Re: [scipion-users] /bin/sh: 1: Syntax error: "(" unexpected

[Grigory S. <sha...@gm...>]

Dear Ana,

you are using wrong syntax (%(JOB_NODES)d) in your hosts.conf file. Please
have a look at
https://scipion-em.github.io/docs/docs/scipion-modes/host-configuration.html


Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Tue, Dec 1, 2020 at 9:59 AM Ana Andreea ARTENI <
ana...@i2...> wrote:

>
>   Morning,
> Can you please help us to sort out this error?
> My kind regards,
>
> The protocols xmipp3-cl2d, relion2D-classification, relion-3D initial
> _model  gives the same error:
>
> Run.stdout:
>  Hostname: CRYOEM-DATA-01.calcul.i2bc.paris-saclay.fr
> 00003:   PID: 1378
> 00004:   pyworkflow: 3.0.7
> 00005:   plugin: xmipp3
> 00006:   currentDir:
> /data/scipion/ana-andreea.arteni/ScipionUserData/projects/TutorialBetagal
> 00007:   workingDir: Runs/002463_XmippProtCL2D
> 00008:   runMode: Restart
> 00009:             MPI: 8
> 00010:         threads: 1
> 00011:    Starting at step: 1
> 00012:    Running steps
> 00013:   STARTED: convertInputStep, step 1, time 2020-12-01 12:35:12.105220
> 00014:   FINISHED: convertInputStep, step 1, time 2020-12-01
> 12:35:17.053899
> 00015:   STARTED: runJob, step 2, time 2020-12-01 12:35:17.165425
> 00016:   mpirun -np %(JOB_NODES)d --map-by node %(COMMAND)s
> 00017:   /bin/sh: 1: Syntax error: "(" unexpected
> 00018:   Traceback (most recent call last):
> 00019:     File
> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 187, in run
> 00020:       self._run()
> 00021:     File
> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 238, in _run
> 00022:       resultFiles = self._runFunc()
> 00023:     File
> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 234, in _runFunc
> 00024:       return self._func(*self._args)
> 00025:     File
> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1338, in runJob
> 00026:       self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
> 00027:     File
> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
> line 65, in runJob
> 00028:       process.runJob(log, programName, params,
> 00029:     File
> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 51, in runJob
> 00030:       return runCommand(command, env, cwd)
> 00031:     File
> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 66, in runCommand
> 00032:       check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr,
> 00033:     File
> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/subprocess.py",
> line 364, in check_call
> 00034:       raise CalledProcessError(retcode, cmd)
> 00035:   subprocess.CalledProcessError: Command 'mpirun -np %(JOB_NODES)d
> --map-by node %(COMMAND)s' returned non-zero exit status 2.
> 00036:   Protocol failed: Command 'mpirun -np %(JOB_NODES)d --map-by node
> %(COMMAND)s' returned non-zero exit status 2.
> 00037:   FAILED: runJob, step 2, time 2020-12-01 12:35:17.220780
> 00038:   *** Last status is failed
> 00039:   ------------------- PROTOCOL FAILED (DONE 2/13)
>
>
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