Failing to sudo apt-get install nest

[IlaCar]

Hello,

I have Ubuntu 20.04.6 LTS and I am trying to install NEST.
I follow the instructions here:
https://nest-simulator.readthedocs.io/en/stable/installation/user.html#user-install

I run:

sudo add-apt-repository ppa:nest-simulator/nest
sudo apt-get update

without problems but when I then run:

sudo apt-get install nest

I get:

Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
gir1.2-goa-1.0 libxmlb1
Use 'sudo apt autoremove' to remove them.
The following NEW packages will be installed:
nest
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/2,104 B of archives.
After this operation, 9,216 B of additional disk space will be used.
Selecting previously unselected package nest.
(Reading database ... 204775 files and directories currently installed.)
Preparing to unpack .../nest_3.6-2ubuntu1ppa1-1512202403260432ubuntu20.04.1_amd64.deb ...
Unpacking nest (3.6-2ubuntu1ppa1-1512202403260432ubuntu20.04.1) ...
Setting up nest (3.6-2ubuntu1ppa1-1512202403260432ubuntu20.04.1) ...
chmod: cannot access '/usr/lib/nest': No such file or directory
dpkg: error processing package nest (--configure):
installed nest package post-installation script subprocess returned error exit status 1
Errors were encountered while processing:
nest
E: Sub-process /usr/bin/dpkg returned an error code (1)

and indeed /usr/lib/nest doen't exist.

Do you have any suggestions?

Thank you.

Best regards,

Ilaria

[jessica-mitchell]

@steffengraber can you take a look at this?

[TesseTiemens]

I am also running into this issue, similarly on ubuntu server 20.04 LTS. I tried manually creating /usr/lib/nest before reinstalling, but, even though the install completed, the folder remained empty, and running nest returns command not found. A quick download and inspection of the .deb shows that in data.tar.xz only usr/share/doc is included, unlike the 22.04 package, which includes all the files

[steffengraber]

It is strange that the packages are still built without errors. I will take a closer look at the issue.

[steffengraber]

A new package of the current NEST v3.7 for Ubuntu 20.04 is now available. @IlaCar @TesseTiemens It would be nice if you could test and give a short feedback here.

[TesseTiemens]

Thanks! I got it it to install now @steffengraber. However, when trying to run pyNest, the kernel crashes due to the fact that pyNest has been built against hdf5 1.14.2, whereas the current version of hdf5 in the ubuntu repo is 1.10.4. This could be an issue on my side, as I upgraded the h5py package yesterday due to similar issues when building from source (which did make it work), but as h5py is supposed to just wrap hdf5, I don't think so. I have attached logs for convenience: testnestlog.txt. Thanks in advance!

[IlaCar]

Hello.

So I tried to install it, and it seemed to have worked but when I try to import nest from python it crashed.
@steffengraber , you can see the error message in the attached file.

Thank you for your help.

CoreDumped.txt

[steffengraber]

I am not able to reproduce it on a clean Ubuntu system. Have you possibly installed hdf5 with another installation tool like pip or conda.

[steffengraber]

However, it is probably also due to a pre-installed h5py version.

[steffengraber]

@IlaCar @TesseTiemens To test the loaded libraries, please execute the following: "ldd /usr/bin/nest". Can you then post the result here?

[TesseTiemens]

@steffengraber Sorry this took so long, but here you go
lddout.txt

[IlaCar]

I tried to install it also on another machine with the same ubuntu distribution and I get the same crash when I import nest from python. About the ldd /usr/bin/nest, here you have the output:

    linux-vdso.so.1 (0x00007ffc3b4ae000)
    libsli_readline.so.3 => /usr/lib/nest/libsli_readline.so.3 (0x00007ff9f0468000)
    libltdl.so.7 => /lib/x86_64-linux-gnu/libltdl.so.7 (0x00007ff9f0447000)
    libmpi_cxx.so.40 => /lib/x86_64-linux-gnu/libmpi_cxx.so.40 (0x00007ff9f0429000)
    libmpi.so.40 => /lib/x86_64-linux-gnu/libmpi.so.40 (0x00007ff9f0304000)
    libhdf5_serial.so.103 => /lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007ff9eff87000)
    libsz.so.2 => /lib/x86_64-linux-gnu/libsz.so.2 (0x00007ff9eff80000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007ff9eff64000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007ff9eff5e000)
    libhdf5_cpp.so.103 => /lib/x86_64-linux-gnu/libhdf5_cpp.so.103 (0x00007ff9efee1000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007ff9efd92000)
    libsli.so.3 => /usr/lib/nest/libsli.so.3 (0x00007ff9efc21000)
    libgsl.so.23 => /lib/x86_64-linux-gnu/libgsl.so.23 (0x00007ff9ef9a3000)
    libgslcblas.so.0 => /lib/x86_64-linux-gnu/libgslcblas.so.0 (0x00007ff9ef961000)
    libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00007ff9ef91f000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007ff9ef8fc000)
    libreadline.so.8 => /lib/x86_64-linux-gnu/libreadline.so.8 (0x00007ff9ef8ac000)
    libncurses.so.6 => /lib/x86_64-linux-gnu/libncurses.so.6 (0x00007ff9ef883000)
    libtinfo.so.6 => /lib/x86_64-linux-gnu/libtinfo.so.6 (0x00007ff9ef851000)
    libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007ff9ef66f000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007ff9ef654000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ff9ef462000)
    libopen-rte.so.40 => /lib/x86_64-linux-gnu/libopen-rte.so.40 (0x00007ff9ef3a8000)
    libopen-pal.so.40 => /lib/x86_64-linux-gnu/libopen-pal.so.40 (0x00007ff9ef2fa000)
    libhwloc.so.15 => /lib/x86_64-linux-gnu/libhwloc.so.15 (0x00007ff9ef2a7000)
    libaec.so.0 => /lib/x86_64-linux-gnu/libaec.so.0 (0x00007ff9ef29e000)
    /lib64/ld-linux-x86-64.so.2 (0x00007ff9f0e9e000)
    libevent-2.1.so.7 => /lib/x86_64-linux-gnu/libevent-2.1.so.7 (0x00007ff9ef248000)
    libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007ff9ef243000)
    libevent_pthreads-2.1.so.7 => /lib/x86_64-linux-gnu/libevent_pthreads-2.1.so.7 (0x00007ff9ef23e000)
    libudev.so.1 => /lib/x86_64-linux-gnu/libudev.so.1 (0x00007ff9ef20f000)