Rebased with main and updated submit.sh for RMG and T3 settings/submit

Author: calvinp0

Servers/Zeus/.bashrc

@@ -1,5 +1,3 @@
-
-
 # User specific aliases and functions
 
 
@@ -37,4 +35,3 @@ alias runs='cd ~/runs'
 alias rmg='python-jl $rmgpy_path/rmg.py input.py  > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)'
 alias sb='qsub submit.sh'
 alias st='qstat -u $USER'
-

Servers/Zeus/.t3/settings.py

@@ -11,7 +11,7 @@
 # If running on a local server, ARC's settings for ``local`` will be used.
 execution_type = {
     'rmg': 'local',
-    'arc': 'incore',
+    'arc': 'local',
 }
 
 servers = {

Servers/Zeus/.t3/t3_submit.py

@@ -4,59 +4,6 @@
 
 # Submission scripts stored as a dictionary with software as the primary key.
 submit_scripts = {
-#     'rmg': """#!/bin/bash -l
-# #SBATCH -J {name}
-# #SBATCH -t 05-00:00:00
-# #SBATCH -o out.txt
-# #SBATCH -e err.txt
-# #SBATCH --ntasks={cpus}
-# #SBATCH --mem-per-cpu={memory / cpus}
-#
-#
-# export PYTHONPATH=$PYTHONPATH:~/Code/RMG-Py/
-#
-# conda activate rmg_env
-#
-# touch initial_time
-#
-# python-jl ~/Code/RMG-Py/rmg.py -n {cpus} input.py{max_iterations}
-#
-# touch final_time
-#
-# """,
-#     'rmg': """Universe      = vanilla
-#
-# +JobName      = "{name}"
-#
-# log           = job.log
-# output        = out.txt
-# error         = err.txt
-#
-# getenv        = True
-#
-# should_transfer_files = no
-#
-# executable = job.sh
-#
-# request_cpus  = {cpus}
-# request_memory = {memory}MB
-#
-# queue
-#
-# """,
-#     'rmg_job': """#!/bin/bash -l
-#
-# touch initial_time
-#
-# source /srv01/technion/$USER/.bashrc
-#
-# conda activate rmg_env
-#
-# python-jl /Local/ce_dana/Code/RMG-Py/rmg.py -n {cpus} input.py{max_iterations}
-#
-# touch final_time
-# 
-# """,
     'rmg': """#!/bin/bash -l
 
 #PBS -N {name}
@@ -73,7 +20,7 @@
 
 touch initial_time
 
-python-jl ~/Code/RMG-Py/rmg.py -n {cpus} input.py{max_iterations}
+python-jl ~/Code/RMG-Py/rmg.py -n {cpus} input.py {max_iterations}
 
 touch final_time
 

Servers/Zeus/ARC/submit.sh

@@ -13,4 +13,3 @@ cd $PBS_O_WORKDIR
 conda activate arc_env
 
 python $arc_code/ARC.py input.yml
-