From 23cae3f230810b1dfd1d7a80de0838b291f42908 Mon Sep 17 00:00:00 2001
From: Daniel J <daniel.jana@epfl.ch>
Date: Thu, 13 Feb 2025 15:04:23 +0100
Subject: [PATCH 1/4] Add namd with tcl support
---
stacks/pinot-noir/definitions_acc_cuda.yaml | 2 +-
stacks/pinot-noir/modules_common.yaml | 1 +
stacks/pinot-noir/packages_acc_cuda.yaml | 2 +-
3 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/stacks/pinot-noir/definitions_acc_cuda.yaml b/stacks/pinot-noir/definitions_acc_cuda.yaml
index 026bd3f..1639b25 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@3.0.1 ^fftw ~mpi
+ - namd@3.0.1 interface=tcl ^fftw ~mpi
- nccl
- cuda_mpi_codes:
diff --git a/stacks/pinot-noir/modules_common.yaml b/stacks/pinot-noir/modules_common.yaml
index fc274c7..135e4d5 100644
--- a/stacks/pinot-noir/modules_common.yaml
+++ b/stacks/pinot-noir/modules_common.yaml
@@ -30,6 +30,7 @@ modules:
'+ilp64': int64
'+int64': int64
'version_suffix=jl': julia
+ 'interface=tcl': tcl
autoload: run
hide_implicits: true
diff --git a/stacks/pinot-noir/packages_acc_cuda.yaml b/stacks/pinot-noir/packages_acc_cuda.yaml
index f4eccc4..173f602 100644
--- a/stacks/pinot-noir/packages_acc_cuda.yaml
+++ b/stacks/pinot-noir/packages_acc_cuda.yaml
@@ -49,7 +49,7 @@ packages:
require: ['+cuda', 'cuda_arch={cuda_arch}']
namd:
- require: ['+cuda', '+single_node_gpu', 'cuda_arch={cuda_arch}']
+ require: ['+cuda', '+single_node_gpu', 'cuda_arch={cuda_arch}', 'interface=tcl']
nvshmem:
require:
--
GitLab
From 6268d796f30d2fec53aef7ea8522a3a79bd176dd Mon Sep 17 00:00:00 2001
From: Daniel J <daniel.jana@epfl.ch>
Date: Fri, 14 Feb 2025 09:16:55 +0100
Subject: [PATCH 2/4] make namd interface=tcl generic
---
stacks/pinot-noir/packages_acc_cuda.yaml | 2 +-
stacks/pinot-noir/packages_stack.yaml | 3 +++
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/stacks/pinot-noir/packages_acc_cuda.yaml b/stacks/pinot-noir/packages_acc_cuda.yaml
index 173f602..f4eccc4 100644
--- a/stacks/pinot-noir/packages_acc_cuda.yaml
+++ b/stacks/pinot-noir/packages_acc_cuda.yaml
@@ -49,7 +49,7 @@ packages:
require: ['+cuda', 'cuda_arch={cuda_arch}']
namd:
- require: ['+cuda', '+single_node_gpu', 'cuda_arch={cuda_arch}', 'interface=tcl']
+ require: ['+cuda', '+single_node_gpu', 'cuda_arch={cuda_arch}']
nvshmem:
require:
diff --git a/stacks/pinot-noir/packages_stack.yaml b/stacks/pinot-noir/packages_stack.yaml
index 4074487..e59f8dc 100644
--- a/stacks/pinot-noir/packages_stack.yaml
+++ b/stacks/pinot-noir/packages_stack.yaml
@@ -234,6 +234,9 @@ packages:
mumps:
require: ['+openmp', '+metis', '+parmetis']
+ namd:
+ require: ['interface=tcl']
+
netcdf-c:
prefer: ['+mpi']
--
GitLab
From dc659d5073810f6c13ba3d59ed894a9aa552f81c Mon Sep 17 00:00:00 2001
From: Daniel J <daniel.jana@epfl.ch>
Date: Fri, 28 Feb 2025 08:35:32 +0100
Subject: [PATCH 3/4] keeping both versions
---
stacks/pinot-noir/definitions_acc_cuda.yaml | 1 +
1 file changed, 1 insertion(+)
diff --git a/stacks/pinot-noir/definitions_acc_cuda.yaml b/stacks/pinot-noir/definitions_acc_cuda.yaml
index 1639b25..d417ff1 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@3.0.1 ^fftw ~mpi
- namd@3.0.1 interface=tcl ^fftw ~mpi
- nccl
--
GitLab
From b8fa18bb997ab33688de93b4cb58ba4b8f15464d Mon Sep 17 00:00:00 2001
From: Daniel Filipe Jana <daniel.jana@epfl.ch>
Date: Fri, 28 Feb 2025 07:51:10 +0000
Subject: [PATCH 4/4] Updating gitlab-ci file since the sysadmins removed the
izar partition
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8b799cd..29d87d3 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -31,7 +31,7 @@ variables:
path_suffix: ['']
- environment: [izar]
- slurm_options: ['-c 20 --gpus 1 -p izar']
+ slurm_options: ['-c 20 --gpus 1 -p gpu']
apptainer_options: ['--nv']
stack: ["pinot-noir"]
app_image: ["registry.c4science.ch/scitas-stack/rhel9-jed"]
--
GitLab