Dear Amber Support Team,
I am attempting to install AmberTools22 and Amber22 on my system but have encountered a linking error during the build process. I'm seeking assistance to resolve this issue.
Environment Details:
- Intel Compiler Modules: compiler-rt, tbb, mpi, mkl, ifort
- INTEL: Intel(R) oneAPI DPC++/C++ Compiler 2024.0.2 (2024.0.2.20231213)
- CUDA Version: 11.8
- GPU: NVIDIA TITAN Xp x4
- NVIDIA Driver Version: 535.104.05
- Operating System: Rocky Linux release 8.9
- Python Version: Python 3.10.13
- MPIRUN: mpirun (Open MPI) 5.0.1
- MPIRUN PATH: amber22/bin/mpirun (installed in compliance with https://ambermd.org/InstCentOS.php )
- GCC: gcc (GCC) 9.2.1 20191120 (Red Hat 9.2.1-2) [Toolset-9]
$ make install (not root)
The issue occurs at 19% of the build process while linking the C shared library libcifparse.so. The specific error message is as follows:
[ 19%] Linking C shared library libcifparse.so
/opt/rh/gcc-toolset-9/root/usr/lib/gcc/x86_64-redhat-linux/9/../../../../bin/ld: CMakeFiles/cifparse.dir/lex.cif.c.o:(.bss+0x0): multiple definition of `cifpin'; CMakeFiles/cifparse.dir/cifparse.c.o:(.bss+0x0): first defined here
icx: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [AmberTools/src/cifparse/CMakeFiles/cifparse.dir/build.make:141: AmberTools/src/cifparse/libcifparse.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:3117: AmberTools/src/cifparse/CMakeFiles/cifparse.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
I have followed the standard installation procedures and also tried modifying the build script (./run_build) as follows:
module load compiler-rt tbb mkl ifort
export AMBER_PREFIX=$(dirname $(dirname `pwd`))
Set the INTELPATH and CC variables
INTELPATH=/opt/intel/oneapi/compiler/2024.0/bin
cmake3 $AMBER_PREFIX/amber22_src \
-DCMAKE_CXX_COMPILER=${INTELPATH}/icpx \
-DCMAKE_C_COMPILER=${INTELPATH}/icx \
-DCMAKE_Fortran_COMPILER=${INTELPATH}/ifx \
-DMKL_ROOT="/opt/intel/oneapi/mkl/latest" \
-DTBB_ROOT="/opt/intel/oneapi/tbb/latest" \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 \
-DCOMPILER=AUTO \
-DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=FALSE \
2>&1 | tee cmake.log
I would greatly appreciate any advice or suggestions on how to resolve this error and successfully complete the installation of AmberTools22 and Amber22.
Thank you for your assistance.
Best regards,
Devashish Das,
PhD Scholar
AIPE Laboratory,
Department of Chemical Engineering
Konkuk University
1 Hwayang-Dong, Gwangjin-Gu
Seoul, South Korea, 143-701
http://aipe.konkuk.ac.kr<
http://aipe.konkuk.ac.kr/>
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Received on Mon Jan 22 2024 - 11:30:02 PST
