T3 rmg zeus submit script

Servers/Zeus/.bashrc

@@ -1,7 +1,4 @@
-
-
 # User specific aliases and functions
-# Note: Change the <user> keyword of the last "st" command to your own username (without the "<" and ">)
 
 
 # RMG-Py
@@ -37,5 +34,4 @@ alias t3code='cd $t3_path'
 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>'
-
+alias st='qstat -u $USER'

Servers/Zeus/.t3/settings.py

@@ -0,0 +1,43 @@
+"""
+T3's settings
+
+You may keep a short version of this file in a local ".t3" folder under your home folder.
+Any definitions made to the local file will take precedence over this file.
+"""
+
+
+# The execution type can be either 'incore', i.e., executed in the same processor,
+# or 'local', i.e., to be submitted to the server queue if running on a server.
+# If running on a local server, ARC's settings for ``local`` will be used.
+execution_type = {
+    'rmg': 'local',
+    'arc': 'local',
+}
+
+servers = {
+    'local': {
+        'cluster_soft': 'PBS',
+        'cpus': 16,
+        'max mem': 40,  # GB
+    },
+}
+
+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  # The initial memory for an RMG job when submitted to the queue, in GB

Servers/Zeus/.t3/t3_submit.py

@@ -0,0 +1,28 @@
+"""
+Submit scripts
+"""
+
+# Submission scripts stored as a dictionary with software as the primary key.
+submit_scripts = {
+    'rmg': """#!/bin/bash -l
+
+#PBS -N {name}
+#PBS -q zeus_long_q
+#PBS -l walltime=168:00:00
+#PBS -l select=1:ncpus={cpus}
+#PBS -o out.txt
+#PBS -e err.txt
+
+PBS_O_WORKDIR={workdir}
+cd $PBS_O_WORKDIR
+
+conda activate rmg_env
+
+touch initial_time
+
+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
-

Servers/Zeus/RMG/submit.sh

@@ -1,13 +1,12 @@
 #!/bin/bash -l
 
-#PBS -N <name>  # Note: Manually change this job name, and delete this comment
-#PBS -q zeus_new_q
-#PBS -l walltime=72:00:00
-#PBS -l select=1:ncpus=10
+#PBS -q zeus_long_q
+#PBS -N {name}
+#PBS -l select=1:ncpus={cpus}:mem={memory}
 #PBS -o out.txt
 #PBS -e err.txt
 
-PBS_O_WORKDIR=~/runs/RMG/x1001/
+PBS_O_WORKDIR={pwd}
 cd $PBS_O_WORKDIR
 
 conda activate rmg_env