Hello Florian,
Yes, the issue has been solved by using an older GCC compiler and OpenMPI.
The OS of my HPC cluster is Rocky 8.10, and here are the scripts and steps I had:
#!/bin/bash
# step 1 - add the GPU support
module load cmake-3.26.5-gcc-11.2.0-ed \
gcc-8.5.0-gcc-11.2.0-kn \
intel-oneapi-mkl-2023.2.0-me \
openblas-0.3.24-5f \
cuda-11.8.0-gcc-11.2.0-66
# edit the run_cmake script:
# -DCMAKE_INSTALL_PREFIX=/packages/apps/amber/24 \
# -DMPI=FALSE -DCUDA=TRUE
export CUDA_HOME=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/cuda-11.8.0-66eeijo
./run_cmake
make install
#!/bin/bash
# step 2 - add the MPI support
module load cmake-3.26.5-gcc-11.2.0-ed \
gcc-8.5.0-gcc-11.2.0-kn \
intel-oneapi-mkl-2023.2.0-me \
openblas-0.3.24-5f \
openmpi/4.1.5 \
cuda-11.8.0-gcc-11.2.0-66
# edit the run_cmake script:
# -DCMAKE_INSTALL_PREFIX=/packages/apps/amber/24 \
# -DMPI=TRUE -DCUDA=TRUE
export CUDA_HOME=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/cuda-11.8.0-66eeijo
./run_cmake
make install
#!/bin/bash
# test script for cuda&mpi build
module load cmake-3.26.5-gcc-11.2.0-ed \
gcc-8.5.0-gcc-11.2.0-kn \
intel-oneapi-mkl-2023.2.0-me \
openblas-0.3.24-5f \
openmpi/4.1.5 \
cuda-11.8.0-gcc-11.2.0-66
cd /packages/apps/amber/24
source amber.sh
export DO_PARALLEL="mpirun -np 4"
make test.cuda.parallel
# Test result
[software.pg002:logs]$ cat test_at_cuda_parallel/at_summary
0 file comparisons passed
0 file comparisons failed
0 tests experienced errors
Test log file saved as /packages/apps/amber/24///logs/test_at_cuda_parallel/2024-07-18_09-14-48.log
No test diffs to save!
[software.pg002:logs]$ pwd
/packages/apps/amber/24/logs
Regards,
Nil Mu
HPC Systems Analyst
Research Computing
Arizona State University
From: "Pertschy, Florian" <florian.pertschy.medunigraz.at>
Date: Tuesday, August 6, 2024 at 8:47 AM
To: Nil Mu <nil.mu.asu.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: Cmake unable to find Mpich
Hello!
Were you able to resolve this? I'm running into similar problems
________________________________
From: Nil Mu via AMBER <amber.ambermd.org>
Sent: 29 June 2024 02:57:24
To: amber.ambermd.org
Subject: [EXT] [AMBER] Cmake unable to find Mpich
Hello,
I’m trying to install Amber 22 or Amber 24 to our HPC cluster, running on Linux Rocky 8.9.
I was able to build the serial version, and then the cuda version without issues. But I wasn’t able to go through building the MPI version.
Here is the installation script I have tried, along with the error messages. It would be super helpful if I can get some insights for this issue, and thanks in advance!
Installation script
****************************************************************************************************************************************************
#!/bin/bash
module load cmake-3.29.6-ab \
gcc-11.2.0-2q \
intel-oneapi-mkl-2023.2.0-me \
openblas-0.3.24-5f \
mamba/latest \
cuda-11.8.0-gcc-11.2.0-66 \
mpich-4.1.2-gcc-11.2.0-cuda-ax
export PATH=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/bin:$PATH
export LD_LIBRARY_PATH=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/lib:$LD_LIBRARY_PATH
export MPI_HOME=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/bin
export MPI_C_INCLUDE_PATH=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/include
export MPI_C_LIBRARIES=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/libmpi.so
export MPI_C=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/lib/libmpi.so
export MPI_CXX=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/lib/libmpicxx.so
export MPI_Fortran=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/lib/libmpicxx.so
export CUDA_HOME=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/cuda-11.8.0-66eeijo
./run_cmake
make install
****************************************************************************************************************************************************
# Edit the run_cmake script
cmake $AMBER_PREFIX/amber24_src \
-DCMAKE_INSTALL_PREFIX=/packages/apps/amber/24_cuda_mpi \
-DCOMPILER=GNU \
-DMPI_C_COMPILER=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/bin/mpicc \
-DMPI_CXX_COMPILER=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/bin/mpicxx \
-DMPI_Fortran_COMPILER=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/bin/mpif90 \
-DMPIEXEC_EXECUTABLE=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/bin/mpiexec \
-DMPI_C_INCLUDE_PATH=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/include \
-DMPI_C_LIBRARIES=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/lib/libmpi.so \
-DCMAKE_PREFIX_PATH=/packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-11.2.0/mpich-4.1.2-axmujgv/bin/ \
-DMPI=TRUE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE
2>&1 | tee cmake.log
****************************************************************************************************************************************************
Error messages
****************************************************************************************************************************************************
-- Setting C compiler to gcc
-- Setting CXX compiler to g++
-- Setting Fortran compiler to gfortran
-- Amber source not found, only building AmberTools
-- The C compiler identification is GNU 11.2.0
-- The CXX compiler identification is GNU 11.2.0
-- The Fortran compiler identification is GNU 11.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-12.3.0/gcc-11.2.0-2qermfr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-12.3.0/gcc-11.2.0-2qermfr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /packages/apps/spack/21.2/opt/spack/x86_64_v3/gcc-12.3.0/gcc-11.2.0-2qermfr/bin/gfortran - skipped
-- Testing if stdlib.h can be included...
-- Testing if stdlib.h can be included... yes
-- Could NOT find MPI_C (missing: MPI_C_WORKS)
-- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS)
-- Could NOT find MPI_Fortran (missing: MPI_Fortran_WORKS)
-- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND MPI_Fortran_FOUND)
CMake Error at cmake/MPIConfig.cmake:12 (message):
You requested MPI, but the MPI C library was not found. Please install one
and try again, or set MPI_C_INCLUDE_PATH and MPI_C_LIBRARIES to point to
your MPI.
Call Stack (most recent call first):
CMakeLists.txt:117 (include)
-- Configuring incomplete, errors occurred!
If errors are reported, search for 'CMake Error' in the cmake.log file.
If the cmake build report looks OK, you should now do the following:
make install
source /packages/apps/build/amber/amber24/amber24/amber.sh
Consider adding the last line to your login startup script, e.g. ~/.bashrc
cat install.sh >install
chmod a+x install
****************************************************************************************************************************************************
Thanks,
Nil Mu
HPC Systems Analyst
Research Computing
Arizona State University
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Received on Tue Aug 06 2024 - 13:30:02 PDT
