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[SOLVED]wrf (intel compiler) crash

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order999

New member
Has anyone seen this error before?

wrf-intel.exe: H5Eint.c:696: H5E_printf_stack: Assertion `cls_id > 0' failed.
forrtl: error (76): Abort trap signal
 
I think that's a netcdf problem and not the intel compiler. Try compiling with classic data model from netCDF-3, without compression.
If you want to use compression, build netcdf with hdf5 without activating parallel I/O.
 
order999 said:
Has anyone seen this error before?

wrf-intel.exe: H5Eint.c:696: H5E_printf_stack: Assertion `cls_id > 0' failed.
forrtl: error (76): Abort trap signal
Click to expand...
I have used intel compilers for another flavor of WRF, the hurricane WRF and I had to do several things to get it to work. If you message me I can walk you through them.
 
Try setting the HDF5 library paths like this before configure:

export HDF5PATH=/hdf5lib_path/hdf5
export PATH=/hdf5lib_path/hdf5/bin:$PATH
export PATH=/hdf5lib_path/hdf5/lib:$PATH
export PATH=/hdf5lib_path/hdf5/include:$PATH
Click to expand...

and then check that HDF5 is correctly linked in configure.wrf
I think these are all the references in the file:
HDF5 = -lhdf5_hl -lhdf5

DEP_LIB_PATH = -L/hdf5lib_path/hdf5/lib

NETCDF4_DEP_LIB = $(DEP_LIB_PATH) $(HDF5) $(ZLIB) $(GPFS) $(CURL)

LIB_EXTERNAL = \
-L$(WRF_SRC_ROOT_DIR)/external/io_netcdf -lwrfio_nf ... -L/hdf5lib_path/hdf5/lib -lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5 -lm -lz

ARCHFLAGS = ...

\
-DHDF5 \
\

HDF5PATH = /hdf5lib_path/hdf5
Click to expand...
 
For the intel compilers are you installing ALL of the intel compliers or just the HPC package? Intel doesn't document it but you need to install all of their packages to get it to work. Here's a snippet of my code for intel compilers.

Bash: 
# download the key to system keyring; this and the following echo command are
# needed in order to install the Intel compilers
wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \
| gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null

# add signed entry to apt sources and configure the APT client to use Intel repository:
echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list

# this update should get the Intel package info from the Intel repository
sudo apt -y update

# install the Intel compilers
sudo apt -y install intel-basekit intel-hpckit
sudo apt -y update

# add the Intel compiler file paths to various environment variables
source /opt/intel/oneapi/setvars.sh

# some of the libraries we install below need one or more of these variables
export CC=icc
export CXX=icpc
export FC=ifort
export F77=ifort
export F90=ifort
export MPIFC=mpiifort
export MPIF77=mpiifort
export MPIF90=mpiifort
export MPICC=mpiicc
export MPICXX=mpiicpc
 
order999 said:
Can you show me how to mark the thread as solved?
Click to expand...
What you do is edit your original post by clicking the 3 dots. Then change the title to put (SOLVED) in front of the title.
Otherwise @kwerner , one of the admins, will do it for you when they can get to it.

Doing it yourself is just a nice thing to do and helps keep the workload low for them.
 
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