Hi Simona,
It appears that mcurl (a URL downloading tool, similar to wget) encountered a certificate issue while attempting to download the Miniforge package from the internet. This appears to be a security issue with your Linux cluster, and I am unsure whether it will occur in future installation steps.
For now, there are several walk-arounds, but perhaps others can have a more professional idea.
1.
Manually obtain the Miniforge configure file (Miniforge3-Linux-x86_64.sh) from here<
https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh> and put it inside the designated folder (in your case, it will be /opt/ambertools25_src/build/CMakeFiles/miniconda/download/, as judged by the cmake output). This will bypass the file check.
OR
2.
Disable miniforge by setting -DDOWNLOAD_MINICONDA=FALSE in the run_cmake file under the "Assume this is Linux" block.
Hope it helps.
Best regards,
Zhen.
_____________________
Zhen Li<
http://lizhen62017.wixsite.com/home>, Ph.D.,
The Merz Research Group<
http://merzgroup.org>,
Michigan State University,
Cleveland Clinic.
________________________________
From: Simona Saporiti via AMBER <amber.ambermd.org>
Sent: Friday, July 18, 2025 4:55 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Problems in installing AmberTools25
Hello,
I am trying to install AmberTools25 on our Linux cluster.
However, when I execute the "run_cmake" file, the installation is blocked due to the following error:
Downloading
https://urldefense.com/v3/__https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh__;!!HXCxUKc!zqtxpmxRnDcYjZ0L__AKRbyjNZ0EVWeTG17ZdVb11JSNatFqUqpcy8aKucV3DaCndyE5zbceOMAjH3c9XVnVKCo$ -> /opt/ambertools25_src/build/CMakeFiles/miniconda/download/Miniforge3-Linux-x86_64.sh
#=#=- #
^M##O=# #
^Mcurl: (60) SSL certificate problem: self-signed certificate in certificate chain
More details here: https://urldefense.com/v3/__https://curl.se/docs/sslcerts.html__;!!HXCxUKc!zqtxpmxRnDcYjZ0L__AKRbyjNZ0EVWeTG17ZdVb11JSNatFqUqpcy8aKucV3DaCndyE5zbceOMAjH3c9DAhsHtU$
curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
CMake Error at cmake/DownloadHttps.cmake:49 (message):
Unable to download file
https://urldefense.com/v3/__https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh__;!!HXCxUKc!zqtxpmxRnDcYjZ0L__AKRbyjNZ0EVWeTG17ZdVb11JSNatFqUqpcy8aKucV3DaCndyE5zbceOMAjH3c9XVnVKCo$
Call Stack (most recent call first):
cmake/UseMiniconda.cmake:113 (download_file_https)
cmake/PythonInterpreterConfig.cmake:72 (download_and_use_miniconda)
CMakeLists.txt:129 (include)
-- Configuring incomplete, errors occurred!
See also "/opt/ambertools25_src/build/CMakeFiles/CMakeOutput.log".
See also "/opt/ambertools25_src/build/CMakeFiles/CMakeError.log".
It seems there is a problem of certificate for the network, is there a way to work around this issue?
Best regards,
Simona
--
Simona Saporiti, PhD
Specialist in Structural Biology
Analytical Regulatory & CMC science
Analytical Excellence & Program Managment (AE&PM)
Global Healthcare Operations
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Received on Fri Jul 18 2025 - 04:00:03 PDT
