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problems following the instructions in INSTALL.md #122

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JamesSuter opened this issue Jun 11, 2019 · 3 comments

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@JamesSuter
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commented Jun 11, 2019

I'm following the instructions listed in INSTALL.md

So far, everything is OK, except for "LAMMPS testing on the local host"

After typing:

fabsim localhost lammps_dummy:lammps_dummy,cores=1,wall_time=1:00:0

I get this error:

[james@localhost] run: mkdir -p /Users/James/FabSim3/config_files; mkdir -p /Users/James/FabSim3/results; mkdir -p /Users/James/FabSim3/scripts; mkdir -p /Users/James/FabSim3/config_files/lammps_dummy
[james@localhost] rsync_project: rsync -pthrvz --rsh='ssh -p 22 ' /Users/james/work/Fabsim3/config_files/lammps_dummy/ james@localhost:/Users/James/FabSim3/config_files/lammps_dummy
[localhost] local: rsync -pthrvz --rsh='ssh -p 22 ' /Users/james/work/Fabsim3/config_files/lammps_dummy/ james@localhost:/Users/James/FabSim3/config_files/lammps_dummy
building file list ... done

sent 68 bytes received 20 bytes 58.67 bytes/sec
total size is 678 speedup is 7.70
SCRIPT: lammps
FabSim Error: could not find template file. FabSim looked for it in the following directories: ['/Users/james/work/Fabsim3/plugins/FabDummy/templates', '/Users/james/work/Fabsim3/deploy/templates']
Traceback (most recent call last):
File "/Users/james/work/FabSim3/bin/fabric_main.py", line 767, in main
*args, **kwargs
File "/usr/local/lib/python3.7/site-packages/fabric/tasks.py", line 387, in execute
multiprocessing
File "/usr/local/lib/python3.7/site-packages/fabric/tasks.py", line 277, in _execute
return task.run(*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/fabric/tasks.py", line 174, in run
return self.wrapped(*args, **kwargs)
File "/Users/james/work/Fabsim3/plugins/FabDummy/FabDummy.py", line 61, in lammps_dummy
job(dict(script='lammps', wall_time = '0:15:0', lammps_input = "in.CG.lammps"),args)
File "/Users/james/work/Fabsim3/base/fab.py", line 465, in job
env.job_script = script_templates(env.batch_header, env.script)
File "/Users/james/work/Fabsim3/deploy/templates.py", line 19, in script_templates
result= "\n".join([script_template_content(name) for name in names]+commands)
TypeError: sequence item 1: expected str instance, NoneType found
Disconnecting from localhost... done.

I am presuming actually requires FabMD plugin, but this is not clear in the documentation.

@JamesSuter

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commented Jun 11, 2019

I've figured it out - it is because I hadn't installed the FabMD plugin. This requirement is not mentioned in INSTALL.md

@arabnejad

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commented Jun 11, 2019

INSTALL.md is updated

@arabnejad arabnejad self-assigned this Jun 11, 2019

@djgroen

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commented Jun 11, 2019

Perhaps it's a bit strange to be installing FabMD as part of INSTALL.md, but the solution works for me. So I'm happy to close this for now, and we can always revisit this after M12.

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