[MOAB-dev] parallel write and restart with variable length tags

Tue Dec 4 01:59:20 CST 2018

Hello,

I apologise for this overflow of information, I know something more, this error is triggered on 0 proc, when I have a variable tag on vertices and edges.

 0  H5M (0.03 s) Reading tag "_App_Datax"
  0  H5M *********** Debug Barrier 51 (@2706)***********
  1  H5M (0.03 s) Reading tag "_App_Datax"
  1  H5M *********** Debug Barrier 51 (@2706)***********
  0  H5M Reading var-len sparse data for tag "_App_Datax"
  1  H5M Reading var-len sparse data for tag "_App_Datax"
  0  H5M Reading file ids for sparse tag "_App_Datax" in 1 chunks
  0  H5M Reading chunk 1 of "_App_Datax" IDs
  1  H5M Reading file ids for sparse tag "_App_Datax" in 1 chunks
  1  H5M Reading chunk 1 of "_App_Datax" IDs
  1  H5M Switching to unordered list for tag handle list
[1]MOAB ERROR: --------------------- Error Message ------------------------------------
[1]MOAB ERROR: Unordered file ids for variable length tag not supported!
[1]MOAB ERROR: read_var_len_tag() line 3335 in src/io/ReadHDF5.cpp
[1]MOAB ERROR: --------------------- Error Message ------------------------------------
[1]MOAB ERROR: ReadHDF5 Failure!
[1]MOAB ERROR: read_tag() line 2769 in src/io/ReadHDF5.cpp
[1]MOAB ERROR: --------------------- Error Message ------------------------------------
[1]MOAB ERROR: ReadHDF5 Failure!
[1]MOAB ERROR: load_file_partial() line 1164 in src/io/ReadHDF5.cpp
  1  H5M (0.04 s) Cleaning up

In particular note, that proc 1 is ok, the problem is on proc 0. Mesh is partitioned with metis and entities are on both processors for both dimensions.

I reading fike with options:

    option = "PARALLEL=READ_PART;"
             "PARALLEL_RESOLVE_SHARED_ENTS;"
             "PARTITION=PARALLEL_PARTITION;DEBUG_IO=5";

Is this something wrong on my side, or rather need to be fixed in moab reader. I can have a go, but need to have some hint how to fix this.

Lukasz

On 4 Dec 2018, at 00:27, Lukasz Kaczmarczyk via moab-dev <moab-dev at mcs.anl.gov<mailto:moab-dev at mcs.anl.gov>> wrote:

Hello,

If that will help, this is debugging IO trace,

H5M (0.02 s) Reading all nodes...
H5M Reading 0 chunks for coordinate coordinates
H5M (0.02 s) Reading chunk 1 of node coords
H5M Closing node coordinate table
H5M Updating ID to handle map for 59 nodes
H5M (0.02 s) Reading all element connectivity...
H5M (0.02 s) READING Edge2 CONNECTIVITY (236 elems in 1 selects)
H5M Reading connectivity in 0 chunks for element group "Edge2"
H5M Reading chunk 1 for "Edge2"
H5M (0.02 s) READING Tet4 CONNECTIVITY (132 elems in 1 selects)
H5M Reading connectivity in 0 chunks for element group "Tet4"
H5M Reading chunk 1 for "Tet4"
H5M (0.02 s) READING Tri3 CONNECTIVITY (310 elems in 1 selects)
H5M Reading connectivity in 0 chunks for element group "Tri3"
H5M Reading chunk 1 for "Tri3"
H5M (0.02 s) Reading all sets...
H5M Reading chunk 1 of set contents
H5M Reading chunk 1 of set children
H5M Reading chunk 1 of set parents
H5M (0.02 s) Reading all adjacencies...
H5M Reading adjacency list in 1 chunks
H5M Reading chunk 1 of adjacency list
H5M Reading adjacency list in 1 chunks
H5M Reading chunk 1 of adjacency list
H5M Reading adjacency list in 1 chunks
H5M Reading chunk 1 of adjacency list
H5M (0.03 s) Reading all tags...
H5M (0.03 s) Reading tag "BLOCK_ATTRIBUTES"
H5M Reading var-len sparse data for tag "BLOCK_ATTRIBUTES"
H5M Reading file ids for sparse tag "BLOCK_ATTRIBUTES" in 0 chunks
H5M Reading chunk 1 of "BLOCK_ATTRIBUTES" IDs
H5M Reading BLOCK_ATTRIBUTES offsets in 0 chunks
H5M Reading chunk 1 of BLOCK_ATTRIBUTES offsets
H5M Reading BLOCK_ATTRIBUTES values in 0 chunks
H5M Reading chunk 1 of BLOCK_ATTRIBUTES values
H5M (0.03 s) Reading tag "BLOCK_HEADER"
H5M Reading sparse data for tag "BLOCK_HEADER"
H5M Reading file ids for sparse tag "BLOCK_HEADER" in 0 chunks
H5M Reading chunk 1 of "BLOCK_HEADER" IDs
H5M Reading sparse values for tag "BLOCK_HEADER" in 0 chunks
H5M Reading chunk 1 of "BLOCK_HEADER" values
H5M (0.03 s) Reading tag "BOX_DIMS"
H5M (0.03 s) Reading tag "CATEGORY"
H5M Reading sparse data for tag "CATEGORY"
H5M Reading file ids for sparse tag "CATEGORY" in 0 chunks
H5M Reading chunk 1 of "CATEGORY" IDs
H5M Reading sparse values for tag "CATEGORY" in 0 chunks
H5M Reading chunk 1 of "CATEGORY" values
H5M (0.03 s) Reading tag "DIRICHLET_SET"
H5M (0.03 s) Reading tag "DIRICHLET_SET__BC_DATA"
H5M (0.03 s) Reading tag "ElemType"
H5M (0.03 s) Reading tag "GEOM_DIMENSION"
H5M Reading sparse data for tag "GEOM_DIMENSION"
H5M Reading file ids for sparse tag "GEOM_DIMENSION" in 0 chunks
H5M Reading chunk 1 of "GEOM_DIMENSION" IDs
H5M Reading sparse values for tag "GEOM_DIMENSION" in 0 chunks
H5M Reading chunk 1 of "GEOM_DIMENSION" values
H5M (0.03 s) Reading tag "GEOM_SENSE_2"
H5M Reading sparse data for tag "GEOM_SENSE_2"
H5M Reading file ids for sparse tag "GEOM_SENSE_2" in 0 chunks
H5M Reading chunk 1 of "GEOM_SENSE_2" IDs
H5M Reading sparse values for tag "GEOM_SENSE_2" in 0 chunks
H5M Reading chunk 1 of "GEOM_SENSE_2" values
H5M (0.03 s) Reading tag "GEOM_SENSE_N_ENTS"
H5M Reading var-len sparse data for tag "GEOM_SENSE_N_ENTS"
H5M Reading file ids for sparse tag "GEOM_SENSE_N_ENTS" in 0 chunks
H5M Reading chunk 1 of "GEOM_SENSE_N_ENTS" IDs
H5M Reading GEOM_SENSE_N_ENTS offsets in 0 chunks
H5M Reading chunk 1 of GEOM_SENSE_N_ENTS offsets
H5M Reading GEOM_SENSE_N_ENTS values in 0 chunks
H5M Reading chunk 1 of GEOM_SENSE_N_ENTS values
H5M (0.03 s) Reading tag "GEOM_SENSE_N_SENSES"
H5M Reading var-len sparse data for tag "GEOM_SENSE_N_SENSES"
H5M Reading file ids for sparse tag "GEOM_SENSE_N_SENSES" in 0 chunks
H5M Reading chunk 1 of "GEOM_SENSE_N_SENSES" IDs
H5M Reading GEOM_SENSE_N_SENSES offsets in 0 chunks
H5M Reading chunk 1 of GEOM_SENSE_N_SENSES offsets
H5M Reading GEOM_SENSE_N_SENSES values in 0 chunks
H5M Reading chunk 1 of GEOM_SENSE_N_SENSES values
H5M (0.03 s) Reading tag "GLOBAL_ID"
H5M Read dense data block for tag "GLOBAL_ID" on "sets"
H5M Reading dense data for tag "GLOBAL_ID data for sets" and group "sets" in 0 chunks
H5M Reading chunk 1 of "GLOBAL_ID data for sets" data
H5M Read dense data block for tag "GLOBAL_ID" on "nodes"
H5M Reading dense data for tag "GLOBAL_ID data for nodes" and group "nodes" in 0 chunks
H5M Reading chunk 1 of "GLOBAL_ID data for nodes" data
H5M Read dense data block for tag "GLOBAL_ID" on "Edge2"
H5M Reading dense data for tag "GLOBAL_ID data for Edge2" and group "Edge2" in 0 chunks
H5M Reading chunk 1 of "GLOBAL_ID data for Edge2" data
H5M Read dense data block for tag "GLOBAL_ID" on "Tet4"
H5M Reading dense data for tag "GLOBAL_ID data for Tet4" and group "Tet4" in 0 chunks
H5M Reading chunk 1 of "GLOBAL_ID data for Tet4" data
H5M Read dense data block for tag "GLOBAL_ID" on "Tri3"
H5M Reading dense data for tag "GLOBAL_ID data for Tri3" and group "Tri3" in 0 chunks
H5M Reading chunk 1 of "GLOBAL_ID data for Tri3" data
H5M (0.03 s) Reading tag "MATERIAL_SET"
H5M Reading sparse data for tag "MATERIAL_SET"
H5M Reading file ids for sparse tag "MATERIAL_SET" in 0 chunks
H5M Reading chunk 1 of "MATERIAL_SET" IDs
H5M Reading sparse values for tag "MATERIAL_SET" in 0 chunks
H5M Reading chunk 1 of "MATERIAL_SET" values
H5M (0.03 s) Reading tag "MOFEM_VERSION"
H5M (0.03 s) Reading tag "NAME"
H5M Reading sparse data for tag "NAME"
H5M Reading file ids for sparse tag "NAME" in 0 chunks
H5M Reading chunk 1 of "NAME" IDs
H5M Reading sparse values for tag "NAME" in 0 chunks
H5M Reading chunk 1 of "NAME" values
H5M (0.03 s) Reading tag "NEUMANN_SET"
H5M (0.03 s) Reading tag "NEUMANN_SET__BC_DATA"
H5M (0.03 s) Reading tag "OBB"
H5M (0.03 s) Reading tag "PARALLEL_PARTITION"
H5M Reading sparse data for tag "PARALLEL_PARTITION"
H5M Reading file ids for sparse tag "PARALLEL_PARTITION" in 0 chunks
H5M Reading chunk 1 of "PARALLEL_PARTITION" IDs
H5M Reading sparse values for tag "PARALLEL_PARTITION" in 0 chunks
H5M Reading chunk 1 of "PARALLEL_PARTITION" values
H5M Read dense data block for tag "PARALLEL_PARTITION" on "Edge2"
H5M Reading dense data for tag "PARALLEL_PARTITION data for Edge2" and group "Edge2" in 0 chunks
H5M Reading chunk 1 of "PARALLEL_PARTITION data for Edge2" data
H5M Read dense data block for tag "PARALLEL_PARTITION" on "Tet4"
H5M Reading dense data for tag "PARALLEL_PARTITION data for Tet4" and group "Tet4" in 0 chunks
H5M Reading chunk 1 of "PARALLEL_PARTITION data for Tet4" data
H5M Read dense data block for tag "PARALLEL_PARTITION" on "Tri3"
H5M Reading dense data for tag "PARALLEL_PARTITION data for Tri3" and group "Tri3" in 0 chunks
H5M Reading chunk 1 of "PARALLEL_PARTITION data for Tri3" data
H5M (0.03 s) Reading tag "PARTITION"
H5M (0.03 s) Reading tag "UNIQUE_ID"
H5M Reading sparse data for tag "UNIQUE_ID"
H5M Reading file ids for sparse tag "UNIQUE_ID" in 0 chunks
H5M Reading chunk 1 of "UNIQUE_ID" IDs
H5M Reading sparse values for tag "UNIQUE_ID" in 0 chunks
H5M Reading chunk 1 of "UNIQUE_ID" values
H5M (0.03 s) Reading tag "_App_DataBUBBLE"
H5M Reading var-len sparse data for tag "_App_DataBUBBLE"
H5M Reading file ids for sparse tag "_App_DataBUBBLE" in 0 chunks
H5M Reading chunk 1 of "_App_DataBUBBLE" IDs
H5M Reading _App_DataBUBBLE offsets in 0 chunks
H5M Reading chunk 1 of _App_DataBUBBLE offsets
H5M Reading _App_DataBUBBLE values in 0 chunks
H5M Reading chunk 1 of _App_DataBUBBLE values
H5M (0.03 s) Reading tag "_App_DataG"
H5M Reading var-len sparse data for tag "_App_DataG"
H5M Reading file ids for sparse tag "_App_DataG" in 0 chunks
H5M Reading chunk 1 of "_App_DataG" IDs
H5M Reading _App_DataG offsets in 0 chunks
H5M Reading chunk 1 of _App_DataG offsets
H5M Reading _App_DataG values in 0 chunks
H5M Reading chunk 1 of _App_DataG values
H5M (0.03 s) Reading tag "_App_DataG0"
H5M Reading var-len sparse data for tag "_App_DataG0"
H5M Reading file ids for sparse tag "_App_DataG0" in 0 chunks
H5M Reading chunk 1 of "_App_DataG0" IDs
H5M Reading _App_DataG0 offsets in 0 chunks
H5M Reading chunk 1 of _App_DataG0 offsets
H5M Reading _App_DataG0 values in 0 chunks
H5M Reading chunk 1 of _App_DataG0 values
H5M (0.03 s) Reading tag "_App_DataP"
H5M Reading var-len sparse data for tag "_App_DataP"
H5M Reading file ids for sparse tag "_App_DataP" in 0 chunks
H5M Reading chunk 1 of "_App_DataP" IDs
H5M Switching to unordered list for tag handle list
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: Unordered file ids for variable length tag not supported!
[0]MOAB ERROR: read_var_len_tag() line 3335 in src/io/ReadHDF5.cpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: ReadHDF5 Failure!
[0]MOAB ERROR: read_tag() line 2769 in src/io/ReadHDF5.cpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: ReadHDF5 Failure!
[0]MOAB ERROR: load_file_impl() line 678 in src/io/ReadHDF5.cpp
H5M (0.03 s) Cleaning up
H5M (0.03 s) READ FAILED (ERROR CODE MB_FAILURE): ReadHDF5 Failure
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: Failed to load file after trying all possible readers!
[0]MOAB ERROR: serial_load_file() line 623 in src/Core.cpp
[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: Failed in step PARALLEL READ!
[0]MOAB ERROR: load_file() line 612 in src/ReadParallel.cpp
[0]MOAB ERROR: load_file() line 263 in src/ReadParallel.cpp
[0]MOAB ERROR: load_file() line 503 in src/Core.cpp
[0]MoFEM ERROR: --------------------- MoFEM Error Message ---------------------------------------------------
[0]MoFEM ERROR: MoFEM version 0.8.17 (MOAB 5.0.2 Petsc Release Version 3.9.3, Jul, 02, 2018 )
[0]MoFEM ERROR: MoFEM git commit id 9fe99b7e4d55b4d664a369dec823ed6f828cab58
[0]MoFEM ERROR: See http://mofem.eng.gla.ac.uk/mofem/html/guidelines_bug_reporting.html for bug reporting.
[0]MoFEM ERROR: Write to https://groups.google.com/forum/#!forum/mofem-group to seek help.
[0]MoFEM ERROR: MOAB error (16) MB_FAILURE
[0]MoFEM ERROR: #1 main() line 59 in /Users/likask/MyBuild/mofem-cephas/mofem/users_modules/eshelbian_plasticty/ep.cpp

On 3 Dec 2018, at 22:23, Lukasz Kaczmarczyk <Lukasz.Kaczmarczyk at glasgow.ac.uk<mailto:Lukasz.Kaczmarczyk at glasgow.ac.uk>> wrote:

This is for partitioning for two processors, and I have variable length tags on vertices, edges, faces and volumes.

On 3 Dec 2018, at 22:15, Lukasz Kaczmarczyk via moab-dev <moab-dev at mcs.anl.gov<mailto:moab-dev at mcs.anl.gov>> wrote:

Hello,

I have this error for parallel when I write, then read in parallel, could you advise how to fix this error,

[1]MOAB ERROR: --------------------- Error Message ------------------------------------
[1]MOAB ERROR: Unordered file ids for variable length tag not supported!
[1]MOAB ERROR: read_var_len_tag() line 3335 in src/io/ReadHDF5.cpp
[1]MOAB ERROR: --------------------- Error Message ------------------------------------
[1]MOAB ERROR: ReadHDF5 Failure!
[1]MOAB ERROR: read_tag() line 2769 in src/io/ReadHDF5.cpp
[1]MOAB ERROR: --------------------- Error Message ------------------------------------
[1]MOAB ERROR: ReadHDF5 Failure!
[1]MOAB ERROR: load_file_partial() line 1164 in src/io/ReadHDF5.cpp

Kind regards,
Lukasz

<restart_1.h5m>

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