scipion-users — Mailing list for Scipion users

Re: [scipion-users] scipion3, own special scipion conda - cluster submission problems/question

[Pablo C. <pc...@cn...>]

Thank, I think I get the issue with the host.conf

I've created an issue: 
https://github.com/scipion-em/scipion-pyworkflow/issues/144

On 16/9/20 16:00, Lugmayr, Wolfgang wrote:
> ad hosts.conf)
> The first time setup it is good that it is generated.
> When calling "scipion config --update" it would be more practical if 
> you just validate it in memory and do not write back the new file 
> without the #SBATCH comments.
> Or you write it back inlcuding the # lines.
> I think it would be enough if you print the validation error messages 
> just to the screen so fixing/adapting the hosts.conf template can be 
> an iterative process.
>
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

Re: [scipion-users] scipion3, own special scipion conda - cluster submission problems/question

[Lugmayr, W. <w.l...@uk...>]

hi, 

ad GPU) 
I will use nvidia-smi for testing 

ad hosts.conf) 
The first time setup it is good that it is generated. 
When calling "scipion config --update" it would be more practical if you just validate it in memory and do not write back the new file without the #SBATCH comments. 
Or you write it back inlcuding the # lines. 
I think it would be enough if you print the validation error messages just to the screen so fixing/adapting the hosts.conf template can be an iterative process. 

I assumed you are validating because of the message: 
All the expected sections and options found in /beegfs/cssb/software/em/scipion/3.0/devel/config/hosts.conf 

Thanks & cheers, 
Wolfgang 



From: "Pablo Conesa" <pc...@cn...> 
To: "Mailing list for Scipion users" <sci...@li...> 
Sent: Monday, 14 September, 2020 18:40:10 
Subject: Re: [scipion-users] scipion3, own special scipion conda - cluster submission problems/question 



Hi Wolfgang, thanks for the feedback. 

Not sure if this will help your pourposes.... 

The number of GPUs go in the template into the: GPU_COUNT variable 

So you can have the number of GPUs un the template. Not sure how can you make us of this since I barely have experience in administering/configuring queue systems. 




Regarding the config......are you running scipion config --update for the scipion.conf? and don't want the host.conf to be replaced? 


May be we can skip the host.conf when making an update? 
On 14/9/20 11:37, Lugmayr, Wolfgang wrote: 



Hi, 

thanks for your help, I think this was my fault. 
We have CPU nodes with no CUDA libs on the cluster and GPU nodes. 
It seems that I've sent the xmipp_cuda_movie_alignment_correlation job to a CPU node where it died immediately without any log message. 
I have to improve my scipion3 hosts.conf template. 
For relion its easy, I check my script if --gpu is on or off. But in scipion3 I cannot determine if its a CPU/GPU job on the cluster submission script level. 

Just to make clear, my python command line came from the template: 
%_(JOB_COMMAND)s 

and due a mpi4py error the settings mentioned below were correct: 
subprocess.CalledProcessError: Command 'mpirun -np 3 -bynode `which python3` "-m" "scipion" "runprotocol" "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_mpirun.py" "/home/lugmayr/ScipionUserData/projects/Scipion3_TestSuite" "Runs/000146_XmippProtMovieCorr/logs/run.db" "146"' returned non-zero exit status 1. 

pip install mpi4py solved it (conda install will also give my mpich, so I used pip). 

Thanks for your help. 
Cheers, 
Wolfgang 

P.S. FYI 
Each time I call scipion3 config --update all my comment lines from the hosts.conf file are removed. But these contain useful SLURM settings like: 
#SBATCH -p %_(JOB_QUEUE)s 
I copy it over the generated one afterwards, but maybe there will be a better solution? 



From: "Pablo Conesa" [ mailto:pc...@cn... | <pc...@cn...> ] 
To: "Mailing list for Scipion users" [ mailto:sci...@li... | <sci...@li...> ] 
Sent: Friday, 11 September, 2020 18:06:18 
Subject: Re: [scipion-users] scipion3, own special scipion conda - cluster submission problems/question 



Let me see if I'm getting it. 

Are you trying to avoid the launching script (scipion3) and instead you want to run "manually" a protocol? 

If so, you need to replicate what the launching script does: 




Here is what I've got in the launching script hightlighting the key lines: 




#!/usr/bin/env python 
# Scipion launcher 
import os 
import sys 
from os.path import dirname, abspath, join, basename 

# Set SCIPION_HOME to the location of this file 
scipionHome = dirname(abspath(__file__)) 
os.environ["SCIPION_TESTS_CMD"] = basename(__file__) + " tests" 
os.environ["LD_LIBRARY_PATH"] = ":".join([os.environ.get("LD_LIBRARY_PATH", ""), join(scipionHome, "software", "lib")]) 
os.environ["PYTHONPATH"] = ":".join([os.environ.get("PYTHONPATH", ""), join(scipionHome, "software", "bindings")]) 

cmd = "" 
if len(sys.argv) > 1 and sys.argv[1] == 'git': 
for repo in ['scipion-app', 'scipion-pyworkflow', 'scipion-em']: 
cmd += ("(cd "+join(scipionHome, repo)+" ; echo ' > in "+repo+":' ;" 
" git "+' '.join(sys.argv[2:])+" ; echo) ; ") 
else: 
# Activate the environment 
cmd = '. /home/pablo/software/scipion/.scipion3env/bin/activate && ' 
cmd += "python -m scipion %s" % " ".join(sys.argv[1:]) 

# Set SCIPION_HOME 
os.environ["SCIPION_HOME"] = scipionHome 
exit(os.WEXITSTATUS(os.system(cmd))) 




A short explanation: 

LD_LIBRARY_PATH and PYTHONPATH are set to allow scipion use xmipp fileformats convertions, metadata utilities and it's viewer. 

SCIPION_HOME, is mandatory, since now the path of pyworkflow (pip package) cannot determine scipion home as it was for scipion2. 




python -m scipion is to run entry point commands but in your case you can skip this. 








On 11/9/20 16:44, Lugmayr, Wolfgang wrote: 

BQ_BEGIN

Hi,

I have re-installed recently scipion3 with its own conda environment. Mainly for the reason that the plugins could overwrite my conda installation e.g. mine is cryolo-1.7 and the scipion plugin creates a cryolo-1.7.2

My new scipion3 conda looks now like:
base                  *  /beegfs/cssb/software/em/scipion/3.0/anaconda3
.scipion3env             /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env
cryolo-1.7.2             /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryolo-1.7.2
cryoloCPU-1.7.2          /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryoloCPU-1.7.2
xmipp_DLTK_v0.3          /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_DLTK_v0.3
xmipp_MicCleaner         /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_MicCleaner

If I run everything locally via scipion3 the task runs fine.

The task script for the cluster contains:
:
source /beegfs/cssb/software/em/scipion/3.0/anaconda3/etc/profile.d/conda.sh
conda activate .scipion3env
which python3
################################
python3 /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/lugmayr/ScipionUserData/projects/Scipion3_TestSuite" "Runs/000146_XmippProtMovieCorr/logs/run.db" 146

Now I get the following error:
### jobid : 5452483  ###
/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/bin/python3
Traceback (most recent call last):
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py", line 39, in <module>
    runProtocolMain(projPath, dbPath, protId)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2167, in runProtocolMain
    protocol = getProtocolFromDb(projectPath, protDbPath, protId, chdir=True)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2249, in getProtocolFromDb
    project.load(dbPath=os.path.join(projectPath, protDbPath), chdir=chdir,
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 244, in load
    self._loadDb(dbPath)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 302, in _loadDb
    self.mapper = self.createMapper(absDbPath)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 211, in createMapper
    classesDict.update(self._domain.getMapperDict())
AttributeError: 'NoneType' object has no attribute 'getMapperDict'

Before when my base conda included all other scipion conda envs the cluster submission was fine.
I have set autoactivation for my base to off in my .condarc.

I have to use the python3 from the .scipion3env otherwise there would not be the pyworkflow package.
What else could I change for submission?

Cheers,
Wolfgang 



-- 
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team 


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BQ_END

-- 
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team 


_______________________________________________ 
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Re: [scipion-users] scipion3, own special scipion conda - cluster submission problems/question

[Pablo C. <pc...@cn...>]

Hi Wolfgang, thanks for the feedback.

Not sure if this will help your pourposes....

The number of GPUs go in the template into the: GPU_COUNT variable

So you can have the number of GPUs un the template. Not sure how can you 
make us of this since I barely have experience in 
administering/configuring queue systems.


Regarding the config......are you running scipion config --update for 
the scipion.conf? and don't want the host.conf to be replaced?

May be we can skip the host.conf when making an update?

On 14/9/20 11:37, Lugmayr, Wolfgang wrote:
> Hi,
>
> thanks for your help, I think this was my fault.
> We have CPU nodes with no CUDA libs on the cluster and GPU nodes.
> It seems that I've sent the xmipp_cuda_movie_alignment_correlation job 
> to a CPU node where it died immediately without any log message.
> I have to improve my scipion3 hosts.conf template.
> For relion its easy, I check my script if --gpu is on or off. But in 
> scipion3 I cannot determine if its a CPU/GPU job on the cluster 
> submission script level.
>
> Just to make clear, my python command line came from the template:
>     %_(JOB_COMMAND)s
>
> and due a mpi4py error the settings mentioned below were correct:
> subprocess.CalledProcessError: Command 'mpirun -np 3 -bynode  `which 
> python3` "-m" "scipion" "runprotocol" 
> "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_mpirun.py" 
> "/home/lugmayr/ScipionUserData/projects/Scipion3_TestSuite" 
> "Runs/000146_XmippProtMovieCorr/logs/run.db" "146"' returned non-zero 
> exit status 1.
>
> pip install mpi4py solved it (conda install will also give my mpich, 
> so I used pip).
>
> Thanks for your help.
> Cheers,
> Wolfgang
>
> P.S. FYI
> Each time I call scipion3 config --update all my comment lines from 
> the hosts.conf file are removed. But these contain useful SLURM 
> settings like:
>     #SBATCH -p %_(JOB_QUEUE)s
> I copy it over the generated one afterwards, but maybe there will be a 
> better solution?
>
>
> ------------------------------------------------------------------------
> *From: *"Pablo Conesa" <pc...@cn...>
> *To: *"Mailing list for Scipion users" 
> <sci...@li...>
> *Sent: *Friday, 11 September, 2020 18:06:18
> *Subject: *Re: [scipion-users] scipion3, own special scipion conda - 
> cluster submission problems/question
>
> Let me see if I'm getting it.
>
> Are you trying to avoid the launching script (scipion3) and instead 
> you want to run "manually" a protocol?
>
> If so, you need to replicate what the launching script does:
>
>
> Here is what I've got in the launching script hightlighting the key lines:
>
>
> #!/usr/bin/env python
> # Scipion launcher
> import os
> import sys
> from os.path import dirname, abspath, join, basename
>
> # Set SCIPION_HOME to the location of this file
> scipionHome = dirname(abspath(__file__))
> os.environ["SCIPION_TESTS_CMD"] = basename(__file__) + " tests"
> os.environ["LD_LIBRARY_PATH"] = 
> ":".join([os.environ.get("LD_LIBRARY_PATH", ""), join(scipionHome, 
> "software", "lib")])
> os.environ["PYTHONPATH"] = ":".join([os.environ.get("PYTHONPATH", ""), 
> join(scipionHome, "software", "bindings")])
>
> cmd = ""
> if len(sys.argv) > 1 and sys.argv[1] == 'git':
>     for repo in ['scipion-app', 'scipion-pyworkflow', 'scipion-em']:
>         cmd += ("(cd "+join(scipionHome, repo)+" ; echo ' > in 
> "+repo+":' ;"
>                 " git "+' '.join(sys.argv[2:])+" ; echo) ; ")
> else:
>     # Activate the environment
>     cmd = '. /home/pablo/software/scipion/.scipion3env/bin/activate && '
>     cmd += "python -m scipion %s" % " ".join(sys.argv[1:])
>
> # Set SCIPION_HOME
> os.environ["SCIPION_HOME"] = scipionHome
> exit(os.WEXITSTATUS(os.system(cmd)))
>
>
> A short explanation:
>
> LD_LIBRARY_PATH and PYTHONPATH are set to allow scipion use xmipp 
> fileformats convertions, metadata utilities and it's viewer.
>
> SCIPION_HOME, is mandatory, since now the path of pyworkflow (pip 
> package) cannot determine scipion home as it was for scipion2.
>
>
> python -m scipion is to run entry point commands but in your case you 
> can skip this.
>
>
>
>
> On 11/9/20 16:44, Lugmayr, Wolfgang wrote:
>
>     Hi,
>
>     I have re-installed recently scipion3 with its own conda environment. Mainly for the reason that the plugins could overwrite my conda installation e.g. mine is cryolo-1.7 and the scipion plugin creates a cryolo-1.7.2
>
>     My new scipion3 conda looks now like:
>     base                  *  /beegfs/cssb/software/em/scipion/3.0/anaconda3
>     .scipion3env             /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env
>     cryolo-1.7.2             /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryolo-1.7.2
>     cryoloCPU-1.7.2          /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryoloCPU-1.7.2
>     xmipp_DLTK_v0.3          /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_DLTK_v0.3
>     xmipp_MicCleaner         /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_MicCleaner
>
>     If I run everything locally via scipion3 the task runs fine.
>
>     The task script for the cluster contains:
>     :
>     source /beegfs/cssb/software/em/scipion/3.0/anaconda3/etc/profile.d/conda.sh
>     conda activate .scipion3env
>     which python3
>     ################################
>     python3 /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/lugmayr/ScipionUserData/projects/Scipion3_TestSuite" "Runs/000146_XmippProtMovieCorr/logs/run.db" 146
>
>     Now I get the following error:
>     ### jobid : 5452483  ###
>     /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/bin/python3
>     Traceback (most recent call last):
>        File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py", line 39, in <module>
>          runProtocolMain(projPath, dbPath, protId)
>        File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2167, in runProtocolMain
>          protocol = getProtocolFromDb(projectPath, protDbPath, protId, chdir=True)
>        File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2249, in getProtocolFromDb
>          project.load(dbPath=os.path.join(projectPath, protDbPath), chdir=chdir,
>        File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 244, in load
>          self._loadDb(dbPath)
>        File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 302, in _loadDb
>          self.mapper = self.createMapper(absDbPath)
>        File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 211, in createMapper
>          classesDict.update(self._domain.getMapperDict())
>     AttributeError: 'NoneType' object has no attribute 'getMapperDict'
>
>     Before when my base conda included all other scipion conda envs the cluster submission was fine.
>     I have set autoactivation for my base to off in my .condarc.
>
>     I have to use the python3 from the .scipion3env otherwise there would not be the pyworkflow package.
>     What else could I change for submission?
>
>     Cheers,
>     Wolfgang
>
> -- 
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

Re: [scipion-users] scipion3, own special scipion conda - cluster submission problems/question

[Lugmayr, W. <w.l...@uk...>]

Hi, 

thanks for your help, I think this was my fault. 
We have CPU nodes with no CUDA libs on the cluster and GPU nodes. 
It seems that I've sent the xmipp_cuda_movie_alignment_correlation job to a CPU node where it died immediately without any log message. 
I have to improve my scipion3 hosts.conf template. 
For relion its easy, I check my script if --gpu is on or off. But in scipion3 I cannot determine if its a CPU/GPU job on the cluster submission script level. 

Just to make clear, my python command line came from the template: 
%_(JOB_COMMAND)s 

and due a mpi4py error the settings mentioned below were correct: 
subprocess.CalledProcessError: Command 'mpirun -np 3 -bynode `which python3` "-m" "scipion" "runprotocol" "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_mpirun.py" "/home/lugmayr/ScipionUserData/projects/Scipion3_TestSuite" "Runs/000146_XmippProtMovieCorr/logs/run.db" "146"' returned non-zero exit status 1. 

pip install mpi4py solved it (conda install will also give my mpich, so I used pip). 

Thanks for your help. 
Cheers, 
Wolfgang 

P.S. FYI 
Each time I call scipion3 config --update all my comment lines from the hosts.conf file are removed. But these contain useful SLURM settings like: 
#SBATCH -p %_(JOB_QUEUE)s 
I copy it over the generated one afterwards, but maybe there will be a better solution? 



From: "Pablo Conesa" <pc...@cn...> 
To: "Mailing list for Scipion users" <sci...@li...> 
Sent: Friday, 11 September, 2020 18:06:18 
Subject: Re: [scipion-users] scipion3, own special scipion conda - cluster submission problems/question 



Let me see if I'm getting it. 

Are you trying to avoid the launching script (scipion3) and instead you want to run "manually" a protocol? 

If so, you need to replicate what the launching script does: 




Here is what I've got in the launching script hightlighting the key lines: 




#!/usr/bin/env python 
# Scipion launcher 
import os 
import sys 
from os.path import dirname, abspath, join, basename 

# Set SCIPION_HOME to the location of this file 
scipionHome = dirname(abspath(__file__)) 
os.environ["SCIPION_TESTS_CMD"] = basename(__file__) + " tests" 
os.environ["LD_LIBRARY_PATH"] = ":".join([os.environ.get("LD_LIBRARY_PATH", ""), join(scipionHome, "software", "lib")]) 
os.environ["PYTHONPATH"] = ":".join([os.environ.get("PYTHONPATH", ""), join(scipionHome, "software", "bindings")]) 

cmd = "" 
if len(sys.argv) > 1 and sys.argv[1] == 'git': 
for repo in ['scipion-app', 'scipion-pyworkflow', 'scipion-em']: 
cmd += ("(cd "+join(scipionHome, repo)+" ; echo ' > in "+repo+":' ;" 
" git "+' '.join(sys.argv[2:])+" ; echo) ; ") 
else: 
# Activate the environment 
cmd = '. /home/pablo/software/scipion/.scipion3env/bin/activate && ' 
cmd += "python -m scipion %s" % " ".join(sys.argv[1:]) 

# Set SCIPION_HOME 
os.environ["SCIPION_HOME"] = scipionHome 
exit(os.WEXITSTATUS(os.system(cmd))) 




A short explanation: 

LD_LIBRARY_PATH and PYTHONPATH are set to allow scipion use xmipp fileformats convertions, metadata utilities and it's viewer. 

SCIPION_HOME, is mandatory, since now the path of pyworkflow (pip package) cannot determine scipion home as it was for scipion2. 




python -m scipion is to run entry point commands but in your case you can skip this. 








On 11/9/20 16:44, Lugmayr, Wolfgang wrote: 



Hi,

I have re-installed recently scipion3 with its own conda environment. Mainly for the reason that the plugins could overwrite my conda installation e.g. mine is cryolo-1.7 and the scipion plugin creates a cryolo-1.7.2

My new scipion3 conda looks now like:
base                  *  /beegfs/cssb/software/em/scipion/3.0/anaconda3
.scipion3env             /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env
cryolo-1.7.2             /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryolo-1.7.2
cryoloCPU-1.7.2          /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryoloCPU-1.7.2
xmipp_DLTK_v0.3          /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_DLTK_v0.3
xmipp_MicCleaner         /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_MicCleaner

If I run everything locally via scipion3 the task runs fine.

The task script for the cluster contains:
:
source /beegfs/cssb/software/em/scipion/3.0/anaconda3/etc/profile.d/conda.sh
conda activate .scipion3env
which python3
################################
python3 /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/lugmayr/ScipionUserData/projects/Scipion3_TestSuite" "Runs/000146_XmippProtMovieCorr/logs/run.db" 146

Now I get the following error:
### jobid : 5452483  ###
/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/bin/python3
Traceback (most recent call last):
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py", line 39, in <module>
    runProtocolMain(projPath, dbPath, protId)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2167, in runProtocolMain
    protocol = getProtocolFromDb(projectPath, protDbPath, protId, chdir=True)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2249, in getProtocolFromDb
    project.load(dbPath=os.path.join(projectPath, protDbPath), chdir=chdir,
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 244, in load
    self._loadDb(dbPath)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 302, in _loadDb
    self.mapper = self.createMapper(absDbPath)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 211, in createMapper
    classesDict.update(self._domain.getMapperDict())
AttributeError: 'NoneType' object has no attribute 'getMapperDict'

Before when my base conda included all other scipion conda envs the cluster submission was fine.
I have set autoactivation for my base to off in my .condarc.

I have to use the python3 from the .scipion3env otherwise there would not be the pyworkflow package.
What else could I change for submission?

Cheers,
Wolfgang 



-- 
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team 


_______________________________________________ 
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Re: [scipion-users] MPI pyworkflow error

[Gabriel R. S. <gab...@ln...>]

Thanks Pablo.

Gabriel Ravanhani Schleder
Nanociências e Materiais avançados - Universidade Federal do ABC
Laboratório Nacional de Nanotecnologia (LNNano)/CNPEM

gab...@ln...<mailto:gab...@ln...>

[https://ci4.googleusercontent.com/proxy/IopjzWOb6ylR_GtG5u-Zq0Y1mfY38261k9R9cRTt4mvcFHhBJiQ9jdJqyZz9bFRhh-8Afvxzo1WXoiG6kICRxixgPuWH7LhkjY7V1aEp_qzCoLTmslvMDpNFwnT1I0LsPrG-vJPz0GuZ6ezdapZ0ysF75gEHWqCWTiyAg81-qkj08_Ziypasdao553zOQn1TYkVWf3diMECDEkRYoQ=s0-d-e1-ft#https://docs.google.com/uc?export=download&id=1VYc_gBmfC5pszxYlE4VRvmsYfUaCft-9&revid=0BzRCD-uA8R9PKzEyQVhwcFp4eEk2cVRXdjh0ZnYzODRQY0lnPQ][https://ci3.googleusercontent.com/proxy/MJIDN1yBIjQxusVQnL3j90ZVVJvigW9KnZqAZTmUe7nf_TIZEBsARPVrz6F5nWlGTQcTYyVvxxHozrAcCleyGYlyUft2g8x8T-epesE1Lz6o_EMGLYHkoEtjqdWE7Uf1JxyS=s0-d-e1-ft#https://drive.google.com/uc?id=1fGLfbjGvalYjDusrpZViRV-yodfbPA83&export=download]

On Sep 11 2020, at 2:44 am, Pablo Conesa <pc...@cn...> wrote:

I've created an issue, so is not lost and will have a look.

https://github.com/scipion-em/scipion-pyworkflow/issues/137

On 10/9/20 18:34, David Maluenda wrote:
Dear all,

I have been getting python errors related to MPI runs on different xmipp3 protocols (alternatively, I tested on relion MPI protocols, which runs correctly). The same protocols run without problems if using threads instead of MPI processes.

It seems like a python2-to-python3 encoding-related issue, as the representative example run traceback below:

00001:   RUNNING PROTOCOL -----------------
00002:   Hostname: node04
00003:   PID: 57882
00004:   pyworkflow: 3.0.1
00005:   plugin: xmipp3
00006:   currentDir: /home/ScipionUserData/projects/Test
00007:   workingDir: Runs/001782_XmippProtExtractParticles
00008:   runMode: Restart
00009:             MPI: 2
00010:         threads: 1
00011:    Starting at step: 1
00012:    Running steps
00013:   STARTED: extractMicrographStep, step 1, time 2020-08-17 13:51:05.684077
00014:   Extracting micrograph: Runs/001557_ProtImportMicrographs/extra/4k_10000001.mrcs
00015:   Sending environment to 1
00016:   'xmipp_coordinates_noisy_zones_filter' have failed for 4k_10000001.mrcs micrograph. We continue...
00017:   Sending environment to 1
00018:   Traceback (most recent call last):
00019:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 149, in run
00020:       self.step._run()  # not self.step.run<http://self.step.run>() , to avoid race conditions
00021:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 239, in _run
00022:       resultFiles = self._runFunc()
00023:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 235, in _runFunc
00024:       return self._func(*self._args)
00025:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocol_particles.py", line 233, in extractMicrographStep
00026:       self._extractMicrograph(mic, *args)
00027:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_extract_particles.py", line 212, in _extractMicrograph
00028:       self.runJob<http://self.runJob>('xmipp_transform_filter',
00029:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1337, in runJob
00030:       self._stepsExecutor.runJob<http://stepsExecutor.runJob>(self._log, program, arguments, **kwargs)
00031:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 352, in runJob
00032:       runJobMPI(programName, params, self.comm<http://self.comm>, node,
00033:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 90, in runJobMPI
00034:       send("env=%s" % dumps(env), mpiComm, mpiDest, TAG_RUN_JOB+mpiDest)
00035:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 77, in send
00036:       raise Exception(str(result).encode(encoding='UTF-8'))
00037:   Exception: b"a bytes-like object is required, not 'str'"
00038:   Protocol failed: b"a bytes-like object is required, not 'str'"
00039:   FAILED: extractMicrographStep, step 1, time 2020-08-17 13:51:08.570543
00040:   ------------------- PROTOCOL FAILED (DONE 1/10)

The errors come from the:
00035:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 77, in send
00036:       raise Exception(str(result).encode(encoding='UTF-8'))

I tested adding ".encode(encoding='UTF-8')" part to the original code, which clearly did not solve the problem. From the traceback, the error seems to come from the string sent by the mpi communications, which I am not acquainted enough to solve.

On a related note, what is the recommended procedure for updating the scipion packages (not plugins)? I updated from the latest available from PyPI.

Best regards,

Gabriel R. Schleder
Universidade Federal do ABC (UFABC)
Laboratório Nacional de Nanotecnologia (LNNano/CNPEM)
--
Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team
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Re: [scipion-users] scipion3, own special scipion conda - cluster submission problems/question

[Pablo C. <pc...@cn...>]

Let me see if I'm getting it.

Are you trying to avoid the launching script (scipion3) and instead you 
want to run "manually" a protocol?

If so, you need to replicate what the launching script does:


Here is what I've got in the launching script hightlighting the key lines:


#!/usr/bin/env python
# Scipion launcher
import os
import sys
from os.path import dirname, abspath, join, basename

# Set SCIPION_HOME to the location of this file
scipionHome = dirname(abspath(__file__))
os.environ["SCIPION_TESTS_CMD"] = basename(__file__) + " tests"
os.environ["LD_LIBRARY_PATH"] = 
":".join([os.environ.get("LD_LIBRARY_PATH", ""), join(scipionHome, 
"software", "lib")])
os.environ["PYTHONPATH"] = ":".join([os.environ.get("PYTHONPATH", ""), 
join(scipionHome, "software", "bindings")])

cmd = ""
if len(sys.argv) > 1 and sys.argv[1] == 'git':
     for repo in ['scipion-app', 'scipion-pyworkflow', 'scipion-em']:
         cmd += ("(cd "+join(scipionHome, repo)+" ; echo ' > in 
"+repo+":' ;"
                 " git "+' '.join(sys.argv[2:])+" ; echo) ; ")
else:
     # Activate the environment
     cmd = '. /home/pablo/software/scipion/.scipion3env/bin/activate && '
     cmd += "python -m scipion %s" % " ".join(sys.argv[1:])

# Set SCIPION_HOME
os.environ["SCIPION_HOME"] = scipionHome
exit(os.WEXITSTATUS(os.system(cmd)))


A short explanation:

LD_LIBRARY_PATH and PYTHONPATH are set to allow scipion use xmipp 
fileformats convertions, metadata utilities and it's viewer.

SCIPION_HOME, is mandatory, since now the path of pyworkflow (pip 
package) cannot determine scipion home as it was for scipion2.


python -m scipion is to run entry point commands but in your case you 
can skip this.




On 11/9/20 16:44, Lugmayr, Wolfgang wrote:
> Hi,
>
> I have re-installed recently scipion3 with its own conda environment. Mainly for the reason that the plugins could overwrite my conda installation e.g. mine is cryolo-1.7 and the scipion plugin creates a cryolo-1.7.2
>
> My new scipion3 conda looks now like:
> base                  *  /beegfs/cssb/software/em/scipion/3.0/anaconda3
> .scipion3env             /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env
> cryolo-1.7.2             /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryolo-1.7.2
> cryoloCPU-1.7.2          /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryoloCPU-1.7.2
> xmipp_DLTK_v0.3          /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_DLTK_v0.3
> xmipp_MicCleaner         /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_MicCleaner
>
> If I run everything locally via scipion3 the task runs fine.
>
> The task script for the cluster contains:
> :
> source /beegfs/cssb/software/em/scipion/3.0/anaconda3/etc/profile.d/conda.sh
> conda activate .scipion3env
> which python3
> ################################
> python3 /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/lugmayr/ScipionUserData/projects/Scipion3_TestSuite" "Runs/000146_XmippProtMovieCorr/logs/run.db" 146
>
> Now I get the following error:
> ### jobid : 5452483  ###
> /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/bin/python3
> Traceback (most recent call last):
>    File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py", line 39, in <module>
>      runProtocolMain(projPath, dbPath, protId)
>    File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2167, in runProtocolMain
>      protocol = getProtocolFromDb(projectPath, protDbPath, protId, chdir=True)
>    File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2249, in getProtocolFromDb
>      project.load(dbPath=os.path.join(projectPath, protDbPath), chdir=chdir,
>    File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 244, in load
>      self._loadDb(dbPath)
>    File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 302, in _loadDb
>      self.mapper = self.createMapper(absDbPath)
>    File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 211, in createMapper
>      classesDict.update(self._domain.getMapperDict())
> AttributeError: 'NoneType' object has no attribute 'getMapperDict'
>
> Before when my base conda included all other scipion conda envs the cluster submission was fine.
> I have set autoactivation for my base to off in my .condarc.
>
> I have to use the python3 from the .scipion3env otherwise there would not be the pyworkflow package.
> What else could I change for submission?
>
> Cheers,
> Wolfgang
>
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

[scipion-users] scipion3, own special scipion conda - cluster submission problems/question

[Lugmayr, W. <w.l...@uk...>]

Hi,

I have re-installed recently scipion3 with its own conda environment. Mainly for the reason that the plugins could overwrite my conda installation e.g. mine is cryolo-1.7 and the scipion plugin creates a cryolo-1.7.2

My new scipion3 conda looks now like:
base                  *  /beegfs/cssb/software/em/scipion/3.0/anaconda3
.scipion3env             /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env
cryolo-1.7.2             /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryolo-1.7.2
cryoloCPU-1.7.2          /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryoloCPU-1.7.2
xmipp_DLTK_v0.3          /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_DLTK_v0.3
xmipp_MicCleaner         /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_MicCleaner

If I run everything locally via scipion3 the task runs fine.

The task script for the cluster contains:
:
source /beegfs/cssb/software/em/scipion/3.0/anaconda3/etc/profile.d/conda.sh
conda activate .scipion3env
which python3
################################
python3 /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/lugmayr/ScipionUserData/projects/Scipion3_TestSuite" "Runs/000146_XmippProtMovieCorr/logs/run.db" 146

Now I get the following error:
### jobid : 5452483  ###
/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/bin/python3
Traceback (most recent call last):
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py", line 39, in <module>
    runProtocolMain(projPath, dbPath, protId)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2167, in runProtocolMain
    protocol = getProtocolFromDb(projectPath, protDbPath, protId, chdir=True)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2249, in getProtocolFromDb
    project.load(dbPath=os.path.join(projectPath, protDbPath), chdir=chdir,
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 244, in load
    self._loadDb(dbPath)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 302, in _loadDb
    self.mapper = self.createMapper(absDbPath)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 211, in createMapper
    classesDict.update(self._domain.getMapperDict())
AttributeError: 'NoneType' object has no attribute 'getMapperDict'

Before when my base conda included all other scipion conda envs the cluster submission was fine.
I have set autoactivation for my base to off in my .condarc.

I have to use the python3 from the .scipion3env otherwise there would not be the pyworkflow package.
What else could I change for submission?

Cheers,
Wolfgang

-- 
Universitätsklinikum Hamburg-Eppendorf (UKE)
@ Centre for Structral Systems Biology (CSSB)
@ Deutsches Elektronen-Synchrotron (DESY)
Notkestrasse 85 Gebäude 15
22607 Hamburg, Germany
Tel.: +49 40 8998-87652
Email: wol...@cs...
http://www.cssb-hamburg.de/

Re: [scipion-users] MPI pyworkflow error

[Pablo C. <pc...@cn...>]

I've created an issue, so is not lost and will have a look.

https://github.com/scipion-em/scipion-pyworkflow/issues/137

On 10/9/20 18:34, David Maluenda wrote:
> Dear all,
> I have been getting python errors related to MPI runs on different 
> xmipp3 protocols (alternatively, I tested on relion MPI protocols, 
> which runs correctly). The same protocols run without problems if 
> using threads instead of MPI processes.
>
> It seems like a python2-to-python3 encoding-related issue, as the 
> representative example run traceback below:
>
> 00001:   RUNNING PROTOCOL -----------------
> 00002:   Hostname: node04
> 00003:   PID: 57882
> 00004:   pyworkflow: 3.0.1
> 00005:   plugin: xmipp3
> 00006:   currentDir: /home/ScipionUserData/projects/Test
> 00007:   workingDir: Runs/001782_XmippProtExtractParticles
> 00008:   runMode: Restart
> 00009:             MPI: 2
> 00010:         threads: 1
> 00011:    Starting at step: 1
> 00012:    Running steps
> 00013:   STARTED: extractMicrographStep, step 1, time 2020-08-17 
> 13:51:05.684077
> 00014:   Extracting micrograph: 
> Runs/001557_ProtImportMicrographs/extra/4k_10000001.mrcs
> 00015:   Sending environment to 1
> 00016: 'xmipp_coordinates_noisy_zones_filter' have failed for 
> 4k_10000001.mrcs micrograph. We continue...
> 00017:   Sending environment to 1
> 00018:   Traceback (most recent call last):
> 00019:     File 
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", 
> line 149, in run
> 00020:       self.step._run()  # not self.step.run 
> <http://self.step.run>() , to avoid race conditions
> 00021:     File 
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 239, in _run
> 00022:       resultFiles = self._runFunc()
> 00023:     File 
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 235, in _runFunc
> 00024:       return self._func(*self._args)
> 00025:     File 
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocol_particles.py", 
> line 233, in extractMicrographStep
> 00026: self._extractMicrograph(mic, *args)
> 00027:     File 
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_extract_particles.py", 
> line 212, in _extractMicrograph
> 00028: self.runJob <http://self.runJob>('xmipp_transform_filter',
> 00029:     File 
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 1337, in runJob
> 00030:       self._stepsExecutor.runJob 
> <http://stepsExecutor.runJob>(self._log, program, arguments, **kwargs)
> 00031:     File 
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", 
> line 352, in runJob
> 00032:       runJobMPI(programName, params, self.comm 
> <http://self.comm>, node,
> 00033:     File 
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", 
> line 90, in runJobMPI
> 00034:       send("env=%s" % dumps(env), mpiComm, mpiDest, 
> TAG_RUN_JOB+mpiDest)
> 00035:     File 
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", 
> line 77, in send
> 00036:       raise Exception(str(result).encode(encoding='UTF-8'))
> 00037:   Exception: b"a bytes-like object is required, not 'str'"
> 00038:   Protocol failed: b"a bytes-like object is required, not 'str'"
> 00039:   FAILED: extractMicrographStep, step 1, time 2020-08-17 
> 13:51:08.570543
> 00040:   ------------------- PROTOCOL FAILED (DONE 1/10)
>
> The errors come from the:
> 00035:     File 
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", 
> line 77, in send
> 00036:       raise Exception(str(result).encode(encoding='UTF-8'))
>
> I tested adding ".encode(encoding='UTF-8')" part to the original code, 
> which clearly did not solve the problem. From the traceback, the error 
> seems to come from the string sent by the mpi communications, which I 
> am not acquainted enough to solve.
>
> On a related note, what is the recommended procedure for updating the 
> scipion packages (not plugins)? I updated from the latest available 
> from PyPI.
> Best regards,
>
> Gabriel R. Schleder
> /Universidade Federal do ABC (UFABC)/
> /Laboratório Nacional de Nanotecnologia (LNNano/CNPEM)/
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

Re: [scipion-users] MPI pyworkflow error

[Gabriel R. S. <gab...@ln...>]

Sounds great.

No problem, thanks David.
Gabriel Ravanhani Schleder
Nanociências e Materiais avançados - Universidade Federal do ABC
Laboratório Nacional de Nanotecnologia (LNNano)/CNPEM
gab...@ln... (mailto:gab...@ln...)

On Sep 10 2020, at 1:34 pm, David Maluenda <dma...@cn...> wrote:
> Hi Gabriel,
>
> It seems like a bug, let us check it and return to you.
>
> Sorry for not replying to you in August.
>
>
> Thanks for reporting.
>
>
>
> _____
> Dr. David Maluenda Niubó
>
> dma...@cn... (mailto:dma...@cn...) - (+34) 619 029 310
> CSIC - Centro Nacional de Biotecnología (http://www.cnb.csic.es)
> BioComputing Unit (http://biocomputingunit.es/)
>
>
> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration.
>
>
>
> On Thu, Sep 10, 2020 at 4:47 PM Gabriel Ravanhani Schleder <gab...@ln... (mailto:gab...@ln...)> wrote:
> > I think this message might not have been seen.
> > Any idea if this is a general error?
> >
> > Gabriel Ravanhani Schleder
> > Nanociências e Materiais avançados - Universidade Federal do ABC
> > Laboratório Nacional de Nanotecnologia (LNNano)/CNPEM
> > gab...@ln... (mailto:gab...@ln...)
> >
> >
> >
> >
> >
> >
> >
> > On Aug 17 2020, at 7:43 pm, Gabriel Ravanhani Schleder <gab...@ln... (mailto:gab...@ln...)> wrote:
> > >
> > > Dear all,
> > >
> > > I have been getting python errors related to MPI runs on different xmipp3 protocols (alternatively, I tested on relion MPI protocols, which runs correctly). The same protocols run without problems if using threads instead of MPI processes.
> > >
> > > It seems like a python2-to-python3 encoding-related issue, as the representative example run traceback below:
> > > 00001: RUNNING PROTOCOL -----------------
> > > 00002: Hostname: node04
> > > 00003: PID: 57882
> > > 00004: pyworkflow: 3.0.1
> > > 00005: plugin: xmipp3
> > > 00006: currentDir: /home/ScipionUserData/projects/Test
> > > 00007: workingDir: Runs/001782_XmippProtExtractParticles
> > > 00008: runMode: Restart
> > > 00009: MPI: 2
> > > 00010: threads: 1
> > > 00011: Starting at step: 1
> > > 00012: Running steps
> > > 00013: STARTED: extractMicrographStep, step 1, time 2020-08-17 13:51:05.684077
> > > 00014: Extracting micrograph: Runs/001557_ProtImportMicrographs/extra/4k_10000001.mrcs
> > > 00015: Sending environment to 1
> > > 00016: 'xmipp_coordinates_noisy_zones_filter' have failed for 4k_10000001.mrcs micrograph. We continue...
> > > 00017: Sending environment to 1
> > > 00018: Traceback (most recent call last):
> > > 00019: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 149, in run
> > > 00020: self.step._run() # not self.step.run (http://self.step.run)() , to avoid race conditions
> > > 00021: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 239, in _run
> > > 00022: resultFiles = self._runFunc()
> > > 00023: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 235, in _runFunc
> > > 00024: return self._func(*self._args)
> > > 00025: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocol_particles.py", line 233, in extractMicrographStep
> > > 00026: self._extractMicrograph(mic, *args)
> > > 00027: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_extract_particles.py", line 212, in _extractMicrograph
> > > 00028: self.runJob (http://self.runJob)('xmipp_transform_filter',
> > > 00029: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1337, in runJob
> > > 00030: self._stepsExecutor.runJob (http://stepsExecutor.runJob)(self._log, program, arguments, **kwargs)
> > > 00031: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 352, in runJob
> > > 00032: runJobMPI(programName, params, self.comm (http://self.comm), node,
> > > 00033: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 90, in runJobMPI
> > > 00034: send("env=%s" % dumps(env), mpiComm, mpiDest, TAG_RUN_JOB+mpiDest)
> > > 00035: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 77, in send
> > > 00036: raise Exception(str(result).encode(encoding='UTF-8'))
> > > 00037: Exception: b"a bytes-like object is required, not 'str'"
> > > 00038: Protocol failed: b"a bytes-like object is required, not 'str'"
> > > 00039: FAILED: extractMicrographStep, step 1, time 2020-08-17 13:51:08.570543
> > > 00040: ------------------- PROTOCOL FAILED (DONE 1/10)
> > >
> > > The errors come from the:
> > > 00035: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 77, in send
> > > 00036: raise Exception(str(result).encode(encoding='UTF-8'))
> > >
> > > I tested adding ".encode(encoding='UTF-8')" part to the original code, which clearly did not solve the problem. From the traceback, the error seems to come from the string sent by the mpi communications, which I am not acquainted enough to solve.
> > > On a related note, what is the recommended procedure for updating the scipion packages (not plugins)? I updated from the latest available from PyPI.
> > >
> > > Best regards,
> > >
> > > Gabriel R. Schleder
> > > Universidade Federal do ABC (UFABC)
> > > Laboratório Nacional de Nanotecnologia (LNNano/CNPEM)
> > >
> > > Aviso Legal: Esta mensagem e seus anexos podem conter informações confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o remetente e apague-a imediatamente.
> > > Disclaimer: This email and its attachments may contain confidential and/or privileged information. Observe its content carefully and consider possible querying to the sender before copying, disclosing or distributing it. If you have received this email by mistake, please notify the sender and delete it immediately.
> > > _______________________________________________
> > > scipion-users mailing list
> > > sci...@li... (mailto:sci...@li...)
> > > https://lists.sourceforge.net/lists/listinfo/scipion-users
> >
> > _______________________________________________
> > scipion-users mailing list
> > sci...@li... (mailto:sci...@li...)
> > https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] MPI pyworkflow error

[David M. <dma...@cn...>]

Hi Gabriel,

It seems like a bug, let us check it and return to you.

Sorry for not replying to you in August.


Thanks for reporting.

<http://ucm.es/>

*_____Dr. David Maluenda Niubó*
dma...@cn... - (+34) 619 029 310
CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
BioComputing Unit <http://biocomputingunit.es/>

This email message and any documents attached to it may contain
confidential or legally protected material and are intended solely for the
use of the individual or organization to whom they are addressed. We remind
you that if you are not the intended recipient of this email message or the
person responsible for processing it, then you are not authorized to read,
save, modify, send, copy or disclose any of its contents. If you have
received this email message by mistake, we kindly ask you to inform the
sender of this and to eliminate both the message and any attachments it
carries from your account. Thank you for your collaboration.



On Thu, Sep 10, 2020 at 4:47 PM Gabriel Ravanhani Schleder <
gab...@ln...> wrote:

> I think this message might not have been seen.
> Any idea if this is a general error?
>
> Gabriel Ravanhani Schleder
> Nanociências e Materiais avançados - Universidade Federal do ABC
> Laboratório Nacional de Nanotecnologia (LNNano)/CNPEM
>
> gab...@ln...
>
> On Aug 17 2020, at 7:43 pm, Gabriel Ravanhani Schleder <
> gab...@ln...> wrote:
>
>
> Dear all,
>
> I have been getting python errors related to MPI runs on different xmipp3
> protocols (alternatively, I tested on relion MPI protocols, which runs
> correctly). The same protocols run without problems if using threads
> instead of MPI processes.
>
> It seems like a python2-to-python3 encoding-related issue, as the
> representative example run traceback below:
>
> 00001:   RUNNING PROTOCOL -----------------
> 00002:   Hostname: node04
> 00003:   PID: 57882
> 00004:   pyworkflow: 3.0.1
> 00005:   plugin: xmipp3
> 00006:   currentDir: /home/ScipionUserData/projects/Test
> 00007:   workingDir: Runs/001782_XmippProtExtractParticles
> 00008:   runMode: Restart
> 00009:             MPI: 2
> 00010:         threads: 1
> 00011:    Starting at step: 1
> 00012:    Running steps
> 00013:   STARTED: extractMicrographStep, step 1, time 2020-08-17
> 13:51:05.684077
> 00014:   Extracting micrograph:
> Runs/001557_ProtImportMicrographs/extra/4k_10000001.mrcs
> 00015:   Sending environment to 1
> 00016:   'xmipp_coordinates_noisy_zones_filter' have failed for
> 4k_10000001.mrcs micrograph. We continue...
> 00017:   Sending environment to 1
> 00018:   Traceback (most recent call last):
> 00019:     File
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
> line 149, in run
> 00020:       self.step._run()  # not self.step.run() , to avoid race
> conditions
> 00021:     File
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 239, in _run
> 00022:       resultFiles = self._runFunc()
> 00023:     File
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 235, in _runFunc
> 00024:       return self._func(*self._args)
> 00025:     File
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocol_particles.py",
> line 233, in extractMicrographStep
> 00026:       self._extractMicrograph(mic, *args)
> 00027:     File
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_extract_particles.py",
> line 212, in _extractMicrograph
> 00028:       self.runJob('xmipp_transform_filter',
> 00029:     File
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1337, in runJob
> 00030:       self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
> 00031:     File
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
> line 352, in runJob
> 00032:       runJobMPI(programName, params, self.comm, node,
> 00033:     File
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py",
> line 90, in runJobMPI
> 00034:       send("env=%s" % dumps(env), mpiComm, mpiDest,
> TAG_RUN_JOB+mpiDest)
> 00035:     File
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py",
> line 77, in send
> 00036:       raise Exception(str(result).encode(encoding='UTF-8'))
> 00037:   Exception: b"a bytes-like object is required, not 'str'"
> 00038:   Protocol failed: b"a bytes-like object is required, not 'str'"
> 00039:   FAILED: extractMicrographStep, step 1, time 2020-08-17
> 13:51:08.570543
> 00040:   ------------------- PROTOCOL FAILED (DONE 1/10)
>
> The errors come from the:
> 00035:     File
> "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py",
> line 77, in send
> 00036:       raise Exception(str(result).encode(encoding='UTF-8'))
>
> I tested adding ".encode(encoding='UTF-8')" part to the original code,
> which clearly did not solve the problem. From the traceback, the error
> seems to come from the string sent by the mpi communications, which I am
> not acquainted enough to solve.
>
> On a related note, what is the recommended procedure for updating the
> scipion packages (not plugins)? I updated from the latest available from
> PyPI.
>
> Best regards,
>
> Gabriel R. Schleder
> *Universidade Federal do ABC (UFABC)*
> *Laboratório Nacional de Nanotecnologia (LNNano/CNPEM)*
>
> Aviso Legal: Esta mensagem e seus anexos podem conter informações
> confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e
> considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou
> distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o
> remetente e apague-a imediatamente.
>
> Disclaimer: This email and its attachments may contain confidential and/or
> privileged information. Observe its content carefully and consider possible
> querying to the sender before copying, disclosing or distributing it. If
> you have received this email by mistake, please notify the sender and
> delete it immediately.
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] MPI pyworkflow error

[Gabriel R. S. <gab...@ln...>]

I think this message might not have been seen.
Any idea if this is a general error?

Gabriel Ravanhani Schleder
Nanociências e Materiais avançados - Universidade Federal do ABC
Laboratório Nacional de Nanotecnologia (LNNano)/CNPEM
gab...@ln... (mailto:gab...@ln...)

On Aug 17 2020, at 7:43 pm, Gabriel Ravanhani Schleder <gab...@ln...> wrote:
>
> Dear all,
>
> I have been getting python errors related to MPI runs on different xmipp3 protocols (alternatively, I tested on relion MPI protocols, which runs correctly). The same protocols run without problems if using threads instead of MPI processes.
>
> It seems like a python2-to-python3 encoding-related issue, as the representative example run traceback below:
> 00001: RUNNING PROTOCOL -----------------
> 00002: Hostname: node04
> 00003: PID: 57882
> 00004: pyworkflow: 3.0.1
> 00005: plugin: xmipp3
> 00006: currentDir: /home/ScipionUserData/projects/Test
> 00007: workingDir: Runs/001782_XmippProtExtractParticles
> 00008: runMode: Restart
> 00009: MPI: 2
> 00010: threads: 1
> 00011: Starting at step: 1
> 00012: Running steps
> 00013: STARTED: extractMicrographStep, step 1, time 2020-08-17 13:51:05.684077
> 00014: Extracting micrograph: Runs/001557_ProtImportMicrographs/extra/4k_10000001.mrcs
> 00015: Sending environment to 1
> 00016: 'xmipp_coordinates_noisy_zones_filter' have failed for 4k_10000001.mrcs micrograph. We continue...
> 00017: Sending environment to 1
> 00018: Traceback (most recent call last):
> 00019: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 149, in run
> 00020: self.step._run() # not self.step.run() , to avoid race conditions
> 00021: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 239, in _run
> 00022: resultFiles = self._runFunc()
> 00023: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 235, in _runFunc
> 00024: return self._func(*self._args)
> 00025: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocol_particles.py", line 233, in extractMicrographStep
> 00026: self._extractMicrograph(mic, *args)
> 00027: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_extract_particles.py", line 212, in _extractMicrograph
> 00028: self.runJob('xmipp_transform_filter',
> 00029: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1337, in runJob
> 00030: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
> 00031: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 352, in runJob
> 00032: runJobMPI(programName, params, self.comm, node,
> 00033: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 90, in runJobMPI
> 00034: send("env=%s" % dumps(env), mpiComm, mpiDest, TAG_RUN_JOB+mpiDest)
> 00035: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 77, in send
> 00036: raise Exception(str(result).encode(encoding='UTF-8'))
> 00037: Exception: b"a bytes-like object is required, not 'str'"
> 00038: Protocol failed: b"a bytes-like object is required, not 'str'"
> 00039: FAILED: extractMicrographStep, step 1, time 2020-08-17 13:51:08.570543
> 00040: ------------------- PROTOCOL FAILED (DONE 1/10)
>
> The errors come from the:
> 00035: File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 77, in send
> 00036: raise Exception(str(result).encode(encoding='UTF-8'))
>
> I tested adding ".encode(encoding='UTF-8')" part to the original code, which clearly did not solve the problem. From the traceback, the error seems to come from the string sent by the mpi communications, which I am not acquainted enough to solve.
> On a related note, what is the recommended procedure for updating the scipion packages (not plugins)? I updated from the latest available from PyPI.
>
> Best regards,
>
> Gabriel R. Schleder
> Universidade Federal do ABC (UFABC)
> Laboratório Nacional de Nanotecnologia (LNNano/CNPEM)
>
> Aviso Legal: Esta mensagem e seus anexos podem conter informações confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o remetente e apague-a imediatamente.
> Disclaimer: This email and its attachments may contain confidential and/or privileged information. Observe its content carefully and consider possible querying to the sender before copying, disclosing or distributing it. If you have received this email by mistake, please notify the sender and delete it immediately.
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] deepEMhancer package installation

[Pablo C. <pc...@cn...>]

Not available in Scipion 2.0.

I think deepEMhancer can be installed alone outside scipion and xmipp: 
https://github.com/rsanchezgarc/deepEMhancer

Shortly, by the end of this month, if all testing/fixing goes well, it 
will be officially released with Scipion3.


On 10/9/20 16:14, Dmitry A. Semchonok wrote:
> So I can not install it with Scipion 2.0?
>
> Thank you
>
> Sincerely,
> Dmitry
>
> On September 10, 2020 5:13:40 PM Pablo Conesa <pc...@cn...> wrote:
>
>> scipion3 installb deepLearningToolkit
>>
>>
>> NOTE: Please, be aware that we still haven't officially released 
>> Scipion3 and xmipp (latest version).
>>
>> I know there are bugs in the installation of deepLearningToolkit 
>> already fixed in "devel" but you probably  will not have them yet.
>>
>>
>> On 10/9/20 15:51, Dmitry Semchonok wrote:
>>>
>>> Dear colleagues,
>>>
>>>
>>>           Small question  - how to install *deepEMhancer***package
>>>           in SCJPION*?*
>>>
>>> Thank you
>>>
>>> Sincerely,
>>>
>>> Dmitry
>>>
>>>
>>>
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>> -- 
>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li... 
>> <mailto:scipion-users%40lists.sourceforge.net>
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

Re: [scipion-users] deepEMhancer package installation

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

So I can not install it with Scipion 2.0?

Thank you

Sincerely,
Dmitry

On September 10, 2020 5:13:40 PM Pablo Conesa <pc...@cn...> wrote:
> scipion3 installb deepLearningToolkit
>
> NOTE: Please, be aware that we still haven't officially released Scipion3 
> and xmipp (latest version).
> I know there are bugs in the installation of deepLearningToolkit already 
> fixed in "devel" but you probably  will not have them yet.
>
> On 10/9/20 15:51, Dmitry Semchonok wrote:
>> Dear colleagues,
>>
>> Small question  - how to install deepEMhancer package in SCJPION?
>>
>> Thank you
>>
>> Sincerely,
>> Dmitry
>>
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
> --
> Pablo Conesa - Madrid Scipion team
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] deepEMhancer package installation

[Pablo C. <pc...@cn...>]

scipion3 installb deepLearningToolkit


NOTE: Please, be aware that we still haven't officially released 
Scipion3 and xmipp (latest version).

I know there are bugs in the installation of deepLearningToolkit already 
fixed in "devel" but you probably  will not have them yet.


On 10/9/20 15:51, Dmitry Semchonok wrote:
>
> Dear colleagues,
>
>
>           Small question  - how to install *deepEMhancer***package in
>           SCJPION*?*
>
> Thank you
>
> Sincerely,
>
> Dmitry
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

[scipion-users] deepEMhancer package installation

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

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--></style></head><body lang=RU link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='color:black'>Dear colleagues,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:black'><o:p>&nbsp;</o:p></span></p><div><h5 style='background:white'><span lang=EN-US style='font-family:"Calibri",sans-serif;color:black'>Small question  - how to install </span><b><span style='font-family:"Calibri",sans-serif;color:black'>deepEMhancer</span></b><b><span style='font-family:"Calibri",sans-serif;color:black'> </span></b><span lang=EN-US style='font-family:"Calibri",sans-serif;color:black'>package in SCJPION<b>?<o:p></o:p></b></span></h5><p class=MsoNormal><span lang=EN-US style='color:black'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:black'>Thank you<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:black'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:black'>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:black'>Dmitry<o:p></o:p></span></p></div><p class=MsoNormal><o:p>&nbsp;</o:p></p></div></body></html>

Re: [scipion-users] Scipion/xmipp v3.0.0 compilation error

[Pablo C. <pc...@cn...>]

Hi, André, we might need some more log lines, some more before the ones 
you've sent?.


Probably if you run the installation again you'll get the same.


On 10/9/20 13:50, André Graça wrote:
>
> Hi,
>
>
> I have gone through other treads that seem to be similar to the 
> problem I am finding during installation of Scipion v3.0.0, but so far 
> nothing made it work.
>
>
> I hope someone here can give me a hint of what going wrong. We are 
> talking about installation with conda on Ubuntu 16.04.
>
> Check the last lines of the log bellow.
>
>
> Thank you,
>
> André
>
>
>
> collect2: error: ld returned 1 exit status
> scons: *** [bin/xmipp_resolution_fsc] Error 1
> scons: building terminated because of errors.
>
> Some error occurred during the compilation of 'xmipp' 
> ('bin/xmipp_resolution_fsc').
>
> Traceback (most recent call last):
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", 
> line 443, in <module>
>     main()
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", 
> line 287, in main
>     installPluginMethods()
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", 
> line 231, in installPluginMethods
>     plugin.installBin({'args': ['-j', numberProcessor]})
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", 
> line 166, in installBin
>     environment.execute()
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", 
> line 748, in execute
>     self._executeTargets(targetList)
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", 
> line 690, in _executeTargets
>     tgt.execute()
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", 
> line 220, in execute
>     command.execute()
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", 
> line 160, in execute
>     assert glob(t), ("target '%s' not built (after "
> AssertionError: target 
> '/home/angr5008/software/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' 
> not built (after running 'cd . && ./xmipp config noAsk &&./xmipp 
> check_config && ./xmipp compileAndInstall N=20 && ln -srf build 
> /home/angr5008/software/scipion/3.0.0/software/em/xmipp && cd - && 
> touch installation_finished && rm bindings_linked 2> /dev/null')
> Error at main: target 
> '/home/angr5008/software/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' 
> not built (after running 'cd . && ./xmipp config noAsk &&./xmipp 
> check_config && ./xmipp compileAndInstall N=20 && ln -srf build 
> /home/angr5008/software/scipion/3.0.0/software/em/xmipp && cd - && 
> touch installation_finished && rm bindings_linked 2> /dev/null')
>
> Something went wrong running:
>  eval "$(/home/angr5008/anaconda3/condabin/conda shell.bash hook)" &&
> conda create  -n .scipion3env python=3 &&
> conda activate .scipion3env &&
> cd /home/angr5008/software/scipion/3.0.0 &&
> mkdir -p software/lib &&
> mkdir -p software/bindings &&
> mkdir -p software/em &&
> export SCIPION_HOME=/home/angr5008/software/scipion/3.0.0 &&
> pip install scipion-pyworkflow &&
> pip install scipion-app &&
> python -m scipion installp -p scipion-em-xmipp -j 20
> Installation cancelled.
>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

[scipion-users] Scipion/xmipp v3.0.0 compilation error

[André G. <and...@um...>]

Hi,


I have gone through other treads that seem to be similar to the problem I am finding during installation of Scipion v3.0.0, but so far nothing made it work.


I hope someone here can give me a hint of what going wrong. We are talking about installation with conda on Ubuntu 16.04.

Check the last lines of the log bellow.


Thank you,

André



collect2: error: ld returned 1 exit status
scons: *** [bin/xmipp_resolution_fsc] Error 1
scons: building terminated because of errors.

Some error occurred during the compilation of 'xmipp' ('bin/xmipp_resolution_fsc').

Traceback (most recent call last):
  File "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 443, in <module>
    main()
  File "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 287, in main
    installPluginMethods()
  File "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods
    plugin.installBin({'args': ['-j', numberProcessor]})
  File "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
    environment.execute()
  File "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
    self._executeTargets(targetList)
  File "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
    tgt.execute()
  File "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute
    command.execute()
  File "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute
    assert glob(t), ("target '%s' not built (after "
AssertionError: target '/home/angr5008/software/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk &&./xmipp check_config && ./xmipp compileAndInstall N=20 && ln -srf build /home/angr5008/software/scipion/3.0.0/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')
Error at main: target '/home/angr5008/software/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk &&./xmipp check_config && ./xmipp compileAndInstall N=20 && ln -srf build /home/angr5008/software/scipion/3.0.0/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')

Something went wrong running:
 eval "$(/home/angr5008/anaconda3/condabin/conda shell.bash hook)" &&
conda create  -n .scipion3env python=3 &&
conda activate .scipion3env &&
cd /home/angr5008/software/scipion/3.0.0 &&
mkdir -p software/lib &&
mkdir -p software/bindings &&
mkdir -p software/em &&
export SCIPION_HOME=/home/angr5008/software/scipion/3.0.0 &&
pip install scipion-pyworkflow &&
pip install scipion-app &&
python -m scipion installp -p scipion-em-xmipp -j 20
Installation cancelled.

[scipion-users] FW: Instruct Course on the development of image processing workflows in streaming and structural data analysis components for Electron Microscopy (Online edition)

[Pablo C. <pc...@cn...>]

This a free, online course for *developers, *you need programing skills. 
Contact Blanca for more details.

Dear Colleagues,

We are pleased to include information about our coming *_Instruct Course 
on the development of image processing workflows in streaming and 
structural data analysis components for Electron Microscopy (Online 
edition). _*

The Online edition of the Instruct Course will take place from October 
26-29, 2020 through the CSIC.Conecta Platform. You can find more 
information at: 
http://i2pc.es/instruct-course-on-the-development-of-image-processing-workflows-in-streaming-and-structural-data-analysis-components-for-electron-microscopy-madrid-october-26-29-2020/

This course will show how to integrate into Scipion any software related 
to electron microscopy data analysis. You will learn the basic Scipion 
architecture and to construct a fully functional plugin containing the 
main elements: protocols, viewers and wizards. The course is aimed at 
programmers, engineers, computational scientists, physicists, 
mathematicians, and in general to information technology related 
scientists with interest in integrating their ideas or software into 
Scipion. Especially welcome are those developers of software packages or 
independent software tools for Electron Microscopy. It is suggested that 
attendees come with their own computer in which they can install 
software development tools.

We look forward meeting you!

The Instruct Image Processing Center team

=====================================================================================

Blanca E. Benitez Silva

Centro Nacional de Biotecnología – CNB

C/Darwin 3, UAM - Campus de Cantoblanco

28049, Madrid, Spain

Telefono: +34 915854922

Fax: +34 913720112

Correo: bl...@cn... <mailto:bl...@cn...>

[scipion-users] MPI pyworkflow error

[Gabriel R. S. <gab...@ln...>]

Dear all,

I have been getting python errors related to MPI runs on different xmipp3 protocols (alternatively, I tested on relion MPI protocols, which runs correctly). The same protocols run without problems if using threads instead of MPI processes.

It seems like a python2-to-python3 encoding-related issue, as the representative example run traceback below:

00001:   RUNNING PROTOCOL -----------------
00002:   Hostname: node04
00003:   PID: 57882
00004:   pyworkflow: 3.0.1
00005:   plugin: xmipp3
00006:   currentDir: /home/ScipionUserData/projects/Test
00007:   workingDir: Runs/001782_XmippProtExtractParticles
00008:   runMode: Restart
00009:             MPI: 2
00010:         threads: 1
00011:    Starting at step: 1
00012:    Running steps
00013:   STARTED: extractMicrographStep, step 1, time 2020-08-17 13:51:05.684077
00014:   Extracting micrograph: Runs/001557_ProtImportMicrographs/extra/4k_10000001.mrcs
00015:   Sending environment to 1
00016:   'xmipp_coordinates_noisy_zones_filter' have failed for 4k_10000001.mrcs micrograph. We continue...
00017:   Sending environment to 1
00018:   Traceback (most recent call last):
00019:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 149, in run
00020:       self.step._run()  # not self.step.run() , to avoid race conditions
00021:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 239, in _run
00022:       resultFiles = self._runFunc()
00023:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 235, in _runFunc
00024:       return self._func(*self._args)
00025:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocol_particles.py", line 233, in extractMicrographStep
00026:       self._extractMicrograph(mic, *args)
00027:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_extract_particles.py", line 212, in _extractMicrograph
00028:       self.runJob('xmipp_transform_filter',
00029:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1337, in runJob
00030:       self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
00031:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 352, in runJob
00032:       runJobMPI(programName, params, self.comm, node,
00033:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 90, in runJobMPI
00034:       send("env=%s" % dumps(env), mpiComm, mpiDest, TAG_RUN_JOB+mpiDest)
00035:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 77, in send
00036:       raise Exception(str(result).encode(encoding='UTF-8'))
00037:   Exception: b"a bytes-like object is required, not 'str'"
00038:   Protocol failed: b"a bytes-like object is required, not 'str'"
00039:   FAILED: extractMicrographStep, step 1, time 2020-08-17 13:51:08.570543
00040:   ------------------- PROTOCOL FAILED (DONE 1/10)

The errors come from the:
00035:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 77, in send
00036:       raise Exception(str(result).encode(encoding='UTF-8'))

I tested adding ".encode(encoding='UTF-8')" part to the original code, which clearly did not solve the problem. From the traceback, the error seems to come from the string sent by the mpi communications, which I am not acquainted enough to solve.

On a related note, what is the recommended procedure for updating the scipion packages (not plugins)? I updated from the latest available from PyPI.

Best regards,

Gabriel R. Schleder
Universidade Federal do ABC (UFABC)
Laboratório Nacional de Nanotecnologia (LNNano/CNPEM)


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[scipion-users] MPI pyworkflow error

[Gabriel R. S. <gab...@ln...>]

Dear all,

I have been getting python errors related to MPI runs on different xmipp3 protocols (alternatively, I tested on relion MPI protocols, which runs correctly). The same protocols run without problems if using threads instead of MPI processes.

It seems like a python2-to-python3 encoding-related issue, as the representative example run traceback below:

00001:   RUNNING PROTOCOL -----------------
00002:   Hostname: node04
00003:   PID: 57882
00004:   pyworkflow: 3.0.1
00005:   plugin: xmipp3
00006:   currentDir: /home/ScipionUserData/projects/Test
00007:   workingDir: Runs/001782_XmippProtExtractParticles
00008:   runMode: Restart
00009:             MPI: 2
00010:         threads: 1
00011:    Starting at step: 1
00012:    Running steps
00013:   STARTED: extractMicrographStep, step 1, time 2020-08-17 13:51:05.684077
00014:   Extracting micrograph: Runs/001557_ProtImportMicrographs/extra/4k_10000001.mrcs
00015:   Sending environment to 1
00016:   'xmipp_coordinates_noisy_zones_filter' have failed for 4k_10000001.mrcs micrograph. We continue...
00017:   Sending environment to 1
00018:   Traceback (most recent call last):
00019:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 149, in run
00020:       self.step._run()  # not self.step.run() , to avoid race conditions
00021:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 239, in _run
00022:       resultFiles = self._runFunc()
00023:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 235, in _runFunc
00024:       return self._func(*self._args)
00025:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocol_particles.py", line 233, in extractMicrographStep
00026:       self._extractMicrograph(mic, *args)
00027:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_extract_particles.py", line 212, in _extractMicrograph
00028:       self.runJob('xmipp_transform_filter',
00029:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1337, in runJob
00030:       self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
00031:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 352, in runJob
00032:       runJobMPI(programName, params, self.comm, node,
00033:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 90, in runJobMPI
00034:       send("env=%s" % dumps(env), mpiComm, mpiDest, TAG_RUN_JOB+mpiDest)
00035:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 77, in send
00036:       raise Exception(str(result).encode(encoding='UTF-8'))
00037:   Exception: b"a bytes-like object is required, not 'str'"
00038:   Protocol failed: b"a bytes-like object is required, not 'str'"
00039:   FAILED: extractMicrographStep, step 1, time 2020-08-17 13:51:08.570543
00040:   ------------------- PROTOCOL FAILED (DONE 1/10)

The errors come from the:
00035:     File "/home/miniconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/mpi.py", line 77, in send
00036:       raise Exception(str(result).encode(encoding='UTF-8'))

I tested adding ".encode(encoding='UTF-8')" part to the original code, which clearly did not solve the problem. From the traceback, the error seems to come from the string sent by the mpi communications, which I am not acquainted enough to solve.

On a related note, what is the recommended procedure for updating the scipion packages (not plugins)? I updated from the latest available from PyPI.

Best regards,

Gabriel R. Schleder
Universidade Federal do ABC (UFABC)
Laboratório Nacional de Nanotecnologia (LNNano/CNPEM)


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Disclaimer: This email and its attachments may contain confidential and/or privileged information. Observe its content carefully and consider possible querying to the sender before copying, disclosing or distributing it. If you have received this email by mistake, please notify the sender and delete it immediately.

Re: [scipion-users] Class 2D averages picutres

[范宏成 <187...@16...>]

Thank you Dario!  I have tried it and it works.


Hongcheng Fan


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制
On 8/6/2020 22:36，Dario Saczko-Brack via scipion-users<sci...@li...> wrote：

Dear Hongcheng,


once you open the images in ImageJ / Fiji, you can also use "Save As - Image sequence" to save all images from the stack as individual images automatically.

Best

Dario




On 06.08.20 16:18, 范宏成 wrote:

Thank you Jose! I will try it according to your advice.  


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制
On 8/6/2020 22:16，Jose Miguel de la Rosa Trevin<del...@gm...> wrote：
Dear Hongcheng, 


You can also open each individual average image in ImageJ and save it, but it is true that it is not very user-friendly right now.


Best,
Jose Miguel




On Thu, Aug 6, 2020 at 3:31 PM 范宏成 <187...@16...> wrote:

OK, I got it. Thank you very much!   


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制
On 8/6/2020 21:28，Pablo Conesa<pc...@cn...> wrote：

Hi Hongcheng Fan,

You can play with the zoom value to increase the size of the averages. This should give you bigger images and better quality.


On 6/8/20 14:38, 范宏成 wrote:

Hi all,
I want to ask a simple question. Can Scipion create the selected class2d averages pictures for publication?  The linux screen capture tool will create the picture that loses some details. Does anyone have better ideas?
Thanks a lot
Hongcheng Fan


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制



_______________________________________________
scipion-users mailing list
sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - Madrid Scipion team
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users




_______________________________________________
scipion-users mailing list
sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] Class 2D averages picutres

[Dario Saczko-B. <dar...@go...>]

Dear Hongcheng,

once you open the images in ImageJ / Fiji, you can also use "Save As - 
Image sequence" to save all images from the stack as individual images 
automatically.

Best

Dario


On 06.08.20 16:18, 范宏成 wrote:
> Thank you Jose! I will try it according to your advice.
>
> 	
> 范宏成
> m18...@16...
>
> <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsmfc69753e7457a6e590754a7cd5492c0d.jpg&items=%5B%22m18717124574%40163.com%22%5D> 
>
> 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail81> 
> 定制
> On 8/6/2020 22:16，Jose Miguel de la Rosa 
> Trevin<del...@gm...> <mailto:del...@gm...> 
> wrote：
>
>     Dear Hongcheng,
>
>     You can also open each individual average image in ImageJ and save
>     it, but it is true that it is not very user-friendly right now.
>
>     Best,
>     Jose Miguel
>
>
>     On Thu, Aug 6, 2020 at 3:31 PM 范宏成 <187...@16...
>     <mailto:187...@16...>> wrote:
>
>         OK, I got it. Thank you very much!
>
>         	
>         范宏成
>         m18...@16...
>
>         <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsmfc69753e7457a6e590754a7cd5492c0d.jpg&items=%5B%22m18717124574%40163.com%22%5D>
>
>         签名由 网易邮箱大师
>         <https://mail.163.com/dashi/dlpro.html?from=mail81> 定制
>         On 8/6/2020 21:28，Pablo Conesa<pc...@cn...>
>         <mailto:pc...@cn...> wrote：
>
>             Hi Hongcheng Fan,
>
>             You can play with the zoom value to increase the size of
>             the averages. This should give you bigger images and
>             better quality.
>
>             On 6/8/20 14:38, 范宏成 wrote:
>>             Hi all,
>>             I want to ask a simple question. Can Scipion create the
>>             selected class2d averages pictures for publication?  The
>>             linux screen capture tool will create the picture that
>>             loses some details. Does anyone have better ideas?
>>             Thanks a lot
>>             Hongcheng Fan
>>
>>             	
>>             范宏成
>>             m18...@16...
>>
>>             <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsmfc69753e7457a6e590754a7cd5492c0d.jpg&items=%5B%22m18717124574%40163.com%22%5D>
>>
>>             签名由 网易邮箱大师
>>             <https://mail.163.com/dashi/dlpro.html?from=mail81> 定制
>>
>>
>>             _______________________________________________
>>             scipion-users mailing list
>>             sci...@li...  <mailto:sci...@li...>
>>             https://lists.sourceforge.net/lists/listinfo/scipion-users
>             -- 
>             Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>         _______________________________________________
>         scipion-users mailing list
>         sci...@li...
>         <mailto:sci...@li...>
>         https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] Class 2D averages picutres

[范宏成 <187...@16...>]

Thank you Jose! I will try it according to your advice.  


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制
On 8/6/2020 22:16，Jose Miguel de la Rosa Trevin<del...@gm...> wrote：
Dear Hongcheng, 


You can also open each individual average image in ImageJ and save it, but it is true that it is not very user-friendly right now.


Best,
Jose Miguel




On Thu, Aug 6, 2020 at 3:31 PM 范宏成 <187...@16...> wrote:

OK, I got it. Thank you very much!   


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制
On 8/6/2020 21:28，Pablo Conesa<pc...@cn...> wrote：

Hi Hongcheng Fan,

You can play with the zoom value to increase the size of the averages. This should give you bigger images and better quality.


On 6/8/20 14:38, 范宏成 wrote:

Hi all,
I want to ask a simple question. Can Scipion create the selected class2d averages pictures for publication?  The linux screen capture tool will create the picture that loses some details. Does anyone have better ideas?
Thanks a lot
Hongcheng Fan


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制



_______________________________________________
scipion-users mailing list
sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - Madrid Scipion team
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] Class 2D averages picutres

[Jose M. de la R. T. <del...@gm...>]

Dear Hongcheng,

You can also open each individual average image in ImageJ and save it, but
it is true that it is not very user-friendly right now.

Best,
Jose Miguel


On Thu, Aug 6, 2020 at 3:31 PM 范宏成 <187...@16...> wrote:

> OK, I got it. Thank you very much!
>
> 范宏成
> m18...@16...
>
> <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsmfc69753e7457a6e590754a7cd5492c0d.jpg&items=%5B%22m18717124574%40163.com%22%5D>
> 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail81> 定制
> On 8/6/2020 21:28，Pablo Conesa<pc...@cn...> <pc...@cn...>
> wrote：
>
> Hi Hongcheng Fan,
>
> You can play with the zoom value to increase the size of the averages.
> This should give you bigger images and better quality.
> On 6/8/20 14:38, 范宏成 wrote:
>
> Hi all,
> I want to ask a simple question. Can Scipion create the selected class2d
> averages pictures for publication?  The linux screen capture tool will
> create the picture that loses some details. Does anyone have better ideas?
> Thanks a lot
> Hongcheng Fan
>
> 范宏成
> m18...@16...
>
> <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsmfc69753e7457a6e590754a7cd5492c0d.jpg&items=%5B%22m18717124574%40163.com%22%5D>
> 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail81> 定制
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] Class 2D averages picutres

[范宏成 <187...@16...>]

OK, I got it. Thank you very much!   


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制
On 8/6/2020 21:28，Pablo Conesa<pc...@cn...> wrote：

Hi Hongcheng Fan,

You can play with the zoom value to increase the size of the averages. This should give you bigger images and better quality.


On 6/8/20 14:38, 范宏成 wrote:

Hi all,
I want to ask a simple question. Can Scipion create the selected class2d averages pictures for publication?  The linux screen capture tool will create the picture that loses some details. Does anyone have better ideas?
Thanks a lot
Hongcheng Fan


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制



_______________________________________________
scipion-users mailing list
sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - Madrid Scipion team