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fix for parallel HDF5 

if filters are applied, writing from one process does not work if the
file is opened for parallel write
This commit is contained in:
Martin Diehl 2021-08-15 08:04:27 +02:00
parent 497bf2c645
commit 4160c4fdb4
6 changed files with 45 additions and 33 deletions
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2
PRIVATE

@ -1 +1 @@
Subproject commit ad4a685d454271a400914c0334c017e3ac0dfc99 Subproject commit 7d783328ff5deac313eb7de951d51d19b5883b84

4
cmake/Compiler-GNU.cmake
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@ -12,9 +12,9 @@ endif ()
if (OPTIMIZATION STREQUAL "OFF") if (OPTIMIZATION STREQUAL "OFF")
set (OPTIMIZATION_FLAGS "-O0") set (OPTIMIZATION_FLAGS "-O0")
elseif (OPTIMIZATION STREQUAL "DEFENSIVE") elseif (OPTIMIZATION STREQUAL "DEFENSIVE")
set (OPTIMIZATION_FLAGS "-O2") set (OPTIMIZATION_FLAGS "-O2 -mtune=generic")
elseif (OPTIMIZATION STREQUAL "AGGRESSIVE") elseif (OPTIMIZATION STREQUAL "AGGRESSIVE")
set (OPTIMIZATION_FLAGS "-O3 -ffast-math -funroll-loops -ftree-vectorize") set (OPTIMIZATION_FLAGS "-O3 -march=native -ffast-math -funroll-loops -ftree-vectorize")
endif () endif ()
set (STANDARD_CHECK "-std=f2018 -pedantic-errors" ) set (STANDARD_CHECK "-std=f2018 -pedantic-errors" )

22
src/grid/grid_mech_FEM.f90
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@ -446,22 +446,26 @@ subroutine grid_mechanical_FEM_restartWrite
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w') fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
groupHandle = HDF5_addGroup(fileHandle,'solver') groupHandle = HDF5_addGroup(fileHandle,'solver')
call HDF5_write(P_aim,groupHandle,'P_aim',.false.)
call HDF5_write(F_aim,groupHandle,'F_aim',.false.)
call HDF5_write(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
call HDF5_write(F,groupHandle,'F') call HDF5_write(F,groupHandle,'F')
call HDF5_write(F_lastInc,groupHandle,'F_lastInc') call HDF5_write(F_lastInc,groupHandle,'F_lastInc')
call HDF5_write(u_current,groupHandle,'u') call HDF5_write(u_current,groupHandle,'u')
call HDF5_write(u_lastInc,groupHandle,'u_lastInc') call HDF5_write(u_lastInc,groupHandle,'u_lastInc')
call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
call HDF5_closeGroup(groupHandle) call HDF5_closeGroup(groupHandle)
call HDF5_closeFile(fileHandle) call HDF5_closeFile(fileHandle)
if (worldrank == 0) then
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','a',.false.)
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_write(P_aim,groupHandle,'P_aim',.false.)
call HDF5_write(F_aim,groupHandle,'F_aim',.false.)
call HDF5_write(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
call HDF5_closeGroup(groupHandle)
call HDF5_closeFile(fileHandle)
endif
call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,ierr) call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr) call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)

12
src/grid/grid_mech_spectral_basic.f90
View File

@ -389,20 +389,24 @@ subroutine grid_mechanical_spectral_basic_restartWrite
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w') fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
groupHandle = HDF5_addGroup(fileHandle,'solver') groupHandle = HDF5_addGroup(fileHandle,'solver')
call HDF5_write(F,groupHandle,'F')
call HDF5_write(F_lastInc,groupHandle,'F_lastInc')
call HDF5_closeGroup(groupHandle)
call HDF5_closeFile(fileHandle)
if (worldrank == 0) then
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','a',.false.)
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_write(P_aim,groupHandle,'P_aim',.false.) call HDF5_write(P_aim,groupHandle,'P_aim',.false.)
call HDF5_write(F_aim,groupHandle,'F_aim',.false.) call HDF5_write(F_aim,groupHandle,'F_aim',.false.)
call HDF5_write(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.) call HDF5_write(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.) call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
call HDF5_write(F,groupHandle,'F')
call HDF5_write(F_lastInc,groupHandle,'F_lastInc')
call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.) call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.) call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
call HDF5_write(C_minMaxAvg,groupHandle,'C_minMaxAvg',.false.) call HDF5_write(C_minMaxAvg,groupHandle,'C_minMaxAvg',.false.)
call HDF5_closeGroup(groupHandle) call HDF5_closeGroup(groupHandle)
call HDF5_closeFile(fileHandle) call HDF5_closeFile(fileHandle)
endif
if (num%update_gamma) call utilities_saveReferenceStiffness if (num%update_gamma) call utilities_saveReferenceStiffness

22
src/grid/grid_mech_spectral_polarisation.f90
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@ -445,22 +445,26 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w') fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
groupHandle = HDF5_addGroup(fileHandle,'solver') groupHandle = HDF5_addGroup(fileHandle,'solver')
call HDF5_write(F_aim,groupHandle,'P_aim',.false.)
call HDF5_write(F_aim,groupHandle,'F_aim',.false.)
call HDF5_write(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
call HDF5_write(F,groupHandle,'F') call HDF5_write(F,groupHandle,'F')
call HDF5_write(F_lastInc,groupHandle,'F_lastInc') call HDF5_write(F_lastInc,groupHandle,'F_lastInc')
call HDF5_write(F_tau,groupHandle,'F_tau') call HDF5_write(F_tau,groupHandle,'F_tau')
call HDF5_write(F_tau_lastInc,groupHandle,'F_tau_lastInc') call HDF5_write(F_tau_lastInc,groupHandle,'F_tau_lastInc')
call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
call HDF5_closeGroup(groupHandle) call HDF5_closeGroup(groupHandle)
call HDF5_closeFile(fileHandle) call HDF5_closeFile(fileHandle)
if (worldrank == 0) then
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','a',.false.)
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_write(F_aim,groupHandle,'P_aim',.false.)
call HDF5_write(F_aim,groupHandle,'F_aim',.false.)
call HDF5_write(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
call HDF5_closeGroup(groupHandle)
call HDF5_closeFile(fileHandle)
endif
if(num%update_gamma) call utilities_saveReferenceStiffness if(num%update_gamma) call utilities_saveReferenceStiffness
call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr) call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)