Hi,
On Fri, Oct 18, 2024 at 09:57:02PM +0530, Nitin Kulhar via AMBER wrote:
> I am trying to install Amber24
> with GCC-11.2.0, CUDA-11.4,
> and MVAPICH2-GDR-2.3.7-1.
>
> I am unable to configure Amber
> with wrapper compilers
> (mpicc, mpicxx, and mpif90)
> from MVAPICH2-GDR.
>
> My approach:
> Edit the run_cmake to direct
> cmake-3.24.2 to use
> MVAPICH2-GDR's wrapper
> compilers, which were edited
> so as to have cmake invoke
> executables, headers, libraries
> from both GCC-11.2.0 and
> CUDA-11.4, via the wrappers.
>
> I could edit the wrappers to
> compile and run primitive
> programs like "Hello World".
> But, I am unable to configure
> the build of Amber24 with the
> 'run_cmake' edited as below:
>
> # Assume this is Linux:
> export CC="mpicc"
> export CXX="mpicxx"
> export FC="mpif90"
> export MV2_USE_CUDA=0
> export MV2_USE_GDRCOPY=0
> cmake $AMBER_PREFIX/amber24_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
> -DMPI=TRUE -DCUDA=TRUE -DNCCL=TRUE \
> -DMVAPICH2GDR_GPU_DIRECT_COMM=TRUE \
> -DCOMPILER=MANUAL \
> -DCMAKE_C_COMPILER=$CC \
> -DCMAKE_CXX_COMPILER=$CXX \
> -DCMAKE_Fortran_COMPILER=$FC \
> -DMPI_C_INCLUDE_PATH=$MV2_INSTALL/include \
> -DMPI_C_LIBRARIES=$MV2_INSTALL/lib64/libmpi.so \
> -DMPI_CXX_INCLUDE_PATH=$MV2_INSTALL/include \
> -DMPI_CXX_LIBRARIES=$MV2_INSTALL/lib64/libmpicxx.so \
> -DMPI_Fortran_INCLUDE_PATH=$MV2_INSTALL/include \
> -DMPI_Fortran_LIBRARIES=$MV2_INSTALL/lib64/libmpifort.so \
> -DBUILD_GUI=FALSE -DBUILD_QUICK=FALSE \
> -DDOWNLOAD_MINICONDA=TRUE \
> -DINSTALL_TESTS=TRUE \
> -DCMAKE_BUILD_TYPE=Debug \
> -DCMAKE_VERBOSE_MAKEFILE=TRUE \
> 2>&1 | tee cmake.log
> fi
>
> PS. PFA the cmake.log.
>
> On Mon, Oct 7, 2024 at 6:55???PM Nitin Kulhar <bo18resch11002.iith.ac.in>
> wrote:
>
> > I am keen on seeing some speedup
> > on multi-node multi-gpu tasks, e.g. with
> > pmemd.cuda.MPI (Amber24).
> >
> > Therefore, I am writing to inquire
> > about the recommended version of
> > cuda drivers (and GNU compilers) with
> > which to install mvapich2-gdr.2.3.7
> > for subsequently building Amber24
> > executables with cuda and/or mpi
> > support.
> >
> > I am also unclear on whether the
> > following switches can be
> > simultaneously turned on while
> > configuring Amber24:
> > -DCUDA
> > -DMVAPICH2GDR_GPU_DIRECT_COMM
> > -DMPI
Your cmake log shows:
...
-- Testing if stdlib.h can be included using -D_BITS_FLOATN_H...
CMake Error at cmake/VerifyCompilerConfig.cmake:96 (message):
Your C compiler could not compile a simple test program using C99 mode to
compile stdlib.h. Build output was: Change Dir:
/scratch/nitin.bt.iith/A24/amber24_src/build/CMakeFiles/CMakeTmp
/scratch/nitin.bt.iith/A24/amber24_src/cmake/test_include_stdlib.c:4:10:
fatal error: stdlib.h: No such file or directory
4 | #include <stdlib.h>
| ^~~~~~~~~~
...
which suggests a basic problem with your compiler installation.
Presumably your hello world program did include some header files?
Have you tried to manually compile the test program
/scratch/nitin.bt.iith/A24/amber24_src/cmake/test_include_stdlib.c ?
With respect to your collection of tools, i am building now with a similar set:
Currently Loaded Modules:
4) gnu/11.2.0
5) cuda/11.7.1
6) mvapich2-gdr/2.3.7-1
mpicc -show
gcc -I/apps/spack/0.17/root/linux-rhel8-zen/cuda/gcc/8.4.1/11.7.1-i3l77ix/include -I/apps/spack/0.17/root/linux-rhel8-zen/cuda/gcc/8.4.1/11.7.1-i3l77ix/include
-lcuda -L/apps/spack/0.17/root/linux-rhel8-zen/cuda/gcc/8.4.1/11.7.1-i3l77ix/lib64/stubs
-L/apps/spack/0.17/root/linux-rhel8-zen/cuda/gcc/8.4.1/11.7.1-i3l77ix/lib64 -lcudart -lrt
-Wl,-rpath,/apps/spack/0.17/root/linux-rhel8-zen/cuda/gcc/8.4.1/11.7.1-i3l77ix/lib64 -Wl,-rpath,XORIGIN/placeholder -Wl,--build-id
-L/apps/spack/0.17/root/linux-rhel8-zen/cuda/gcc/8.4.1/11.7.1-i3l77ix/lib64/ -lm -I/apps/mvapich2-gdr/gnu/11.2/2.3.7-1/include
-L/apps/mvapich2-gdr/gnu/11.2/2.3.7-1/lib64 -Wl,-rpath -Wl,/apps/mvapich2-gdr/gnu/11.2/2.3.7-1/lib64 -Wl,--enable-new-dtags -lmpi
cmake /tmp/amber -DCMAKE_INSTALL_PREFIX=/tmp/amber24 -DCOMPILER=GNU -DMPI=TRUE -DCUDA=TRUE -DOPENMP=FALSE -DMVAPICH2GDR_GPU_DIRECT_COMM=TRUE -DBUILD_GUI=TRUE -DBUILD_QUICK=TRUE -DBUILD_REAXFF_PUREMD=TRUE -DINSTALL_TESTS=TRUE -DBUILD_PYTHON=TRUE -DDOWNLOAD_MINICONDA=TRUE -DCHECK_UPDATES=TRUE -DAPPLY_UPDATES=FALSE -DCMAKE_BUILD_TYPE=Release -DCOLOR_CMAKE_MESSAGES=FALSE -DCMAKE_VERBOSE_MAKEFILE=TRUE
Note that i do not specify the compilers manually.
This set of tools has been put in my path, via the modules, and i just let
cmake find them, eg:
which mpicc
/apps/mvapich2-gdr/gnu/11.2/2.3.7-1/bin/mpicc
grep mpicc cmake.log
-- MPI C Compiler: /apps/mvapich2-gdr/gnu/11.2/2.3.7-1/bin/mpicc
oschelp,
scott
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Received on Fri Oct 18 2024 - 12:00:02 PDT
