Search found 17 matches

by acnavasolive
Fri Sep 21, 2018 5:05 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Ok, we have understand what was the cause of it: My $PATH was something like: /home/andrea/anaconda3/bin :/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/local/cuda-8.0/bin:/usr/local/cuda-8.0/lib64:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/j...
by acnavasolive
Fri Sep 21, 2018 4:07 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Current conda install: platform : linux-64 conda version : 4.3.30 conda is private : False conda-env version : 4.3.30 conda-build version : not installed python version : 2.7.13.final.0 requests version : 2.14.2 root environment : /home/andrea/anaconda3 (writable) default environment : /home/andrea...
by acnavasolive
Thu Sep 20, 2018 10:38 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

It's finally installed!

I tried with the GCC4.8 and it worked!

Thank you so much!!
by acnavasolive
Thu Sep 20, 2018 8:09 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

I have trying to focus on those errors too. As all these errors mention the GLIBCXX_3.4.21 and GLIBCXX_3.4.20, /home/andrea/neuron/iv/x86_64/lib/libIVhines.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_strin...
by acnavasolive
Wed Sep 19, 2018 11:44 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Ok. I have now tried with the git version, compiling it with different options. These are my results: Successfully installed: ./configure --prefix=/home/andrea/neuron/neuronbin --with-iv=/home/andrea/neuron/iv ./configure --prefix=/home/andrea/neuron/neuronbin --with-iv=/home/andrea/neuron/iv --with...
by acnavasolive
Wed Sep 19, 2018 7:31 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

I installed them but still same errors. I have now been focusing on those undefined references previous to the compilation error, such: ./.libs/libnrniv.so: undefined reference to `vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' and, as y...
by acnavasolive
Tue Sep 18, 2018 10:00 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Same errors happen if I repeat with:

Code: Select all

$ make distclean
$ ./configure --prefix=`pwd` --with-paranrn --with-iv=$HOME/neuron/iv --with-nrnpython=/home/andrea/anaconda3/envs/py27/bin/python --disable-rx3d >& /home/andrea/Escritorio/configure.txt
$ make -j install >& /home/andrea/Escritorio/make.txt
by acnavasolive
Tue Sep 18, 2018 8:44 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Oh! I haven't noticed that either. $ base="build-essential libreadline-dev libx11-dev libxext-dev libncurses-dev zlib1g-dev" $ sudo apt install $base Leyendo lista de paquetes... Hecho Creando árbol de dependencias Leyendo la información de estado... Hecho Nota, seleccionando «libncurses5-dev» en lu...
by acnavasolive
Tue Sep 18, 2018 6:41 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

I am a beginner with OpenMPI, so I can't really do much with it right now, but I have been trying to check if it worked ok running easy examples. Here it is what I did: $ mpirun -np 4 mpi_hello_world -------------------------------------------------------------------------- [[3509,1],0]: A high-perf...
by acnavasolive
Tue Sep 18, 2018 4:15 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

No... it fails again, same errors.
Here there are the resulted files from the >&:
https://www.dropbox.com/sh/ifvzb94sgn0z ... pEgja?dl=0

There is also information about my current version of OpenMPI in ompi_info.txt
by acnavasolive
Mon Sep 17, 2018 11:43 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

I installed mpich with: sudo apt install mpich and I have just uninstalled it with: sudo apt remove mpich To install it again, I did as you said: $ sudo apt install libopenmpi-dev Leyendo lista de paquetes... Hecho Creando arbol de dependencias Leyendo la informacion de estado... Hecho libopenmpi-de...
by acnavasolive
Mon Sep 17, 2018 5:39 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Hi! Yes, all mpicc, mpic++, mpicxx and mpiexec are in /usr/bin/ Also, the interviews installation was ok, since $HOME/neuron/iv/x86_64/bin/idraw worked. There was just an error message: "invalid font name -*-Symbol-*-12-*-*-*-*-*-*-*, substituting fixed font", but except for that, it was alright. Th...
by acnavasolive
Fri Sep 14, 2018 4:19 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

I downloaded the 7.6 version and again, there was no problems with the iv installation, and the same errors when I tried to compile NEURON: collect2: error: ld returned 1 exit status Makefile:746: recipe for target 'nrniv' failed make[3]: *** [nrniv] Error 1 make[3]: Leaving directory '/home/andrea/...
by acnavasolive
Wed Sep 12, 2018 7:34 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 9123

Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Hi everyone! I want to use the parallel version of NEURON, so I uninstalled my old one to start from the beginning. I have an Ubuntu 16.04. I started installing MPICH. Then, following the main instructions for IV: # Compiling iv: $ ./configure --prefix=`pwd` $ make $ make install and then for NEURON...