An error of run gadget2.0.7 with hdf5 IC

From: ¡ <wu-cl_at_outlook.com>
Date: Sun, 13 Nov 2022 10:14:47 +0000

Dear gadget2 user

Im a postgraduate and I am learning how to run gadget2.0.7

I understand from user-guide that I can run my IC with hdf5 format , and my tutor said I can use hdf5 snapshot file to be the IC , so I tried use a snapshot from galaxy.param and galaxy_littleendian.dat , but it dont work and return me an error level of 1 .

I wonder whether I use the wrong file format or I should write a new hdf5 IC by other different way?

Heres the error it return:



reading file `./test.hdf5' on task=0 (contains 400 particles.)

distributing this file to tasks 0-0

Type 0 (gas): 0 (tot= 0000000000) masstab=0

Type 1 (halo): 0 (tot= 0000000000) masstab=0

Type 2 (disk): 400 (tot= 0000000400) masstab=0

Type 3 (bulge): 0 (tot= 0000000000) masstab=0

Type 4 (stars): 0 (tot= 0000000000) masstab=0

Type 5 (bndry): 0 (tot= 0000000000) masstab=0



reading done.

Total number of particles : 0000000400



allocated 0.0762939 Mbyte for ngb search.



Allocated 0.796875 MByte for BH-tree. 64



domain decomposition...

done with snapshot.



Setting next time for snapshot file to Time_next= 0.1





Begin Step 0, Time: 0, Systemstep: 0

domain decomposition...

NTopleaves= 127

work-load balance=1 memory-balance=1

domain decomposition done.

begin Peano-Hilbert order...

Peano-Hilbert done.

Start force computation...

Tree construction.

task 0: endrun called with an error level of 1





NTopleaves= 127

work-load balance=1 memory-balance=1

domain decomposition done.

begin Peano-Hilbert order...

Peano-Hilbert done.

Begin Ngb-tree construction.

Ngb-Tree contruction finished



Setting next time for snapshot file to Time_next= 0





writing snapshot file...

--------------------------------------------------------------------------

Primary job terminated normally, but 1 process returned

a non-zero exit code. Per user-direction, the job has been aborted.

--------------------------------------------------------------------------

task 0: maximum number 480 of tree-nodes reached.

for particle 335



Allocated 0.0389099 MByte for particle storage. 68





reading file `./test.hdf5' on task=0 (contains 400 particles.)

distributing this file to tasks 0-0

Type 0 (gas): 0 (tot= 0000000000) masstab=0

Type 1 (halo): 0 (tot= 0000000000) masstab=0

Type 2 (disk): 400 (tot= 0000000400) masstab=0

Type 3 (bulge): 0 (tot= 0000000000) masstab=0

Type 4 (stars): 0 (tot= 0000000000) masstab=0

Type 5 (bndry): 0 (tot= 0000000000) masstab=0



application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5Gdeprec.c line 326 in H5Gopen1(): unable to open group

    major: Symbol table

    minor: Can't open object

  #001: H5Gint.c line 320 in H5G__open_name(): group not found

    major: Symbol table

    minor: Object not found

  #002: H5Gloc.c line 430 in H5G_loc_find(): can't find object

    major: Symbol table

    minor: Object not found

  #003: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed

    major: Symbol table

    minor: Object not found

  #004: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed

    major: Symbol table

    minor: Callback failed

  #005: H5Gloc.c line 385 in H5G_loc_find_cb(): object 'PartType2' doesn't exist

    major: Symbol table

   minor: Object not found

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5Ddeprec.c line 244 in H5Dopen1(): not a location

    major: Invalid arguments to routine

    minor: Inappropriate type

  #001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

    major: Invalid arguments to routine

    minor: Bad value

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5Dio.c line 140 in H5Dread(): not a dataset

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5D.c line 415 in H5Dclose(): not a dataset

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5Ddeprec.c line 244 in H5Dopen1(): not a location

    major: Invalid arguments to routine

    minor: Inappropriate type

  #001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

    major: Invalid arguments to routine

    minor: Bad value

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5Dio.c line 140 in H5Dread(): not a dataset

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5D.c line 415 in H5Dclose(): not a dataset

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5Ddeprec.c line 244 in H5Dopen1(): not a location

    major: Invalid arguments to routine

    minor: Inappropriate type

  #001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

    major: Invalid arguments to routine

    minor: Bad value

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5Dio.c line 140 in H5Dread(): not a dataset

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5D.c line 415 in H5Dclose(): not a dataset

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5Ddeprec.c line 244 in H5Dopen1(): not a location

    major: Invalid arguments to routine

    minor: Inappropriate type

  #001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

    major: Invalid arguments to routine

    minor: Bad value

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5Dio.c line 140 in H5Dread(): not a dataset

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5D.c line 415 in H5Dclose(): not a dataset

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:

  #000: H5G.c line 811 in H5Gclose(): not a group

    major: Invalid arguments to routine

    minor: Inappropriate type

task 0: endrun called with an error level of 1





--------------------------------------------------------------------------

mpirun detected that one or more processes exited with non-zero status, thus causing

the job to be terminated. The first process to do so was:



  Process name: [[31325,1],0]

  Exit code: 1



In addition , I use 1.8.13 version of hdf5 package , but I think maybe its not the problem , the error also happened in 1.6.10 version of hdf5



Best wishes

wood

Received on 2022-11-13 11:15:01

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