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Implement openPMD I/O for grid arrays #165

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Jul 4, 2023
Merged

Implement openPMD I/O for grid arrays #165

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183eeec
CarpetX: Poison boundaries when reading variables from file
eschnett Jul 4, 2023
8223cda
TestOutput: Apply boundary conditions after recovering
eschnett Jul 4, 2023
85a71d3
TestOutput: Add openPMD checkpoint/recovery test cases
eschnett Jul 4, 2023
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540 changes: 453 additions & 87 deletions CarpetX/src/io_openpmd.cxx
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10 changes: 9 additions & 1 deletion TestOutput/schedule.ccl
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Expand Up @@ -3,9 +3,17 @@
SCHEDULE TestOutput_SetVarsLocal AT initial
{
LANG: C
WRITES: gf(everywhere)
WRITES: gf(interior)
SYNC: gf
} "Set up local test variables"

SCHEDULE TestOutput_Sync AT post_recover_variables
{
LANG: C
OPTIONS: global
SYNC: gf
} "Synchronize local test variables"

SCHEDULE TestOutput_SetVarsGlobal AT initial
{
LANG: C
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6 changes: 5 additions & 1 deletion TestOutput/src/SetVars.cxx
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Expand Up @@ -5,11 +5,15 @@ namespace TestOutput {
extern "C" void TestOutput_SetVarsLocal(CCTK_ARGUMENTS) {
DECLARE_CCTK_ARGUMENTSX_TestOutput_SetVarsLocal;

grid.loop_all<0, 0, 0>(grid.nghostzones, [=](const Loop::PointDesc &p) {
grid.loop_int<0, 0, 0>(grid.nghostzones, [=](const Loop::PointDesc &p) {
gf(p.I) = p.z * 10000 + p.y * 100 + p.x;
});
}

extern "C" void TestOutput_Sync(CCTK_ARGUMENTS) {
DECLARE_CCTK_ARGUMENTSX_TestOutput_Sync;
}

extern "C" void TestOutput_SetVarsGlobal(CCTK_ARGUMENTS) {
DECLARE_CCTK_ARGUMENTSX_TestOutput_SetVarsGlobal;

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46 changes: 46 additions & 0 deletions TestOutput/test/checkpoint-openpmd.par
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@@ -0,0 +1,46 @@
ActiveThorns = "
CarpetX
IOUtil
TestOutput
"

Cactus::cctk_itlast = 0
Cactus::presync_mode = "mixed-error"

CarpetX::ncells_x = 32
CarpetX::ncells_y = 32
CarpetX::ncells_z = 32

CarpetX::xmin = 0.0
CarpetX::ymin = 0.0
CarpetX::zmin = 0.0
CarpetX::xmax = 32.0
CarpetX::ymax = 32.0
CarpetX::zmax = 32.0

CarpetX::boundary_x = "linear extrapolation"
CarpetX::boundary_y = "linear extrapolation"
CarpetX::boundary_z = "linear extrapolation"
CarpetX::boundary_upper_x = "linear extrapolation"
CarpetX::boundary_upper_y = "linear extrapolation"
CarpetX::boundary_upper_z = "linear extrapolation"

IO::out_dir = $parfile
IO::parfile_write = "no"
IO::out_every = 1

CarpetX::out_metadata = no

CarpetX::out_tsv_vars = "
TestOutput::gf
TestOutput::sc
TestOutput::a1
TestOutput::a2
TestOutput::a3
"

CarpetX::checkpoint_method = "openpmd"
IO::checkpoint_dir = "../checkpoints"
IO::checkpoint_ID = yes
IO::checkpoint_every = 1
IO::checkpoint_on_terminate = yes
11 changes: 11 additions & 0 deletions TestOutput/test/checkpoint-openpmd/testoutput-a1.it000000.x.tsv
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10 changes: 10 additions & 0 deletions TestOutput/test/checkpoint-openpmd/testoutput-a2.it000000.x.tsv
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9 changes: 9 additions & 0 deletions TestOutput/test/checkpoint-openpmd/testoutput-a2.it000000.y.tsv
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8 changes: 8 additions & 0 deletions TestOutput/test/checkpoint-openpmd/testoutput-a3.it000000.x.tsv
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7 changes: 7 additions & 0 deletions TestOutput/test/checkpoint-openpmd/testoutput-a3.it000000.y.tsv
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6 changes: 6 additions & 0 deletions TestOutput/test/checkpoint-openpmd/testoutput-a3.it000000.z.tsv
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36 changes: 36 additions & 0 deletions TestOutput/test/checkpoint-openpmd/testoutput-gf.it000000.x.tsv
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36 changes: 36 additions & 0 deletions TestOutput/test/checkpoint-openpmd/testoutput-gf.it000000.y.tsv
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36 changes: 36 additions & 0 deletions TestOutput/test/checkpoint-openpmd/testoutput-gf.it000000.z.tsv
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# 1:iteration 2:time 3:patch 4:level 5:i 6:j 7:k 8:x 9:y 10:z 11:gf
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2 changes: 2 additions & 0 deletions TestOutput/test/checkpoint-openpmd/testoutput-sc.it000000.tsv
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# 1:iteration 2:time 3:sc
0 0.0000000000000000e+00 4.2000000000000000e+01
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3 changes: 3 additions & 0 deletions TestOutput/test/checkpoints-openpmd/checkpoint.chkpt.it00000000.bp5/profiling.json
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[
{ "rank":0, "start":"Tue_Jul_04_15:42:21_2023", "bytes":0, "AWD":{"mus":1187, "nCalls":1}, "close_ts":{"mus":157, "nCalls":1}, "meta_lvl1":{"mus":13, "nCalls":1}, "meta_lvl2":{"mus":191, "nCalls":1}, "endstep":{"mus":1550, "nCalls":1}, "transport_0":{"type":"File_POSIX", "close":{"mus":48, "nCalls":1}, "write":{"mus":74, "nCalls":1}, "open":{"mus":124, "nCalls":1}}, "transport_1":{"type":"File_POSIX", "close":{"mus":39, "nCalls":1}, "write":{"mus":65, "nCalls":5}, "open":{"mus":132, "nCalls":1}} }
]
1 change: 1 addition & 0 deletions TestOutput/test/checkpoints-openpmd/checkpoint.chkpt.openpmd.visit
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checkpoint.chkpt.it00000000.bp5
7 changes: 7 additions & 0 deletions TestOutput/test/output-arrays.par
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Expand Up @@ -18,6 +18,13 @@ CarpetX::xmax = 32.0
CarpetX::ymax = 32.0
CarpetX::zmax = 32.0

CarpetX::boundary_x = "linear extrapolation"
CarpetX::boundary_y = "linear extrapolation"
CarpetX::boundary_z = "linear extrapolation"
CarpetX::boundary_upper_x = "linear extrapolation"
CarpetX::boundary_upper_y = "linear extrapolation"
CarpetX::boundary_upper_z = "linear extrapolation"

IO::out_dir = $parfile
IO::parfile_write = "no"
IO::out_every = 1
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