search

CoBrALab / antsRegistration-MAGeT

A reimplementation of MAGeTbrain using only ANTs tools.
Other
16 stars 6 forks source link

bc: command not found #44

Closed jakeopolis closed 8 years ago

jakeopolis commented 8 years ago

When running new MAGeT on Scinet, got bc: command not found error as follows:

lsscinet02-ib0-$ mb.sh -- run 2016-07-22 17:21:25 UTC [ info] Found: 2016-07-22 17:21:25 UTC [ info] 5 atlases in input/atlas 2016-07-22 17:21:25 UTC [ info] 1 labels in input/atlas 2016-07-22 17:21:25 UTC [ info] 3 templates in input/template 2016-07-22 17:21:25 UTC [ info] 6 subjects in input/subject 2016-07-22 17:21:25 UTC [ info] 0 models in input/models 2016-07-22 17:21:25 UTC [ info] Progress: 2016-07-22 17:21:25 UTC [ info] 0 of 15 atlas-template registrations completed 2016-07-22 17:21:25 UTC [ info] 0 of 15 template-subject registrations completed 2016-07-22 17:21:25 UTC [ info] 0 of 90 resample labels completed 2016-07-22 17:21:25 UTC [ info] 0 of 6 voted labels completed 2016-07-22 17:21:25 UTC [ info] Checking Resolution of First Atlas awk: fatal: division by zero attempted 2016-07-22 17:21:37 UTC [ info] Found average: 2016-07-22 17:21:37 UTC [ info] Checking Resolution of First Template awk: fatal: division by zero attempted 2016-07-22 17:21:37 UTC [ info] Found average: 2016-07-22 17:21:37 UTC [ info] Checking Resolution of First Subject awk: fatal: division by zero attempted 2016-07-22 17:21:37 UTC [ info] Found average: 2016-07-22 17:21:37 UTC [ notice] MAGeTbrain makes no attempt to find the maximum resolution file, if you have mixed resolutions, make your highest resoluition file the first file /home/m/mchakrav/shejos/antsRegistration-MAGeT/bin/stages.sh: line 33: bc: command not found /home/m/mchakrav/shejos/antsRegistration-MAGeT/bin/stages.sh: line 34: bc: command not found /home/m/mchakrav/shejos/antsRegistration-MAGeT/bin/stages.sh: line 40: bc: command not found /home/m/mchakrav/shejos/antsRegistration-MAGeT/bin/stages.sh: line 41: bc: command not found /home/m/mchakrav/shejos/antsRegistration-MAGeT/bin/stages.sh: line 49: bc: command not found /home/m/mchakrav/shejos/antsRegistration-MAGeT/bin/stages.sh: line 54: bc: command not found /home/m/mchakrav/shejos/antsRegistration-MAGeT/bin/stages.sh: line 57: bc: command not found /home/m/mchakrav/shejos/antsRegistration-MAGeT/bin/stages.sh: line 60: bc: command not found /home/m/mchakrav/shejos/antsRegistration-MAGeT/bin/stages.sh: line 64: bc: command not found 2016-07-22 17:28:12 UTC [ info] Cleaning up. Done

gdevenyi commented 8 years ago

looks like you're on a login node, even with this issue resolved, you need to actually be on a dev node to submit jobs

You do not have the standard mchakrav bashrc template

Specially, you're missing the extras module, which is loaded by default in the mchakrav template.

To fix:

> cp /project/m/mchakrav/bashrc-template ~/.bashrc
gdevenyi commented 8 years ago

bc replaced with bash math and python. No longer an issue either way.