIZING -DMIN_NP=128 -DVPIC_USE_LEGACY_SORT -DVPIC_USE_OPENMP -DUSE_V4_AVX2 -DUSE_V8_AVX2 -DVPIC_ENABLE_HDF5 -g -O2 -ffast-math -fno-unsafe-math-optimizations -fomit-frame-pointer -fno-strict-aliasing -Winline -rdynamic -dynamic -fopenmp -I -std=c++11  -DVPIC_USE_LEGACY_SORT -fopenmp -DVPIC_USE_OPENMP -DUSE_V4_AVX2 -DUSE_V8_AVX2 -I. -I/global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/src -I -std=c++11  -DVPIC_USE_LEGACY_SORT -fopenmp -DVPIC_USE_OPENMP -DUSE_V4_AVX2 -DUSE_V8_AVX2 -DINPUT_DECK=reconnection.cc /global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/deck/main.cc /global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/deck/wrapper.cc -o reconnection.Linux -Wl,-rpath,/global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/build -L/global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/build -lvpic     -lpthread -ldl
In file included from ./test_particle/tracer.hh:87,
                 from ./reconnection.cc:14,
                 from /global/homes/h/hyzhou/vpic/vpic_hdf5_rebase/deck/wrapper.cc:4:
./test_particle/test_particle.h:8:10: fatal error: Kokkos_DualView.hpp: No such file or directory
    8 | #include "Kokkos_DualView.hpp"
      |          ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [Makefile_perlmutter_cpu:6: all] Error 1