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Installing QuantumATK-U-2022.12-Linux64.bin

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hagelberg:
Thanks for your instructions - I deinstalled the earlier version of  QuantumATK-U-2022.12  and followed your description when installing QuantumATK-U-2022.12-SP1.

Here is my test script:

#!/bin/bash
#SBATCH --nodes 1
#SBATCH --ntasks-per-node 8
#SBATCH --cpus-per-task 1
#SBATCH --exclusive
#SBATCH --mem=50g
#SBATCH -p batch
#SBATCH -A cnms
#SBATCH -t 4:00:00

module load PE-intel
export SNPSLMD_LICENSE_FILE="27020@151.141.244.36"

/home/fhagelberg/QuantumATK/QuantumATK-U-2022.12-SP1/mpi/bin/mpiexec.hydra -n 1 /home/fhagelberg/QuantumATK/QuantumATK-U-2022.12-SP1/atkpython/bin/atkpython Fgraphene-half-spinit-lower-edge.py > Fgraphene-half-spinit-lower-edge.log
#END

Once more, the job fails with an error message:

Traceback (most recent call last):
  File "/home/fhagelberg/QuantumATK/QuantumATK-U-2022.12-SP1/atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 837, in __run_atkpython
  File "<frozen zipimport>", line 281, in load_module
  File "zipdir/NL/__init__.py", line 13, in <module>
  File "zipdir/NL/ATKLicenseHelpers.py", line 193, in atkpythonLicenseCheck
  File "zipdir/NL/ATKLicenseHelpers.py", line 167, in atkpythonLicenseCheck
  File "<frozen zipimport>", line 281, in load_module
  File "zipdir/NLEngine.py", line 21, in <module>
ImportError: /software/tools/compilers/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpifort.so.12: undefined symbol: MPI_UNWEIGHTED

I submitted the installbuilder file in a separate post. Please let me know about any other relevant information I could supply.
 
Frank

filipr:
Hi Frank,

It appears the installation was successful this time. We did have an issue with using relative paths for installation directories in the past, but it should have been fixed in version 2022.12, so it's still unknown what the original issue was. Most likely something system specific.

Anyway, you new problem is that the program finds the libraries of an existing Intel MPI installation from 2016 (/software/tools/compilers/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpifort.so.12). Maybe that's what you load with module load PE-intel? Try to remove that from your submission script. Also be sure that your PATH and LD_LIBRARY_PATH environment variables do not contain directories to any MPI libraries, and that no environment variables called I_MPI_ROOT and MKLROOT exist. Typically these are set in e.g. your .bashrc by sourcing environment scripts shipped by Intel software like source /path/to/intel/mpi/mpivars.sh, so be sure none of that is done. You don't want your shell environment to contain any traces of MPI, whether it is OpenMPI, MPICH or Intel-MPI.

hagelberg:
Removing the line 'module load PE-intel' from the script settled the issue.
Thanks so much,

Frank

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