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104 Views 4 Replies Latest reply: Mar 19, 2021 3:09 PM by Brendan McAndrew RSS
Currently Being Moderated

Mar 13, 2021 5:45 PM

LDT killed

I was able to successfully compile LDT but when I try to run the first testcase from https://lis.gsfc.nasa.gov/tests/lis which is https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase1_ldt_par ms_2020.tar.gz

The program gets killed. I am using the latest version from github i.e. LISF-7.4.0-557WW/ld

 

$ ./LDT ldt.config.noah36_params

Killed

 

 

An ldtlog.000 file is getting generated which is as follows

 

  Start of LDT parameter processing

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

local domain:(          28          22 )

local domain without halo:(          28          22 )

running domain:(          28          22 )

local domain:    34.37500       39.62500      -102.8750      -96.12500

-------------------- LDT/LIS Domain ----------------------

(           1 ,  0.0000000E+00 )

(           2 ,   28.00000     )

(           3 ,   22.00000     )

(           4 ,   34.37500     )

(           5 ,  -102.8750     )

(           6 ,   128.0000     )

(           7 ,   39.62500     )

(           8 ,  -96.12500     )

(           9 ,  0.2500000     )

(          10 ,  0.2500000     )

(          11 ,   64.00000     )

(          12 ,  0.0000000E+00 )

(          13 ,  0.0000000E+00 )

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

LSM User-selected:  Noah.3.6

  - - - - - - MODEL PARAMETERS (NOT Selected) - - - - - - -

Regional mask data source: not defined

  -- Opening LDT Mask-Parameter Fill log file --

[INFO]  - - - - - - -  SURFACE TYPES  - - - - - - - -

[INFO] Initializing and Summing Surface Types

[INFO] ... Surface types selected:

  ... LSM       Openwater

[INFO] Finished initializing surface types

  [INFO] - - - - - - - - - Landcover/Landmask Parameters - - - - - - - - - - -

  -- 'NONE' Parameter-Mask Agreement Option Selected for Landcover

Param_Check: Vegetation tiles are being created ...

[INFO] Reading landcover values

[INFO] Reading landcover file: ./INPUT/LS_PARAMETERS/noah_2dparms/igbp.bin

 

I checked whether the file ./INPUT/LS_PARAMETERS/noah_2dparms/igbp.bin exists and it does.

 

Following is my make/configure.ldt file

 

FC              = /opt/intel/oneapi/mpi/2021.1.1//bin/mpiifort

FC77            = /opt/intel/oneapi/mpi/2021.1.1//bin/mpiifort

LD              = /opt/intel/oneapi/mpi/2021.1.1//bin/mpiifort

CC              = /opt/intel/oneapi/mpi/2021.1.1//bin/mpiicc

AR              = ar

MOD_ESMF        = /home/DEP/ESMF/mod/modO/Linux.intel.64.intelmpi.default

LIB_ESMF        = /home/DEP/ESMF/lib/libO/Linux.intel.64.intelmpi.default

INC_JPEG2000      = /home/DEP/JASPER/include/

LIB_JPEG2000      = /home/DEP/JASPER/lib64/

INC_ECCODES     = /home/DEP/ECCODES/include/

LIB_ECCODES     = /home/DEP/ECCODES/lib/

INC_NETCDF      = /home/DEP/NETCDF/include/

LIB_NETCDF      = /home/DEP/NETCDF/lib/

INC_HDF4        = /home/DEP/HDF4/include/

LIB_HDF4        = /home/DEP/HDF4/lib/

INC_HDF5        = /home/DEP/HDF5/include/

LIB_HDF5        = /home/DEP/HDF5/lib/

INC_HDFEOS      = /home/DEP/HDF-EOS2/test_/include/

LIB_HDFEOS      = /home/DEP/HDF-EOS2/test_/lib/

INC_FORTRANGIS1 =

INC_FORTRANGIS2 =

LIB_FORTRANGIS  =

INC_LIBGEOTIFF  =

LIB_LIBGEOTIFF  =

LIB_GDAL        =

CFLAGS          = -c  -DIFC

FFLAGS77        = -c -O1 -nomixed_str_len_arg -names lowercase -convert big_endian -assume byterecl  -DIFC -I$(MOD_ESMF) -DUSE_INCLUDE_MPI -I$(INC_ECCODES) -I$(INC_NETCDF)  -I$(INC_HDFEOS)  -I$(INC_HDF4)  -I$(INC_HDF5)

FFLAGS          =  -c -O1 -u -traceback -fpe0  -nomixed_str_len_arg -names lowercase -convert big_endian -assume byterecl -DIFC -I$(MOD_ESMF) -DUSE_INCLUDE_MPI -I$(INC_ECCODES) -I$(INC_NETCDF)  -I$(INC_HDFEOS)  -I$(INC_HDF4)  -I$(INC_HDF5)

LDFLAGS         =  -L$(LIB_ESMF) -lesmf -lstdc++ -limf -lm -lrt -lz -L$(LIB_ECCODES) -leccodes_f90 -leccodes -L$(LIB_JPEG2000) -ljasper -L$(LIB_NETCDF) -lnetcdff -lnetcdf -L$(LIB_HDFEOS) -lhdfeos -lGctp -L$(LIB_HDF4) -lmfhdf -ldf -ljpeg -lz  -L$(LIB_HDF5) -lhdf5_fortran -lhdf5_hl -lhdf5 -ldl

    • Currently Being Moderated
      Mar 15, 2021 4:51 PM (in response to Manmeet Singh)
      Re: LDT killed

      Hi Manmeet,

       

      It is worth a try. The igbp.bin file is fairly large (~900M) so I wonder if the run is being killed for exceeding memory quota on a login node (if that's where you're running)? I recall encountering a crash in a similar location while trying to run LDT within a container with a limited memory allocation.

       

      Please let me know if using `mpirun` also fails and I'll escalate your question.

       

      Thanks,

      Brendan

        • Currently Being Moderated
          Mar 19, 2021 3:09 PM (in response to Manmeet Singh)
          Re: LDT killed

          Hi Manmeet,

           

          Sorry for the delay; the notification about your reply just arrived in my inbox.

           

          Are you using a Singularity or Docker container? If the former, I may have some suggestions based on my limited experimentation with LISF + Singularity. I'm not very familiar with Docker, however.

           

          We most commonly run LISF on HPC (no container). If you have access to HPC it may be worth a shot running there, but you'd have to set up the LISF build environment there again.

           

          Brendan

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