T3 rmg zeus submit script

Servers/Zeus/.bashrc

@@ -1,7 +1,6 @@
 
 
 # User specific aliases and functions
-# Note: Change the <user> keyword of the last "st" command to your own username (without the "<" and ">)
 
 
 # RMG-Py
@@ -36,11 +35,11 @@ alias dbcode='cd $rmgdb_path'
 alias arcode='cd $arc_path'
 alias t3code='cd $t3_path'
 
-alias rmg='python-jl $rmgpy_path/rmg.py input.py  > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)'
-alias arkane='python-jl $rmgpy_path/Arkane.py input.py  > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)'
+alias rmg='python $rmgpy_path/rmg.py input.py  > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)'
+alias arkane='python $rmgpy_path/Arkane.py input.py  > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)'
 alias arc='python $arc_path/ARC.py input.yml  > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)'
 alias arcrestart='python $arc_path/ARC.py restart.yml  > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)'
 alias t3='python $t3_path/T3.py input.yml  > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)'
 
 alias sb='qsub submit.sh'
-alias st='qstat -u <user>'
+alias st='qstat -u $USER'

Servers/Zeus/.t3/t3_settings.py

@@ -0,0 +1,49 @@
+"""
+Local T3 settings for the Zeus (PBS) cluster.
+
+T3 loads this file from ``~/.t3/t3_settings.py`` and any variable defined here
+overrides the corresponding one in T3's built-in ``t3/settings/t3_settings.py``.
+Each override replaces the whole variable, so dicts below are kept complete.
+"""
+
+# Execution type per software:
+#   'incore' - run in the calling T3 process
+#   'local'  - submit a job to this server's queue
+# RMG is submitted to the Zeus queue; ARC runs in-process and submits its own
+# ESS jobs via Servers/Zeus/ARC/.arc.
+execution_type = {
+    'rmg': 'local',
+    'arc': 'incore',
+}
+
+servers = {
+    'local': {  # Each Zeus node has 80 cores and 378 GB RAM
+        'cluster_soft': 'PBS',
+        'cpus': 16,
+        'max mem': 40,  # GB
+    },
+}
+
+# Zeus keeps its PBS binaries under /opt/pbs/bin (matches Servers/Zeus/ARC/.arc/settings.py).
+check_status_command = {
+    'OGE': 'export SGE_ROOT=/opt/sge; /opt/sge/bin/lx24-amd64/qstat -u $USER',
+    'Slurm': '/usr/bin/squeue -u $USER',
+    'PBS': '/opt/pbs/bin/qstat -u $USER',
+    'HTCondor': """condor_q -cons 'Member(Jobstatus,{1,2})' -af:j '{"0","P","R","X","C","H",">","S"}[JobStatus]' RequestCpus RequestMemory JobName '(Time() - EnteredCurrentStatus)'""",
+}
+
+submit_command = {
+    'OGE': 'export SGE_ROOT=/opt/sge; /opt/sge/bin/lx24-amd64/qsub',
+    'Slurm': '/usr/bin/sbatch',
+    'PBS': '/opt/pbs/bin/qsub',
+    'HTCondor': 'condor_submit',
+}
+
+submit_filenames = {
+    'OGE': 'submit.sh',
+    'Slurm': 'submit.sl',
+    'PBS': 'submit.sh',
+    'HTCondor': 'submit.sub',
+}
+
+rmg_initial_memory = 25  # GB, initial memory for an RMG job submitted to the queue

Servers/Zeus/.t3/t3_submit.py

@@ -0,0 +1,30 @@
+"""
+Local T3 submit scripts for the Zeus (PBS) cluster.
+
+T3 loads this file from ``~/.t3/t3_submit.py`` and updates its built-in
+``submit_scripts`` with the entries below. T3 fills the 'rmg' template via
+str.format() with: name, cpus, memory, workdir, max_iterations.
+"""
+
+submit_scripts = {
+    'rmg': """#!/bin/bash -l
+
+#PBS -N {name}
+#PBS -q alon_q
+#PBS -l walltime=72:00:00
+#PBS -l select=1:ncpus={cpus}:host=n170
+#PBS -o out.txt
+#PBS -e err.txt
+
+PBS_O_WORKDIR={workdir}
+cd $PBS_O_WORKDIR
+
+conda activate rmg_env
+
+touch initial_time
+
+python $rmgpy_path/rmg.py {max_iterations} -n {cpus} input.py
+
+touch final_time
+""",
+}

Servers/Zeus/RMG/submit.sh

@@ -12,5 +12,5 @@ cd $PBS_O_WORKDIR
 
 conda activate rmg_env
 
-python-jl $rmg_code/rmg.py -n 10 input.py
+python $rmgpy_path/rmg.py -n 10 input.py