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ornladios / ADIOS

The old ADIOS 1.x code repository. Look for ADIOS2 for new repo
https://csmd.ornl.gov/adios
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bp2ncd not working on skel benchmark output #191

Closed khou2020 closed 5 years ago

khou2020 commented 5 years ago

Hi:

I tried to convert output of the gts and s3d benchmark generated by the built in skel tool. It report error parsing the header.

~/Desktop/ADIOS/examples/skel/gts$ ls
gts.xml
~/Desktop/ADIOS/examples/skel/gts$ skel xml gts
~/Desktop/ADIOS/examples/skel/gts$ skel params gts
~/Desktop/ADIOS/examples/skel/gts$ ls
gts.xml  gts_params.xml  gts_skel.xml
~/Desktop/ADIOS/examples/skel/gts$ skel source gts
~/Desktop/ADIOS/examples/skel/gts$ skel makefile gts
~/Desktop/ADIOS/examples/skel/gts$ make
mpif90 -g -O2 `/home/khl7265/.local/bin/../bin/adios_config -fc`           -o gts_skel_restart_write gts_skel_restart_write.f90 -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/7/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/7/../../.. -lgfortran -lm -lquadmath `/home/khl7265/.local/bin/../bin/adios_config -fl` -L/home/khl7265/.local/bin/../lib/skel -lskel
~/Desktop/ADIOS/examples/skel/gts$ ls
Makefile  gts.xml  gts_params.xml  gts_skel.xml  gts_skel_restart_write  gts_skel_restart_write.f90

I got some error message when I try to run the benchmark, I don't know if they related to the error in bp2ncd

~/Desktop/ADIOS/examples/skel/gts$ mpiexec -np 128 ./gts_skel_restart_write
ERROR: Parameter name ***skel-parameters*** is not recognized by the POSIX write method
... (same error repeat)
ERROR: Parameter name ***skel-parameters*** is not recognized by the POSIX write method
 \n
 **************************
   Groupsize:                 28916
   Open Time:    10.492516040802002
 Access Time:   0.11841320991516113
  Close Time:    3.8680129051208496
  Total Time:    14.664496183395386
 **************************
 \n

I use bp2ncd to convert it to a NetCDF file, but I got following errors.

~/Desktop/ADIOS/examples/skel/gts$ ls
Makefile  gts.xml  gts_params.xml  gts_skel.xml  gts_skel_restart_write  gts_skel_restart_write.f90  out_restart_write_1  out_restart_write_1.dir  skel_time.xml
~/Desktop/ADIOS/examples/skel/gts$ bp2ncd out_restart_write_1
ERROR: adios_parse_process_group_header_v1requires a buffer of at least 24 bytes. Only 0 were provided
ERROR: adios_parse_vars_header_v1requires a buffer of at least 12 bytes. Only 0 were provided
ERROR: adios_parse_attributes_header_v1requires a buffer of at least 10 bytes.  Only 0 were provided
... (same error repeat)

The result is an empty NetCDF file

~/Desktop/ADIOS/examples/skel/gts$ ls
Makefile  gts.xml  gts_params.xml  gts_skel.xml  gts_skel_restart_write  gts_skel_restart_write.f90  out_restart_write_1  out_restart_write_1.dir  out_restart_write_1.nc  skel_time.xml
~/Desktop/ADIOS/examples/skel/gts$ ncdump out_restart_write_1.nc
netcdf out_restart_write_1 {
}

I am using the master branch of the git repository on commit 9edc5b6984009c413fe60753b67e9c5f02985e8a

The NetCDF version I used to build bp2ncd is 4.6.2-development of Oct 9 2018