Keywords for svpost in .slurm files

[Alessandro Ruggeri]

Dear all,

I've some trouble in generating .txt velocity, flow and pressure average files after converting results.
Actually, i'm working without a GUI in a server that is Linux-based. I run simulations after uploading all simulation files in a directory and by running a .slurm file.
Simulation run fine, and i can reduce results and obtain .vtu and .vtp files, but i can take .txt average files.

The general structure of .slurm file that i use is the following:

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#!/bin/bash -l

#SBATCH --nodes=1
#SBATCH --ntasks=16
#SBATCH --partition=debug
#SBATCH --job-name=test

WORK_DIR=/home/
EXE_DIR=/opt/svSolver-build/svSolver-build/bin

module purge
module load mpi/openmpi3-x86_64
export LD_LIBRARY_PATH=/usr/local/lib64:$LD_LIBRARY_PATH

cd ${WORK_DIR}/$SLURM_JOB_NAME

#launch simulation
mpirun ${EXE_DIR}/svsolver > ./log

#reduce results
${EXE_DIR}/svpost -all -indir ./$SLURM_NTASKS-procs_case -outdir ./ -start 4546 -stop 5054 -incr 2 -vtkcombo -vtp $SLURM_JOB_NAME.vtp -vtu $SLURM_JOB_NAME.vtu

I've found this instruction for svpost, but I don't know how to make those work in .slurm file

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create-flow-files --mesh-directory /home/test/mesh-complete/mesh-surfaces/    --output-directory /home/test/  --results-directory /home/test/  --single-file no --skip-walls yes  --units cm

Can you help me?

Best regards,
Alessandro

[David Parker]

Hi Alessandro,

There is no functionality in svpost to create flow files.

The create-flow-files you refer to is I think a program I wrote to create flow files (see https://github.com/ktbolt/cardiovascula ... flow-files).

I've never built this guy on an HPC cluster but you can download the C++ source and try to build it (needs CMake and VTK).

Cheers,
Dave

[Alessandro Ruggeri]

Dear Dave,
thank you for your kindly answer.

I'll try to build the program!

[Alessandro Ruggeri]

Dear Dave,
I've build succesfully. However, when i try to convert the result of the cylinder example, nothing happens.

This is the code i run with slurm

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#!/bin/bash -l

#SBATCH --nodes=1
#SBATCH --ntasks=2
#SBATCH --partition=debug
#SBATCH --job-name=steady_rcr

WORK_DIR=/home/michelec/SimVascular/Test_resuts_cilindro
EXE_DIR=/home/michelec/SimVascular/results2flow/build

module purge
module load mpi/openmpi3-x86_64
export LD_LIBRARY_PATH=/usr/local/lib64:$LD_LIBRARY_PATH

mkdir ${WORK_DIR}/$SLURM_JOB_NAME/flow-files
#cd ${WORK_DIR}/$SLURM_JOB_NAME/

${EXE_DIR}/create-flow-files --mesh-directory ${WORK_DIR}/$SLURM_JOB_NAME/mesh-complete/mesh-surfaces   --output-directory ${WORK_DIR}/$SLURM_JOB_NAME/flow-files  --results-directory ${WORK_DIR}/$SLURM_JOB_NAME/$SLURM_NTASKS-procs_case  --single-file no --skip-walls yes  --units cm

This is the directory tree:
-steady_rcr --> main project folder
|-------------2procs-case-----------> here i have restart files, and also converted results as depicted below
|-------------converted-results-----> here i save converted results by svpost; both vtu and vtp, one for each timestep, including the "0" timestep
|-------------flow-files---------------> here i want to save the flow files generated by create-flow-files code
|-------------mesh-complete--------> here i have mesh, and subfolders, generated properly by svpre

This is the output i've receved:

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Output directory: /home/michelec/SimVascular/Test_resuts_cilindro/steady_rcr/flow-files
Number of converted results files: 0
Number of face files: 3

I don't understand where i have to point when declaring the "--results-directory".
I've tried pointing to the folder with the converted results, but i receive the output mentioned above.
The same happens pointing to the folder with the restart files.
And again, pointing to a folder that conotains btoh restart files and converted results.

What am i doing wrong?

Thanks for your help!

Best regards,
Alessandro

[David Parker]

Hi Alessandro,

The --results-directory argument is the directory of the simulation results converted to VTK .vtp and .vtu files typically in a <NAME>-converted-results directory (see https://github.com/ktbolt/cardiovascula ... flow-files).

Cheers,
Dave

[Alessandro Ruggeri]

Hi Dave,
thanks for the answer.

I've tried again and i think the folders are correctly pointed, however, no flow file where creted.
The output message always say

Number of converted results files: 0
Number of face files: 3

Am i drown in an inch of water, or may be there is a bug in the code?
I've tried also with more complex simulations, but the flow files creation wont work.

Can you help me If i upload an explicative video?

Thanks in advance.

Have a nice day,
Alessandro

[David Parker]

Hi Alessandro,

The --results-directory parameter is the directory containing the VTK files you converted from you simulation files using svpost.

The Number of converted results files: 0 message means that the program could not find any VTK files. These files should be named like

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all_results_00100.vtp
all_results_00200.vtu
all_results_00400.vtp	
all_results_00500.vtu	
all_results_00100.vtu

The program is expecting the files named all_results_*.

Cheers,
Dave