From 5b975e502932029fd0e5f383e2a8921cc8deed05 Mon Sep 17 00:00:00 2001 From: Youjia Li Date: Tue, 12 Nov 2024 16:49:09 -0600 Subject: [PATCH 1/5] add instructions for quick install --- README.md | 6 ++++++ docs/source/installation/install.rst | 8 ++++++-- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ae1b755..ca15fbd 100644 --- a/README.md +++ b/README.md @@ -15,6 +15,12 @@ scalable I/O performance. * MPI C library and Python package, [mpi4py](https://mpi4py.readthedocs.io/en/stable/install.html). * [PnetCDF C library](https://github.com/Parallel-netCDF/PnetCDF), built with shared libraries. +### Quick Installation +* Make sure have a working MPI and pnetcdf-C software and then use pip to install pnetcdf-Python library from PyPI + ``` + CC=/path/to/mpicc PNETCDF_DIR=/path/to/pnetcdf/dir/ pip install pnetcdf + ``` + ### Developer Installation * Clone this GitHub repository * Required software for developer installation: diff --git a/docs/source/installation/install.rst b/docs/source/installation/install.rst index 0b9d954..af7c81e 100644 --- a/docs/source/installation/install.rst +++ b/docs/source/installation/install.rst @@ -6,8 +6,12 @@ Installation Quick Install =================================== -Quick installation via pip install is currently unavailable as this library has not yet been uploaded to PyPI. -Please follow building from source instructions provided below to set up the library. +Software Requirements + - PnetCDF C library (built with shared libraries) and MPI C library + +Make sure have a working MPI and pnetcdf-C software and then use pip to install pnetcdf-Python library from PyPI +.. code-block:: bash + $ CC=/path/to/mpicc PNETCDF_DIR=/path/to/pnetcdf/dir/ pip install pnetcdf Install from Source ============================================ From 7adcf0035fc82975fcb68f185eb288c29a48d8ae Mon Sep 17 00:00:00 2001 From: Youjia Li Date: Tue, 12 Nov 2024 16:53:22 -0600 Subject: [PATCH 2/5] fixed typo in instructions --- README.md | 2 +- docs/source/installation/install.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ca15fbd..55e09d9 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ scalable I/O performance. * [PnetCDF C library](https://github.com/Parallel-netCDF/PnetCDF), built with shared libraries. ### Quick Installation -* Make sure have a working MPI and pnetcdf-C software and then use pip to install pnetcdf-Python library from PyPI +* Make sure you have a working MPI and pnetcdf-C software and then use pip to install pnetcdf-Python library from PyPI ``` CC=/path/to/mpicc PNETCDF_DIR=/path/to/pnetcdf/dir/ pip install pnetcdf ``` diff --git a/docs/source/installation/install.rst b/docs/source/installation/install.rst index af7c81e..cdcfedf 100644 --- a/docs/source/installation/install.rst +++ b/docs/source/installation/install.rst @@ -9,7 +9,7 @@ Quick Install Software Requirements - PnetCDF C library (built with shared libraries) and MPI C library -Make sure have a working MPI and pnetcdf-C software and then use pip to install pnetcdf-Python library from PyPI +Make sure you have a working MPI and pnetcdf-C software and then use pip to install pnetcdf-Python library from PyPI .. code-block:: bash $ CC=/path/to/mpicc PNETCDF_DIR=/path/to/pnetcdf/dir/ pip install pnetcdf From d0da5d3bf359898238aa5e884ad55afa24a3ae49 Mon Sep 17 00:00:00 2001 From: Youjia Li Date: Tue, 12 Nov 2024 17:24:25 -0600 Subject: [PATCH 3/5] update MPICH version to 4.2.2 in github actions --- .github/workflows/pnetcdf_c_master.yml | 2 +- .github/workflows/pnetcdf_c_official.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pnetcdf_c_master.yml b/.github/workflows/pnetcdf_c_master.yml index 4429e75..e7b2699 100644 --- a/.github/workflows/pnetcdf_c_master.yml +++ b/.github/workflows/pnetcdf_c_master.yml @@ -19,7 +19,7 @@ jobs: runs-on: ubuntu-latest timeout-minutes: 60 env: - MPICH_VERSION: 4.2.0 + MPICH_VERSION: 4.2.2 MPICH_DIR: ${{ github.workspace }}/mpich-install PNETCDF_VERSION: repo PNETCDF_DIR: ${{ github.workspace }}/PnetCDF-install diff --git a/.github/workflows/pnetcdf_c_official.yml b/.github/workflows/pnetcdf_c_official.yml index 7749f82..c09d4cd 100644 --- a/.github/workflows/pnetcdf_c_official.yml +++ b/.github/workflows/pnetcdf_c_official.yml @@ -19,7 +19,7 @@ jobs: runs-on: ubuntu-latest timeout-minutes: 60 env: - MPICH_VERSION: 4.2.0 + MPICH_VERSION: 4.2.2 MPICH_DIR: ${{ github.workspace }}/mpich-install PNETCDF_VERSION: 1.13.0 PNETCDF_DIR: ${{ github.workspace }}/PnetCDF-install From c2f9d1e3538d1eebb12c40d5f85781c6bab98e17 Mon Sep 17 00:00:00 2001 From: Youjia Li Date: Tue, 12 Nov 2024 17:39:13 -0600 Subject: [PATCH 4/5] modified user guide --- docs/source/installation/install.rst | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/docs/source/installation/install.rst b/docs/source/installation/install.rst index cdcfedf..37f6345 100644 --- a/docs/source/installation/install.rst +++ b/docs/source/installation/install.rst @@ -9,9 +9,11 @@ Quick Install Software Requirements - PnetCDF C library (built with shared libraries) and MPI C library -Make sure you have a working MPI and pnetcdf-C software and then use pip to install pnetcdf-Python library from PyPI -.. code-block:: bash - $ CC=/path/to/mpicc PNETCDF_DIR=/path/to/pnetcdf/dir/ pip install pnetcdf +Install PnetCDF-python library from PyPI + .. code-block:: bash + + $ CC=/path/to/mpicc PNETCDF_DIR=/path/to/pnetcdf/dir/ pip install pnetcdf + Install from Source ============================================ From 0ea8f7980a89e9b957dd8b703b67b0dc164fe7e9 Mon Sep 17 00:00:00 2001 From: wkliao Date: Tue, 12 Nov 2024 18:05:35 -0600 Subject: [PATCH 5/5] MPICH 4.2.2 is required when using mpi4py 4.0 This is because MPI 4.0's large-count feature is only properly supported by MPICH starting from 4.2.2. --- README.md | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 55e09d9..9574ec5 100644 --- a/README.md +++ b/README.md @@ -12,11 +12,16 @@ scalable I/O performance. ### Software Dependencies * Python 3.9 or later. * [numpy](http://www.numpy.org/) Python package. -* MPI C library and Python package, [mpi4py](https://mpi4py.readthedocs.io/en/stable/install.html). -* [PnetCDF C library](https://github.com/Parallel-netCDF/PnetCDF), built with shared libraries. +* MPI C library and Python package, + [mpi4py](https://mpi4py.readthedocs.io/en/stable/install.html). + + Note when using mpi4py 4.0 and MPICH, MPICH version 4.2.2 and later is + required. +* [PnetCDF C library](https://github.com/Parallel-netCDF/PnetCDF), built with + shared libraries. ### Quick Installation -* Make sure you have a working MPI and pnetcdf-C software and then use pip to install pnetcdf-Python library from PyPI +* Make sure you have a working MPI and PnetCDF-C software installed. +* Run pip command below to install PnetCDF-Python library from PyPI: ``` CC=/path/to/mpicc PNETCDF_DIR=/path/to/pnetcdf/dir/ pip install pnetcdf ```