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Easy PSANA everywhere!
With the latest environment, the following error is met on SDF compute nodes:
[fpoitevi@rome0023 singularity_images]$ conda activate skopi-ana-none-4.0.28-py3
(skopi-ana-none-4.0.28-py3) [fpoitevi@rome0023 singularity_images]$ python
Python 3.7.10 | packaged by conda-forge | (default, Feb 19 2021, 16:07:37)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import mpi4py
>>> from mpi4py import MPI
[rome0023:122763] pmix_mca_base_component_repository_open: unable to open mca_gds_ds12: /scratch/fpoitevi/conda/envs/skopi-ana-none-4.0.28-py3/bin/../lib/libmca_common_dstore.so.1: undefined symbol: pmix_output_check_verbosity (ignored)
[rome0023:122763] pmix_mca_base_component_repository_open: unable to open mca_gds_ds21: /scratch/fpoitevi/conda/envs/skopi-ana-none-4.0.28-py3/bin/../lib/libmca_common_dstore.so.1: undefined symbol: pmix_output_check_verbosity (ignored)
*** An error occurred in MPI_Init_thread
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[rome0023:122763] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
I will try the container approach soon. We might have to compile openmpi directly in the image...
Weird bug... When I do the following and the output .yml already exists under docker/
I get this error. Removing the .yml
solves the issue but I'm not sure why...
(ezpsana) [fpoitevi@sdf-login03 ezpsana]$ ./create-container.py -b yaml/ana-4.0.28-py3.yml -a yaml/skopi.yml -o skopi-ana-none-4.0.28-py3.yml -r skopi-ana -t none-4.0.28-py3 -u fpoitevi
>> Reading base environment YAML file: yaml/ana-4.0.28-py3.yml
Traceback (most recent call last):
File "./create-container.py", line 108, in <module>
base_env = yaml.safe_load(fh)
AttributeError: module 'yaml' has no attribute 'safe_load'```
Sorry for asking naive questions, it'd be great if I could be walked through the docker setup; I suspect this is what is causing this for me:
(ezpsana) [fpoitevi@sdf-login03 ezpsana]$ ./create-container.py -b yaml/ana-4.0.28-py3.yml -a yaml/skopi.yml -o skopi-ana-none-4.0.28-py3.yml -r skopi-ana -t none-4.0.28-py3 -u fpoitevi -d
>> Reading base environment YAML file: yaml/ana-4.0.28-py3.yml
>> Reading additional environment YAML file: yaml/skopi.yml
>> Adding custom dependencies to base environment
>> Writing output YAML file: docker/skopi-ana-none-4.0.28-py3.yml
>> Building docker image with tag: fpoitevi/skopi-ana:none-4.0.28-py3. Please wait (it can take several minutes)
Error accessing the docker service from the system: Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
Instead of having a specific environment for ezpsana, let's use the generic building environment.
It would be nice if create_container.py
could do that. I'll try to add this feature soon
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