Re: [scipion-users] shire cryo training protocol failed from running

[Dmitry A. S. <sem...@gm...>]

Dear Wolfgang,

Thanks a lot!
I will try that.

Sincerely,
Dmitry


------ Original Message ------
From: "Lugmayr, Wolfgang" <w.l...@uk...>
To: "Mailing list for Scipion users" 
<sci...@li...>
Sent: 08-Jun-20 1:27:05 PM
Subject: Re: [scipion-users] shire cryo training protocol failed from 
running

>hi dmitry,
>
>we use a cryolo installation outside of scipion and added the following 
>lines to the config/scipion.conf
>
>CONDA_ACTIVATION_CMD = source 
>/beegfs/cssb/software/anaconda3/etc/profile.d/conda.sh
>CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7
>
>cheers,
>wolfgang
>
>
>--------------------------------------------------------------------------------
>From: "Grigory Sharov" <sha...@gm...>
>To: "Mailing list for Scipion users" 
><sci...@li...>
>Sent: Thursday, 4 June, 2020 14:54:20
>Subject: Re: [scipion-users] shire cryo training protocol failed from 
>running
>
>Hi Dmitry,
>
>Here is the error message:
>
>2020-06-04 14:19:55.483884
>00022:   WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying 
>on conda being in the PATH
>00023:    conda activate cryolo-1.6.1 && cryolo_train.py -c config.json 
>-w 5  -g 0 -e 10 --fine_tune
>00024:   /bin/sh: conda: command not found
>
>You need to have conda command in your path or define the variable as 
>it says
>
>Grigory.
>
>
>On Thu, Jun 4, 2020, 13:40 Dmitry Semchonok <Sem...@gm...> 
>wrote:
>>Dear colleagues,
>>
>>I have a problems running shire cryo training protocol in SCIPION.
>>
>>Do you know how to fix it?
>>
>>
>>Thank you!
>>
>>Sincerely,
>>Dmitry
>>
>>
>>
>>==============
>>RUNSTDOUT
>>===============
>>
>>UNNING PROTOCOL -----------------
>>00002:        HostName: dataanalysisserver1
>>00003:             PID: 69964
>>00004:         Scipion: v2.0 (2019-04-23) Diocletian
>>00005:      currentDir: 
>>/home/user/Data/ScipionUserData/projects/Colette__03_06__20
>>00006:      workingDir: Runs/000317_SphireProtCRYOLOTraining
>>00007:         runMode: Restart
>>00008:             MPI: 1
>>00009:         threads: 1
>>00010:    Starting at step: 1
>>00011:    Running steps
>>00012:   STARTED: convertInputStep, step 1
>>00013:     2020-06-04 14:19:55.349748
>>00014:   FINISHED: convertInputStep, step 1
>>00015:     2020-06-04 14:19:55.477612
>>00016:   STARTED: createConfigStep, step 2
>>00017:     2020-06-04 14:19:55.480179
>>00018:   FINISHED: createConfigStep, step 2
>>00019:     2020-06-04 14:19:55.481720
>>00020:   STARTED: cryoloModelingStep, step 3
>>00021:     2020-06-04 14:19:55.483884
>>00022:   WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying 
>>on conda being in the PATH
>>00023:    conda activate cryolo-1.6.1 && cryolo_train.py -c 
>>config.json -w 5  -g 0 -e 10 --fine_tune
>>00024:   /bin/sh: conda: command not found
>>00025:   Traceback (most recent call last):
>>00026:     File "/usr/local/scipion/pyworkflow/protocol/protocol.py", 
>>line 186, in run
>>00027:       self._run()
>>00028:     File "/usr/local/scipion/pyworkflow/protocol/protocol.py", 
>>line 237, in _run
>>00029:       resultFiles = self._runFunc()
>>00030:     File "/usr/local/scipion/pyworkflow/protocol/protocol.py", 
>>line 233, in _runFunc
>>00031:       return self._func(*self._args)
>>00032:     File 
>>"/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", 
>>line 246, in cryoloModelingStep
>>00033:       self.runCryoloTrain(5, extraArgs=extraArgs)
>>00034:     File 
>>"/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", 
>>line 243, in runCryoloTrain
>>00035:       cwd=self._getWorkDir())
>>00036:     File 
>>"/usr/local/scipion/software/lib/python2.7/site-packages/sphire/__init__.py", 
>>line 220, in runCryolo
>>00037:       protocol.runJob(fullProgram, args, env=cls.getEnviron(), 
>>cwd=cwd)
>>00038:     File "/usr/local/scipion/pyworkflow/protocol/protocol.py", 
>>line 1311, in runJob
>>00039:       self._stepsExecutor.runJob(self._log, program, arguments, 
>>**kwargs)
>>00040:     File "/usr/local/scipion/pyworkflow/protocol/executor.py", 
>>line 70, in runJob
>>00041:       env=env, cwd=cwd, gpuList=self.getGpuList())
>>00042:     File "/usr/local/scipion/pyworkflow/utils/process.py", line 
>>52, in runJob
>>00043:       return runCommand(command, env, cwd)
>>00044:     File "/usr/local/scipion/pyworkflow/utils/process.py", line 
>>67, in runCommand
>>00045:       env=env, cwd=cwd)
>>00046:     File 
>>"/usr/local/scipion/software/lib/python2.7/subprocess.py", line 190, 
>>in check_call
>>00047:       raise CalledProcessError(retcode, cmd)
>>00048:   CalledProcessError: Command ' conda activate cryolo-1.6.1 && 
>>cryolo_train.py -c config.json -w 5  -g 0 -e 10 --fine_tune' returned 
>>non-zero exit status 127
>>00049:   Protocol failed: Command ' conda activate cryolo-1.6.1 && 
>>cryolo_train.py -c config.json -w 5  -g 0 -e 10 --fine_tune' returned 
>>non-zero exit status 127
>>00050:   FAILED: cryoloModelingStep, step 3
>>00051:     2020-06-04 14:19:55.510445
>>00052:   *** Last status is failed
>>00053:   ------------------- PROTOCOL FAILED (DONE 3/4)
>>
>>============================================================
>>========
>>RUN LOG
>>=======
>>RUNNING PROTOCOL -----------------
>>00002:        HostName: dataanalysisserver1
>>00003:             PID: 69964
>>00004:         Scipion: v2.0 (2019-04-23) Diocletian
>>00005:      currentDir: 
>>/home/user/Data/ScipionUserData/projects/Colette__03_06__20
>>00006:      workingDir: Runs/000317_SphireProtCRYOLOTraining
>>00007:         runMode: Restart
>>00008:             MPI: 1
>>00009:         threads: 1
>>00010:    Starting at step: 1
>>00011:    Running steps
>>00012:   STARTED: convertInputStep, step 1
>>00013:     2020-06-04 14:19:55.349748
>>00014:   FINISHED: convertInputStep, step 1
>>00015:     2020-06-04 14:19:55.477612
>>00016:   STARTED: createConfigStep, step 2
>>00017:     2020-06-04 14:19:55.480179
>>00018:   FINISHED: createConfigStep, step 2
>>00019:     2020-06-04 14:19:55.481720
>>00020:   STARTED: cryoloModelingStep, step 3
>>00021:     2020-06-04 14:19:55.483884
>>00022:   WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying 
>>on conda being in the PATH
>>00023:    conda activate cryolo-1.6.1 && cryolo_train.py -c 
>>config.json -w 5  -g 0 -e 10 --fine_tune
>>00024:   /bin/sh: conda: command not found
>>00025:   Traceback (most recent call last):
>>00026:     File "/usr/local/scipion/pyworkflow/protocol/protocol.py", 
>>line 186, in run
>>00027:       self._run()
>>00028:     File "/usr/local/scipion/pyworkflow/protocol/protocol.py", 
>>line 237, in _run
>>00029:       resultFiles = self._runFunc()
>>00030:     File "/usr/local/scipion/pyworkflow/protocol/protocol.py", 
>>line 233, in _runFunc
>>00031:       return self._func(*self._args)
>>00032:     File 
>>"/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", 
>>line 246, in cryoloModelingStep
>>00033:       self.runCryoloTrain(5, extraArgs=extraArgs)
>>00034:     File 
>>"/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", 
>>line 243, in runCryoloTrain
>>00035:       cwd=self._getWorkDir())
>>00036:     File 
>>"/usr/local/scipion/software/lib/python2.7/site-packages/sphire/__init__.py", 
>>line 220, in runCryolo
>>00037:       protocol.runJob(fullProgram, args, env=cls.getEnviron(), 
>>cwd=cwd)
>>00038:     File "/usr/local/scipion/pyworkflow/protocol/protocol.py", 
>>line 1311, in runJob
>>00039:       self._stepsExecutor.runJob(self._log, program, arguments, 
>>**kwargs)
>>00040:     File "/usr/local/scipion/pyworkflow/protocol/executor.py", 
>>line 70, in runJob
>>00041:       env=env, cwd=cwd, gpuList=self.getGpuList())
>>00042:     File "/usr/local/scipion/pyworkflow/utils/process.py", line 
>>52, in runJob
>>00043:       return runCommand(command, env, cwd)
>>00044:     File "/usr/local/scipion/pyworkflow/utils/process.py", line 
>>67, in runCommand
>>00045:       env=env, cwd=cwd)
>>00046:     File 
>>"/usr/local/scipion/software/lib/python2.7/subprocess.py", line 190, 
>>in check_call
>>00047:       raise CalledProcessError(retcode, cmd)
>>00048:   CalledProcessError: Command ' conda activate cryolo-1.6.1 && 
>>cryolo_train.py -c config.json -w 5  -g 0 -e 10 --fine_tune' returned 
>>non-zero exit status 127
>>00049:   Protocol failed: Command ' conda activate cryolo-1.6.1 && 
>>cryolo_train.py -c config.json -w 5  -g 0 -e 10 --fine_tune' returned 
>>non-zero exit status 127
>>00050:   FAILED: cryoloModelingStep, step 3
>>00051:     2020-06-04 14:19:55.510445
>>00052:   *** Last status is failed
>>00053:   ------------------- PROTOCOL FAILED (DONE 3/4)
>>
>>_______________________________________________
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>
>
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