Skip to content

changing batch scripts for SVMBIR jobs #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

changing batch scripts for SVMBIR jobs #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion backend/ALS_batch_recon.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
import ALS_recon_functions as als
import ALS_recon_helper as helper

MAX_JOB_SECONDS = 80*60 # 1 hour 20 min
MAX_JOB_SECONDS = 300*60 # 5 hour 00 min

def get_batch_template(algorithm="astra"):
""" Gets path to appropriate batch scrpit template, depending on whether using Astra or SVMBIR, on Cori or Perlmutter """
Expand Down
18 changes: 16 additions & 2 deletions backend/ALS_recon_functions.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -481,8 +481,22 @@ def cache_svmbir_projector(num_rays,num_angles,save_to_default_cache=True):


def get_svmbir_cache_dir():
""" Sets location of SVMBIR system matrix cache. Must be accessible by all users, otherwise SVMBIR will take prohibitively long """
return '//global/cfs/cdirs/als/users/tomography_notebooks/svmbir_cache'
""" Sets location of SVMBIR system matrix cache. Must be accessible by all users, otherwise SVMBIR will take prohibitively long

If the global cache directory does raise a permission error, you can set the cache directory to your scratch directory by setting up cache_path as follows:

For Perlmutter:
cache_path = '/pscratch/sd/h/*YOUR_USER_NAME*/svmbir_cache'
For Cori:
cache_path = '/global/cscratch1/sd/h/*YOUR_USER_NAME*/svmbir_cache'

---------------
Returns:
_type_: globally accessible file path to SVMBIR cache

"""
cache_path = '//global/cfs/cdirs/als/users/tomography_notebooks/svmbir_cache'
return cache_path

def get_scratch_path():
""" Gets path to user's scratch if on NERSC, otherwise returns current directory """
Expand Down
5 changes: 3 additions & 2 deletions slurm_scripts/svmbir_template_job-cori.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,11 @@
#SBATCH --image=dperl/als832:mpi
#SBATCH --volume=/global/cfs/cdirs/als/data_mover/share/<username>:/alsuser;/global/cfs/cdirs/als/data_mover/8.3.2/raw:/alsdata:ro
#SBATCH -C haswell
#SBATCH -N 100
#SBATCH -n 100
#SBATCH -N 10
#SBATCH -n 10
#SBATCH --ntasks-per-node 1
#SBATCH --cpus-per-task 32
#SBATCH --mem 96000
#SBATCH --time=00:15:00
#SBATCH -J als832-svmbir

Expand Down
4 changes: 2 additions & 2 deletions slurm_scripts/svmbir_template_job-perlmutter.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@
#SBATCH --image=dperl/als832:mpi
#SBATCH --volume=/global/cfs/cdirs/als/data_mover/share/<username>:/alsuser;/global/cfs/cdirs/als/data_mover/8.3.2/raw:/alsdata:ro
#SBATCH -C cpu
#SBATCH -N 100
#SBATCH -n 100
#SBATCH -N 10
#SBATCH -n 10
#SBATCH --ntasks-per-node 1
#SBATCH --cpus-per-task 256
#SBATCH --time=00:15:00
Expand Down