Server Submit & Setting Scripts

t3/imports.py

@@ -4,9 +4,19 @@
 
 import os
 import sys
+import socket
 
-import t3.settings.settings as t3_settings
-from t3.settings.t3_submit import submit_scripts
+
+
+if socket.gethostname() == 'zeus.technion.ac.il':
+    import t3.settings.settings_zeus as t3_settings
+    from t3.settings.submit_zeus import submit_scripts
+elif socket.gethostname() == 'tech-ui02.hep.technion.ac.il':
+    import t3.settings.settings_atlas as t3_settings
+    from t3.settings.submit_atlas import submit_scripts
+else:
+    import t3.settings.settings as t3_settings
+    from t3.settings.t3_submit import submit_scripts
 
 
 # Common imports where the user can optionally put a modified copy of settings.py or t3_submit.py file under ~/.t3

t3/settings/settings_atlas.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': 'incore',
+}
+
+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': '/usr/local/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': '/usr/local/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

t3/settings/settings_zeus.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': 'incore',
+}
+
+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

t3/settings/submit_atlas.py

@@ -0,0 +1,60 @@
+"""
+Submit scripts
+"""
+
+# 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=9500
+#
+#
+# export PYTHONPATH=$PYTHONPATH:~/Code/RMG-Py/
+#
+# conda activate rmg_env
+#
+# touch initial_time
+#
+# python-jl ~/Code/RMG-Py/rmg.py -n {cpus} input.py
+#
+# touch final_time
+#
+# """,
+    'rmg': """Universe      = vanilla
+
++JobName      = "{name}"
+
+log           = job.log
+output        = out.txt
+error         = err.txt
+
+getenv        = True
+
+should_transfer_files = no
+
+executable = job.sh
+
+request_cpus  = {cpus}
+request_memory = {memory}MB
+
+queue
+
+""",
+    'rmg_job': """#!/bin/bash -l
+
+touch initial_time
+
+source /srv01/technion/$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
+
+""",
+}

t3/settings/submit_zeus.py

@@ -0,0 +1,81 @@
+"""
+Submit scripts
+"""
+
+# 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}
+#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
+
+""",
+}