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Broken NEST installation, fatal SLIStartup [resolved] #749

rpgowers opened this issue Jun 12, 2017 · 3 comments

Broken NEST installation, fatal SLIStartup [resolved] #749

rpgowers opened this issue Jun 12, 2017 · 3 comments


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@rpgowers rpgowers commented Jun 12, 2017

[Issue probably resolved]
Consistently achieving broken NEST installation.

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

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 install

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/", line 329, in run
  File "/home/robert/anaconda/lib/python2.7/site-packages/nose/", 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:

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.

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 Broken NEST installation, fatal SLIStartup Broken NEST installation, fatal SLIStartup [resolved] Jun 12, 2017
@rpgowers rpgowers closed this Jun 12, 2017
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@muffgaga 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 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 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

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