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

[Ana A. A. <ana...@i2...>]

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)