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