azazellochg
commented
3 years ago mpirun: Error: unknown option "--pickname" means that you have not configured Scipion to point to your relion installation.
Closed FraaaMazzz closed 3 years ago
azazellochg
commented
3 years ago mpirun: Error: unknown option "--pickname" means that you have not configured Scipion to point to your relion installation.
FraaaMazzz
commented
3 years ago How can I do this?
I think I'm having some troubles getting Relion to work.
I have removed Relion via the plugin manager and tried reinstalling but I get errors
.
This is the Plugin.err
_0001: https://codeload.github.com/3dem/relion/tar.gz/4.0:
00002: 2021-10-20 12:06:07 ERROR 404: Not Found.
00003: tar: This does not look like a tar archive
00004:
00005: gzip: stdin: unexpected end of file
00006: tar: Child returned status 1
00007: tar: Error is not recoverable: exiting now
00008: --- Logging error ---
00009: Traceback (most recent call last):
00010: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_manager.py", line 772, in _applyOperations
00011: op.runOperation(self.numberProcessors.get(), not self.skipBinaries.get())
00012: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_manager.py", line 242, in runOperation
00013: plugin.installBin({'args': ['-j', processors]})
00014: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
00015: environment.execute()
00016: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
00017: self._executeTargets(targetList)
00018: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
00019: tgt.execute()
00020: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute
00021: command.execute()
00022: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute
00023: assert glob(t), ("target '%s' not built (after "
00024: AssertionError: target '/home/em-group/Programs/software/em/relion-4.0' not built (after running 'tar -xf relion-4.0.tgz')
00025:
00026: During handling of the above exception, another exception occurred:
00027:
00028: Traceback (most recent call last):
00029: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/logging/init.py", line 1085, in emit
00030: msg = self.format(record)
00031: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/logging/init.py", line 929, in format
00032: return fmt.format(record)
00033: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/logging/init.py", line 668, in format
00034: record.message = record.getMessage()
00035: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/logging/init.py", line 373, in getMessage
00036: msg = msg % self.args
00037: TypeError: not all arguments converted during string formatting
00038: Call stack:
00039: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/threading.py", line 890, in _bootstrap
00040: self._bootstrap_inner()
00041: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/threading.py", line 932, in _bootstrap_inner
00042: self.run()
00043: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/threading.py", line 870, in run
00044: self._target(*self._args, **self._kwargs)
00045: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_manager.py", line 793, in _applyOperations
00046: self.plug_errorslog.error(redStr(strErr), False)
00047: Message: '\x1b[31mError executing the operation: install scipion-em-relion\x1b[0m'
00048: Arguments: (False,)
azazellochg
commented
3 years ago Hi, I'll fix the error. In the meantime, tick "Skip binaries" when installing relion plugin. We do not provide relion4 binaries, you have to install them yourself.
azazellochg
commented
3 years ago Error msg updated
FraaaMazzz
commented
3 years ago I think I have successfully and correctly installed Relion, I have even specified the relion location in scipion.conf, but I still get the mpirun: Error: unknown option "--pickname"
azazellochg
commented
3 years ago Okay, can you post here output from the following commands: 1) scipion config -p relion 2) scipion run relion_refine --version 3) mpirun -np 4 hostname
FraaaMazzz
commented
3 years ago 1) scipion3 config -p relion
Scipion v3.0.9 - Eugenius Variables defined by plugin 'relion':
RELION_HOME = /home/em-group/Programs/software/em/relion-4.0/ RELION_CUDA_LIB = /usr/local/cuda-11.4/lib64 RELION_PYTHON = None
These variables can be added/edited in '/home/em-group/Programs/config/scipion.conf'
2) scipion3 run relion_refine --version
Scipion v3.0.9 - Eugenius
relion command detected
** Running command: relion_refine "--version"
/bin/sh: 1: relion_refine: not found
Traceback (most recent call last):
File "/home/em-group/miniconda3/envs/scipion3/bin/emprogram", line 8, in
3) mpirun -np 4 hostname Invalid MIT-MAGIC-COOKIE-1 keyCryo-EM-Worktsation Cryo-EM-Worktsation Cryo-EM-Worktsation Cryo-EM-Worktsation
azazellochg
commented
3 years ago Hm, does scipion installp -h show scipion-em-relion plugin version 4.0 ? If you cd /home/em-group/Programs/software/em/relion-4.0/bin and then run mpirun -np 3 relion_refine --version, does it work?
FraaaMazzz
commented
3 years ago scipion installp -h shows: scipion-em-relion 4.0b3 [X]
I don't have the "bin" directory in relion-4.0 so I can only go until cd /home/em-group/Programs/software/em/relion-4.0/
In the relion directory mpirun -np 3 relion_refine --version returns the following: Invalid MIT-MAGIC-COOKIE-1 key-------------------------------------------------------------------------- mpirun was unable to find the specified executable file, and therefore did not launch the job. This error was first reported for process rank 0; it may have occurred for other processes as well.
NOTE: A common cause for this error is misspelling a mpirun command line parameter option (remember that mpirun interprets the first unrecognized command line token as the executable).
3 total processes failed to start
azazellochg
commented
3 years ago Voila! This is the problem. Inside relion-4.0 you are expected to have bin, lib and other stuff. What do you have inside?
FraaaMazzz
commented
3 years ago Nothing :(
azazellochg
commented
3 years ago Oh well, you have not installed relion binaries correctly then. Did you clone the git repo as per instructions?
FraaaMazzz
commented
3 years ago In ~/Programs/software/em/ I also have a relion folder that has the following folders: AUTHORS build CMakeLists.txt data LICENSE relion.h src betaGuide.pdf cmake COPYING external README.md scripts tests
azazellochg
commented
3 years ago okay, that looks good! It seems that you have installed your relion into ~/Programs/software/em/relion then. Remove relion-4.0 folder and make a symbolic link:
cd /home/em-group/Programs/software/em/ ln -s /home/em-group/Programs/software/em/relion/build relion-4.0
FraaaMazzz
commented
3 years ago Yes!!!! It finally worked!!!!! Thank you so much! :)
azazellochg
commented
3 years ago Great! You are welcome
I have obtained my micrographs and I now want to pick the particles for SPA. So I launch Relion - auto-picking LoG but it fails immediately.
I'm working with Scipion v3.0.9
run.stdout
_00047: Logging configured. STDOUT --> Runs/001888_ProtRelionAutopickLoG/logs/run.stdout , STDERR --> Runs/001888_ProtRelionAutopickLoG/logs/run.stderr 00048: RUNNING PROTOCOL ----------------- 00049: Protocol starts 00050: Hostname: Cryo-EM-Worktsation 00051: PID: 41947 00052: pyworkflow: 3.0.17 00053: plugin: relion 00054: plugin v: 3.1.3 00055: currentDir: /home/em-group/ScipionUserData/Mazzotta/ApoFer 00056: workingDir: Runs/001888_ProtRelionAutopickLoG 00057: runMode: Continue 00058: MPI: 4 00059: threads: 1 00060: Starting at step: 1 00061: Running steps 00062: STARTED: pickMicrographStep, step 1, time 2021-10-19 13:33:00.458358 00063: Picking micrograph: Runs/000655_XmippProtMovieCorr/extra/190117_02_00001_UnderDefocus0.7um_frameImage_aligned_mic.mrc 00064: Some paths do not exist in: /usr/local/cuda-10.1/lib64 00065: mpirun -np 4
which relion_autopick_mpi--pickname autopick --odir "./" --LoG --shrink 0 --lowpass 20.000 --i input_micrographs.star --LoG_diam_min 100.000 --LoG_diam_max 200.000 --LoG_adjust_threshold 0.000 --LoG_upper_threshold 999.000 00066: Protocol failed: Command ' mpirun -np 4which relion_autopick_mpi--pickname autopick --odir "./" --LoG --shrink 0 --lowpass 20.000 --i input_micrographs.star --LoG_diam_min 100.000 --LoG_diam_max 200.000 --LoG_adjust_threshold 0.000 --LoG_upperthreshold 999.000' returned non-zero exit status 1. 00067: FAILED: pickMicrographStep, step 1, time 2021-10-19 13:33:00.481998 00068: *** Last status is failed 00069: ------------------- PROTOCOL FAILED (DONE 1/21)run.stderr
_00059: mpirun: Error: unknown option "--pickname" 00060: Type 'mpirun --help' for usage. 00061: Traceback (most recent call last): 00062: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run 00063: self._run() 00064: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run 00065: resultFiles = self._runFunc() 00066: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc 00067: return self._func(self._args) 00068: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_particles_picking.py", line 241, in pickMicrographStep 00069: self._pickMicrograph(mic, args) 00070: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_autopick.py", line 44, in _pickMicrograph 00071: self._pickMicrographList([mic], args) 00072: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_autopick.py", line 54, in _pickMicrographList 00073: self._pickMicrographsFromStar(micStar, micsDir, args) 00074: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_autopick_log.py", line 161, in _pickMicrographsFromStar 00075: self.runJob(program, params, cwd=cwd) 00076: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1388, in runJob 00077: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) 00078: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob 00079: process.runJob(log, programName, params, 00080: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob 00081: return runCommand(command, env, cwd) 00082: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand 00083: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, 00084: File "/home/em-group/miniconda3/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call 00085: raise CalledProcessError(retcode, cmd) 00086: subprocess.CalledProcessError: Command ' mpirun -np 4
which relion_autopick_mpi--pickname autopick --odir "./" --LoG --shrink 0 --lowpass 20.000 --i input_micrographs.star --LoG_diam_min 100.000 --LoG_diam_max 200.000 --LoG_adjust_threshold 0.000 --LoG_upper_threshold 999.000' returned non-zero exit status 1. 00087: Protocol failed: Command ' mpirun -np 4which relion_autopick_mpi--pickname autopick --odir "./" --LoG --shrink 0 --lowpass 20.000 --i input_micrographs.star --LoG_diam_min 100.000 --LoG_diam_max 200.000 --LoG_adjust_threshold 0.000 --LoG_upperthreshold 999.000' returned non-zero exit status 1.Can you help me understand what I'm doing wrong?