WIP: GROMACS 2024.2 with NVSHMEM & cuFFTMp fixes for Slingshot

docs/uenv-gromacs.md

@@ -44,6 +44,30 @@ The `plumed` view contains GROMACS 2022.5 (older version) with PLUMED 2.9.0. Thi
 
 The `gromacs` view contains the newest GROMACS 2024.1 that has been configured and tested for the highest performance on the Grace-Hopper nodes.
 
+### Build from Source
+
+Users that require customized variants of the packages can build their own using the `develop` view. One can use the following set of commands to do the same.
+
+```bash
+uenv start gromacs/2024:v1 
+
+# this sets PATH, LD_LIBRARY_PATH and PKG_CONFIG_PATH with the dependencies of gromacs and plumed
+uenv view develop
+
+# load GROMACS source from repo/tarball and cd to it
+mkdir build
+cd build
+CXX=mpic++ CC=mpicc ftn=mpif90
+cmake .. -DGMX_MPI=on -DGMX_GPU=CUDA -DGMX_SIMD=ARM_NEON_ASIMD
+make
+make check
+make install
+source /usr/local/gromacs/bin/GMXRC
+
+# same for plumed
+# set CXX, etc and call the build system
+```
+
 ### How to Run
 
 To start a job, 2 bash scripts are required: a standard SLURM submission script, and a wrapper to start the CUDA MPS daemon (in order to have multiple MPI ranks per GPU).

recipes/gromacs/2024.2/gh200-mpi/compilers.yaml

@@ -0,0 +1,5 @@
+bootstrap:
+  spec: gcc@12
+gcc:
+  specs:
+  - [email protected]

recipes/gromacs/2024.2/gh200-mpi/config.yaml

@@ -0,0 +1,7 @@
+name: gromacs-gh200
+store: /user-environment
+description: GPU-optimised GROMACS with and without PLUMED, and the toolchain to build your own GROMACS.
+spack:
+  repo: https://github.com/spack/spack.git
+  commit: v0.22.0
+modules: false

recipes/gromacs/2024.2/gh200-mpi/environments.yaml

@@ -0,0 +1,35 @@
+gromacs:
+  compiler:
+  - toolchain: gcc
+    spec: [email protected]
+  unify: when_possible
+  specs:
+  - cmake
+  - cuda
+  - [email protected]
+  - blas
+  - lapack
+  - hwloc
+  - fftw
+  - [email protected]
+  - [email protected] +cuda +mpi +hwloc +cufftmp
+  - [email protected] +cuda ~shared +mpi +hwloc +cufftmp +plumed
+  mpi:
+    spec: [email protected]
+    gpu: cuda
+  variants:
+  - +mpi
+  - +cuda
+  - cuda_arch=90
+  views:
+    develop:
+      exclude: ['gromacs']
+    gromacs: 
+      exclude: ['gromacs+plumed']
+      link: run
+    plumed:
+      exclude: ['[email protected]']
+      link: run
+  packages:
+  - perl
+

recipes/gromacs/2024.2/gh200-mpi/modules.yaml

@@ -0,0 +1,23 @@
+modules:
+  # Paths to check when creating modules for all module sets
+  prefix_inspections:
+    bin:
+      - PATH
+    lib:
+      - LD_LIBRARY_PATH
+    lib64:
+      - LD_LIBRARY_PATH
+
+  default:
+    arch_folder: false
+    # Where to install modules
+    roots:
+      tcl: /user-environment/modules
+    tcl:
+      all:
+        autoload: none
+      hash_length: 0
+      exclude_implicits: true
+      exclude: ['%[email protected]', 'gcc %[email protected]']
+      projections:
+        all: '{name}/{version}'

recipes/gromacs/2024.2/gh200-mpi/repo/packages/gromacs/gmxDetectCpu-cmake-3.14.patch

@@ -0,0 +1,12 @@
+--- a/cmake/gmxDetectCpu.cmake
++++ b/cmake/gmxDetectCpu.cmake
+@@ -83,7 +83,7 @@ function(gmx_run_cpu_detection TYPE)
+                 set(GCC_INLINE_ASM_DEFINE "-DGMX_X86_GCC_INLINE_ASM=0")
+             endif()
+
+-            set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${PROJECT_SOURCE_DIR}/src -DGMX_CPUINFO_STANDALONE ${GMX_STDLIB_CXX_FLAGS} -DGMX_TARGET_X86=${GMX_TARGET_X86_VALUE}")
++            set(_compile_definitions ${GCC_INLINE_ASM_DEFINE} -I${PROJECT_SOURCE_DIR}/src -DGMX_CPUINFO_STANDALONE ${GMX_STDLIB_CXX_FLAGS} -DGMX_TARGET_X86=${GMX_TARGET_X86_VALUE})
+             set(LINK_LIBRARIES "${GMX_STDLIB_LIBRARIES}")
+             try_compile(CPU_DETECTION_COMPILED
+                 "${PROJECT_BINARY_DIR}"
+

recipes/gromacs/2024.2/gh200-mpi/repo/packages/gromacs/gmxDetectSimd-cmake-3.14.patch

@@ -0,0 +1,11 @@
+--- a/cmake/gmxDetectSimd.cmake
++++ b/cmake/gmxDetectSimd.cmake
+@@ -77,7 +77,7 @@ function(gmx_suggest_simd _suggested_simd)
+     else()
+         set(GMX_TARGET_X86_VALUE 0)
+     endif()
+-    set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${CMAKE_SOURCE_DIR}/src -DGMX_CPUINFO_STANDALONE ${GMX_STDLIB_CXX_FLAGS} -DGMX_TARGET_X86=${GMX_TARGET_X86_VALUE}")
++    set(_compile_definitions ${GCC_INLINE_ASM_DEFINE} -I${CMAKE_SOURCE_DIR}/src -DGMX_CPUINFO_STANDALONE ${GMX_STDLIB_CXX_FLAGS} -DGMX_TARGET_X86=${GMX_TARGET_X86_VALUE})
+
+     # Prepare a default suggestion
+     set(OUTPUT_SIMD "None")