make error when build the source

[niuniu800]

Hello Phoebe developers!

I have trained a machine learning potential and would like to use LAMMPS as the calculator to compute the second and third-order force constants, so I searched for Phoebe. However, I encountered some issues while installing Phoebe in the conda environment.

The file cmake_log.txt is the compilation log that appears after running cmake .. and there are no obvious errors. The file make_log.txt is the compilation log that appears after running make, and it always throws an error after reaching 100%.

Here is my system version information:
NAME="Red Hat Enterprise Linux"
VERSION="8.10 (Ootpa)"
ID="rhel"
ID_LIKE="fedora"
VERSION_ID="8.10"
PLATFORM_ID="platform:el8"
PRETTY_NAME="Red Hat Enterprise Linux 8.10 (Ootpa)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:redhat:enterprise_linux:8::baseos"
HOME_URL="https://www.redhat.com/"
DOCUMENTATION_URL="https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/8"
BUG_REPORT_URL="https://issues.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 8"
REDHAT_BUGZILLA_PRODUCT_VERSION=8.10
REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="8.10"

gcc --version:
gcc (conda-forge gcc 13.3.0-2) 13.3.0
path: ~/anaconda3/envs/deepmd-cpu/bin/gcc

g++ --version:
g++ (conda-forge gcc 13.3.0-2) 13.3.0
path: ~/anaconda3/envs/deepmd-cpu/bin/g++

gfortran --version:
GNU Fortran (conda-forge gcc 13.3.0-2) 13.3.0
path: ~/anaconda3/envs/deepmd-cpu/bin/gfortran

Could you please check what might be causing the installation failure? I look forward to your reply.
cmake_log.txt
make_log.txt

[jcoulter12]

Hi @niuniu800,

Thanks for using Phoebe -- let's see if we can get the code to build for you correctly.

It's hard for me to deduce exactly the problem without having access to your system, but if one googles some of the error messages in your output, things like this turn up,
https://stackoverflow.com/questions/9303037/cannot-compile-simple-c-program-in-ubuntu
where almost all suggestions point to either 1) a problem with the installation of compilers on your system, causing it to be unable to compile even simple C++ programs, or 2) there's some issue where copies of things from different installations are being used in different parts of the build.

My suspicion would really be that using conda compilers is very tricky and often leads to issues where system copies of compilers/tools are mixed in with the conda ones, causing sometimes difficult to diagnose problems. Looking at your output suggests that it's always finding conda copies of things, but there could be a system copy of something on your file path that's still being picking up and causing this conflict. In the same vein, I often find that when one builds with conda envs, one often gets sub-optimal computational performance compared to using standard installations of computational tools. Maybe inspecting build/CMakeCache.txt files to make sure that only conda copies are found, or otherwise maybe retrying your conda env setup?

Also -- Is there a reason you're using conda instead of native copies of things? Phoebe typically can be installed without too much trouble on linux machines and clusters, because it's dependencies are very common tools.

Hopefully we can get this working for you without too much trouble,
Jenny