diff --git a/Servers/Zeus/.bashrc b/Servers/Zeus/.bashrc index 3904fdc..bc1e75d 100644 --- a/Servers/Zeus/.bashrc +++ b/Servers/Zeus/.bashrc @@ -1,7 +1,4 @@ - - # User specific aliases and functions -# Note: Change the 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 ' - +alias st='qstat -u $USER' diff --git a/Servers/Zeus/.t3/settings.py b/Servers/Zeus/.t3/settings.py new file mode 100755 index 0000000..0df8d38 --- /dev/null +++ b/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 diff --git a/Servers/Zeus/.t3/t3_submit.py b/Servers/Zeus/.t3/t3_submit.py new file mode 100755 index 0000000..169aecb --- /dev/null +++ b/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 + +""", +} diff --git a/Servers/Zeus/ARC/submit.sh b/Servers/Zeus/ARC/submit.sh index 81052c5..2503da5 100644 --- a/Servers/Zeus/ARC/submit.sh +++ b/Servers/Zeus/ARC/submit.sh @@ -13,4 +13,3 @@ cd $PBS_O_WORKDIR conda activate arc_env python $arc_code/ARC.py input.yml - diff --git a/Servers/Zeus/RMG/submit.sh b/Servers/Zeus/RMG/submit.sh index a184b0d..6a473a8 100644 --- a/Servers/Zeus/RMG/submit.sh +++ b/Servers/Zeus/RMG/submit.sh @@ -1,13 +1,12 @@ #!/bin/bash -l -#PBS -N # 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