From aa3511a9649570ee6a2a206019805275c0132485 Mon Sep 17 00:00:00 2001 From: James Chen <jchen.6727@gmail.com> Date: Tue, 17 Sep 2024 10:15:09 -0400 Subject: [PATCH 1/2] d/w expanse setup, moved {env} {res} {custom} --- netpyne/batchtools/search.py | 1 + netpyne/batchtools/submits.py | 10 +++++----- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/netpyne/batchtools/search.py b/netpyne/batchtools/search.py index 93a52cc05..79045706b 100644 --- a/netpyne/batchtools/search.py +++ b/netpyne/batchtools/search.py @@ -225,6 +225,7 @@ def run(config): ('sh', 'sfs' ): constructors(runtk.dispatchers.SFSDispatcher , submits.SHSubmitSFS), }#TODO, just say "socket"? + """ some shim functions before ray_search """ diff --git a/netpyne/batchtools/submits.py b/netpyne/batchtools/submits.py index ad033f188..587843a37 100644 --- a/netpyne/batchtools/submits.py +++ b/netpyne/batchtools/submits.py @@ -179,9 +179,8 @@ class SlurmSubmit(Submit): #SBATCH --mail-user={email} #SBATCH --mail-type=end export JOBID=$SLURM_JOB_ID -{res} +{env} {custom} -source ~/.bashrc cd {project_path} {command} wait @@ -227,8 +226,8 @@ class SlurmSubmitSFS(SlurmSubmit): export JOBID=$SLURM_JOB_ID export OUTFILE="{output_path}/{label}.out" export SGLFILE="{output_path}/{label}.sgl" +{env} {custom} -source ~/.bashrc cd {project_path} {command} wait @@ -254,8 +253,8 @@ class SlurmSubmitSOCK(SlurmSubmit): #SBATCH --mail-type=end export JOBID=$SLURM_JOB_ID export SOCNAME="{sockname}" +{env} {custom} -source ~/.bashrc cd {project_path} {command} wait @@ -263,4 +262,5 @@ class SlurmSubmitSOCK(SlurmSubmit): script_handles = {runtk.SUBMIT: '{output_path}/{label}.sh', runtk.STDOUT: '{output_path}/{label}.run', runtk.SOCKET: '{sockname}' - } \ No newline at end of file + } + From 15de957059b20ca5b36c48b49492e89a4f75118b Mon Sep 17 00:00:00 2001 From: James Chen <jchen.6727@gmail.com> Date: Thu, 26 Sep 2024 13:11:14 -0500 Subject: [PATCH 2/2] quickfix -- runners validation now referring to mapping rather than coll --- netpyne/batchtools/runners.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/netpyne/batchtools/runners.py b/netpyne/batchtools/runners.py index 8289c8421..389ad2993 100644 --- a/netpyne/batchtools/runners.py +++ b/netpyne/batchtools/runners.py @@ -65,7 +65,7 @@ def update_items(d, u, force_match = False): for k, v in u.items(): try: force_match and validate(k, d) - if isinstance(v, collections.abc.Container): + if isinstance(v, collections.abc.Mapping): #TODO this will currently break on lists of dicts d[k] = update_items(d.get(k), v, force_match) else: d[k] = v