atomisation example compilation and execution problem

[Harsh Agarwal]

Hello, 

I have installed basilisk in WSL environment in "/home/gopu" directory my windows PC also on college HPC cluster. Their I prepare the code file "atomisation.c" in "/home/gopu/myfiles" directory as reccomended in example. 

 

1)- Approach first:

 

 Then I produce the source code on my local PC as recommended in the example using:

qcc -source -grid=octree -D_MPI=1 atomisation.c

Then I copy the source code "_atomisation.c" from my local PC to my college HPC cluster using:

scp _atomisation.c javedm@clustername:/home/javedm/myfiles 

Their I prepare the run script which I am attaching as "run.sh" to upload the job script on the cluster, but I am getting the error file and output file containing error, which are named respectively as "log_compilation" and "atomout_compilation_error".

From analysing the errors, I am suggesting that the compilation using mpicc is not being done, as it might be searching the files in "/home/gopu/basilisk.." instead of "/home/javedm/basilisk..". Therefore, not producing the executable file.

Please suggest me something to solve this error.

 

2)- Approach second:

 

As in first approach I produced the source code on local PC, but this time I compile the source code on the login node of the HPC by loading the required module:

module load compiler/openmpi/gcc/4.0.2

module load compiler/intel/2020.2.254

compiling using:

mpicc -Wall -std=c99 -D_XOPEN_SOURCE=700 -O2 _atomisation.c -o atomisation -L/home/javedm/basilisk/src/gl -lglutils -lfb_tiny -lm

This produce executable file naming “atomisation”, then I submit the run script with run command only naming “run1.sh”

This produce an error file and a output file respectively naming as “log_run2” and “basilisk2.output”

 

3)- Approach third:

 

Instead of producing the source code on the local PC, I tried to produce the source code on the HPC using the same:

qcc -source -grid=octree -D_MPI=1 atomisation.c

with some parsing errors it produces source code "_atomisation.c". The errors file naming “comp_onlog.docx”.

Then I upload the same "run.sh" script hoping successful compilation and execution, but now also the compilation doesn’t work. Therefore, no point of execution also.

I am attaching the error file as "log_hpc" and also the output file as "basilisk3.output"

Please suggest me something to solve this error.

4)- Approach fourth:

 

As in third approach produce source code on HPC and this time doing the compilation on the login node as well by loading the required module:

module load compiler/openmpi/gcc/4.0.2

module load compiler/intel/2020.2.254

then doing the compilation using:

mpicc -Wall -std=c99 -D_XOPEN_SOURCE=700 -O2 _atomisation.c -o atomisation -L/home/javedm/basilisk/src/gl -lglutils -lfb_tiny -lm

which produce an executable file “atomisation”.

Then for executing the code I upload the job script naming “run4.sh”, which in return produces error and output file as “log_run4” and “basilisk4.output” respaectively.

 

5)- Approach fifth:

 

Produced the source code on local PC, compiled on login node and running on HPC using run script but containing the run command for single environment i.e.

./atomisation

Which produces the files but they are as I want them to be.

If anyone one of you can suggest a proper procedure then please suggest me, or if I am doing some silly mistake in my procedure then please also suggest.