Hi all,
I am attempting to compile Amber24 on our Rock9.1 HPC cluster, but I'm running into an error when cmake attempts to download and build local miniconda:
I run module load cmake to load the system's cmake (3.24.2). When I run the ./run_cmake command (in step 4 of the installation instructions), cmake hangs indefinitely when it attempts to download and build a local miniconda at the "unpacking payload" step.
-- **************************************************************************
-- Starting configuration of Amber version 24.0.0...
-- CMake Version: 3.24.2
-- For how to use this build system, please read this wiki:
--
http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
-- For a list of important CMake variables, check here:
--
http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
-- **************************************************************************
-- Setting C compiler to gcc
-- Setting CXX compiler to g++
-- Setting Fortran compiler to gfortran
-- Amber source found, building AmberTools and Amber
-- The C compiler identification is GNU 11.5.0
-- The CXX compiler identification is GNU 11.5.0
-- The Fortran compiler identification is GNU 11.5.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/bin/gfortran - skipped
-- Testing if stdlib.h can be included...
-- Testing if stdlib.h can be included... yes
-- Downloading Python 3 Miniforge
-- Detected Linux OS. Downloading the Linux installer
-- Using 64 bit miniforge3
Downloading
https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -> /groups/nl2960_gp/software/amber24_src/build/CMakeFiles/miniconda/download/Miniforge3-Linux-x86_64.sh
############################################################################################################################################################################################### 100.0%
Installing Miniforge Python.
PREFIX=/groups/nl2960_gp/software/amber24_src/build/CMakeFiles/miniconda/install
Unpacking payload ...
I have verified that I don't have conda or miniconda variables in my PATH, but I'm not sure how to proceed from here. Has anyone else encountered this error before?
Thanks so much,
Naomi
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Received on Thu Mar 20 2025 - 07:00:02 PDT
