igrmonty-osg
A simple setup for running a large number of igrmonty
jobs on the
Open Science Grid (OSG) using HTCondor.
Usage
This git repository is designed to be cloned to OSG connect as a run/work directory for both submitting a large OSG job and gathering the output.
It is recommended to place the output of your OSG jobs at your OSG
connect home /home/<user>
.
Therefore, to start,
ssh <user>@login<ID>.osgconnect.net
mkdir -p runs
cd runs
git clone git@github.com:bhpire/igrmonty-osg.git Ma+0.94_w5_SED
cd Ma+0.94_w5_SED
All the scripts are placed inside bin/
.
The empty directories log/
, and out/
will be used to stage OSG run
logs and grmonty output.
It is recommended to place the (large) input of your OSG jobs at the
public directory /public/<user>
.
I.e.,
ssh <user>@login<ID>.osgconnect.net
cd /public/<user>
mkdir -p eht/sgra/{bias,md5,rho0,Ma+0.94_w5}
cd eht/sgra
# Populate information tables in `bias/`, `md5/`, and `rho0/`
rsync -rav <supercomputer>:/GRMHD/snapshots/ Ma+0.94_w5/
Before submitting a job, one needs to copy a static linked grmonty
binary to bin/
ssh <user>@login<ID>.osgconnect.net
mkdir -p src
cd src
git clone https://github.com/AFD-Illinois/igrmonty.git
cd igrmonty
# Change the default N_THBINS in `/model/iharm/model.h` to a larger number, e.g.,
# #define N_THBINS 18
# Edit `make` so that the CFLAGS line contains `-static`; e.g.,
# CFLAGS = -static -std=gnu99 -O3 -fopenmp -funroll-loops -Wall -Wextra
module load gsl hdf5
make
cd ~/runs/Ma+0.94_w5_SED
cp ~/src/igrmonty/grmonty bin
Also make sure that you update the md5sum of grmonty in bin/wrapper
, e.g.,
grmd5="22691ef253e109166acb1eb5d5ac1084"
You may also need to edit bin/pargen
to generate the necessary
parameter sets.
Then, simply submit an OSG job by
bin/batches
bin/batches
will create a table of input parameters of Condor and
put it in par/BATCH.ALL
. However, because at the EHT we are running
a large number of jobs, they may exceed the maximum allowed jobs on
your queue. Therefore, bin/batches
also split par/BATCH.ALL
into
smaller files par/batch.p00
, par/batch.p01
, ... and try to submit
each of them individually. Once a job is submitted successfully, it
will be renamed as par/BATCH.D00
. You may simply rerun
bin/batches
multiple times. Every time it will try to submit the
last unsubmitted par/batch.pXX
file.
bin/batches
uses bin/submit
under the hood, which is a standard
Condor submission script starts with a hashbang directive to use the
system condor_submit
.
It uses bin/parget
to get the list of parameters from the
corresponding file in par/
.
These parameter sets are then passed to bin/wrapper
on the worker
machines as command line arguments.
bin/wrapper
will automatically generate a grmonty
parameter file
based on the arguments, and start grmonty
with it.
All Condor logs, stdout
, and stderr
will be sent to log/
.
The parameter files, hotcross data, and spectrum output will be saved
to out/
.
Their file names are transform according to the rules described in
bin/submit
.