4/18/2023 0 Comments Anaconda virtual environment![]() ![]() memacs/.libs/libmemacs.so: undefined reference to error: ld returned 1 exit status memacs/.libs/libmemacs.so: undefined reference to. sundials/.libs/libsundials.so: undefined reference to `MPI_Allreduce' sundials/.libs/libsundials.so: undefined reference to `MPI_Comm_size' sundials/.libs/libsundials.so: undefined reference to `ompi_mpi_long' sundials/.libs/libsundials.so: undefined reference to `ompi_mpi_double' sundials/.libs/libsundials.so: undefined reference to `nrnmpi_comm' sundials/.libs/libsundials.so: undefined reference to `ompi_mpi_op_max' sundials/.libs/libsundials.so: undefined reference to `ompi_mpi_op_min' sundials/.libs/libsundials.so: undefined reference to `ompi_mpi_op_sum' readline/.libs/libreadline.so -lncurses -ltinfo -lm -ldl -pthread -Wl,-rpath -Wl,/home/marcelo/neuron/nrn-7.7/x86_64/lib -Wl,-rpath -Wl,/usr/local/iv/x86_64/lib -Wl,-rpath -Wl,/home/marcelo/anaconda3/envs/modals_env/lib nrnpython/.libs/libnrnpython.so -L/home/marcelo/anaconda3/envs/modals_env/lib -lpython2.7 -lpthread -lutil. mesch/.libs/libmeschach.so /usr/local/iv/x86_64/lib/libIVhines.so. Last part of the errors is shown below:Ĭode: Select all libtool: link: g++ -pthread -g -O2 -o. If Anaconda is already installed and added to PATH, I get many errors after ‘make –j’ for neuron (but nor for iv). If I install anaconda after this, create a virtual environment and try to run neuron inside it, it stops working again.ģ.Ĝompiling neuron from source (with Anaconda previously installed and added to path) As I said, I would like to run it inside a virtual environment. This is the only situation where it actually works, but it runs with python3 and without any virtual environment. I have also tried to compile neuron from source following these instructions (. ![]() "/home/marcelo/anaconda3/etc/profile.d/conda.sh"Įxport PATH="/home/marcelo/anaconda3/bin:$PATH"Įxport PATH=$PATH:/usr/local/nrn/x86_64/binĮxport PYTHONPATH=/home/usr/local/nrn/lib/python 2.Ĝompiling neuron from source (without Anaconda installed) _conda_setup="$('/home/marcelo/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" # !! Contents within this block are managed by 'conda init' !! Did I do it right?Ĭode: Select all # > conda initialize > I have tried to add neuron to PATH and PYTHONPATH by editing the bashrc file (last lines shown below), re-openning the terminal and trying to run neuron again, but it still doesn’t work. ![]() The quickguide mentions "If this doesn’t work, it’s probably a PATH or PYTHONPATH issue.", but it doesn’t give any direction on how to solve it. It seems it was installed, but I cannot run neuron (‘from neuron import h, gui') either inside ‘my_env’ (which has python2) or outside it (both situations return ‘No module named neuron’). I have downloaded Neuron7.5.deb ( ) and installed it following your quickguide (. deb file (with Anaconda previously installed) Please let me number what I have done so far to facilitate any answer.ġ.ĝownloading. It seems like a PATH problem to me, but I’m not sure. Some solutions to related problems found in this forum involved removing anaconda, but I cannot do that since I use it in other projects. So, the general idea here is to create a virtual environment with python2 using Anaconda (e.g.: 'conda create -n my_env python=2.7'), install neuron in it and then run it. Anaconda is already installed with python3, which I use for other projects, and I want to run neuron with python2. I am trying to install and run neuron 7.5 inside a virtual environment in Ubuntu18.04.3. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |