Python process not reponding when writing file to EFS docker volume












0















After setting up a docker swarm with cloudformation using the info from https://docs.docker.com/docker-for-aws/. The swarm runs a Django stack (django, nginx, celery) and for media storage a docker EFS volume is used (same setup as the shared storage volume in https://docs.docker.com/docker-for-aws/persistent-data-volumes/).



When I'm uploading a file through the website (using a django FileField) the django container hangs and in the corresponding EC2 instance I see the following kernel errors:



Nov 25 22:05:47 moby kernel: INFO: task uwsgi:6951 blocked for more than 120 seconds.
Nov 25 22:05:47 moby kernel: Not tainted 4.9.114-moby #1
Nov 25 22:05:47 moby kernel: "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message.
Nov 25 22:05:47 moby kernel: uwsgi D 0 6951 6504 0x00000100
Nov 25 22:05:47 moby kernel: 00000000000190c0 0000000000000000 ffff9a00a6e9a400 ffff9a009ee5c340
Nov 25 22:05:47 moby kernel: ffff9a00b2e80d00 ffff9a00b6e190c0 ffffffffb583caf6 0000000000000002
Nov 25 22:05:47 moby kernel: ffff9a00b2e80d00 ffffa767c0bdfce0 7fffffffffffffff 0000000000000002
Nov 25 22:05:47 moby kernel: Call Trace:
Nov 25 22:05:47 moby kernel: [<ffffffffb583caf6>] ? __schedule+0x35f/0x43d
Nov 25 22:05:47 moby kernel: [<ffffffffb583cf26>] ? bit_wait+0x2a/0x2a
Nov 25 22:05:47 moby kernel: [<ffffffffb583cc52>] ? schedule+0x7e/0x87
Nov 25 22:05:47 moby kernel: [<ffffffffb583e8de>] ? schedule_timeout+0x43/0x101
Nov 25 22:05:47 moby kernel: [<ffffffffb5019808>] ? xen_clocksource_read+0x11/0x12
Nov 25 22:05:47 moby kernel: [<ffffffffb512e281>] ? timekeeping_get_ns+0x19/0x2c
Nov 25 22:05:47 moby kernel: [<ffffffffb583c739>] ? io_schedule_timeout+0x99/0xf7
Nov 25 22:05:47 moby kernel: [<ffffffffb583c739>] ? io_schedule_timeout+0x99/0xf7
Nov 25 22:05:47 moby kernel: [<ffffffffb583cf3d>] ? bit_wait_io+0x17/0x34
Nov 25 22:05:47 moby kernel: [<ffffffffb583d009>] ? __wait_on_bit+0x48/0x76
Nov 25 22:05:47 moby kernel: [<ffffffffb519e758>] ? wait_on_page_bit+0x7c/0x96
Nov 25 22:05:47 moby kernel: [<ffffffffb510f99e>] ? autoremove_wake_function+0x35/0x35
Nov 25 22:05:47 moby kernel: [<ffffffffb519e842>] ? __filemap_fdatawait_range+0xd0/0x12b
Nov 25 22:05:47 moby kernel: [<ffffffffb519e8ac>] ? filemap_fdatawait_range+0xf/0x23
Nov 25 22:05:47 moby kernel: [<ffffffffb51a060c>] ? filemap_write_and_wait_range+0x3a/0x4f
Nov 25 22:05:47 moby kernel: [<ffffffffb52bcf98>] ? nfs_file_fsync+0x54/0x187
Nov 25 22:05:47 moby kernel: [<ffffffffb51f6c4d>] ? filp_close+0x39/0x66
Nov 25 22:05:47 moby kernel: [<ffffffffb51f6c99>] ? SyS_close+0x1f/0x47
Nov 25 22:05:47 moby kernel: [<ffffffffb50033b7>] ? do_syscall_64+0x69/0x79
Nov 25 22:05:47 moby kernel: [<ffffffffb583f64e>] ? entry_SYSCALL_64_after_swapgs+0x58/0xc6
Nov 25 22:06:28 moby kernel: nfs: server fs-d5eb171d.efs.eu-west-1.amazonaws.com not responding, still trying


I could resort to using S3 buckets, but this will take quite an effort. Is there something obvious that I'm missing/doing wrong? Or do I need to take an alternative route for storage?










share|improve this question



























    0















    After setting up a docker swarm with cloudformation using the info from https://docs.docker.com/docker-for-aws/. The swarm runs a Django stack (django, nginx, celery) and for media storage a docker EFS volume is used (same setup as the shared storage volume in https://docs.docker.com/docker-for-aws/persistent-data-volumes/).



    When I'm uploading a file through the website (using a django FileField) the django container hangs and in the corresponding EC2 instance I see the following kernel errors:



    Nov 25 22:05:47 moby kernel: INFO: task uwsgi:6951 blocked for more than 120 seconds.
    Nov 25 22:05:47 moby kernel: Not tainted 4.9.114-moby #1
    Nov 25 22:05:47 moby kernel: "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message.
    Nov 25 22:05:47 moby kernel: uwsgi D 0 6951 6504 0x00000100
    Nov 25 22:05:47 moby kernel: 00000000000190c0 0000000000000000 ffff9a00a6e9a400 ffff9a009ee5c340
    Nov 25 22:05:47 moby kernel: ffff9a00b2e80d00 ffff9a00b6e190c0 ffffffffb583caf6 0000000000000002
    Nov 25 22:05:47 moby kernel: ffff9a00b2e80d00 ffffa767c0bdfce0 7fffffffffffffff 0000000000000002
    Nov 25 22:05:47 moby kernel: Call Trace:
    Nov 25 22:05:47 moby kernel: [<ffffffffb583caf6>] ? __schedule+0x35f/0x43d
    Nov 25 22:05:47 moby kernel: [<ffffffffb583cf26>] ? bit_wait+0x2a/0x2a
    Nov 25 22:05:47 moby kernel: [<ffffffffb583cc52>] ? schedule+0x7e/0x87
    Nov 25 22:05:47 moby kernel: [<ffffffffb583e8de>] ? schedule_timeout+0x43/0x101
    Nov 25 22:05:47 moby kernel: [<ffffffffb5019808>] ? xen_clocksource_read+0x11/0x12
    Nov 25 22:05:47 moby kernel: [<ffffffffb512e281>] ? timekeeping_get_ns+0x19/0x2c
    Nov 25 22:05:47 moby kernel: [<ffffffffb583c739>] ? io_schedule_timeout+0x99/0xf7
    Nov 25 22:05:47 moby kernel: [<ffffffffb583c739>] ? io_schedule_timeout+0x99/0xf7
    Nov 25 22:05:47 moby kernel: [<ffffffffb583cf3d>] ? bit_wait_io+0x17/0x34
    Nov 25 22:05:47 moby kernel: [<ffffffffb583d009>] ? __wait_on_bit+0x48/0x76
    Nov 25 22:05:47 moby kernel: [<ffffffffb519e758>] ? wait_on_page_bit+0x7c/0x96
    Nov 25 22:05:47 moby kernel: [<ffffffffb510f99e>] ? autoremove_wake_function+0x35/0x35
    Nov 25 22:05:47 moby kernel: [<ffffffffb519e842>] ? __filemap_fdatawait_range+0xd0/0x12b
    Nov 25 22:05:47 moby kernel: [<ffffffffb519e8ac>] ? filemap_fdatawait_range+0xf/0x23
    Nov 25 22:05:47 moby kernel: [<ffffffffb51a060c>] ? filemap_write_and_wait_range+0x3a/0x4f
    Nov 25 22:05:47 moby kernel: [<ffffffffb52bcf98>] ? nfs_file_fsync+0x54/0x187
    Nov 25 22:05:47 moby kernel: [<ffffffffb51f6c4d>] ? filp_close+0x39/0x66
    Nov 25 22:05:47 moby kernel: [<ffffffffb51f6c99>] ? SyS_close+0x1f/0x47
    Nov 25 22:05:47 moby kernel: [<ffffffffb50033b7>] ? do_syscall_64+0x69/0x79
    Nov 25 22:05:47 moby kernel: [<ffffffffb583f64e>] ? entry_SYSCALL_64_after_swapgs+0x58/0xc6
    Nov 25 22:06:28 moby kernel: nfs: server fs-d5eb171d.efs.eu-west-1.amazonaws.com not responding, still trying


    I could resort to using S3 buckets, but this will take quite an effort. Is there something obvious that I'm missing/doing wrong? Or do I need to take an alternative route for storage?










    share|improve this question

























      0












      0








      0








      After setting up a docker swarm with cloudformation using the info from https://docs.docker.com/docker-for-aws/. The swarm runs a Django stack (django, nginx, celery) and for media storage a docker EFS volume is used (same setup as the shared storage volume in https://docs.docker.com/docker-for-aws/persistent-data-volumes/).



      When I'm uploading a file through the website (using a django FileField) the django container hangs and in the corresponding EC2 instance I see the following kernel errors:



      Nov 25 22:05:47 moby kernel: INFO: task uwsgi:6951 blocked for more than 120 seconds.
      Nov 25 22:05:47 moby kernel: Not tainted 4.9.114-moby #1
      Nov 25 22:05:47 moby kernel: "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message.
      Nov 25 22:05:47 moby kernel: uwsgi D 0 6951 6504 0x00000100
      Nov 25 22:05:47 moby kernel: 00000000000190c0 0000000000000000 ffff9a00a6e9a400 ffff9a009ee5c340
      Nov 25 22:05:47 moby kernel: ffff9a00b2e80d00 ffff9a00b6e190c0 ffffffffb583caf6 0000000000000002
      Nov 25 22:05:47 moby kernel: ffff9a00b2e80d00 ffffa767c0bdfce0 7fffffffffffffff 0000000000000002
      Nov 25 22:05:47 moby kernel: Call Trace:
      Nov 25 22:05:47 moby kernel: [<ffffffffb583caf6>] ? __schedule+0x35f/0x43d
      Nov 25 22:05:47 moby kernel: [<ffffffffb583cf26>] ? bit_wait+0x2a/0x2a
      Nov 25 22:05:47 moby kernel: [<ffffffffb583cc52>] ? schedule+0x7e/0x87
      Nov 25 22:05:47 moby kernel: [<ffffffffb583e8de>] ? schedule_timeout+0x43/0x101
      Nov 25 22:05:47 moby kernel: [<ffffffffb5019808>] ? xen_clocksource_read+0x11/0x12
      Nov 25 22:05:47 moby kernel: [<ffffffffb512e281>] ? timekeeping_get_ns+0x19/0x2c
      Nov 25 22:05:47 moby kernel: [<ffffffffb583c739>] ? io_schedule_timeout+0x99/0xf7
      Nov 25 22:05:47 moby kernel: [<ffffffffb583c739>] ? io_schedule_timeout+0x99/0xf7
      Nov 25 22:05:47 moby kernel: [<ffffffffb583cf3d>] ? bit_wait_io+0x17/0x34
      Nov 25 22:05:47 moby kernel: [<ffffffffb583d009>] ? __wait_on_bit+0x48/0x76
      Nov 25 22:05:47 moby kernel: [<ffffffffb519e758>] ? wait_on_page_bit+0x7c/0x96
      Nov 25 22:05:47 moby kernel: [<ffffffffb510f99e>] ? autoremove_wake_function+0x35/0x35
      Nov 25 22:05:47 moby kernel: [<ffffffffb519e842>] ? __filemap_fdatawait_range+0xd0/0x12b
      Nov 25 22:05:47 moby kernel: [<ffffffffb519e8ac>] ? filemap_fdatawait_range+0xf/0x23
      Nov 25 22:05:47 moby kernel: [<ffffffffb51a060c>] ? filemap_write_and_wait_range+0x3a/0x4f
      Nov 25 22:05:47 moby kernel: [<ffffffffb52bcf98>] ? nfs_file_fsync+0x54/0x187
      Nov 25 22:05:47 moby kernel: [<ffffffffb51f6c4d>] ? filp_close+0x39/0x66
      Nov 25 22:05:47 moby kernel: [<ffffffffb51f6c99>] ? SyS_close+0x1f/0x47
      Nov 25 22:05:47 moby kernel: [<ffffffffb50033b7>] ? do_syscall_64+0x69/0x79
      Nov 25 22:05:47 moby kernel: [<ffffffffb583f64e>] ? entry_SYSCALL_64_after_swapgs+0x58/0xc6
      Nov 25 22:06:28 moby kernel: nfs: server fs-d5eb171d.efs.eu-west-1.amazonaws.com not responding, still trying


      I could resort to using S3 buckets, but this will take quite an effort. Is there something obvious that I'm missing/doing wrong? Or do I need to take an alternative route for storage?










      share|improve this question














      After setting up a docker swarm with cloudformation using the info from https://docs.docker.com/docker-for-aws/. The swarm runs a Django stack (django, nginx, celery) and for media storage a docker EFS volume is used (same setup as the shared storage volume in https://docs.docker.com/docker-for-aws/persistent-data-volumes/).



      When I'm uploading a file through the website (using a django FileField) the django container hangs and in the corresponding EC2 instance I see the following kernel errors:



      Nov 25 22:05:47 moby kernel: INFO: task uwsgi:6951 blocked for more than 120 seconds.
      Nov 25 22:05:47 moby kernel: Not tainted 4.9.114-moby #1
      Nov 25 22:05:47 moby kernel: "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message.
      Nov 25 22:05:47 moby kernel: uwsgi D 0 6951 6504 0x00000100
      Nov 25 22:05:47 moby kernel: 00000000000190c0 0000000000000000 ffff9a00a6e9a400 ffff9a009ee5c340
      Nov 25 22:05:47 moby kernel: ffff9a00b2e80d00 ffff9a00b6e190c0 ffffffffb583caf6 0000000000000002
      Nov 25 22:05:47 moby kernel: ffff9a00b2e80d00 ffffa767c0bdfce0 7fffffffffffffff 0000000000000002
      Nov 25 22:05:47 moby kernel: Call Trace:
      Nov 25 22:05:47 moby kernel: [<ffffffffb583caf6>] ? __schedule+0x35f/0x43d
      Nov 25 22:05:47 moby kernel: [<ffffffffb583cf26>] ? bit_wait+0x2a/0x2a
      Nov 25 22:05:47 moby kernel: [<ffffffffb583cc52>] ? schedule+0x7e/0x87
      Nov 25 22:05:47 moby kernel: [<ffffffffb583e8de>] ? schedule_timeout+0x43/0x101
      Nov 25 22:05:47 moby kernel: [<ffffffffb5019808>] ? xen_clocksource_read+0x11/0x12
      Nov 25 22:05:47 moby kernel: [<ffffffffb512e281>] ? timekeeping_get_ns+0x19/0x2c
      Nov 25 22:05:47 moby kernel: [<ffffffffb583c739>] ? io_schedule_timeout+0x99/0xf7
      Nov 25 22:05:47 moby kernel: [<ffffffffb583c739>] ? io_schedule_timeout+0x99/0xf7
      Nov 25 22:05:47 moby kernel: [<ffffffffb583cf3d>] ? bit_wait_io+0x17/0x34
      Nov 25 22:05:47 moby kernel: [<ffffffffb583d009>] ? __wait_on_bit+0x48/0x76
      Nov 25 22:05:47 moby kernel: [<ffffffffb519e758>] ? wait_on_page_bit+0x7c/0x96
      Nov 25 22:05:47 moby kernel: [<ffffffffb510f99e>] ? autoremove_wake_function+0x35/0x35
      Nov 25 22:05:47 moby kernel: [<ffffffffb519e842>] ? __filemap_fdatawait_range+0xd0/0x12b
      Nov 25 22:05:47 moby kernel: [<ffffffffb519e8ac>] ? filemap_fdatawait_range+0xf/0x23
      Nov 25 22:05:47 moby kernel: [<ffffffffb51a060c>] ? filemap_write_and_wait_range+0x3a/0x4f
      Nov 25 22:05:47 moby kernel: [<ffffffffb52bcf98>] ? nfs_file_fsync+0x54/0x187
      Nov 25 22:05:47 moby kernel: [<ffffffffb51f6c4d>] ? filp_close+0x39/0x66
      Nov 25 22:05:47 moby kernel: [<ffffffffb51f6c99>] ? SyS_close+0x1f/0x47
      Nov 25 22:05:47 moby kernel: [<ffffffffb50033b7>] ? do_syscall_64+0x69/0x79
      Nov 25 22:05:47 moby kernel: [<ffffffffb583f64e>] ? entry_SYSCALL_64_after_swapgs+0x58/0xc6
      Nov 25 22:06:28 moby kernel: nfs: server fs-d5eb171d.efs.eu-west-1.amazonaws.com not responding, still trying


      I could resort to using S3 buckets, but this will take quite an effort. Is there something obvious that I'm missing/doing wrong? Or do I need to take an alternative route for storage?







      python docker amazon-cloudformation nfs amazon-efs






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      asked Nov 25 '18 at 22:31









      roelioroelio

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          Apparently I needed to downgrade from Docker 18.06 to 18.03



          Now it all works :)






          share|improve this answer























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            Apparently I needed to downgrade from Docker 18.06 to 18.03



            Now it all works :)






            share|improve this answer




























              0














              Apparently I needed to downgrade from Docker 18.06 to 18.03



              Now it all works :)






              share|improve this answer


























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                0







                Apparently I needed to downgrade from Docker 18.06 to 18.03



                Now it all works :)






                share|improve this answer













                Apparently I needed to downgrade from Docker 18.06 to 18.03



                Now it all works :)







                share|improve this answer












                share|improve this answer



                share|improve this answer










                answered Nov 26 '18 at 16:36









                roelioroelio

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