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Merge pull request #41 from BIDS-Apps/fix/parallel
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Remove -parallel
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@chrisgorgo
chrisgorgo authored Apr 22, 2018
2 parents 0ff9f93 + 0a8bcbb commit b63b6ce
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Showing 2 changed files with 10 additions and 10 deletions.
4 changes: 2 additions & 2 deletions circle.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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16 changes: 8 additions & 8 deletions run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand All @@ -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,
Expand All @@ -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,
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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)
Expand Down

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