diff --git a/installer/centos/README.md b/installer/centos/README.md
index 96849540e..d448187fc 100644
--- a/installer/centos/README.md
+++ b/installer/centos/README.md
@@ -64,10 +64,10 @@ Open a bash terminal and run these commands (from [Docker Compose installation](
```
3. The HNN GUI should show up. Make sure that you can run simulations by clicking the 'Run Simulation' button. This will run a simulation with the default configuration. After it completes, graphs should be displayed in the main window.
- * If the GUI doesn't show up, check the [Docker troubleshooting section](../docker/troubleshooting.md) (also links the bottom of this page)
+ - If the GUI doesn't show up, check the [Docker troubleshooting section](../docker/troubleshooting.md) (also links the bottom of this page). It may be necessary to run the `xhost +local:docker` command to open up permissions to display the GUI on your local machine.
4. You can now proceed to running the tutorials at [https://hnn.brown.edu/index.php/tutorials/](https://hnn.brown.edu/index.php/tutorials/) . Some things to note:
- * A directory called "hnn_out" exists both inside the container (at /home/hnn_user/hnn_out) and outside (in the directory set by step 2) that can be used to share files between the container and your host OS.
- * The HNN repository with sample data and parameter files exists at /home/hnn_user/hnn_source_code
+ - A directory called "hnn_out" exists both inside the container (at /home/hnn_user/hnn_out) and outside (in the directory set by step 2) that can be used to share files between the container and your host OS.
+ - The HNN repository with sample data and parameter files exists at /home/hnn_user/hnn_source_code
5. To quit HNN and shut down container, first press 'Quit' within the GUI. Then run `./hnn_docker.sh stop`.
```bash
diff --git a/installer/centos/centos7-installer.sh b/installer/centos/centos7-installer.sh
index 4f7eb237f..65db42d35 100755
--- a/installer/centos/centos7-installer.sh
+++ b/installer/centos/centos7-installer.sh
@@ -22,16 +22,16 @@ cd $startdir && \
mkdir nrn && \
cd nrn && \
git clone https://github.com/neuronsimulator/nrn src && \
- cd /home/hnn_user/nrn/src && \
+ cd $startdir/nrn/src && \
./build.sh && \
./configure --with-nrnpython=python3 --with-paranrn --disable-rx3d \
--without-iv --without-nrnoc-x11 --with-mpi \
- --prefix=/home/hnn_user/nrn/build && \
+ --prefix=$startdir/nrn/build && \
make -j4 && \
make install -j4 && \
cd src/nrnpython && \
python3 setup.py install --user && \
- cd /home/hnn_user/nrn/ && \
+ cd $startdir/nrn/ && \
rm -rf src && \
sudo yum clean all
diff --git a/installer/centos/native_install.md b/installer/centos/native_install.md
index 5bbee62a0..d676a8d07 100644
--- a/installer/centos/native_install.md
+++ b/installer/centos/native_install.md
@@ -1,18 +1,27 @@
# HNN native install (CentOS)
The scripts below can be used to install HNN and its prerequisites. However, there is a greater possibility that your base environment will not be compatible with the script and installation might require additional troubleshooting. Thus, we do not recommend this method. For the recommended Docker-based installation, please see the instructions below.
- - Alternative: [Docker install instructions](README.md)
+
+- Alternative: [Docker install instructions](README.md)
See the scripts in this directory:
-* CentOS 6: [centos6-installer.sh](centos6-installer.sh)
-* CentOS 7: [centos7-installer.sh](centos7-installer.sh)
- ```
+
+- CentOS 7: [centos7-installer.sh](centos7-installer.sh)
+
+ ```bash
chmod +x ./centos7-installer.sh
./centos7-installer.sh
```
-# Troubleshooting
+- CentOS 6 (no longer maintained): [centos6-installer.sh](centos6-installer.sh)
+
+ ```bash
+ chmod +x ./centos6-installer.sh
+ ./centos6-installer.sh
+ ```
+
+## Troubleshooting
If you run into other issues with the installation, please [open an issue on our GitHub](https://github.com/jonescompneurolab/hnn/issues). Our team monitors these issues and will be able to suggest possible fixes.
-For other HNN software issues, please visit the [HNN bulletin board](https://www.neuron.yale.edu/phpBB/viewforum.php?f=46)
\ No newline at end of file
+For other HNN software issues, please visit the [HNN bulletin board](https://www.neuron.yale.edu/phpBB/viewforum.php?f=46)
diff --git a/installer/docker/troubleshooting.md b/installer/docker/troubleshooting.md
index 960096ad2..b5117636c 100644
--- a/installer/docker/troubleshooting.md
+++ b/installer/docker/troubleshooting.md
@@ -4,65 +4,52 @@ Common problems that one might encounter running the HNN docker container are li
Make sure to check the log hnn_docker.log for more verbose error messages that will hint at which of the sections to go to below.
-* [Failed to start HNN on any X port](#xdisplay)
+* [Failed to start HNN (No GUI)](#xdisplay)
* [Starting HNN fails with 'Drive has not been shared'](#shared)
* [This computer doesn't have VT-x/AMD-v enabled](#vtx)
* [Image operating system linux cannot be used on this platform](#image)
-# Failed to start HNN
+## Failed to start HNN (No GUI)
Output from `./docker_hnn.sh start`:
```none
-Starting HNN... failed to start HNN. Please see hnn_docker.log for more details
+Starting HNN... failed
+Please see hnn_docker.log for more details
```
-Check the contents of `hnn_docker.log` to determine which of the following issue applies
+Check the contents of `hnn_docker.log`. Most likely, they will be something similar to below:
-
-
-## Failed to start HNN on any X port
-
-`hnn_docker.log` contents:
```none
-Starting HNN GUI...
-No protocol specified
-qt.qpa.xcb: could not connect to display localhost:0
-qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
-This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
-
-Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.
-
-/home/hnn_user/start_hnn.sh: line 41: 147 Aborted python3 hnn.py
-
-...[more output]...
-
-Failed to start HNN on any X port
-Connection to localhost closed.
+Creating hnn_container ... done
+Attaching to hnn_container
+hnn_container | Starting HNN GUI...
+hnn_container | No protocol specified
+hnn_container | qt.qpa.xcb: could not connect to display :0
+hnn_container | qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
+hnn_container | This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
+hnn_container |
+hnn_container | Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.
+hnn_container |
```
-macOS only: try forcing a restart of the container:
+The important line for troubleshooting is the next line and will look something like this:
-```bash
-./hnn_docker.sh -r start
-```
-
-Then try to start HNN manually:
-```bash
-docker exec -ti hnn_container bash
+```none
+hnn_container | /home/hnn_user/start_hnn.sh: line 41: 147 Aborted python3 hnn.py
```
-Try starting HNN manually:
+OR
-```bash
-python3 hnn.py
+```none
+hnn_container | /home/hnn_user/start_hnn.sh: line 45: 12 Aborted (core dumped) python3 hnn.py
```
-If that doesn't work, troubleshooting steps diverge for each operating system.
+Troubleshooting steps diverge for each operating system.
* Mac/Windows
- 1. Check that the X server is started (VcXsrv for Windows and XQuartz for Mac).
+ 1. Check that the X server is started (VcXsrv for Windows and XQuartz for Mac) and verify that it works with other applications, such as with ssh X-forwarding, if possible.
* Linux
@@ -70,11 +57,9 @@ If that doesn't work, troubleshooting steps diverge for each operating system.
```bash
xhost +local:docker
- cd hnn/installer/docker
- docker-compose restart
```
-If issues persist, please include output from the above commands in a new [GitHub issue](https://github.com/jonescompneurolab/hnn/issues)
+If issues persist, we'd greatly appreciate it if you would report the issue on our [GitHub Issues](https://github.com/jonescompneurolab/hnn/issues). Please include output from hnn_docker.log and the above commands
@@ -89,16 +74,17 @@ ERROR: for hnn_container Cannot create container for service hnn: b'Drive has n
ERROR: for hnn Cannot create container for service hnn: b'Drive has not been shared'
```
+
This will happen when starting the HNN container for the first time on Windows. When it is starting, there will be a prompt in the lower-right asking you to share the drive C:. Rerun the script to see the prompt again
-# This computer doesn't have VT-x/AMD-v enabled
+## This computer doesn't have VT-x/AMD-v enabled
[MetaCell documentation link](https://github.com/MetaCell/NetPyNE-UI/wiki/Docker-installation#problem-this-computer-doesnt-have-vt-xamd-v-enabled)
-# Image operating system linux cannot be used on this platform
+## Image operating system linux cannot be used on this platform
[MetaCell documentation link](https://github.com/MetaCell/NetPyNE-UI/wiki/Docker-installation#problem-image-operating-system-linux-cannot-be-used-on-this-platform)
diff --git a/installer/ubuntu/README.md b/installer/ubuntu/README.md
index 2f8d442ba..e6b45885e 100644
--- a/installer/ubuntu/README.md
+++ b/installer/ubuntu/README.md
@@ -63,7 +63,7 @@ Open a bash terminal and run these commands (from [Docker Compose installation](
```
3. The HNN GUI should show up. Make sure that you can run simulations by clicking the 'Run Simulation' button. This will run a simulation with the default configuration. After it completes, graphs should be displayed in the main window.
- * If the GUI doesn't show up, check the [Docker troubleshooting section](../docker/troubleshooting.md) (also links the bottom of this page)
+ * If the GUI doesn't show up, check the [Docker troubleshooting section](../docker/troubleshooting.md) (also links the bottom of this page). It may be necessary to run the `xhost +local:docker` command to open up permissions to display the GUI on your local machine.
4. You can now proceed to running the tutorials at [https://hnn.brown.edu/index.php/tutorials/](https://hnn.brown.edu/index.php/tutorials/) . Some things to note:
* A directory called "hnn_out" exists both inside the container (at /home/hnn_user/hnn_out) and outside (in the directory set by step 2) that can be used to share files between the container and your host OS.
* The HNN repository with sample data and parameter files exists at /home/hnn_user/hnn_source_code
diff --git a/installer/ubuntu/installer.sh b/installer/ubuntu/installer.sh
index a677bf470..02de935e4 100755
--- a/installer/ubuntu/installer.sh
+++ b/installer/ubuntu/installer.sh
@@ -20,16 +20,16 @@ cd $startdir && \
mkdir nrn && \
cd nrn && \
git clone https://github.com/neuronsimulator/nrn src && \
- cd /home/hnn_user/nrn/src && \
+ cd $startdir/nrn/src && \
./build.sh && \
./configure --with-nrnpython=python3 --with-paranrn --disable-rx3d \
--without-iv --without-nrnoc-x11 --with-mpi \
- --prefix=/home/hnn_user/nrn/build && \
+ --prefix=$startdir/nrn/build && \
make -j4 && \
make install -j4 && \
cd src/nrnpython && \
python3 setup.py install --user && \
- cd /home/hnn_user/nrn/ && \
+ cd $startdir/nrn/ && \
rm -rf src && \
sudo apt-get -y remove --purge bison flex python3-dev zlib1g-dev python && \
sudo apt-get autoremove -y --purge && \