scipion-users

[scipion-users] config looking for mpi.h in wrong location on Ubuntu?

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

Hi -

I'm trying to configure Scipion cloned from the git repo on an Ubuntu 
18.04 machine and get the following error message:

-----------------
Checking paths in /root/scipion/config/scipion.conf ...
   Path to MPI_LIBDIR (/usr/lib64/mpi/gcc/openmpi/lib) should exist but 
it doesn't.
   Path to MPI_INCLUDE (/usr/lib64/mpi/gcc/openmpi/include) should exist 
but it doesn't.
   Cannot find file: /usr/lib64/mpi/gcc/openmpi/include/mpi.h
Errors found.
-----------------

I think it's looking for the MPI header file in the wrong location for 
Ubuntu?  It's here:

   /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h


Also, minor point.  The installation instructions have a list of 
dependencies that need to be installed which includes "libreadline6". 
There's no installation candidate for this, I think it needs to be 
lib64readline6-dev instead.

Re: [scipion-users] config looking for mpi.h in wrong location on Ubuntu?

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

Hi Patrick,

We have default values for the paths of several dependencies, like MPI 
or JAVA.


Our current default values do not match Ubuntu paths.

At this point you can:

1.- run:  ./scipion config --overwrite

This tries to guess those paths, and in Ubuntu 14 --> 16 works fine. 
Sorry never tried on ubuntu 18!

2.- Manually, edit the config file: this file can be found at 
<SCIPION_HOME>/config/scipion.conf


Regarding the libreadline6,....could this be a change related to ubuntu 18?

To me, it seems that libreadline6 hasn't made it to bionic, yet?:

<https://packages.ubuntu.com/trusty/libreadline6,%20yet>


Whereas, the dev version has made it!

<https://packages.ubuntu.com/trusty/libreadline6-dev>



I have added a note in our wiki!! Thanks for the feedback!

Patrick, probably you are the first one to install Scipion in Ubuntu 18. 
Please let us know how it goes, whether if it goes right  and more 
importantly if something does wrong.

All the best, Pablo.

On 18/04/18 19:40, Patrick Goetz wrote:
> Hi -
>
> I'm trying to configure Scipion cloned from the git repo on an Ubuntu 
> 18.04 machine and get the following error message:
>
> -----------------
> Checking paths in /root/scipion/config/scipion.conf ...
>   Path to MPI_LIBDIR (/usr/lib64/mpi/gcc/openmpi/lib) should exist but 
> it doesn't.
>   Path to MPI_INCLUDE (/usr/lib64/mpi/gcc/openmpi/include) should 
> exist but it doesn't.
>   Cannot find file: /usr/lib64/mpi/gcc/openmpi/include/mpi.h
> Errors found.
> -----------------
>
> I think it's looking for the MPI header file in the wrong location for 
> Ubuntu?  It's here:
>
>   /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h
>
>
> Also, minor point.  The installation instructions have a list of 
> dependencies that need to be installed which includes "libreadline6". 
> There's no installation candidate for this, I think it needs to be 
> lib64readline6-dev instead.
>
> ------------------------------------------------------------------------------ 
>
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] config looking for mpi.h in wrong location on Ubuntu?

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

Hi Pablo -

Thanks very much for your help with this.  I will try the config 
suggestions you provided; meanwhile, regarding libreadline6:


On 04/19/2018 12:49 AM, Pablo Conesa wrote:
> To me, it seems that libreadline6 hasn't made it to bionic, yet?:
> 


My bad; I should have checked the Xenial (16.04) package list first. 
However, it doesn't look like libreadline6 is going to make it into 
Bionic (18.04).  Here is the related package list obtained by searching 
the package directories on packages.ubuntu.com for "libreadline":

   Package libreadline-dev  [this is version 7]

   Package libreadline5

   Package libreadline5-dbg

   Package libreadline6-dev

   Package libreadline7

   Package libreadline7-dbg


Looks like they went to version 7, while retaining version 5, but not 6. 
  Is this a compile time or a run time dependency?  If compile time, one 
would usually need the -dev  version anyway.

Re: [scipion-users] config looking for mpi.h in wrong location on Ubuntu?

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

Hi Patrick, to be honest , I don't know how libreadline6 is used,,, I 
would say that since it is not _dev we don't need it at compile time but 
at runtime

But I might be wrong. Try dev_7 ? Will it work?


On 19/04/18 15:59, Patrick Goetz wrote:
> Hi Pablo -
>
> Thanks very much for your help with this.  I will try the config 
> suggestions you provided; meanwhile, regarding libreadline6:
>
>
> On 04/19/2018 12:49 AM, Pablo Conesa wrote:
>> To me, it seems that libreadline6 hasn't made it to bionic, yet?:
>>
>
>
> My bad; I should have checked the Xenial (16.04) package list first. 
> However, it doesn't look like libreadline6 is going to make it into 
> Bionic (18.04).  Here is the related package list obtained by 
> searching the package directories on packages.ubuntu.com for 
> "libreadline":
>
>   Package libreadline-dev  [this is version 7]
>
>   Package libreadline5
>
>   Package libreadline5-dbg
>
>   Package libreadline6-dev
>
>   Package libreadline7
>
>   Package libreadline7-dbg
>
>
> Looks like they went to version 7, while retaining version 5, but not 
> 6.  Is this a compile time or a run time dependency?  If compile time, 
> one would usually need the -dev  version anyway.
>
>
> ------------------------------------------------------------------------------ 
>
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

[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

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

[Kyle D. <kyl...@ep...>]

Hi Patrick,

(I'm not a Scipion dev but have some suggestions.)


On 04/24/2018 11:21 PM, Patrick Goetz wrote:
>
>
> 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)?
>
>
>   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
>
>

Actually it looks like that error is coming from a call to a system 
command and is not directly caused by anything in Python. Exit status 
127 is returned when either 1) the file does not exist or 2) the file 
does not have execute permission for your user or group. Could you 
verify that spider_linux_mp_intel64 exists and has execute permissions 
set? You can use the command

ls -l /root/scipion/software/em/spider-21.13/spider/bin/ | grep 
spider_linux_mp_intel64

and check that an 'x' exists for the user/group? (I assume it's the root 
user.)

I would also think that you should give everyone read/write access to 
the ScipionUserData folder since you want multiple users to have access 
to it; this may not be true in your case since it is buried inside a 
folder belonging to root.

Finally, there are log files for stdout and stderr that are written to 
the ScipionUserData folder when you run a workflow or test. In my 
experience you can get more information about any errors from these files.

Hope this helps,
Kyle

-- 
Kyle M. Douglass, PhD
Post-doctoral researcher
The Laboratory of Experimental Biophysics
EPFL, Lausanne, Switzerland
http://kmdouglass.github.io
http://leb.epfl.ch

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

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

Hi Kyle

On 04/25/2018 01:31 AM, Kyle Douglass wrote:
> verify that spider_linux_mp_intel64 exists and has execute permissions 
> set? You can use the command
> 
> ls -l /root/scipion/software/em/spider-21.13/spider/bin/ | grep 
> spider_linux_mp_intel64
> 

This was the problem.  I didn't notice that the spider package needs to 
be installed separately even though it's right there in the 
documentation.  Now the test works as advertised.

Thanks for your help with this.

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
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

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

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

On 04/25/2018 02:07 AM, Jose Miguel de la Rosa Trevin wrote:
> 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.
> 

That's very nice, actually.  So all I need to do is move the Scipion 
folder to a publicly accessible location (e.g. /opt/scipion or 
/usr/local/scipion), make sure the users can find the scipion command, 
and make sure that the read/write/execute permissions are properly set?

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

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

The users only need read/execution permissions and a way to find the
scipion script inside the installation folder.

On Wed, Apr 25, 2018 at 3:48 PM, Patrick Goetz <pg...@ma...>
wrote:

>
> On 04/25/2018 02:07 AM, Jose Miguel de la Rosa Trevin wrote:
>
>> 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.
>>
>>
> That's very nice, actually.  So all I need to do is move the Scipion
> folder to a publicly accessible location (e.g. /opt/scipion or
> /usr/local/scipion), make sure the users can find the scipion command, and
> make sure that the read/write/execute permissions are properly set?
>
>
>
>
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

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

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

On 04/25/2018 09:06 AM, Jose Miguel de la Rosa Trevin wrote:
> The users only need read/execution permissions and a way to find the 
> scipion script inside the installation folder.
> 

What about the ScipionUserData folder -- does this just need to be 
located in parallel to scipion, or is there a way I can put scipion into 
/opt and ScipionUserData in /var or /home/per_user?  And presumably 
users would need permission to write to this folder?

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

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

ScipionUserData is a folder independent from the scipion installation
folder and each user has its own ScipionUserData...by default it goes to
~/ScipionUserData.

On Wed, Apr 25, 2018 at 4:15 PM, Patrick Goetz <pg...@ma...>
wrote:

> On 04/25/2018 09:06 AM, Jose Miguel de la Rosa Trevin wrote:
>
>> The users only need read/execution permissions and a way to find the
>> scipion script inside the installation folder.
>>
>>
> What about the ScipionUserData folder -- does this just need to be located
> in parallel to scipion, or is there a way I can put scipion into /opt and
> ScipionUserData in /var or /home/per_user?  And presumably users would need
> permission to write to this folder?
>
>
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