Hello
I have installed Amber24 and Ambertools24 on my RTX 4090 system with GPU compatibility. I am working on WSL ubuntu 24 version and downloded the cuda-11.8 wsl-ubunutu version
I am stuck due to problems in compatibility issue in nvidia drivers and cuda versions.
Please find the attached outputs of my setting and files.
Any lead would be highly appreciated.
Thank you
bioinfo2025.Bioinformatics2:~$ nvidia-smi
Mon Jan 13 11:55:04 2025
+-----------------------------------------------------------------------------------------+
| NVIDIA-SMI 550.120 Driver Version: 556.12 CUDA Version: 12.5 |
|-----------------------------------------+------------------------+----------------------+
| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|=========================================+========================+======================|
| 0 NVIDIA GeForce RTX 4090 On | 00000000:01:00.0 On | Off |
| 31% 27C P8 9W / 450W | 565MiB / 24564MiB | 0% Default |
| | | N/A |
+-----------------------------------------+------------------------+----------------------+
+-----------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=========================================================================================|
| No running processes found |
+-----------------------------------------------------------------------------------------+
bioinfo2025.Bioinformatics2:~$ sudo update-alternatives --config cuda
[sudo] password for bioinfo2025:
There is 1 choice for the alternative cuda (providing /usr/local/cuda).
Selection Path Priority Status
------------------------------------------------------------
* 0 /usr/local/cuda-11.8 100 auto mode
1 /usr/local/cuda-11.8 100 manual mode
Press <enter> to keep the current choice[*], or type selection number:
bioinfo2025.Bioinformatics2:~$ sudo update-alternatives --config gcc
There are 2 choices for the alternative gcc (providing /usr/bin/gcc).
Selection Path Priority Status
------------------------------------------------------------
* 0 /usr/bin/gcc-10 10 auto mode
1 /usr/bin/gcc-10 10 manual mode
2 /usr/bin/gcc-9 9 manual mode
Press <enter> to keep the current choice[*], or type selection number:
bioinfo2025.Bioinformatics2:~$ sudo update-alternatives --config gfortran
There are 2 choices for the alternative gfortran (providing /usr/bin/gfortran).
Selection Path Priority Status
------------------------------------------------------------
* 0 /usr/bin/gfortran-10 100 auto mode
1 /usr/bin/gfortran-10 100 manual mode
2 /usr/bin/gfortran-9 100 manual mode
Press <enter> to keep the current choice[*], or type selection number:
bioinfo2025.Bioinformatics2:~$ nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2022 NVIDIA Corporation
Built on Wed_Sep_21_10:33:58_PDT_2022
Cuda compilation tools, release 11.8, V11.8.89
Build cuda_11.8.r11.8/compiler.31833905_0
sudo apt install nvidia-driver-550
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
nvidia-driver-550 is already the newest version (550.120-0ubuntu0.24.04.1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
./run_cmake
-- **************************************************************************
-- Starting configuration of Amber version 24.0.0...
-- CMake Version: 3.28.3
-- 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
-- **************************************************************************
-- Amber source found, building AmberTools and Amber
-- MPI C Compiler: /usr/bin/mpicc
-- MPI CXX Compiler: /usr/bin/mpicxx
-- MPI Fortran Compiler: /usr/bin/mpif90
-- If these are not the correct MPI wrappers, then set MPI_<language>_COMPILER to the correct wrapper and reconfigure.
CMake Warning (dev) at cmake/CudaConfig.cmake:12 (find_package):
Policy CMP0146 is not set: The FindCUDA module is removed. Run "cmake
--help-policy CMP0146" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
Call Stack (most recent call first):
CMakeLists.txt:119 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- CUDA version 11.5 detected
-- Configuring for SM3.5, SM5.0, SM5.2, SM5.3, SM6.0, SM6.1, SM7.0, SM7.5 and SM8.0
-- Checking CUDA and GNU versions -- compatible
CMake Error at cmake/LibraryTracking.cmake:153 (message):
Attempt to import library cublas from nonexistant path
"/usr/local/cuda-11.5/lib64/libcublas.so"
Call Stack (most recent call first):
cmake/CudaConfig.cmake:147 (import_library)
CMakeLists.txt:119 (include)
-- Configuring incomplete, errors occurred!
If errors are reported, search for 'CMake Error' in the cmake.log file.
If the cmake build report looks OK, you should now do the following:
make install
source /home/bioinfo2025/amber24/amber.sh
Consider adding the last line to your login startup script, e.g. ~/.bashrc
Bash file
# ~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples
# If not running interactively, don't do anything
case $- in
*i*) ;;
*) return;;
esac
# don't put duplicate lines or lines starting with space in the history.
# See bash(1) for more options
HISTCONTROL=ignoreboth
# append to the history file, don't overwrite it
shopt -s histappend
# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
HISTSIZE=1000
HISTFILESIZE=2000
# check the window size after each command and, if necessary,
# update the values of LINES and COLUMNS.
shopt -s checkwinsize
# If set, the pattern "**" used in a pathname expansion context will
# match all files and zero or more directories and subdirectories.
#shopt -s globstar
# make less more friendly for non-text input files, see lesspipe(1)
[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"
# set variable identifying the chroot you work in (used in the prompt below)
if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
debian_chroot=$(cat /etc/debian_chroot)
fi
# set a fancy prompt (non-color, unless we know we "want" color)
case "$TERM" in
xterm-color|*-256color) color_prompt=yes;;
esac
# uncomment for a colored prompt, if the terminal has the capability; turned
# off by default to not distract the user: the focus in a terminal window
# should be on the output of commands, not on the prompt
#force_color_prompt=yes
if [ -n "$force_color_prompt" ]; then
if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
# We have color support; assume it's compliant with Ecma-48
# (ISO/IEC-6429). (Lack of such support is extremely rare, and such
# a case would tend to support setf rather than setaf.)
color_prompt=yes
else
color_prompt=
fi
fi
if [ "$color_prompt" = yes ]; then
PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u.\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
else
PS1='${debian_chroot:+($debian_chroot)}\u.\h:\w\$ '
fi
unset color_prompt force_color_prompt
# If this is an xterm set the title to user.host:dir
case "$TERM" in
xterm*|rxvt*)
PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u.\h: \w\a\]$PS1"
;;
*)
;;
esac
# enable color support of ls and also add handy aliases
if [ -x /usr/bin/dircolors ]; then
test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
alias ls='ls --color=auto'
#alias dir='dir --color=auto'
#alias vdir='vdir --color=auto'
alias grep='grep --color=auto'
alias fgrep='fgrep --color=auto'
alias egrep='egrep --color=auto'
fi
# colored GCC warnings and errors
#export GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'
# some more ls aliases
alias ll='ls -alF'
alias la='ls -A'
alias l='ls -CF'
# Add an "alert" alias for long running commands. Use like so:
# sleep 10; alert
alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal || echo error)" "$(history|tail -n1|sed -e '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'
# Alias definitions.
# You may want to put all your additions into a separate file like
# ~/.bash_aliases, instead of adding them here directly.
# See /usr/share/doc/bash-doc/examples in the bash-doc package.
if [ -f ~/.bash_aliases ]; then
. ~/.bash_aliases
fi
# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
if [ -f /usr/share/bash-completion/bash_completion ]; then
. /usr/share/bash-completion/bash_completion
elif [ -f /etc/bash_completion ]; then
. /etc/bash_completion
fi
fi
export AMBERHOME=/home/bioinfo2025/amber24_src/src
export PATH=/usr/local/cuda-11.8/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda-11.8/lib64:$LD_LIBRARY_PATH
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Received on Mon Jan 13 2025 - 05:30:02 PST
