MS4 container creation error creating mount source path '/etc/localtime': mkdir /etc/localtime: file exists.

[nahawtho]

Is it possible the container already has a localtime file? It appears the Makefile is trying to map in something that already exists. I do not know if the localtime mapping ( -v /etc/localtime:/etc/localtime:ro ) is necessary ? If so maybe make sure to delete the old localtime file when creating the image?

sf2env) home@Mes-MacBook-Pro examples % python3 example_mountainsort4.py ===== Hither: running [mountainsort4] in container: docker://magland/sf-mountainsort4:0.3.2 #############################################################

            #!/bin/bash

            exec docker run --name Iyoclvbu_mountainsort4 -i  \
                -v /etc/localtime:/etc/localtime:ro \
                -v /etc/passwd:/etc/passwd -u 'id -u':'id -g' \
                -v $KACHERY_STORAGE_DIR:/kachery-storage \
                -v /Users/home/Desktop/code/spikeforest2/spikeforest2_container/spikeforest2/examples/tmp/tmp_hither_run_in_container_mountainsort4_idqqj5bm:/run_in_container \
                -v /tmp:/tmp \
                -v $HOME:$HOME \
                -v /Users/home/Desktop/code/spikeforest2/spikeforest2_container/spikeforest2/examples/tmp/tmp_hither_run_in_container_mountainsort4_idqqj5bm/outputs:/outputs \
                magland/sf-mountainsort4:0.3.2 \
                bash /run_in_container/run.sh

############################################################# docker: Error response from daemon: error while creating mount source path '/etc/localtime': mkdir /etc/localtime: file exists. ERRO[0000] error waiting for container: context canceled Traceback (most recent call last): File "example_mountainsort4.py", line 14, in <module> sorting_out=hither.File() File "/Users/home/Desktop/code/spikeforest2/hither_sf/_core.py", line 271, in run _run_job(job) File "/Users/home/Desktop/code/spikeforest2/hither_sf/_core.py", line 464, in _run_job timeout=_job_timeout File "/Users/home/Desktop/code/spikeforest2/hither_sf/_run_function_in_container.py", line 263, in run_function_in_container raise Exception('Non-zero exit code ({}) running [{}] in container {}'.format(retcode, label, container)) Exception: Non-zero exit code (125) running [mountainsort4] in container docker://magland/sf-mountainsort4:0.3.2

(sf2env) home@Mes-MacBook-Pro examples % python3 --version Python 3.7.7 (sf2env) home@Mes-MacBook-Pro examples % docker --version Docker version 19.03.8, build afacb8b

^ I tried adding /etc/localtime to make sure I can support mounting those files but I don't think that's the issue. There's probably something obvious i'm missing... thanks!

[nahawtho]

I realize now I failed to actually mount a directory, so if anyone has this issue, you may need to do this, mounting /etc and /private/etc instead:

[nahawtho]

now this is my issue (sf2env) home@Mes-MacBook-Pro examples % chmod 777 ms4Out (sf2env) home@Mes-MacBook-Pro examples % export KACHERY_STORAGE_DIR=/Users/home/Desktop/code/spikeforest2/examples/ms4Out (sf2env) home@Mes-MacBook-Pro examples % python3 example_mountainsort4.py ===== Hither: running [mountainsort4] in container: docker://magland/sf-mountainsort4:0.3.2 #############################################################

!/bin/bash

            exec docker run --name bTimFZai_mountainsort4 -i  \
                -v /etc/localtime:/etc/localtime:ro \
                -v /etc/passwd:/etc/passwd -u `id -u`:`id -g` \
                -v $KACHERY_STORAGE_DIR:/kachery-storage \
                -v /Users/home/Desktop/code/spikeforest2/examples/ms4Out/tmp/tmp_hither_run_in_container_mountainsort4_a6a909h8:/run_in_container \
                -v /tmp:/tmp \
                -v $HOME:$HOME \
                -v /Users/home/Desktop/code/spikeforest2/examples/ms4Out/tmp/tmp_hither_run_in_container_mountainsort4_a6a909h8/outputs:/outputs \
                magland/sf-mountainsort4:0.3.2 \
                bash /run_in_container/run.sh

############################################################# docker: Error response from daemon: Mounts denied: EOF. ERRO[0000] error waiting for container: context canceled Traceback (most recent call last): File "example_mountainsort4.py", line 14, in <module> sorting_out=hither.File() File "/Users/home/Desktop/code/spikeforest2/hither_sf/_core.py", line 271, in run _run_job(job) File "/Users/home/Desktop/code/spikeforest2/hither_sf/_core.py", line 464, in _run_job timeout=_job_timeout File "/Users/home/Desktop/code/spikeforest2/hither_sf/_run_function_in_container.py", line 263, in run_function_in_container raise Exception('Non-zero exit code ({}) running [{}] in container {}'.format(retcode, label, container)) Exception: Non-zero exit code (125) running [mountainsort4] in container docker://magland/sf-mountainsort4:0.3.2 (sf2env) home@Mes-MacBook-Pro examples %