From 7f45be8050b0c4fad5616bd033f373088a1bf516 Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Sat, 21 Apr 2018 18:51:05 -0700 Subject: [PATCH 1/2] remove parallel --- run.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/run.py b/run.py index 43170ee..08a7237 100755 --- a/run.py +++ b/run.py @@ -224,12 +224,12 @@ def run(command, env={}, ignore_errors=False): fsid = "sub-%s_ses-%s" % (subject_label, session_label) stages = " ".join(["-" + stage for stage in args.stages]) - cmd = "recon-all -subjid %s -sd %s %s %s -parallel -openmp %d" % (fsid, + cmd = "recon-all -subjid %s -sd %s %s %s -openmp %d" % (fsid, output_dir, input_args, stages, args.n_cpus) - resume_cmd = "recon-all -subjid %s -sd %s %s -parallel -openmp %d" % (fsid, + resume_cmd = "recon-all -subjid %s -sd %s %s -openmp %d" % (fsid, output_dir, stages, args.n_cpus) @@ -254,7 +254,7 @@ def run(command, env={}, ignore_errors=False): input_args = " ".join(["-tp %s" % tp for tp in timepoints]) fsid = "sub-%s" % subject_label stages = " ".join(["-" + stage for stage in args.stages]) - cmd = "recon-all -base %s -sd %s %s %s -parallel -openmp %d" % (fsid, + cmd = "recon-all -base %s -sd %s %s %s -openmp %d" % (fsid, output_dir, input_args, stages, @@ -280,7 +280,7 @@ def run(command, env={}, ignore_errors=False): # longitudinally process all timepoints fsid = "sub-%s" % subject_label stages = " ".join(["-" + stage for stage in args.stages]) - cmd = "recon-all -long %s %s -sd %s %s -parallel -openmp %d" % (tp, + cmd = "recon-all -long %s %s -sd %s %s -openmp %d" % (tp, fsid, output_dir, stages, @@ -333,12 +333,12 @@ def run(command, env={}, ignore_errors=False): fsid = "sub-%s" % subject_label stages = " ".join(["-" + stage for stage in args.stages]) - cmd = "recon-all -subjid %s -sd %s %s %s -parallel -openmp %d" % (fsid, + cmd = "recon-all -subjid %s -sd %s %s %s -openmp %d" % (fsid, output_dir, input_args, stages, args.n_cpus) - resume_cmd = "recon-all -subjid %s -sd %s %s -parallel -openmp %d" % (fsid, + resume_cmd = "recon-all -subjid %s -sd %s %s -openmp %d" % (fsid, output_dir, stages, args.n_cpus) @@ -391,12 +391,12 @@ def run(command, env={}, ignore_errors=False): fsid = "sub-%s" % subject_label stages = " ".join(["-" + stage for stage in args.stages]) - cmd = "recon-all -subjid %s -sd %s %s %s -parallel -openmp %d" % (fsid, + cmd = "recon-all -subjid %s -sd %s %s %s -openmp %d" % (fsid, output_dir, input_args, stages, args.n_cpus) - resume_cmd = "recon-all -subjid %s -sd %s %s -parallel -openmp %d" % (fsid, + resume_cmd = "recon-all -subjid %s -sd %s %s -openmp %d" % (fsid, output_dir, stages, args.n_cpus) From 0a8bcbb1ef971e92831fbceb68d697bfa232264c Mon Sep 17 00:00:00 2001 From: Chris Filo Gorgolewski Date: Sat, 21 Apr 2018 18:58:48 -0700 Subject: [PATCH 2/2] --no-check-certificate --- circle.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/circle.yml b/circle.yml index a34b48b..0c273b4 100644 --- a/circle.yml +++ b/circle.yml @@ -16,8 +16,8 @@ dependencies: - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi - if [[ ! -d ~/data/ds114_test1 ]]; then wget -c -O ${HOME}/ds114_test1.tar "https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/57e54a326c613b01d7d3ed90" && mkdir -p ${HOME}/data && tar xf ${HOME}/ds114_test1.tar -C ${HOME}/data; fi - if [[ ! -d ~/data/ds114_test2 ]]; then wget -c -O ${HOME}/ds114_test2.tar "https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/57e549f9b83f6901d457d162" && mkdir -p ${HOME}/data && tar xf ${HOME}/ds114_test2.tar -C ${HOME}/data; fi - - if [[ ! -d ~/data/ds114_test1_freesurfer_precomp_v6.0.0 ]]; then wget -c -O ${HOME}/ds114_test1_freesurfer_precomp_v6.0.0.tar "https://osf.io/j6zk2/?action=download&version=1" && mkdir -p ${HOME}/data && tar xf ${HOME}/ds114_test1_freesurfer_precomp_v6.0.0.tar -C ${HOME}/data; fi - - if [[ ! -d ~/data/ds114_test2_freesurfer_precomp_v6.0.0 ]]; then wget -c -O ${HOME}/ds114_test2_freesurfer_precomp_v6.0.0.tar "https://osf.io/yhzzj/?action=download&version=1" && mkdir -p ${HOME}/data && tar xf ${HOME}/ds114_test2_freesurfer_precomp_v6.0.0.tar -C ${HOME}/data; fi + - if [[ ! -d ~/data/ds114_test1_freesurfer_precomp_v6.0.0 ]]; then wget -c --no-check-certificate -O ${HOME}/ds114_test1_freesurfer_precomp_v6.0.0.tar "https://osf.io/j6zk2/?action=download&version=1" && mkdir -p ${HOME}/data && tar xf ${HOME}/ds114_test1_freesurfer_precomp_v6.0.0.tar -C ${HOME}/data; fi + - if [[ ! -d ~/data/ds114_test2_freesurfer_precomp_v6.0.0 ]]; then wget -c --no-check-certificate -O ${HOME}/ds114_test2_freesurfer_precomp_v6.0.0.tar "https://osf.io/yhzzj/?action=download&version=1" && mkdir -p ${HOME}/data && tar xf ${HOME}/ds114_test2_freesurfer_precomp_v6.0.0.tar -C ${HOME}/data; fi - git describe --tags > version - docker build -t bids/${CIRCLE_PROJECT_REPONAME} . : timeout: 21600