Hello Dr Brozell
>
>
> Nevertheless, I suggest removing those lines above and trying again.
>
I ran into the same error
despite removing the flags
that you pointed out.
Snippet of 'run_cmake':
# Assume this is Linux:
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="mpicc" -DCMAKE_CXX_COMPILER="mpicxx"
-DCMAKE_Fortran_COMPILER="mpif90"
\
-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
PFA the 'cmake.log' for
your kind reference.
Thanks and regards
Nitin Kulhar
On Tue, Oct 22, 2024 at 6:25 AM Scott Brozell <sbrozell.comcast.net> wrote:
> Hi,
>
> You should not have to specify these paths and libraries:
>
> -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 \
>
> I suspect that is the cause of this unusual error:
>
> CMake Error at cmake/LibraryTracking.cmake:219 (message):
> Incorrect usage. At least one LIBRARY should be provided.
>
> However, I am unable to trigget this error by specifying those.
> Nevertheless, I suggest removing those lines above and trying again.
>
> FWIW, my build was successful.
>
> scott
>
> On Sat, Oct 19, 2024 at 06:30:18PM +0530, Nitin Kulhar via AMBER wrote:
> > Thanks for the mail, Dr Brozell.
> >
> > Noting the output of `mpicc -show`
> > shared by you, I made changes in
> > my mpicc, which helped the
> > configuration along, albeit not all
> > the way.
> >
> > A snippet of cmake.log:
> > -- Found MPI_C: /path/to/mpicc (found version "3.1")
> > -- Found MPI_CXX: /path/to/mpicxx (found version "3.1")
> > -- Found MPI_Fortran: /path/to/mpif90 (found version "3.1")
> > -- Found MPI: TRUE (found version "3.1")
> > -- MPI C Compiler: /path/to/mpicc
> > -- MPI CXX Compiler: /path/to/mpicxx
> > -- MPI Fortran Compiler: /path/to/mpif90
> > -- If these are not the correct MPI wrappers, then set
> > MPI_<language>_COMPILER to the correct wrapper and reconfigure.
> > CMake Error at cmake/LibraryTracking.cmake:219 (message):
> > Incorrect usage. At least one LIBRARY should be provided.
> > Call Stack (most recent call first):
> > cmake/MPIConfig.cmake:122 (import_libraries)
> > CMakeLists.txt:117 (include)
> > Full log attached herewith
> > for your kind reference.
> >
> > With respect to your collection of tools, i am building now with a
> similar
> > > set:
> > > Currently Loaded Modules:
> > > 4) gnu/11.2.0
> >
> >
> > Note that i do not specify the compilers manually.
> >
> > The rpm build of MVAPICH2-GDR
> > compatible with our HPC hardware
> > requires GCC-11.2.0, which is not
> > currently available on the HPC. So,
> > I installed GCC-11.2.0 in my user
> > space, followed by primitive tests
> > with a few headers. Hence, the
> > -DCOMPILER=MANUAL in my
> > run_cmake.
> >
> > Presumably your hello world program did include some header files?
> >
> > Yes.
> >
> > Have you tried to manually compile the test program
> > > /scratch/nitin.bt.iith/A24/amber24_src/cmake/test_include_stdlib.c ?
> >
> > Yes, it worked as below:
> > *nitin.bt.iith.login01: build$* mpicc -g -o test-include.out
> > ../cmake/test_include_stdlib.c
> > *nitin.bt.iith.login01: build$* srun -v -p gpu ./test-include.out
> > ...
> > srun: launch/slurm: _task_start: Node gpu003, 1 tasks started
> > srun: launch/slurm: _task_finish: Received task exit notification for 1
> > task of StepId=203117.0 (*status=0x0000*).
> > srun: launch/slurm: _task_finish: gpu003: task 0: Completed
> >
> > I would be grateful for any help
> > in this regard.
> > Thanks
> > Nitin Kulhar
> > On Sat, Oct 19, 2024 at 12:14???AM Scott Brozell <sbrozell.comcast.net>
> wrote:
> >
> > > 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
> > >
> > > scott
>
--
Disclaimer:- This footer text is to convey that this email is sent by one
of the users of IITH. So, do not mark it as SPAM.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 21 2024 - 21:00:01 PDT
