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Broken NEST installation, fatal SLIStartup [resolved] #749

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rpgowers opened this Issue Jun 12, 2017 · 3 comments

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rpgowers commented Jun 12, 2017

[Issue probably resolved]
Description
Consistently achieving broken NEST installation.

Version
I am trying to install NEST 2.12.0 on Ubuntu 16.04 with Python 2.7.11 (anaconda version 4.3.21)

Steps
I installed NEST with the following steps,
cmake -DCMAKE_INSTALL_PREFIX:PATH=../nest-install -Dwith-mpi=ON -Dwith-readline=OFF -DCMAKE_C_COMPILER=cc -DCMAKE_CXX_COMPILER=c++ -DMPI_C_COMPILER=mpicc -DMPI_CXX_COMPILER=mpicxx ../nest-simulator
make
make install

Results
installcheck is mostly successful, except for one SLI failure and being unable to run PyNEST tests. These errors read as follows,

Running  ../nest-install/bin/sli ../nest-install/share/doc/nest/mpitests/issue-281.sli
SLI v2.12.0 (C) 2004 The NEST Initiative
N_MPI: 1
N_MPI: 2
N_MPI: 4

Jun 12 09:24:31 unittest::assert_or_die [Fatal]: 
    Assertion failed: unittest::distributed_pass_or_die: collected results.

Jun 12 09:24:31 unittest::assert_or_die [Fatal]: 
    Exiting with code 1
Traceback (most recent call last):
  File "/home/robert/anaconda/lib/python2.7/unittest/case.py", line 329, in run
    testMethod()
  File "/home/robert/anaconda/lib/python2.7/site-packages/nose/failure.py", line 42, in runTest
    raise self.exc_class(self.exc_val)
OSError: No such file /home/robert/repositories/nest-install/lib/python2.7/site-packages/nest/tests


However, when I try to run nest I am given the following error message (full output here:
output.txt)

Jun 12 09:33:34 SLIStartup [Fatal]: 
    Your NEST installation seems broken. 

Additional Info
Sometimes when I have reinstalled NEST this error message does not appear at first, but appears later when trying to run nest later. Furthermore, attempting to import nest in Python results in "no module named nest". I am not sure if this is part of the same problem or a separate issue.

EDIT
Issue seems to be resolved by using absolute rather than relative paths in the cmake step, ie
cmake -DCMAKE_INSTALL_PREFIX:PATH=~/repositories/nest-install -Dwith-mpi=ON -Dwith-readline=OFF -DCMAKE_C_COMPILER=cc -DCMAKE_CXX_COMPILER=c++ -DMPI_C_COMPILER=mpicc -DMPI_CXX_COMPILER=mpicxx ~/repositories/nest-simulator

@rpgowers rpgowers changed the title from Broken NEST installation, fatal SLIStartup to Broken NEST installation, fatal SLIStartup [resolved] Jun 12, 2017

@rpgowers rpgowers closed this Jun 12, 2017

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muffgaga Jun 19, 2017

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IMHO the path provided to CMAKE_INSTALL_PREFIX:PATH should be automatically canonicalized to a absolute path (using realpath or similar); it's a quite common "mistake" to provide relative installation paths.

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muffgaga commented Jun 19, 2017

IMHO the path provided to CMAKE_INSTALL_PREFIX:PATH should be automatically canonicalized to a absolute path (using realpath or similar); it's a quite common "mistake" to provide relative installation paths.

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heplesser Jun 29, 2017

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@muffgaga Your suggestion is plausible, but as a comment to a closed issue, there is a high risk it will get lost. Could you open a new issue or, even better, create a pull request implementing your suggestion?

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heplesser commented Jun 29, 2017

@muffgaga Your suggestion is plausible, but as a comment to a closed issue, there is a high risk it will get lost. Could you open a new issue or, even better, create a pull request implementing your suggestion?

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muffgaga Jul 10, 2017

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Done, cf. #783.

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muffgaga commented Jul 10, 2017

Done, cf. #783.

muffgaga added a commit to electronicvisions/nest-simulator that referenced this issue Aug 2, 2017

jougs added a commit that referenced this issue Aug 3, 2017

Merge pull request #796 from electronicvisions/use_abspath_for_nest_p…
…refix

Use absolute path for compile-time NEST_PREFIX (cf. #749)
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