From adc6ce4c535cb2ba8012b9906fd08a6f20884932 Mon Sep 17 00:00:00 2001 From: Daniel J <daniel.jana@epfl.ch> Date: Tue, 28 Jan 2025 10:47:02 +0100 Subject: [PATCH 1/4] Added namd@3.0.1 to stack (gpu-only) --- stacks/pinot-noir/definitions_acc_cuda.yaml | 1 + stacks/pinot-noir/packages_acc_cuda.yaml | 3 +++ 2 files changed, 4 insertions(+) diff --git a/stacks/pinot-noir/definitions_acc_cuda.yaml b/stacks/pinot-noir/definitions_acc_cuda.yaml index 23cc17d..30bdd68 100644 --- a/stacks/pinot-noir/definitions_acc_cuda.yaml +++ b/stacks/pinot-noir/definitions_acc_cuda.yaml @@ -4,6 +4,7 @@ definitions: - cuda_serial_codes: - cuda - cudnn + - namd ^fftw ~mpi - nccl - cuda_mpi_codes: diff --git a/stacks/pinot-noir/packages_acc_cuda.yaml b/stacks/pinot-noir/packages_acc_cuda.yaml index 8bb0498..3c9c4b0 100644 --- a/stacks/pinot-noir/packages_acc_cuda.yaml +++ b/stacks/pinot-noir/packages_acc_cuda.yaml @@ -45,6 +45,9 @@ packages: libxc: require: ['+cuda', 'cuda_arch={cuda_arch}'] + namd: + require: ['+cuda', '+single_node_gpu', 'cuda_arch={cuda_arch}'] + nvshmem: require: - spec: '+cuda cuda_arch={cuda_arch} +nccl +ucx +mpi' -- GitLab From abf94ab19c81a5f06b6a9316c06a4628dd387365 Mon Sep 17 00:00:00 2001 From: Daniel J <daniel.jana@epfl.ch> Date: Tue, 28 Jan 2025 18:08:26 +0100 Subject: [PATCH 2/4] Force charmpp to ~cuda --- stacks/pinot-noir/definitions_acc_cuda.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stacks/pinot-noir/definitions_acc_cuda.yaml b/stacks/pinot-noir/definitions_acc_cuda.yaml index 30bdd68..596c814 100644 --- a/stacks/pinot-noir/definitions_acc_cuda.yaml +++ b/stacks/pinot-noir/definitions_acc_cuda.yaml @@ -4,7 +4,7 @@ definitions: - cuda_serial_codes: - cuda - cudnn - - namd ^fftw ~mpi + - namd ^fftw ~mpi ^charmpp ~cuda - nccl - cuda_mpi_codes: -- GitLab From 2c90965668043cd2d1b7fb321a14ac2d12d44036 Mon Sep 17 00:00:00 2001 From: Daniel J <daniel.jana@epfl.ch> Date: Wed, 29 Jan 2025 16:29:50 +0100 Subject: [PATCH 3/4] Constrain charmpp further --- stacks/pinot-noir/definitions_acc_cuda.yaml | 2 +- stacks/pinot-noir/packages_acc_cuda.yaml | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/stacks/pinot-noir/definitions_acc_cuda.yaml b/stacks/pinot-noir/definitions_acc_cuda.yaml index 596c814..30bdd68 100644 --- a/stacks/pinot-noir/definitions_acc_cuda.yaml +++ b/stacks/pinot-noir/definitions_acc_cuda.yaml @@ -4,7 +4,7 @@ definitions: - cuda_serial_codes: - cuda - cudnn - - namd ^fftw ~mpi ^charmpp ~cuda + - namd ^fftw ~mpi - nccl - cuda_mpi_codes: diff --git a/stacks/pinot-noir/packages_acc_cuda.yaml b/stacks/pinot-noir/packages_acc_cuda.yaml index 3c9c4b0..f4eccc4 100644 --- a/stacks/pinot-noir/packages_acc_cuda.yaml +++ b/stacks/pinot-noir/packages_acc_cuda.yaml @@ -16,6 +16,9 @@ packages: amber: require: ['+nccl'] + charmpp: + require: ['+smp', '~cuda'] + cuda: prefer: - spec: "^gcc-runtime@{gcc_version} target={target}" -- GitLab From 79c1d4b664d04e09bcee32919ac0e9801f64039e Mon Sep 17 00:00:00 2001 From: Daniel J <daniel.jana@epfl.ch> Date: Wed, 29 Jan 2025 19:10:52 +0100 Subject: [PATCH 4/4] Force namd to 3.0.1 --- stacks/pinot-noir/definitions_acc_cuda.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stacks/pinot-noir/definitions_acc_cuda.yaml b/stacks/pinot-noir/definitions_acc_cuda.yaml index 30bdd68..026bd3f 100644 --- a/stacks/pinot-noir/definitions_acc_cuda.yaml +++ b/stacks/pinot-noir/definitions_acc_cuda.yaml @@ -4,7 +4,7 @@ definitions: - cuda_serial_codes: - cuda - cudnn - - namd ^fftw ~mpi + - namd@3.0.1 ^fftw ~mpi - nccl - cuda_mpi_codes: -- GitLab