SLURM Errors

[hermeckerogg]

Hi all.

I'm trying to build a subject-specific template for some pediatric timeseries data.

antsMultivariateTemplateConstruction2.sh -d 4 -j 6 -k 1 -n 0 -r 1 -t SyN -c 5 -o MY sub-M87192301_Session1_task-restopen_bold.nii.gz sub-M87192301_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restopen_bold.nii.gz

All of the timeseries are in a folder, but the slurm scripts being generated don't seem to look like slurm scripts and it looks like the variables are not passing either.

Same issue even when I submit it as a SLURM job.

Any advice would be appreciated.

Thanks in advance!

antsMultivariateTemplateConstruction2.sh -d 4 -j 6 -k 1 -n 0 -r 1 -t SyN -c 5 -o MY sub-M87192301_Session1_task-restopen_bold.nii.gz sub-M87192301_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restopen_bold.nii.gz

job_0_0_metriclog.txt job_1_0_metriclog.txt job_2_0_metriclog.txt job_3_0_metriclog.txt

ANTs_Slurm_Error.zip

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Creating template MYtemplate0.nii.gz from a population average image from the inputs. sub-M87192301_Session1_task-restopen_bold.nii.gz sub-M87192301_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restopen_bold.nii.gzpwd

/trdapps/linux-x86_64/bin/ants/bin/antsMultivariateTemplateConstruction2.sh: line 272: 223250 Segmentation fault ${ANTSPATH}/AverageImages $dim $output 1 ${images[*]} sbatch: error: Batch job submission failed: No partition specified or system default partition sbatch: error: Batch job submission failed: No partition specified or system default partition sbatch: error: Batch job submission failed: No partition specified or system default partition ^C User pressed CTRL + C \n Performing cleanup, please wait \n killing: 223312 /trdapps/linux-x86_64/bin/ants/bin/antsMultivariateTemplateConstruction2.sh: line 448: kill: (223312) - No such process [tderamus@trendscn001 Template_Maker]$ antsMultivariateTemplateConstruction2.sh -d 4 -j 6 -k 1 -n 0 -r 1 -t SyN -c 5 -o MY sub-M87192301_Session1_task-restopen_bold.nii.gz sub-M87192301_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restopen_bold.nii.gz

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Creating template MYtemplate0.nii.gz from a population average image from the inputs. sub-M87192301_Session1_task-restopen_bold.nii.gz sub-M87192301_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restopen_bold.nii.gz

bigimage 4 maxSize [82, 82, 56] Setting physcal space of output average image based on largest image Averaging 4 images with dim = 3 vector components 1 reading sub-M87192301_Session1_task-restopen_bold.nii.gz reading sub-M87192301_Session1_task-restclosed_bold.nii.gz reading sub-M68290751_Session1_task-restclosed_bold.nii.gz reading sub-M68290751_Session1_task-restopen_bold.nii.gz writing output sbatch: error: Batch job submission failed: No partition specified or system default partition sbatch: error: Batch job submission failed: No partition specified or system default partition sbatch: error: Batch job submission failed: No partition specified or system default partition sbatch: error: Batch job submission failed: No partition specified or system default partition

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Starting ANTS rigid registration on SLURM cluster. Submitted 4 jobs

Waiting for 0 jobs: No more jobs in queue

/trdapps/linux-x86_64/bin/ants/bin/AverageImages 3 MYtemplate0.nii.gz 1 ./rigid0_0_sub-M87192301_Session1_task-restopen_bold.nii.gz ./rigid1_0_sub-M87192301_Session1_task-restclosed_bold.nii.gz ./rigid2_0_sub-M68290751_Session1_task-restclosed_bold.nii.gz ./rigid3_0_sub-M68290751_Session1_task-restopen_bold.nii.gz /trdapps/linux-x86_64/bin/ants/bin/antsMultivariateTemplateConstruction2.sh: line 272: 223458 Segmentation fault ${ANTSPATH}/AverageImages $dim $output 1 ${images[*]}

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Start to build templates: MYtemplate0.nii.gz

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Mapping parameters

ANTSPATH is /trdapps/linux-x86_64/bin/ants/bin

Dimensionality: 3 Do N4 bias correction: 0 Back up each iteration: 0 Similarity metric: CC Gradient step: 0.25 Transformation: SyN Max iterations: 100x100x70x20 Smoothing factors: 3x2x1x0 Shrink factors: 6x4x2x1 Output prefix: MY Template: MYtemplate Template update steps: 4 Template population: sub-M87192301_Session1_task-restopen_bold.nii.gz sub-M87192301_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restopen_bold.nii.gz Number of modalities: 1 Madality weights: Image statistic: 1

sbatch: error: Batch job submission failed: No partition specified or system default partition sbatch: error: Batch job submission failed: No partition specified or system default partition sbatch: error: Batch job submission failed: No partition specified or system default partition sbatch: error: Batch job submission failed: No partition specified or system default partition

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Starting ANTS registration on SLURM cluster. Submitted 4 jobs

Waiting for 0 jobs: No more jobs in queue

ls: cannot access MYWarp.nii.gz: No such file or directory ls: cannot access MYGenericAffine.mat: No such file or directory shapeupdatetotemplate()

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shapeupdatetotemplate---voxel-wise averaging of the warped images to the current template Mon Nov 18 16:10:31 EST 2019

ls: cannot access MYtemplate0*WarpedToTemplate.nii.gz: No such file or directory ERROR shapeupdatedtotemplate - imagelist length is 0

[ntustison]

Can you repost over at the ANTs/ANTs repo?

[hermeckerogg]

Of course. My apologies.

[hermeckerogg]

Done. Closing.