Issue with atlas building
helena.g...@googlemail.com
I am trying to run atlas building on a cluster that uses Slurm (without GNU) using the 2017 fast-ashs code. The terminal has been returning the current commands that are added to the nohup.out file for three days (using tail -f nohup.out) but has now stopped outputting any further commands in the past two days even though the system notes that the job is still running. The nohup.out file is now so large that it can no longer be opened. I copied and pasted the last output from the terminal into the attached document.
When inspecting the files generated so far, here is what now exists in my directory: The “atlas” folder contains a subfolder for every image used for atlas construction (containing 22 files). The “train” folder only contains “main_left” and “main_right” with empty subfolders. The “template_build” folder contains many files with warped and resliced images for the input T2 images for atlas building and “prereg” has many files with two subjects being referenced. I have checked the last modification dates and it looks like the folders have not been modified in the past days, so it seems to me something is going wrong.
Do you know what might be happening here? I have run the commands listed below:
export ASHS_ROOT=/home/ashs/ashs-1.0.0
$ASHS_ROOT/bin/ashs_train.sh \
-D ashs_data_manifest.txt \
-L ashs_labels.txt \
-w /home/ashs_atlas \
-r ashs_heuristics.txt \
| tee ashs_train.log
Also, when I use the command “nohup bash ./runme.sh &” with the specification to write to ashs_train.log, no log file is created.
It would be really helpful if you have any idea what might be going wrong and if there are any steps I can try to fix this.
Thanks so much!
Best,
Helena