Dockerfile dependency error

[koetjen]

In the docker, pyjnius is looking for libjvm.so in the wrong place.

ashlar 'exemplar-001-cycle-01.ome.tiff' 'exemplar-001-cycle-02.ome.tiff' 'exemplar-001-cycle-03.ome.tiff' -m 30 --ffp exemplar-001-cycle-01-ffp.tif exemplar-001-cycle-02-ffp.tif exemplar-001-cycle-03-ffp.tif --dfp exemplar-001-cycle-01-dfp.tif exemplar-001-cycle-02-dfp.tif exemplar-001-cycle-03-dfp.tif --pyramid -f exemplar-001.ome.tif

  Traceback (most recent call last):
    File "/usr/local/bin/ashlar", line 5, in <module>
      from ashlar.scripts.ashlar import main
    File "/usr/local/lib/python3.7/dist-packages/ashlar/scripts/ashlar.py", line 8, in <module>
      from .. import reg
    File "/usr/local/lib/python3.7/dist-packages/ashlar/reg.py", line 37, in <module>
      import jnius
    File "/usr/local/lib/python3.7/dist-packages/jnius/__init__.py", line 42, in <module>
      from .reflect import *  # noqa
    File "/usr/local/lib/python3.7/dist-packages/jnius/reflect.py", line 20, in <module>
      class Class(with_metaclass(MetaJavaClass, JavaClass)):
    File "/usr/lib/python3/dist-packages/six.py", line 827, in __new__
      return meta(name, bases, d)
    File "jnius/jnius_export_class.pxi", line 119, in jnius.MetaJavaClass.__new__
    File "jnius/jnius_export_class.pxi", line 179, in jnius.MetaJavaClass.resolve_class
    File "jnius/jnius_env.pxi", line 11, in jnius.get_jnienv
    File "jnius/jnius_jvm_dlopen.pxi", line 134, in jnius.get_platform_jnienv
    File "jnius/jnius_jvm_dlopen.pxi", line 101, in jnius.create_jnienv
  SystemError: Error calling dlopen(b'/opt/ibm/jre/lib/server/libjvm.so': b'/opt/ibm/jre/lib/server/libjvm.so: cannot open shared object file: No such file or directory'

As a workaround, I added to the dockerfile

RUN mkdir -p /opt/ibm/jre/lib/server/ \
&& ln -s /usr/lib/jvm/java-11-openjdk-amd64/lib/server/libjvm.so /opt/ibm/jre/lib/server/libjvm.so

possibly related... kivy/pyjnius#428

[jmuhlich]

Could you tell me what exact version of the container you are using? Did you build your own or pull an image from labsyspharm/ashlar on Dockerhub? I don't see this issue in the current latest image on Dockerhub.

[koetjen]

Sorry for not including the full example. It's the labsyspharm/ashlar image from Dockerhub on our computing cluster. I'm not seeing this problem when I run locally, so I will try to identify the problem in the computing environment instead

[koetjen@compute1-client-1 ~]$ bsub -Is -q general-interactive -a 'docker(labsyspharm/ashlar)' /bin/bash
Job <870401> is submitted to queue <general-interactive>.
<<Waiting for dispatch ...>>
<<Starting on compute1-exec-132.ris.wustl.edu>>
Using default tag: latest
latest: Pulling from labsyspharm/ashlar
3f2411103a12: Pull complete 
4da04088b2c2: Pull complete 
ab1184837b6f: Pull complete 
354c6da61dcc: Pull complete 
4b506cc51d18: Pull complete 
e004abadf190: Pull complete 
cb553601e103: Pull complete 
576359f27547: Pull complete 
f445b3192f2a: Pull complete 
Digest: sha256:a595c0f548c00c2c8b1ed55b3299c612b527f73bfa21aaadb11c40ac253c9a46
Status: Downloaded newer image for labsyspharm/ashlar:latest
docker.io/labsyspharm/ashlar:latest
koetjen@compute1-exec-132:~$ ashlar
Traceback (most recent call last):
  File "/usr/local/bin/ashlar", line 5, in <module>
    from ashlar.scripts.ashlar import main
  File "/usr/local/lib/python3.7/dist-packages/ashlar/scripts/ashlar.py", line 8, in <module>
    from .. import reg
  File "/usr/local/lib/python3.7/dist-packages/ashlar/reg.py", line 37, in <module>
    import jnius
  File "/usr/local/lib/python3.7/dist-packages/jnius/__init__.py", line 42, in <module>
    from .reflect import *  # noqa
  File "/usr/local/lib/python3.7/dist-packages/jnius/reflect.py", line 20, in <module>
    class Class(with_metaclass(MetaJavaClass, JavaClass)):
  File "/usr/lib/python3/dist-packages/six.py", line 827, in __new__
    return meta(name, bases, d)
  File "jnius/jnius_export_class.pxi", line 119, in jnius.MetaJavaClass.__new__
  File "jnius/jnius_export_class.pxi", line 179, in jnius.MetaJavaClass.resolve_class
  File "jnius/jnius_env.pxi", line 11, in jnius.get_jnienv
  File "jnius/jnius_jvm_dlopen.pxi", line 134, in jnius.get_platform_jnienv
  File "jnius/jnius_jvm_dlopen.pxi", line 101, in jnius.create_jnienv
SystemError: Error calling dlopen(b'/opt/ibm/jre/lib/server/libjvm.so': b'/opt/ibm/jre/lib/server/libjvm.so: cannot open shared object file: No such file or directory'