From 9013b9da8a7ce2eadf91d415ef9dcbde4b5100b9 Mon Sep 17 00:00:00 2001 From: AmauryC <87360587+Amaury070@users.noreply.github.com> Date: Wed, 23 Oct 2024 15:10:39 +0200 Subject: [PATCH 01/10] Update lammps.rst --- docs/source/lammps.rst | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/docs/source/lammps.rst b/docs/source/lammps.rst index e2808c9..2ef7454 100644 --- a/docs/source/lammps.rst +++ b/docs/source/lammps.rst @@ -28,7 +28,7 @@ For instance, from the terminal, download the last stable release: LAMMPS -Compile LAMMPS +Compile LAMMPS with make -------------- For compiling in serial, simply navidate to the ``src/`` folder, and type: @@ -50,6 +50,26 @@ Then, from the ``src/`` folder, type: make mpi +Compile LAMMPS with cmake using guix environment +-------------- + +source your guix environment and install the following package(specified the openmpi version, some issues were observed on dahu cluster with openmpi 5) +.. code-block:: bash +source /applis/site/guix-start.sh +guix install cmake +guix install gcc-toolchain +guix install openmpi@4.1.6 +guix install clang +guix install ffmpeg +.. code-block:: bash +navigate into your lammps home, create a folder build and compile : +.. code-block:: bash +mkdir build +cd build +cmake ../cmake -D PKG_MOLECULE=on -D PKG_KSPACE=on -D PKG_RIGID=on +.. code-block:: bash + +It creates an executable lmp in the directory. You can add as many packages as you want and create different build if you need it. Run LAMMPS ---------- From 3cff83bfa59f9d3b404ab0203d3f501f96bf61cf Mon Sep 17 00:00:00 2001 From: AmauryC <87360587+Amaury070@users.noreply.github.com> Date: Wed, 23 Oct 2024 15:11:25 +0200 Subject: [PATCH 02/10] Update lammps.rst --- docs/source/lammps.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source/lammps.rst b/docs/source/lammps.rst index 2ef7454..6d3e5ea 100644 --- a/docs/source/lammps.rst +++ b/docs/source/lammps.rst @@ -54,20 +54,20 @@ Compile LAMMPS with cmake using guix environment -------------- source your guix environment and install the following package(specified the openmpi version, some issues were observed on dahu cluster with openmpi 5) -.. code-block:: bash +.. code-block:: guix source /applis/site/guix-start.sh guix install cmake guix install gcc-toolchain guix install openmpi@4.1.6 guix install clang guix install ffmpeg -.. code-block:: bash +.. code-block:: guix navigate into your lammps home, create a folder build and compile : -.. code-block:: bash +.. code-block:: cmake mkdir build cd build cmake ../cmake -D PKG_MOLECULE=on -D PKG_KSPACE=on -D PKG_RIGID=on -.. code-block:: bash +.. code-block:: cmake It creates an executable lmp in the directory. You can add as many packages as you want and create different build if you need it. Run LAMMPS From 82831ecb897276b50720878d91c9aac96f8d4b83 Mon Sep 17 00:00:00 2001 From: AmauryC <87360587+Amaury070@users.noreply.github.com> Date: Wed, 23 Oct 2024 15:12:39 +0200 Subject: [PATCH 03/10] Update lammps.rst --- docs/source/lammps.rst | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/docs/source/lammps.rst b/docs/source/lammps.rst index 6d3e5ea..813f8ca 100644 --- a/docs/source/lammps.rst +++ b/docs/source/lammps.rst @@ -55,21 +55,22 @@ Compile LAMMPS with cmake using guix environment source your guix environment and install the following package(specified the openmpi version, some issues were observed on dahu cluster with openmpi 5) .. code-block:: guix -source /applis/site/guix-start.sh -guix install cmake -guix install gcc-toolchain -guix install openmpi@4.1.6 -guix install clang -guix install ffmpeg -.. code-block:: guix + source /applis/site/guix-start.sh + guix install cmake + guix install gcc-toolchain + guix install openmpi@4.1.6 + guix install clang + guix install ffmpeg + navigate into your lammps home, create a folder build and compile : .. code-block:: cmake -mkdir build -cd build -cmake ../cmake -D PKG_MOLECULE=on -D PKG_KSPACE=on -D PKG_RIGID=on -.. code-block:: cmake + mkdir build + cd build + cmake ../cmake -D PKG_MOLECULE=on -D PKG_KSPACE=on -D PKG_RIGID=on ... It creates an executable lmp in the directory. You can add as many packages as you want and create different build if you need it. + + Run LAMMPS ---------- From 49d7dea12a9046c493f83ae54b005eff628b57a0 Mon Sep 17 00:00:00 2001 From: AmauryC <87360587+Amaury070@users.noreply.github.com> Date: Wed, 23 Oct 2024 15:13:22 +0200 Subject: [PATCH 04/10] Update lammps.rst --- docs/source/lammps.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/source/lammps.rst b/docs/source/lammps.rst index 813f8ca..635c47b 100644 --- a/docs/source/lammps.rst +++ b/docs/source/lammps.rst @@ -54,6 +54,7 @@ Compile LAMMPS with cmake using guix environment -------------- source your guix environment and install the following package(specified the openmpi version, some issues were observed on dahu cluster with openmpi 5) + .. code-block:: guix source /applis/site/guix-start.sh guix install cmake @@ -63,6 +64,7 @@ source your guix environment and install the following package(specified the ope guix install ffmpeg navigate into your lammps home, create a folder build and compile : + .. code-block:: cmake mkdir build cd build From 3cdc397c9aa170505bbeb04db5264a10590ea878 Mon Sep 17 00:00:00 2001 From: AmauryC <87360587+Amaury070@users.noreply.github.com> Date: Wed, 23 Oct 2024 15:15:03 +0200 Subject: [PATCH 05/10] Update lammps.rst --- docs/source/lammps.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source/lammps.rst b/docs/source/lammps.rst index 635c47b..c7d6f80 100644 --- a/docs/source/lammps.rst +++ b/docs/source/lammps.rst @@ -55,21 +55,21 @@ Compile LAMMPS with cmake using guix environment source your guix environment and install the following package(specified the openmpi version, some issues were observed on dahu cluster with openmpi 5) -.. code-block:: guix +``` source /applis/site/guix-start.sh guix install cmake guix install gcc-toolchain guix install openmpi@4.1.6 guix install clang guix install ffmpeg - +``` navigate into your lammps home, create a folder build and compile : -.. code-block:: cmake +``` mkdir build cd build cmake ../cmake -D PKG_MOLECULE=on -D PKG_KSPACE=on -D PKG_RIGID=on ... - +``` It creates an executable lmp in the directory. You can add as many packages as you want and create different build if you need it. From 1f07ae01fae4111c503de634d56c3159279ead6e Mon Sep 17 00:00:00 2001 From: AmauryC <87360587+Amaury070@users.noreply.github.com> Date: Wed, 23 Oct 2024 15:16:15 +0200 Subject: [PATCH 06/10] Update lammps.rst --- docs/source/lammps.rst | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/docs/source/lammps.rst b/docs/source/lammps.rst index c7d6f80..f0f624a 100644 --- a/docs/source/lammps.rst +++ b/docs/source/lammps.rst @@ -55,21 +55,23 @@ Compile LAMMPS with cmake using guix environment source your guix environment and install the following package(specified the openmpi version, some issues were observed on dahu cluster with openmpi 5) -``` +.. code-block:: + source /applis/site/guix-start.sh guix install cmake guix install gcc-toolchain guix install openmpi@4.1.6 guix install clang guix install ffmpeg -``` + navigate into your lammps home, create a folder build and compile : -``` +.. code-block:: + mkdir build cd build cmake ../cmake -D PKG_MOLECULE=on -D PKG_KSPACE=on -D PKG_RIGID=on ... -``` + It creates an executable lmp in the directory. You can add as many packages as you want and create different build if you need it. From 89b939a59c5e41063fd1b8aecbb4676bd4584e7a Mon Sep 17 00:00:00 2001 From: AmauryC <87360587+Amaury070@users.noreply.github.com> Date: Wed, 23 Oct 2024 15:17:03 +0200 Subject: [PATCH 07/10] Update lammps.rst --- docs/source/lammps.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/lammps.rst b/docs/source/lammps.rst index f0f624a..3673c9d 100644 --- a/docs/source/lammps.rst +++ b/docs/source/lammps.rst @@ -70,7 +70,7 @@ navigate into your lammps home, create a folder build and compile : mkdir build cd build - cmake ../cmake -D PKG_MOLECULE=on -D PKG_KSPACE=on -D PKG_RIGID=on ... + cmake ../cmake -D PKG_MOLECULE=on -D PKG_KSPACE=on -D PKG_RIGID=on It creates an executable lmp in the directory. You can add as many packages as you want and create different build if you need it. From b1a7ab711c1afc683d63b95de334fccd80ca9b91 Mon Sep 17 00:00:00 2001 From: AmauryC <87360587+Amaury070@users.noreply.github.com> Date: Wed, 23 Oct 2024 15:19:17 +0200 Subject: [PATCH 08/10] Update lammps.rst --- docs/source/lammps.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/lammps.rst b/docs/source/lammps.rst index 3673c9d..5620f3f 100644 --- a/docs/source/lammps.rst +++ b/docs/source/lammps.rst @@ -64,7 +64,7 @@ source your guix environment and install the following package(specified the ope guix install clang guix install ffmpeg -navigate into your lammps home, create a folder build and compile : +navigate into your lammps home, create a folder ``build/``. From the ``build/`` folder, compile LAMMPS: .. code-block:: From a751f6eab2cf69d42a46f2f242d1cbcb5f579c8f Mon Sep 17 00:00:00 2001 From: AmauryC <87360587+Amaury070@users.noreply.github.com> Date: Wed, 23 Oct 2024 15:22:03 +0200 Subject: [PATCH 09/10] Update lammps.rst --- docs/source/lammps.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/lammps.rst b/docs/source/lammps.rst index 5620f3f..15708ef 100644 --- a/docs/source/lammps.rst +++ b/docs/source/lammps.rst @@ -72,7 +72,7 @@ navigate into your lammps home, create a folder ``build/``. From the ``build/`` cd build cmake ../cmake -D PKG_MOLECULE=on -D PKG_KSPACE=on -D PKG_RIGID=on -It creates an executable lmp in the directory. You can add as many packages as you want and create different build if you need it. +It creates an executable lmp in the directory. You can add as many packages as you want and you can create different build if you need it. Run LAMMPS From ce059183decaaae4e7aec5742cfa0c2107f424cc Mon Sep 17 00:00:00 2001 From: AmauryC <87360587+Amaury070@users.noreply.github.com> Date: Wed, 23 Oct 2024 15:25:37 +0200 Subject: [PATCH 10/10] Update lammps.rst --- docs/source/lammps.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/lammps.rst b/docs/source/lammps.rst index 15708ef..5a8c85e 100644 --- a/docs/source/lammps.rst +++ b/docs/source/lammps.rst @@ -59,6 +59,7 @@ source your guix environment and install the following package(specified the ope source /applis/site/guix-start.sh guix install cmake + guix install glibc-locales guix install gcc-toolchain guix install openmpi@4.1.6 guix install clang