[scipion-users] scipion installed, now what?

[Patrick G. <pg...@ma...>]

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)?

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)?


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/spider-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/spider-21.13/spider/bin/spider_linux_mp_intel64 
  stk @cp_endian' returned non-zero exit status 127
('Creating project at: ', 
'/root/ScipionUserData/projects/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