Could not detect memory capacity of Docker container.

[mcmahonmc]

Describe the bug What were you trying to do when the crash happened?

xcpengine-docker \ -d Volumes/schnyer/Aging_DecMem/Scan_Data/fmriprep/anat-antsct.dsn \ -c Volumes/schnyer/Aging_DecMem/Scan_Data/fmriprep/anat_cohort.csv \ -o Volumes/schnyer/Aging_DecMem/Scan_Data/fmriprep/xcp_output \ -t 1 \ -r Volumes/schnyer/Aging_DecMem/Scan_Data/fmriprep/fmriprep

Cohort file Paste cohort file between the triple backticks

id0,img
30004,fmriprep/sub-30004/anat/sub-30004_desc-preproc_T1w.nii.gz
30008,fmriprep/sub-30008/anat/sub-30008_desc-preproc_T1w.nii.gz
30009,fmriprep/sub-30009/anat/sub-30009_desc-preproc_T1w.nii.gz
30012,fmriprep/sub-30012/anat/sub-30012_desc-preproc_T1w.nii.gz
30015,fmriprep/sub-30015/anat/sub-30015_desc-preproc_T1w.nii.gz
30019,fmriprep/sub-30019/anat/sub-30019_desc-preproc_T1w.nii.gz
30020,fmriprep/sub-30020/anat/sub-30020_desc-preproc_T1w.nii.gz
30023,fmriprep/sub-30023/anat/sub-30023_desc-preproc_T1w.nii.gz
30040,fmriprep/sub-30040/anat/sub-30040_desc-preproc_T1w.nii.gz
30057,fmriprep/sub-30057/anat/sub-30057_desc-preproc_T1w.nii.gz
30064,fmriprep/sub-30064/anat/sub-30064_desc-preproc_T1w.nii.gz
30066,fmriprep/sub-30066/anat/sub-30066_desc-preproc_T1w.nii.gz
30069,fmriprep/sub-30069/anat/sub-30069_desc-preproc_T1w.nii.gz
30074,fmriprep/sub-30074/anat/sub-30074_desc-preproc_T1w.nii.gz
30085,fmriprep/sub-30085/anat/sub-30085_desc-preproc_T1w.nii.gz
30088,fmriprep/sub-30088/anat/sub-30088_desc-preproc_T1w.nii.gz
30090,fmriprep/sub-30090/anat/sub-30090_desc-preproc_T1w.nii.gz
30091,fmriprep/sub-30091/anat/sub-30091_desc-preproc_T1w.nii.gz
30095,fmriprep/sub-30095/anat/sub-30095_desc-preproc_T1w.nii.gz
30096,fmriprep/sub-30096/anat/sub-30096_desc-preproc_T1w.nii.gz
30105,fmriprep/sub-30105/anat/sub-30105_desc-preproc_T1w.nii.gz
30116,fmriprep/sub-30116/anat/sub-30116_desc-preproc_T1w.nii.gz
30118,fmriprep/sub-30118/anat/sub-30118_desc-preproc_T1w.nii.gz
30119,fmriprep/sub-30119/anat/sub-30119_desc-preproc_T1w.nii.gz
30128,fmriprep/sub-30128/anat/sub-30128_desc-preproc_T1w.nii.gz
30181,fmriprep/sub-30181/anat/sub-30181_desc-preproc_T1w.nii.gz
30217,fmriprep/sub-30217/anat/sub-30217_desc-preproc_T1w.nii.gz
30227,fmriprep/sub-30227/anat/sub-30227_desc-preproc_T1w.nii.gz
30236,fmriprep/sub-30236/anat/sub-30236_desc-preproc_T1w.nii.gz
30242,fmriprep/sub-30242/anat/sub-30242_desc-preproc_T1w.nii.gz
30255,fmriprep/sub-30255/anat/sub-30255_desc-preproc_T1w.nii.gz
30274,fmriprep/sub-30274/anat/sub-30274_desc-preproc_T1w.nii.gz
30283,fmriprep/sub-30283/anat/sub-30283_desc-preproc_T1w.nii.gz
30295,fmriprep/sub-30295/anat/sub-30295_desc-preproc_T1w.nii.gz
30330,fmriprep/sub-30330/anat/sub-30330_desc-preproc_T1w.nii.gz
30346,fmriprep/sub-30346/anat/sub-30346_desc-preproc_T1w.nii.gz
30376,fmriprep/sub-30376/anat/sub-30376_desc-preproc_T1w.nii.gz
30395,fmriprep/sub-30395/anat/sub-30395_desc-preproc_T1w.nii.gz
30400,fmriprep/sub-30400/anat/sub-30400_desc-preproc_T1w.nii.gz
30403,fmriprep/sub-30403/anat/sub-30403_desc-preproc_T1w.nii.gz
30412,fmriprep/sub-30412/anat/sub-30412_desc-preproc_T1w.nii.gz
30426,fmriprep/sub-30426/anat/sub-30426_desc-preproc_T1w.nii.gz
30432,fmriprep/sub-30432/anat/sub-30432_desc-preproc_T1w.nii.gz
30466,fmriprep/sub-30466/anat/sub-30466_desc-preproc_T1w.nii.gz
30469,fmriprep/sub-30469/anat/sub-30469_desc-preproc_T1w.nii.gz
30476,fmriprep/sub-30476/anat/sub-30476_desc-preproc_T1w.nii.gz
30478,fmriprep/sub-30478/anat/sub-30478_desc-preproc_T1w.nii.gz
30568,fmriprep/sub-30568/anat/sub-30568_desc-preproc_T1w.nii.gz
30570,fmriprep/sub-30570/anat/sub-30570_desc-preproc_T1w.nii.gz
30581,fmriprep/sub-30581/anat/sub-30581_desc-preproc_T1w.nii.gz
30584,fmriprep/sub-30584/anat/sub-30584_desc-preproc_T1w.nii.gz
30588,fmriprep/sub-30588/anat/sub-30588_desc-preproc_T1w.nii.gz
40160,fmriprep/sub-40160/anat/sub-40160_desc-preproc_T1w.nii.gz
40175,fmriprep/sub-40175/anat/sub-40175_desc-preproc_T1w.nii.gz
40288,fmriprep/sub-40288/anat/sub-40288_desc-preproc_T1w.nii.gz
40351,fmriprep/sub-40351/anat/sub-40351_desc-preproc_T1w.nii.gz
40496,fmriprep/sub-40496/anat/sub-40496_desc-preproc_T1w.nii.gz
40512,fmriprep/sub-40512/anat/sub-40512_desc-preproc_T1w.nii.gz
40515,fmriprep/sub-40515/anat/sub-40515_desc-preproc_T1w.nii.gz
40519,fmriprep/sub-40519/anat/sub-40519_desc-preproc_T1w.nii.gz
40522,fmriprep/sub-40522/anat/sub-40522_desc-preproc_T1w.nii.gz
40524,fmriprep/sub-40524/anat/sub-40524_desc-preproc_T1w.nii.gz
40547,fmriprep/sub-40547/anat/sub-40547_desc-preproc_T1w.nii.gz
40550,fmriprep/sub-40550/anat/sub-40550_desc-preproc_T1w.nii.gz
40619,fmriprep/sub-40619/anat/sub-40619_desc-preproc_T1w.nii.gz
40623,fmriprep/sub-40623/anat/sub-40623_desc-preproc_T1w.nii.gz
40624,fmriprep/sub-40624/anat/sub-40624_desc-preproc_T1w.nii.gz
40629,fmriprep/sub-40629/anat/sub-40629_desc-preproc_T1w.nii.gz
40649,fmriprep/sub-40649/anat/sub-40649_desc-preproc_T1w.nii.gz
40650,fmriprep/sub-40650/anat/sub-40650_desc-preproc_T1w.nii.gz
40655,fmriprep/sub-40655/anat/sub-40655_desc-preproc_T1w.nii.gz
40656,fmriprep/sub-40656/anat/sub-40656_desc-preproc_T1w.nii.gz
40664,fmriprep/sub-40664/anat/sub-40664_desc-preproc_T1w.nii.gz
40668,fmriprep/sub-40668/anat/sub-40668_desc-preproc_T1w.nii.gz
40672,fmriprep/sub-40672/anat/sub-40672_desc-preproc_T1w.nii.gz
40694,fmriprep/sub-40694/anat/sub-40694_desc-preproc_T1w.nii.gz
40720,fmriprep/sub-40720/anat/sub-40720_desc-preproc_T1w.nii.gz
40738,fmriprep/sub-40738/anat/sub-40738_desc-preproc_T1w.nii.gz
40743,fmriprep/sub-40743/anat/sub-40743_desc-preproc_T1w.nii.gz
40750,fmriprep/sub-40750/anat/sub-40750_desc-preproc_T1w.nii.gz
40758,fmriprep/sub-40758/anat/sub-40758_desc-preproc_T1w.nii.gz
40769,fmriprep/sub-40769/anat/sub-40769_desc-preproc_T1w.nii.gz
40773,fmriprep/sub-40773/anat/sub-40773_desc-preproc_T1w.nii.gz
40775,fmriprep/sub-40775/anat/sub-40775_desc-preproc_T1w.nii.gz
40777,fmriprep/sub-40777/anat/sub-40777_desc-preproc_T1w.nii.gz
40778,fmriprep/sub-40778/anat/sub-40778_desc-preproc_T1w.nii.gz
40779,fmriprep/sub-40779/anat/sub-40779_desc-preproc_T1w.nii.gz
40782,fmriprep/sub-40782/anat/sub-40782_desc-preproc_T1w.nii.gz
40784,fmriprep/sub-40784/anat/sub-40784_desc-preproc_T1w.nii.gz
40796,fmriprep/sub-40796/anat/sub-40796_desc-preproc_T1w.nii.gz
40803,fmriprep/sub-40803/anat/sub-40803_desc-preproc_T1w.nii.gz
40811,fmriprep/sub-40811/anat/sub-40811_desc-preproc_T1w.nii.gz

Design File Paste your entire design (.dsn) file between the triple backticks

#!/usr/bin/env bash

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

###################################################################
# This design file stores the values of all variables required to
# execute a complete task-free functional connectivity pipeline.
# You may execute the analysis specified in this design file by
# calling (in any bash terminal):
#
# xcpEngine -d <design> -c <cohort> -o <output> <options>
#
# Variables fall into five general categories:
# * ANALYSIS VARIABLES are used at all stages of this analysis.
# * PIPELINE specifies the modules that comprise the analysis.
# * GLOBAL VARIABLES are used at all stages of all analyses.
# * MODULE VARIABLES are used during one stage of the analysis.
#                  These are typically array variables with array
#                  indices equal to the index of the analysis
#                  stage during which they are used.
# * OUTPUT VARIABLES may be used at all stages of the analysis.
#                  These are sometimes array variables with array
#                  indices equal to the value of the primary
#                  subject identifier. They will appear only in
#                  localised design files.
###################################################################

###################################################################
# ANALYSIS VARIABLES
###################################################################

analysis=struc-ACCELERATOR
design=${XCPEDIR}/designs/anat-antsct.dsn
sequence=anatomical
standard=MNI%1x1x1

###################################################################
# PIPELINE
###################################################################

pipeline=struc,roiquant,qcanat

###################################################################
# 1 STRUC
###################################################################

struc_denoise_anat[1]=0
struc_prior_weight[1]=0.25
struc_posterior_formulation[1]='Socrates[1]'
struc_keepBEImages[1]=0
struc_floating_point[1]=0
struc_random_seed[1]=0
struc_bspline[1]=0
struc_fit[1]=0.3
struc_quick[1]=0
struc_seg_priors[1]=1
struc_rerun[1]=0
struc_cleanup[1]=1
struc_process[1]=ACT

###################################################################
# 2 ROIQUANT
###################################################################

roiquant_atlas[2]=all
roiquant_vol[2]=1
roiquant_rerun[2]=0
roiquant_cleanup[2]=1

###################################################################
# 3 QCANAT
###################################################################

qcanat_gm[3]=Y
qcanat_gm_val[3]=2,4
qcanat_wm[3]=Y
qcanat_wm_val[3]=3
qcanat_csf[3]=Y
qcanat_csf_val[3]=1
qcanat_cort[3]=Y
qcanat_cort_val[3]=4
qcanat_rerun[3]=0
qcanat_cleanup[3]=1

Error message Paste your error message between the backticks

docker: Error response from daemon: OCI runtime create failed: container_linux.go:344: starting container process caused "exec: \"free\": executable file not found in $PATH": unknown.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?

Runtime Information How were you running the software? Docker? Singularity? Directly? If Directly, please consider using Docker or Singluarity first before submitting a bug report.

Additional context Add any other context about the problem here.

[mattcieslak]

Hi! Are you running this from your root directory? If not, you might want to try adding a / before your directories. Could you try this version?

xcpengine-docker \
    --image pennbbl/xcpengine:latest \
    -d /Volumes/schnyer/Aging_DecMem/Scan_Data/fmriprep/anat-antsct.dsn \
    -c /Volumes/schnyer/Aging_DecMem/Scan_Data/fmriprep/anat_cohort.csv \
    -o /Volumes/schnyer/Aging_DecMem/Scan_Data/fmriprep/xcp_output \
    -t 1 \
    -r /Volumes/schnyer/Aging_DecMem/Scan_Data/fmriprep/fmriprep

And if this doesn't work could you double check your docker installation with something like

docker run hello-world

[mcmahonmc]

Hi Matt,

Sorry, yes I had a / before my directories earlier but somehow left it out later on!

I ran this command:

xcpengine-docker \ --image pennbbl/xcpengine:latest \ -d /Volumes/schnyer/Aging_DecMem/Scan_Data/fmriprep/anat-antsct.dsn \ -c /Volumes/schnyer/Aging_DecMem/Scan_Data/fmriprep/anat_cohort.csv \ -o /Volumes/schnyer/Aging_DecMem/Scan_Data/fmriprep/xcp_output \ -t 1 \ -r /Volumes/schnyer/Aging_DecMem/Scan_Data/fmriprep

but I am still getting the same error message:

docker: Error response from daemon: OCI runtime create failed: container_linux.go:344: starting container process caused "exec: \"free\": executable file not found in $PATH": unknown. Could not detect memory capacity of Docker container. Do you have permission to run docker?

I ran docker run hello-world, and it says the installation is working correctly.

Any other ideas?

Megan On Apr 30, 2019, 4:03 PM -0500, PennBBL/xcpEngine reply@reply.github.com, wrote:

docker run hello-world

[mattcieslak]

Could you do

docker pull pennbbl/xcpengine:latest

to make sure you've got the updated image and try again?

[mcmahonmc]

That fixed it! Thank you Matt! On May 1, 2019, 1:34 PM -0500, Matt Cieslak notifications@github.com, wrote:

Could you do docker pull pennbbl/xcpengine:latest to make sure you've got the updated image and try again? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[mattcieslak]

Excellent!