Hello Hector,
Thank you very much for your kind message !
so I need firstly clean the wrong installation using the ./clean_build
script and then modify the run_cmake ?
This is also the run_cmake script (for linux section):
# Assume this is Linux:
cmake $AMBER_PREFIX/amber24_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
-DCOMPILER=GNU \
-DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE \
2>&1 | tee cmake.log
fi
Where exactly should these two lines be added ??
Many thanks in advance !
Enrico
Il giorno mar 24 set 2024 alle ore 16:57 Hector A. Baldoni <
hbaldoni.unsl.edu.ar> ha scritto:
> Dear Enrico,
>
> The error message you encountered indicates that the object files in
> `libmc.a` were not compiled with the `-fPIC` flag, which is required for
> creating shared objects on 64-bit architectures. To resolve this, please
> add the following lines to your CMake file before running `make clean`
> and `make`:
>
> set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
> set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
>
> I hope this helps resolve the compilation issue.
>
> Best regards,
> Hector.
>
>
>
> El 2024-09-24 09:50, Enrico Martinez via AMBER escribió:
> > Dear Amber Users !
> >
> > I am trying to install Amber 24 on the local gpu cluster with CUDA
> > support
> > This is the current versions of the compilers and cuda:
> >
> > cmake/3.10.2
> > cuda/11.1.105
> > gcc81/3.1.0
> >
> > The only one option which was activated in cmake script is CUDA
> > support.
> >
> > Here is the error during the compilation
> >
> > [ 65%] Linking CXX static library libcpptraj_core.a
> > [ 65%] Built target cpptraj_core
> > Scanning dependencies of target libcpptraj
> > [ 65%] Building CXX object
> > AmberTools/src/cpptraj/src/CMakeFiles/libcpptraj.dir/Action_Esander.cpp.o
> > [ 65%] Building CXX object
> > AmberTools/src/cpptraj/src/CMakeFiles/libcpptraj.dir/Command.cpp.o
> > [ 65%] Building CXX object
> > AmberTools/src/cpptraj/src/CMakeFiles/libcpptraj.dir/Cpptraj.cpp.o
> > [ 65%] Building CXX object
> > AmberTools/src/cpptraj/src/CMakeFiles/libcpptraj.dir/Energy_Sander.cpp.o
> > [ 65%] Building CXX object
> > AmberTools/src/cpptraj/src/CMakeFiles/libcpptraj.dir/ReadLine.cpp.o
> > [ 65%] Linking CXX shared library libcpptraj.so
> > /usr/bin/ld: ../../c9x-complex/libmc.a(cmplx.c.o): relocation
> > R_X86_64_32
> > against `.rodata' can not be used when making a shared object;
> > recompilé
> > avec -fPIC
> > /usr/bin/ld: ../../c9x-complex/libmc.a(stubs.c.o): relocation
> > R_X86_64_32
> > against `.rodata' can not be used when making a shared object;
> > recompilé
> > avec -fPIC
> > /usr/bin/ld : échec de l'édition de liens finale : Section
> > non-représentable sur la sortie
> > collect2: error: ld a retourné le statut de sortie 1
> > make[2]: *** [AmberTools/src/cpptraj/src/libcpptraj.so] Erreur 1
> > make[1]: *** [AmberTools/src/cpptraj/src/CMakeFiles/libcpptraj.dir/all]
> > Erreur 2
> >
> > How could it be fixed ? Otherwise alternatively is it possible not to
> > install cpptraj at all if the solution is complicated?
> >
> > Many thanks in advance !
> >
> > Enrico
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> --------------------------------------
> Dr Hector A. Baldoni
> Professor (FQByF - UNSL)
> Adjunct Researcher (IMIBIO-SL - CONICET)
> Department of General and Inorganic Chemistry
> National University of San Luis
> Ejercito de los Andes 950 (D5700HHW)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.: +54-(0)266-4520300 ext. 6157
> --------------------------------------
>
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Received on Tue Sep 24 2024 - 08:30:01 PDT
