[Flash-X-users] Error while Running CCSN DeleptonizationWave

kiyarash Taghiniyarami kiyarash.niyarami at gmail.com
Thu Dec 14 05:30:21 CST 2023


Dear Users,
I tried to make core collapse supernova with +weaklib, +spark, and
+thornado with the setup command of:

 ./setup DeleptonizationWave -auto -1d +spherical +pm4dev -objdir Delep
-nxb=16 --with-unit=physics/Hydro/HydroMain/Spark/NonTelescoping +nolwf
--with-unofficial=physics/Hydro/HydroMain/Spark/NonTelescoping
nontelescoping=True +weaklib +thornado -maxblocks=64  nE=16 swE=1
nSpecies=6 nNodes=2 nMoments=4 momentClosure=MINERBO thornadoOrder=ORDER_V
Bittree=True

. After successful setup and compilation then tried to run it but face the
following error:


HDF5-DIAG: Error detected in HDF5 (1.14.3) MPI-process 0:
  #000: /home/taghinia/FLASH/HDF5/hdf5-1.14.3/src/H5F.c line 660 in
H5Fcreate(): unable to synchronously create file
    major: File accessibility
    minor: Unable to create file
  #001: /home/taghinia/FLASH/HDF5/hdf5-1.14.3/src/H5F.c line 614 in
H5F__create_api_common(): unable to create file
    major: File accessibility
    minor: Unable to open file
  #002: /home/taghinia/FLASH/HDF5/hdf5-1.14.3/src/H5VLcallback.c line 3605
in H5VL_file_create(): file create failed
    major: Virtual Object Layer
    minor: Unable to create file
  #003: /home/taghinia/FLASH/HDF5/hdf5-1.14.3/src/H5VLcallback.c line 3571
in H5VL__file_create(): file create failed
    major: Virtual Object Layer
    minor: Unable to create file
  #004: /home/taghinia/FLASH/HDF5/hdf5-1.14.3/src/H5VLnative_file.c line 94
in H5VL__native_file_create(): unable to create file
    major: File accessibility
    minor: Unable to open file
  #005: /home/taghinia/FLASH/HDF5/hdf5-1.14.3/src/H5Fint.c line 1851 in
H5F_open(): unable to open file: name = 'chk/delep_hdf5_chk_0000',
tent_flags = 13
    major: File accessibility
    minor: Unable to open file
  #006: /home/taghinia/FLASH/HDF5/hdf5-1.14.3/src/H5FD.c line 769 in
H5FD_open(): open failed
    major: Virtual File Layer
    minor: Unable to initialize object
  #007: /home/taghinia/FLASH/HDF5/hdf5-1.14.3/src/H5FDsec2.c line 323 in
H5FD__sec2_open(): unable to open file: name = 'chk/delep_hdf5_chk_0000',
errno = 2, error message = 'No such file or directory', flags = 13, o_flags
= 242
    major: File accessibility
    minor: Unable to open file
 Error: unable to initialize file

Can anyone help me with that? Is that something due to netcdf and HDF5
locking? I also tried export HDF5_USE_FILE_LOCKING=FALSE  but it did not
help.

Best,
Kiya
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