UBUNTU VM installation failure

[yashg16422-design]

Describe the bug
On services like a VM or distrobox or even docker the installation often fails after so much wait because the cmake version compatible is ~3.5, on force downloading it also whenever main installation run is made version 4.2 or latest is automatically downloaded forcing it to stop

To Reproduce
Steps to reproduce the behavior:

1. From official documentation perform all prerequisites.
2. Install Bidynamo by main curl command..
3. Wait till it fails due to Cmake compatibility even if on your clean system you have downloaded compatible version or are automatically downloading it without performing prerequisites..

Setup (please complete the following information):

• OS: Primary Windows but tried on Virtual box VMs and clean Distrobox Environments
• BioDynaMo version [e.g. v0.1.0-152-ge3d39e6]

Additional context
Also tried on Ubuntu(VM) after clean setup without even installing cmake just installing 3.19 due to prerequisite documentation and still automatically 4.2 was installed..

[romanbauer111]

Hi, thanks for raising this. Could you please create a post on the BioDynaMo Google Forum (https://groups.google.com/g/biodynamo-forum)? That way it will be easier to communicate with the various experienced users and developers. Thanks, Roman

[sportokalidis]

Hi @yashg16422-design!

Hi! Could you please provide a few details so we can reproduce?

1. Ubuntu version (in the VM/container): please paste the output of:

   • lsb_release -a (or cat /etc/os-release)

2. The exact command(s) you ran:

   • the full curl/install command from the docs (copy/paste)
   • any additional commands you ran before/after

3. The logs from the failing run

[yashg16422-design]

Sure @sportokalidis!

1. Ubuntu Version-

yosh@yosh-VirtualBox:~$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 20.04.6 LTS Release: 20.04 Codename: focal

2.Commands Sequential Run

To ensure all the prerequisites match the documentation, i followed up with these commands and everything went on smoothly...

`sudo apt-get update
sudo apt-get install -y wget curl make gcc g++
libblas-dev liblapack-dev libopenmpi-dev libomp5 libomp-d/ev \
libnuma-dev freeglut3-dev libpthread-stubs0-dev

curl -L -O https://github.com/Kitware/CMake/releases/download/v3.19.3/cmake-3.19.3-Linux-x86_64.sh
chmod +x cmake-3.19.3-Linux-x86_64.sh
sudo ./cmake-3.19.3-Linux-x86_64.sh --skip-license --prefix=/usr/local`

Since I have 20.04 I ran
sudo apt-get install -y libssl-dev zlib1g-dev libbz2-dev libreadline-dev \ libsqlite3-dev xz-utils tk-dev libffi-dev liblzma-dev python-openssl

and then
curl https://pyenv.run | bash export PATH="$HOME/.pyenv/bin:$PATH" eval "$(pyenv init --path)" eval "$(pyenv init -)" PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.1

Since Ive had similar issues in past with Cmake and Cmake-data versions almost everytime, i checked

yosh@yosh-VirtualBox:~$ cmake --version cmake version 3.19.3 CMake suite maintained and supported by Kitware (kitware.com/cmake). yosh@yosh-VirtualBox:~$

Then after this I ran the main command for Biodynamo installation
curl https://biodynamo.github.io/install | bash

There was an early fail also where cmake and cmake-data version were not matching so i added the following flag command and both were of the same version
sudo apt-get install --allow-downgrades cmake-data=3.19.3-0kitware1ubuntu20.04.1

3.Error

After 10-12 minutes of continuous successful installations, this is the temp log data

`Hit:6 http://archive.ubuntu.com/ubuntu focal-backports InRelease
Hit:3 https://apt.llvm.org/focal llvm-toolchain-focal-10
InReleaseReading package lists...
Building dependency tree...
Reading state information...
15 packages can be upgraded.
Run 'apt list --upgradable' to see them.WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED: cmake
The following packages will be DOWNGRADED: cmake-data
0 upgraded, 0 newly installed, 1 downgraded, 1 to remove and 15 not upgraded.
E: Packages were downgraded and -y was used without --allow-downgrades.
Something went wrong with the installation.
For more details check the log file: /tmp/tmp.gCMQE7BMh0/biodynamo/installation.log
yosh@yosh-VirtualBox:~$ cmake --version
cmake version 3.19.3

CMake suite maintained and supported by Kitware (kitware.com/cmake).
`

But this time cmake-data version changed again

yosh@yosh-VirtualBox:~$ dpkg -s cmake-data | grep Version Version: 4.2.3-0kitware1ubuntu20.04.1 yosh@yosh-VirtualBox:~$

[yashg16422-design]

@sportokalidis

My primary error before cmake and cmake-data mismatch was

ERROR

-- Check if compiler accepts -pthread - yes CMake Error at build/third_party/paraview/lib/cmake/rkcommon-1.5.1/FindTBB.cmake:40 (cmake_minimum_required): Compatibility with CMake < 3.5 has been removed from CMake. Update the VERSION argument <min> value. Or, use the <min>...<max> syntax to tell CMake that the project requires at least <min> but has been updated to work with policies introduced by <max> or earlier. Or, add -DCMAKE_POLICY_VERSION_MINIMUM=3.5 to try configuring anyway.

[sportokalidis]

Hi @yashg16422-design!

Thanks for the report.

I managed to get past the installer failure on my side by pinning CMake to a known-working version and making sure it’s the one found first in PATH.

What worked for me (Ubuntu VM / clean environment):

wget https://github.com/Kitware/CMake/releases/download/v3.19.3/cmake-3.19.3-linux-x86_64.sh
sudo mkdir /opt/cmake
sudo bash cmake-3.19.3-linux-x86_64.sh --prefix=/opt/cmake --skip-license
export PATH=/opt/cmake/bin:$PATH

After exporting PATH like above the installation no longer auto-pulled CMake 4.x and it completed successfully.

[yashg16422-design]

Thank You for this Solution, I will try to replicate it...

…

On Wed, Mar 18, 2026 at 9:04 PM Stavros Portokalidis < ***@***.***> wrote: *sportokalidis* left a comment (BioDynaMo/biodynamo#465) <#465 (comment)> Hi @yashg16422-design <https://github.com/yashg16422-design>! Thanks for the report. I managed to get past the installer failure on my side by pinning CMake to a known-working version and making sure it’s the one found first in PATH. What worked for me (Ubuntu VM / clean environment): wget https://github.com/Kitware/CMake/releases/download/v3.19.3/cmake-3.19.3-linux-x86_64.sh sudo mkdir /opt/cmake sudo bash cmake-3.19.3-linux-x86_64.sh --prefix=/opt/cmake --skip-licenseexport PATH=/opt/cmake/bin:$PATH After exporting PATH like above the installation no longer auto-pulled CMake 4.x and it completed successfully. — Reply to this email directly, view it on GitHub <#465 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BWWKGPWGXFGYIARLHTBWMNL4RK6YJAVCNFSM6AAAAACWMDCBOWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DAOBTGQ4DSNBQGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>