Running CDFT Tutorial Calculation on Cluster

Brian Day 22b... at
Mon Jul 30 20:00:41 UTC 2018

Hi Nico,

I use the following intel compilers: module load intel/2017.3.196 
intel-mpi/2017.3.196 cp2k/6.1

Summarized below are the conditions I used and the results I got:
nodes = 1, tasks = 14, executable = cp2k.popt -i *.inp -o *.out ---> Cube 
files generated without issue
nodes = 1, tasks = 14, executable = mpirun -np $SLURM_NTASKS cp2k.popt -i 
*.inp -o *.out ---> 

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Image              PC                Routine            Line        Source

cp2k.popt          000000000D730E14  Unknown               Unknown  Unknown

libpthread-2.17.s  00002ABEB44735E0  Unknown               Unknown  Unknown   00002ABEB61E74DC  cfree                 Unknown  Unknown

cp2k.popt          000000000D767FA8  Unknown               Unknown  Unknown

cp2k.popt          000000000109F105  qs_dispersion_typ         135  

cp2k.popt          0000000000B88BFF  qs_environment_ty        1476  

cp2k.popt          0000000000B13020  force_env_types_m         232  

cp2k.popt          0000000000EE66E0  f77_interface_mp_         335  

cp2k.popt          000000000043BEF8  cp2k_runs_mp_run_         405  

cp2k.popt          0000000000432814  MAIN__                    281  cp2k.F

cp2k.popt          000000000043151E  Unknown               Unknown  Unknown   00002ABEB6188C05  __libc_start_main     Unknown  Unknown

cp2k.popt          0000000000431429  Unknown               Unknown  Unknown
Note that I had to run these simulations on a different cluster here, as 
the one I was using previously requires the submission file to declare a 
minimum of 2 nodes. I can talk to our computing center and see if they can 
test this themselves. 

To (hopefully) clarify my earlier message, when I ran with 2 nodes, the 
last line in the cp2k output file would be:

 The sum of alpha and beta density is written in cube file format to the 

and the electron density file would appear in the submission directory, but 
it would be empty. If I re-ran the simulation and passed this blank file to 
the cluster which I was running on, it would run successfully, but when 
trying to open the file in another program such as Avogadro, or using it in 
a subsequent simulation, it would not work. Maybe this is because it is 
only partially writing as you pointed out. 

I will try and update this with the compiling information and a detailed 
debugging output. (Sorry if any of the above does not make sense, I am 
still fairly new to computational work). 

Thanks again.

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