Comments (7)
Moelf
commented on June 2, 2024
@jpivarski this is a head-scratcher. There are a few special features of this file:
- footer's extension links are not empty, meaning at some point more fields and columns are created after the writing process has started
- because of that, it may not be very surprising, that the first
clusterand the secondclusterhave different numbers of storage columns (835 for 1st cluster, 869 for 2nd cluster and all the subsequent ones)
869 matches the number of total column records after appending the ones found int footer to that of the header
none of these directly explain why the offset/content would misalign suddenly though, my understanding is the field and column records in the footer extension should just be "appended" to the header ones, so in theory they shouldn't mess up the indexing of storage column, thus everything I can read from 1st cluster should continue to work in 2nd cluster.
from unroot.jl.
Moelf
commented on June 2, 2024
I think that might be red herring:
# remember Julia is 1-based index
julia> rf.header.field_records[182:201]
20-element rVector{UnROOT.FieldRecord}:
UnROOT.FieldRecord(field_version=0x00000000, type_version=0xffffffff, parent_field_id=0x000000b5, struct_role=0x0002, flags=0x0000, repetition=0, field_name="AntiKt4TruthDressedWZJetsAux:", type_name="xAOD::JetAuxContainer_v1", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0xffffffff, parent_field_id=0x000000b5, struct_role=0x0002, flags=0x0000, repetition=0, field_name=":_0", type_name="xAOD::AuxContainerBase", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0xffffffff, parent_field_id=0x000000b6, struct_role=0x0002, flags=0x0000, repetition=0, field_name=":_0", type_name="SG::IAuxStore", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0xffffffff, parent_field_id=0x000000b7, struct_role=0x0002, flags=0x0000, repetition=0, field_name=":_0", type_name="SG::IConstAuxStore", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0xffffffff, parent_field_id=0x000000b6, struct_role=0x0002, flags=0x0000, repetition=0, field_name=":_1", type_name="SG::IAuxStoreIO", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0xffffffff, parent_field_id=0x000000b6, struct_role=0x0002, flags=0x0000, repetition=0, field_name=":_2", type_name="SG::IAuxStoreHolder", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0xffffffff, parent_field_id=0x000000b6, struct_role=0x0002, flags=0x0000, repetition=0, field_name=":_3", type_name="ILockable", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0x00000000, parent_field_id=0x000000b5, struct_role=0x0001, flags=0x0000, repetition=0, field_name="pt", type_name="std::vector<float>", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0x00000000, parent_field_id=0x000000bc, struct_role=0x0000, flags=0x0000, repetition=0, field_name="_0", type_name="float", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0x00000000, parent_field_id=0x000000b5, struct_role=0x0001, flags=0x0000, repetition=0, field_name="eta", type_name="std::vector<float>", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0x00000000, parent_field_id=0x000000be, struct_role=0x0000, flags=0x0000, repetition=0, field_name="_0", type_name="float", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0x00000000, parent_field_id=0x000000b5, struct_role=0x0001, flags=0x0000, repetition=0, field_name="phi", type_name="std::vector<float>", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0x00000000, parent_field_id=0x000000c0, struct_role=0x0000, flags=0x0000, repetition=0, field_name="_0", type_name="float", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0x00000000, parent_field_id=0x000000b5, struct_role=0x0001, flags=0x0000, repetition=0, field_name="m", type_name="std::vector<float>", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0x00000000, parent_field_id=0x000000c2, struct_role=0x0000, flags=0x0000, repetition=0, field_name="_0", type_name="float", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0x00000000, parent_field_id=0x000000b5, struct_role=0x0001, flags=0x0000, repetition=0, field_name="constituentLinks", type_name="std::vector<std::vector<ElementLink<DataVector<xAOD::IParticle> >>>", type_alias="xAOD::JetAuxContainer_v1::ConstituentLinks_t", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0x00000000, parent_field_id=0x000000c4, struct_role=0x0001, flags=0x0000, repetition=0, field_name="_0", type_name="std::vector<ElementLink<DataVector<xAOD::IParticle> >>", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0xffffffff, parent_field_id=0x000000c5, struct_role=0x0002, flags=0x0000, repetition=0, field_name="_0", type_name="ElementLink<DataVector<xAOD::IParticle> >", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0xffffffff, parent_field_id=0x000000c6, struct_role=0x0002, flags=0x0000, repetition=0, field_name=":_0", type_name="ElementLinkBase", type_alias="", field_desc="", )
UnROOT.FieldRecord(field_version=0x00000000, type_version=0x00000000, parent_field_id=0x000000c7, struct_role=0x0000, flags=0x0000, repetition=0, field_name="m_persKey", type_name="std::uint32_t", type_alias="SG::sgkey_t", field_desc="", )
julia> collect(rnt.var"AntiKt4TruthDressedWZJetsAux:")
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000bc, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0011, nbits=0x0020, field_id=0x000000bd, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000be, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0011, nbits=0x0020, field_id=0x000000bf, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000c0, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0011, nbits=0x0020, field_id=0x000000c1, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000c2, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0011, nbits=0x0020, field_id=0x000000c3, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000c4, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000c5, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0014, nbits=0x0020, field_id=0x000000c8, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0014, nbits=0x0020, field_id=0x000000c9, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000ca, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000cb, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0011, nbits=0x0020, field_id=0x000000cc, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000bc, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0011, nbits=0x0020, field_id=0x000000bd, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000be, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0011, nbits=0x0020, field_id=0x000000bf, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000c0, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0011, nbits=0x0020, field_id=0x000000c1, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000c2, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0011, nbits=0x0020, field_id=0x000000c3, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000c4, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x000e, nbits=0x0040, field_id=0x000000c5, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0014, nbits=0x0020, field_id=0x000000c8, flags=0x00000000, first_ele_idx=0, )
field.columnrecord = UnROOT.ColumnRecord(type=0x0014, nbits=0x0020, field_id=0x000000c9, flags=0x00000000, first_ele_idx=0, )none of the columns touched have flags=0x08 in this case.
from unroot.jl.
Moelf
commented on June 2, 2024
julia> rnt = LazyTree("./DAOD_TRUTH1.zprime125.rntuple.root", "RNT:CollectionTree", "AntiKt4TruthDressedWZJetsAux:");
julia> rnt.var"AntiKt4TruthDressedWZJetsAux:".rn.schema
RNTupleSchema with 1 top fields
└─ Symbol("AntiKt4TruthDressedWZJetsAux:") ⇒ Struct
├─ :m ⇒ Vector
│ ├─ :offset ⇒ Leaf{UnROOT.Index64}(col=38)
│ └─ :content ⇒ Leaf{Float32}(col=39)
├─ :pt ⇒ Vector
│ ├─ :offset ⇒ Leaf{UnROOT.Index64}(col=32)
│ └─ :content ⇒ Leaf{Float32}(col=33)
├─ :eta ⇒ Vector
│ ├─ :offset ⇒ Leaf{UnROOT.Index64}(col=34)
│ └─ :content ⇒ Leaf{Float32}(col=35)
├─ :constituentWeights ⇒ Vector
│ ├─ :offset ⇒ Leaf{UnROOT.Index64}(col=44)
│ └─ :content ⇒ Vector
│ ├─ :offset ⇒ Leaf{UnROOT.Index64}(col=45)
│ └─ :content ⇒ Leaf{Float32}(col=46)
├─ :phi ⇒ Vector
│ ├─ :offset ⇒ Leaf{UnROOT.Index64}(col=36)
│ └─ :content ⇒ Leaf{Float32}(col=37)
└─ :constituentLinks ⇒ Vector
├─ :offset ⇒ Leaf{UnROOT.Index64}(col=40)
└─ :content ⇒ Vector
├─ :offset ⇒ Leaf{UnROOT.Index64}(col=41)
└─ :content ⇒ Struct
└─ Symbol(":_0") ⇒ Struct
├─ :m_persKey ⇒ Leaf{UInt32}(col=42)
└─ :m_persIndex ⇒ Leaf{UInt32}(col=43)
let's manually check all the columns under the :constituentLinks, and specifically in the second cluster, see if they are consistent:
julia> io = rnt.var"AntiKt4TruthDressedWZJetsAux:".rn.io;
julia> rnt.var"AntiKt4TruthDressedWZJetsAux:"[1]; # fill the pagelinks cache
julia> cluster_group = rnt.var"AntiKt4TruthDressedWZJetsAux:".rn.pagelinks[1];
julia> cluster_group.cluster_summaries[2] # we're interested in the second cluster
UnROOT.ClusterSummary(528, 1432)
julia> cluster_group.nested_page_locations[2][40] # this is col=40 in the schema, we converted already
1-element UnROOT.RNTupleListNoFrame{UnROOT.PageDescription}:
UnROOT.PageDescription(0x00000598, UnROOT.Locator(num_bytes=816, offset=0x0000000003f3eb4a, )
)
# ├─ :offset ⇒ Leaf{UnROOT.Index64}(col=40)
julia> reinterpret(UnROOT.Index64, UnROOT.read_pagedesc(io, cluster_group.nested_page_locations[2][40], 64; split=true)) |> cumsum .|> Int
1432-element Vector{Int64}:
9
30
36
43
57
65
⋮
12906
12919
12930
julia> cluster_group.nested_page_locations[2][41] # this is col=41 in the schema, we converted already
2-element UnROOT.RNTupleListNoFrame{UnROOT.PageDescription}:
UnROOT.PageDescription(0x00002000, UnROOT.Locator(num_bytes=4740, offset=0x0000000003c6ab67, )
)
UnROOT.PageDescription(0x00001282, UnROOT.Locator(num_bytes=2770, offset=0x0000000003f3eea4, )
)
# this is split and delta encoded
# ├─ :offset ⇒ Leaf{UnROOT.Index64}(col=41)
julia> reinterpret(UnROOT.Index64, UnROOT.read_pagedesc(io, cluster_group.nested_page_locations[2][41], 64; split=true)) |> cumsum .|> Int
12930-element Vector{Int64}:
30
34
52
66
...
209999
210008
julia> cluster_group.nested_page_locations[2][42]
8-element UnROOT.RNTupleListNoFrame{UnROOT.PageDescription}:
UnROOT.PageDescription(0x00004000, UnROOT.Locator(num_bytes=38, offset=0x000000000196af81, )
)
UnROOT.PageDescription(0x00004000, UnROOT.Locator(num_bytes=38, offset=0x0000000001f361e0, )
)
UnROOT.PageDescription(0x00004000, UnROOT.Locator(num_bytes=38, offset=0x00000000024cac93, )
)
UnROOT.PageDescription(0x00004000, UnROOT.Locator(num_bytes=38, offset=0x0000000002ac8a47, )
)
UnROOT.PageDescription(0x00004000, UnROOT.Locator(num_bytes=38, offset=0x00000000030d9f71, )
)
UnROOT.PageDescription(0x00004000, UnROOT.Locator(num_bytes=38, offset=0x00000000036576d6, )
)
UnROOT.PageDescription(0x00004000, UnROOT.Locator(num_bytes=38, offset=0x0000000003c710aa, )
)
UnROOT.PageDescription(0x00003648, UnROOT.Locator(num_bytes=38, offset=0x0000000003f3f9a0, )
)
julia> julia> reinterpret(UInt32, UnROOT.read_pagedesc(io, cluster_group.nested_page_locations[2][42], 32; split=true))
128584-element reinterpret(UInt32, ::Vector{UInt8}):
0x2784318b
0x2784318b
0x2784318b
0x2784318b
0x2784318b
0x2784318b
0x2784318b
0x2784318bfrom unroot.jl.
Moelf
commented on June 2, 2024
First cluster seems to match:
ROOT
In [39]: df = ROOT.RDataFrame("RNT:CollectionTree", "./DAOD_TRUTH1.zprime125.rntuple.root")
In [41]: df.GetColumnType("AntiKt4TruthDressedWZJetsAux:.constituentLinks.:_0.m_persKey")
Out[41]: 'ROOT::VecOps::RVec<ROOT::VecOps::RVec<std::uint32_t>>'
In [67]: list(list(list(df.Take['ROOT::VecOps::RVec<ROOT::VecOps::RVec<std::uint32_t>>']("AntiKt4TruthDressedWZJetsAux:.constituentLinks.:_0.m_persIndex"))[3])[2])
Out[67]: [748, 932, 936, 935, 934]
In [68]: list(list(list(df.Take['ROOT::VecOps::RVec<ROOT::VecOps::RVec<std::uint32_t>>']("AntiKt4TruthDressedWZJetsAux:.constituentLinks.:_0.m_persKey"))[3])[2])
Out[68]: [662974859, 662974859, 662974859, 662974859, 662974859]
In [62]: list(list(list(df.Take['ROOT::VecOps::RVec<ROOT::VecOps::RVec<std::uint32_t>>']("AntiKt4TruthDressedWZJetsAux:.constituentLinks.:_0.m_persIndex"))[527])[7])
Out[62]: [1575, 2481, 435, 2480, 2477, 2532]
In [63]: list(list(list(df.Take['ROOT::VecOps::RVec<ROOT::VecOps::RVec<std::uint32_t>>']("AntiKt4TruthDressedWZJetsAux:.constituentLinks.:_0.m_persKey"))[527])[7])
Out[63]: [662974859, 662974859, 662974859, 662974859, 662974859, 662974859]UnROOT
julia> br = rnt.var"AntiKt4TruthDressedWZJetsAux:";
julia> [Int(x[1].m_persIndex) for x in br[4].constituentLinks[3]]
5-element Vector{Int64}:
748
932
936
935
934
julia> [Int(x[1].m_persKey) for x in br[4].constituentLinks[3]]
5-element Vector{Int64}:
662974859
662974859
662974859
662974859
662974859
julia> [Int(x[1].m_persIndex) for x in br[528].constituentLinks[8]]
6-element Vector{Int64}:
1575
2481
435
2480
2477
2532
julia> [Int(x[1].m_persKey) for x in br[528].constituentLinks[8]]
6-element Vector{Int64}:
662974859
662974859
662974859
662974859
662974859
662974859from unroot.jl.
Moelf
commented on June 2, 2024
Scond cluster
ROOT
In [65]: list(list(list(df.Take['ROOT::VecOps::RVec<ROOT::VecOps::RVec<std::uint32_t>>']("AntiKt4TruthDressedWZJetsAux:.constituentLinks.:_0.m_persIndex"))[528])[0])
Out[65]:
[1709,
1122,
1132,
1808,
1807,
...
In [92]: list(list(list(df.Take['ROOT::VecOps::RVec<ROOT::VecOps::RVec<std::uint32_t>>']("AntiKt4TruthDressedWZJetsAux:.constituentLinks.:_0.m_persIndex"))[528+1432-1])[-1])
Out[92]: [1427, 900, 546, 849, 1433, 1425, 1431, 845, 964]Julia
we crash here, so using debug output:
# @show inside second cluster
length(content) = 128584
[Int((x[1]).m_persIndex) for x = first(content, 5)] = [1709, 1122, 1132, 1808, 1807]
[Int((x[1]).m_persIndex) for x = last(content, 9)] = [1427, 900, 546, 849, 1433, 1425, 1431, 845, 964]So it looks like we have all the data we want, just somehow the index are not aligned ....
what about total amount of data in 2nd cluster?
# be warned: this is slow
a = []
In [116]: for i in range(528, 528+1432):
...: ns = list(list(df.Take['ROOT::VecOps::RVec<ROOT::VecOps::RVec<std::uint32_t>>']("AntiKt4TruthDressedWZJetsAux:.constituentLinks.:_0.m_persIndex"))[i])
...: for n in ns:
...: a.append(len(list(n)))
In [121]: sum(a)
Out[121]: 128584well, I'm not missing any data here, so idk what the is going on
from unroot.jl.
Moelf
commented on June 2, 2024
Given the content column is fine, now I suspect we're doing something wrong with the offset column:
field.offset_col = Leaf{UnROOT.Index64}(col=41)and sure enough, this is that weird column we weren't able to read earlier, because we couldn't inflate 29 bytes into 131072
Let's compare the offsets
ROOT
In [8]: a[:10]
Out[8]: [30, 4, 18, 14, 5, 8, 10, 7, 8, 18]UnROOT
Int.(first(offset, 10)) = [30, 34, 52, 66, 71, 79, 89, 96, 104, 122]
diff([0; Int.(first(offset, 10))]) = [30, 4, 18, 14, 5, 8, 10, 7, 8, 18]so they start out agreeing!
from unroot.jl.
Moelf
commented on June 2, 2024
Compare the content of col=41
They appear to be the same at first glance, in fact they start and end the same:
julia> length(my_offset) == length(ref_offset)
true
julia> first(my_offset, 10) == first(ref_offset, 10)
true
julia> last(my_offset, 10) == last(ref_offset, 10)
trueah, it's because of
0x01 64 Index64 Mother columns of (nested) collections, counting is relative to the cluster
0x02 32 Index32 Mother columns of (nested) collections, counting is relative to the cluster
specifically, "counting is relative to the cluster" was not clear to me. But what it means is, if you have 2 pages of Index64 for a column in this cluster, after "de-split encoding" you will get these two arrays:
first page: [30, 4, 18, 14, 5, 8, 10, 7, 8, 18, ..., 22, 1, 16, 14, 14, 12, 4, 7, 15, 24]
first page after cumsum: [..., 81317, 81318, 81334, 81348, 81362, 81374, 81378, 81385, 81400, 81424]
second page: [81428, 13, 9, 7, 5, 20, 21, 4, 8, 6, ..., 8, 3, 4, 9, 14, 18, 8, 14, 16, 6, 8, 7, 11, 9]you can see that the second page doesn't start with 4, instead, it starts with a huge number 81428. I guess it means index pages are to be interpreted individually within the cluster.
see also: root-project/root#14982
from unroot.jl.
Related Issues (20)
- Pre-compilation failure after upgrading to v1.9.3 HOT 6
- Performance for trees with a large number of branches HOT 13
- Fix Documentation due to their 1.0 release
- `RNTuple` reading extremely slow
- `nanoAOD_ttbar` latency HOT 26
- CI broken on nighly due to MD5.jl using SHA.jl internals
- RNTuple RC2 compatibility
- Do not manage to read a TTree with a structure of arrays of basic types HOT 17
- Cannot read empty collections from a RNTuple file HOT 1
- ConcurrencyViolationError when reading with XRootD HOT 2
- [RNTuple] accessing nested structs is not lazy enough HOT 1
- [WIP] 0.11.0 breaking changes items
- Re-write resources with `Base.Lockable`
- [RNTuple] OutOfMemoryError in show() HOT 2
- Reading a file with Branches and Leafs HOT 11
- [RNTuple] miss-aligned column in DAOD_TLA with RNTuple RC2 HOT 2
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from unroot.jl.