Re: [scipion-users] scipion installed, now what?

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

Hi Patrick,

Find some clarification below, on top of the suggestions from Kyle.




On Tue, Apr 24, 2018 at 11:21 PM, Patrick Goetz <pg...@ma...>
wrote:

> Hi -
>
> I've managed to install Scipion (with --no-opencv) on Ubuntu 18.04.
>
> Missing from the instructions is the need for this package:
> libreadline-dev
>
> The readline.h header file is needed for the sqlite compilation.
>
> Also, the file ~/scipion/config/scipion.conf required several
> modifications to MPI, CUDA, and Matlab paths.
>
> I also installed EMAN2 using:  ./scipion install --no-xmipp eman-2.12
>
> Now unfortunately I have a number of questions.
>
> 1.
> I cloned the git repo into /root, and now everything is installed under
>
>    /root/scipion
>
> How should I make the software available to users?  It seems that source
> and binaries are heavily intertwined here.  The scipion command is in
> /root/scipion, but everything else is installed in /root/scipion/software?
>
> Presumably this also means setting some environment variables (at least a
> path)?
>

It is true that source and binaries are intertwined now, we want to improve
this in the future.
We have designed scipion to avoid modifying you environment...so, user only
need to point to the scipion python script from the installation folder.
Two possibilities are:
a) Define an alias to that: alias scipion='/path/to/scipion/scipion'
b) Add the /path/to/scipion to the user PATH environment variable
All the environment settings for each process are done on the fly, this
means that will not interfere between packages or with the system
libraries.

>
> 2.
> I tried running one of the small tests (scipion tests
> em.workflows.test_workflow_spiderMDA), but this failed with a couple of
> python runtime errors.  These look like internal errors, but could this
> have something to do with the fact that I'm trying to run the test from a
> (non-graphical) terminal as root (because of the install location)?
>
> As Kyle pointed out, the error is a missing binary file. My guess would be
that you haven't installed spider (scipion install spider --no-xmipp) and
you are trying to run a test that use it.
The test data sets are written in /path/to/scipion/data/tests, so, if this
folder belong to root, you will need to run the tests with root or give
user access. Additionally, the projects that are
generated by each test go to the same data folder of each user
(~/ScipionUserData by default)

Hope this helps
Best,
Jose Miguel


>
> Fetching files of dataset "hemoglobin_mda"...
> #################################################
> ** Running command: 'python /root/scipion/scipion runprotocol
> pw_protocol_run.py "/root/ScipionUserData/projects/TestSpiderConvert"
> "Runs/000002_ProtImportParticles/logs/run.db" 2'
>
> Scipion v1.2 (2018-04-02) Caligula
>
> >>>>> python  /root/scipion/pyworkflow/apps/pw_protocol_run.py
> "/root/ScipionUserData/projects/TestSpiderConvert"
> "Runs/000002_ProtImportParticles/logs/run.db" "2"
> stackFn:  /root/ScipionUserData/projects/TestSpiderConvert/stack.stk
> ** Running command: /root/scipion/software/em/spid
> er-21.13/spider/bin/spider_linux_mp_intel64  stk @cp_endian
> /bin/sh: 1: /root/scipion/software/em/spider-21.13/spider/bin/spider_linux_mp_intel64:
> not found
> [   FAILED ] TestSpiderConvert.test_convert
>
> Traceback (most recent call last):
>   File "/root/scipion/software/lib/python2.7/unittest/case.py", line 329,
> in run
>     testMethod()
>   File "/root/scipion/pyworkflow/tests/em/workflows/test_workflow_spiderMDA.py",
> line 62, in test_convert
>     writeSetOfImages(protImport.outputParticles, stackFn, selFn)
>   File "/root/scipion/pyworkflow/em/packages/spider/convert.py", line 86,
> in writeSetOfImages
>     convertEndian(stackFn, imgSet.getSize())
>   File "/root/scipion/pyworkflow/em/packages/spider/convert.py", line
> 103, in convertEndian
>     }, cwd=fnDir)
>   File "/root/scipion/pyworkflow/em/packages/spider/spider.py", line 177,
> in runTemplate
>     runScript(outputScript, ext, log, cwd)
>   File "/root/scipion/pyworkflow/em/packages/spider/spider.py", line 183,
> in runScript
>     runJob(log, SPIDER, args, env=dict(environment), cwd=cwd)
>   File "/root/scipion/pyworkflow/utils/process.py", line 51, in runJob
>     return runCommand(command, env, cwd)
>   File "/root/scipion/pyworkflow/utils/process.py", line 65, in runCommand
>     check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
> env=env, cwd=cwd)
>   File "/root/scipion/software/lib/python2.7/subprocess.py", line 186, in
> check_call
>     raise CalledProcessError(retcode, cmd)
> CalledProcessError: Command '/root/scipion/software/em/spi
> der-21.13/spider/bin/spider_linux_mp_intel64  stk @cp_endian' returned
> non-zero exit status 127
> ('Creating project at: ', '/root/ScipionUserData/project
> s/TestSpiderWorkflow/project.sqlite')
> >>>> python /root/scipion/scipion testdata --download hemoglobin_mda
>
> Scipion v1.2 (2018-04-02) Caligula
>
> >>>>> python  scripts/sync_data.py --download hemoglobin_mda
> Selected datasets: hemoglobin_mda
> Local copy of dataset hemoglobin_mda detected.
> Checking for updates...
> Regenerating local MANIFEST...
> Verifying MD5s...
> ...done. Updated files: 0
> ** Running command: 'python /root/scipion/scipion runprotocol
> pw_protocol_run.py "/root/ScipionUserData/projects/TestSpiderWorkflow"
> "Runs/000002_ProtImportParticles/logs/run.db" 2'
>
> Scipion v1.2 (2018-04-02) Caligula
>
> >>>>> python  /root/scipion/pyworkflow/apps/pw_protocol_run.py
> "/root/ScipionUserData/projects/TestSpiderWorkflow"
> "Runs/000002_ProtImportParticles/logs/run.db" "2"
> ** Running command: 'python /root/scipion/scipion runprotocol
> pw_protocol_run.py "/root/ScipionUserData/projects/TestSpiderWorkflow"
> "Runs/000070_SpiderProtFilter/logs/run.db" 70'
>
> Scipion v1.2 (2018-04-02) Caligula
>
> >>>>> python  /root/scipion/pyworkflow/apps/pw_protocol_run.py
> "/root/ScipionUserData/projects/TestSpiderWorkflow"
> "Runs/000070_SpiderProtFilter/logs/run.db" "70"
>
> >>> ERROR running protocol scipion - filter particles
> [   FAILED ] TestSpiderWorkflow.test_mdaWorkflow
>
> Traceback (most recent call last):
>   File "/root/scipion/software/lib/python2.7/unittest/case.py", line 329,
> in run
>     testMethod()
>   File "/root/scipion/pyworkflow/tests/em/workflows/test_workflow_spiderMDA.py",
> line 104, in test_mdaWorkflow
>     self.launchProtocol(protFilter)
>   File "/root/scipion/pyworkflow/tests/tests.py", line 106, in
> launchProtocol
>     raise Exception("ERROR: Protocol not finished")
> Exception: ERROR: Protocol not finished
>
> [==========] run 2 tests (46.593 secs)
> [  FAILED  ] 2 tests
> [  PASSED  ] 0 tests
>
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