Add fesom2_ci image with OASIS and XIOS preinstalled

.github/workflows/docker-publish.yml

@@ -34,6 +34,7 @@ jobs:
   build:
     needs: generate-matrix
     strategy:
+      fail-fast: false
       matrix:
         dockerfile: ${{fromJson(needs.generate-matrix.outputs.matrix)}}
     runs-on: ubuntu-latest

fesom2_ci/Dockerfile

@@ -0,0 +1,96 @@
+# FESOM2 CI build-test image
+#
+# Provides the toolchain used by FESOM/fesom2's build-test workflow:
+#   - GCC + OpenMPI + NetCDF/HDF5 + LAPACK
+#   - OASIS3-MCT prebuilt at /oasis (CMake build)
+#   - XIOS 2.5 prebuilt at /xios (make_xios with arch-GCC_LINUX, sequential netcdf)
+#
+# Source for OASIS and XIOS lives next to this Dockerfile (./oasis/ and ./xios/),
+# committed to FESOM/FESOM2_Docker so the docker build doesn't depend on
+# gitlab.dkrz.de being reachable from GHA runners (it isn't).
+#
+# Built and published by .github/workflows/docker-publish.yml in this repo to
+# ghcr.io/fesom/fesom2_docker:fesom2_ci-<version>. FESOM/fesom2's
+# fesom2_build_tests.yml runs inside this image and copies /oasis and /xios
+# into the workspace before configuring CMake.
+
+FROM ubuntu:22.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV TZ=UTC
+
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    cmake \
+    make \
+    git \
+    wget \
+    curl \
+    gfortran \
+    gcc \
+    g++ \
+    libopenmpi-dev \
+    openmpi-bin \
+    libnetcdf-dev \
+    libnetcdf-mpi-dev \
+    libnetcdff-dev \
+    libhdf5-dev \
+    libhdf5-openmpi-dev \
+    libhdf5-fortran-102 \
+    libhdf5-openmpi-fortran-102 \
+    liblapack-dev \
+    libblas-dev \
+    libopenblas-dev \
+    pkg-config \
+    perl \
+    uuid-dev \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+ENV OMPI_ALLOW_RUN_AS_ROOT=1
+ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+ENV FC=mpifort
+ENV CC=mpicc
+ENV CXX=mpicxx
+ENV LAPACK_LIBRARIES=/usr/lib/x86_64-linux-gnu/liblapack.so.3
+ENV CMAKE_ARGS=-DLAPACK_LIBRARIES=/usr/lib/x86_64-linux-gnu/liblapack.so.3
+ENV FESOM_PLATFORM_STRATEGY=ubuntu
+
+# OASIS3-MCT: copy source + CMake build to /oasis. The fesom2 workflow then
+# does `cp -rf /oasis ../` and FESOM's FindOASIS.cmake picks it up.
+COPY oasis /oasis
+RUN cd /oasis \
+    && mkdir -p build \
+    && cd build \
+    && cmake ../ -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
+    && make -j$(nproc)
+
+# XIOS 2.5: copy source + make_xios build to /xios. Sequential NetCDF is
+# sufficient for a build/link test of FESOM's __XIOS code path (CI doesn't
+# run XIOS). FCM_NEW is used (FCM_OLD removed to keep the source commit
+# small); extern/boost and extern/blitz are kept bundled because XIOS's
+# bld.cfg has hardcoded -I${PWD}/extern/{boost,blitz}/include paths that
+# --use_extern_boost/blitz don't rewrite.
+#
+# Two arch-GCC_LINUX overrides:
+#   - .env: upstream hardcodes $HOME/hdf5 and $HOME/netcdf4; rewrite to Ubuntu
+#     serial library paths so make_xios's `source arch.env` gives valid roots.
+#   - .fcm: upstream BASE_CFLAGS sets -ansi (= C++98) which forbids C++11
+#     lambdas as template args. XIOS 2.5 uses those (e.g. distribute_file_server2.cpp).
+#     Append -std=c++11 to override -ansi for C++ compilation.
+# arch-GCC_LINUX.path is left untouched — it already references the env vars
+# sourced from .env.
+COPY xios /xios
+RUN printf '%s\n' \
+        'export HDF5_INC_DIR=/usr/include/hdf5/serial' \
+        'export HDF5_LIB_DIR=/usr/lib/x86_64-linux-gnu/hdf5/serial' \
+        'export NETCDF_INC_DIR=/usr/include' \
+        'export NETCDF_LIB_DIR=/usr/lib/x86_64-linux-gnu' \
+        > /xios/arch/arch-GCC_LINUX.env \
+    && sed -i 's|^%BASE_CFLAGS .*|%BASE_CFLAGS    -ansi -w -fPIC -std=c++11|' \
+        /xios/arch/arch-GCC_LINUX.fcm \
+    && cd /xios \
+    && ./make_xios --arch GCC_LINUX --fcm new \
+                   --netcdf_lib netcdf4_seq --job $(nproc)
+
+WORKDIR /

fesom2_ci/README.md

@@ -0,0 +1,16 @@
+# fesom2_ci
+
+CI build-test image for [FESOM/fesom2](https://github.com/FESOM/fesom2). Provides:
+
+- Ubuntu 22.04 base
+- GCC, OpenMPI, NetCDF, HDF5, LAPACK
+- OASIS3-MCT prebuilt at `/oasis` (CMake, position-independent)
+- XIOS 2.5 prebuilt at `/xios` (`make_xios --arch GCC_LINUX --netcdf_lib netcdf4_seq`)
+
+Published by this repo's `docker-publish.yml` to
+`ghcr.io/fesom/fesom2_docker:fesom2_ci-<version>`.
+
+FESOM/fesom2's `.github/workflows/fesom2_build_tests.yml` runs inside this image and
+copies `/oasis` and `/xios` into the workspace before configuring CMake. XIOS is
+built with sequential NetCDF since CI only build-and-link-tests the XIOS path; it
+does not run XIOS at runtime.

fesom2_ci/oasis/.gitignore

@@ -0,0 +1,27 @@
+util/make_dir/COMP.err
+util/make_dir/COMP.log
+util/make_dir/COMP-shared.err
+util/make_dir/COMP-shared.log
+util/make_dir/COMP-pyoasis.err
+util/make_dir/COMP-pyoasis.log
+*.o
+*.mod
+*~
+examples/test_interpolation/model1
+examples/test_interpolation/model2
+examples/test_interpolation/test_interpolation_*
+doc/*.aux
+doc/*.cb
+doc/*.cb2
+doc/*.idx
+doc/*.log
+doc/*.toc
+arch_ecearth
+util/make_dir/make.ece.inc
+
+
+build/
+lib/libmct.a
+lib/libmpeu.a
+lib/libpsmile.a
+lib/libscrip.a

fesom2_ci/oasis/CMakeLists.txt

@@ -0,0 +1,11 @@
+cmake_minimum_required(VERSION 3.4)
+
+# set default build type cache entry (do so before project(...) is called, which would create this cache entry on its own)
+if(NOT CMAKE_BUILD_TYPE)
+	message(STATUS "setting default build type: Release")
+	set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: None(CMAKE_CXX_FLAGS or CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel.")
+endif()
+
+project(oasis3-mct)
+
+add_subdirectory(lib/psmile)

fesom2_ci/oasis/LICENSE

@@ -0,0 +1,106 @@
+OASIS3-MCT license and copyright statement
+------------------------------------------
+
+Copyright © 2021 Centre Européen de Recherche et Formation
+Avancée en Calcul Scientifique (CERFACS).  
+
+This software and ancillary information called OASIS3-MCT is free
+software.  CERFACS has rights to use, reproduce, and distribute
+OASIS3-MCT. The public may copy, distribute, use, prepare derivative works
+and publicly display OASIS3-MCT under the terms of the Lesser GNU General
+Public License (LGPL) as published by the Free Software Foundation,
+provided that this notice and any statement of authorship are
+reproduced on all copies. If OASIS3-MCT is modified to produce derivative
+works, such modified software should be clearly marked, so as not to
+confuse it with the OASIS3-MCT version available from CERFACS.
+
+The developers of the OASIS3-MCT software are researchers attempting to
+build a modular and user-friendly coupler accessible to the climate
+modelling community. Although we use the tool ourselves and have made
+every effort to ensure its accuracy, we can not make any
+guarantees. We provide the software to you for free. In return,
+you - the user - assume full responsibility for use of the software. The
+OASIS3-MCT software comes without any warranties (implied or expressed)
+and is not guaranteed to work for you or on your computer. Specifically,
+CERFACS and the various individuals involved in development and
+maintenance of the OASIS3-MCT software are not responsible for any damage
+that may result from correct or incorrect use of this software.
+
+============================================================================
+
+MCT copyright statement
+-----------------------
+
+              Modeling Coupling Toolkit (MCT) Software
+
+Copyright © 2021, UChicago Argonne, LLC as Operator of Argonne
+National Laboratory. All rights reserved. 
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met: 
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer. 
+2. Redistributions in binary form must reproduce the above copyright
+   notice, this list of conditions and the following disclaimer in the
+   documentation and/or other materials provided with the distribution. 
+3. The end-user documentation included with the redistribution, if
+   any, must include the following acknowledgment: "This product includes
+   software developed by the UChicago Argonne, LLC, as Operator of
+   Argonne National Laboratory." Alternately, this acknowledgment may
+   appear in the software itself, if and wherever such third-party
+   acknowledgments normally appear. 
+   This software was authored by:
+   * Argonne National Laboratory Climate Modeling Group,
+     Mathematics and Computer Science Division,
+     Argonne National Laboratory
+     Argonne IL 60439 
+   * Robert Jacob, tel: (630) 252-2983
+     E-mail: jacob@mcs.anl.gov
+   * Jay Larson
+     E-mail: larson@mcs.anl.gov
+   * Everest Ong
+   * Ray Loy
+4. WARRANTY DISCLAIMER. THE SOFTWARE IS SUPPLIED "AS IS" WITHOUT
+   WARRANTY OF ANY KIND. THE COPYRIGHT HOLDER, THE UNITED STATES, THE
+   UNITED STATES DEPARTMENT OF ENERGY, AND THEIR EMPLOYEES: (1) DISCLAIM
+   ANY WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY
+   IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
+   PURPOSE, TITLE OR NON-IN- FRINGEMENT, (2) DO NOT ASSUME ANY LEGAL
+   LIABILITY OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR
+   USEFULNESS OF THE SOFTWARE, (3) DO NOT REPRESENT THAT USE OF THE
+   SOFTWARE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS, (4) DO NOT WARRANT
+   THAT THE SOFTWARE WILL FUNCTION UNINTERRUPTED, THAT IT IS ERROR-FREE
+   OR THAT ANY ERRORS WILL BE CORRECTED.  
+5. LIMITATION OF LIABILITY. IN NO EVENT WILL THE COPYRIGHT HOLDER, THE
+   UNITED STATES, THE UNITED STATES DEPARTMENT OF ENERGY, OR THEIR
+   EMPLOYEES: BE LIABLE FOR ANY INDIRECT, INCIDENTAL, CONSEQUENTIAL,
+   SPECIAL OR PUNITIVE DAMAGES OF ANY KIND OR NATURE, INCLUDING BUT NOT
+   LIMITED TO LOSS OF PROFITS OR LOSS OF DATA, FOR ANY REASON WHATSOEVER,
+   WHETHER SUCH LIABILITY IS ASSERTED ON THE BASIS OF CONTRACT, TORT
+   (INCLUDING NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE, EVEN IF ANY
+   OF SAID PARTIES HAS BEEN WARNED OF THE POSSIBILITY OF SUCH LOSS OR
+   DAMAGES. 
+
+============================================================================
+
+The SCRIP 1.4 license copyright statement
+-----------------------------------------
+
+The SCRIP 1.4 copyright statement reads as follows:
+"Copyright © 1997, 1998 the Regents of the University of California.
+This software and ancillary information (herein called SOFTWARE)
+called SCRIP is made available under the terms described here. The
+SOFTWARE has been approved for release with associated LA-CC Number
+98-45. Unless otherwise indicated, this SOFTWARE has been authored by
+an employee or employees of the University of California, operator of
+Los Alamos National Laboratory under Contract No. W-7405-ENG-36 with
+the United States Department of Energy. The United States Government
+has rights to use, reproduce, and distribute this SOFTWARE. The public
+may copy, distribute, prepare derivative works and publicly display
+this SOFTWARE without charge, provided that this Notice and any
+statement of authorship are reproduced on all copies. Neither the
+Government nor the University makes any warranty, express or implied,
+or assumes any liability or responsibility for the use of this
+SOFTWARE. If SOFTWARE is modified to produce derivative works, such
+modified SOFTWARE should be clearly marked, so as not to confuse it
+with the version available from Los Alamos National Laboratory."

fesom2_ci/oasis/README.md

@@ -0,0 +1,17 @@
+This is the branch of the OASIS3-MCT climate coupler currently recommended for users. It corresponds to the official OASIS3-MCT_5.0 released in December 2022 + important bugfixes since then.
+
+Developments for the future OASIS3-MCT_6.0 will be done in other branches and then merged to the master branch.
+
+For changes between the different versions of OASIS3-MCT, please refer to Appendix B of the User Guide (in oasis3-mct/doc/oasis3mct_UserGuide.pdf).
+
+Please keep us informed of your progress with OASIS3-MCT and do not forget to cite the following latest reference in your paper describing your coupled model results.::
+A. Craig, S. Valcke, L. Coquart, 2017: Development and performance of a new version of the OASIS coupler, OASIS3-MCT_3.0, Geosci. Model Dev., 10, 3297-3308,https://doi.org/10.5194/gmd-10-3297-2017, 2017.   
+
+If you have problems or questions, please check the forum on the OASIS3-MCT web site (https://www.cerfacs.fr/site-oasis/forum/oa_main.php) or contact us at oasishelp@cerfacs.fr .
+
+Bugfixes since OASIS3-MCT_5.0 official release:
+
+- 31/10/2022: Add support for multiple grids per partition
+- 01/06/2022: Bugfix for load balacing analysis freezing when all processes are not involved in the coupling observed and solved by Eric
+- 01/06/2022: Fix use of uninitialized rglo for mask in grid writing.
+- 01/06/2022: Add oasis_def_var interface with 2d id_var_shape.  id_var_shape is not used anymore, but we provide an interface with a 1d and 2d argument for backwards compatibility.

fesom2_ci/oasis/cmake/FindBLAS.cmake

@@ -0,0 +1,61 @@
+
+
+
+# BLAS_<lang>_FOUND
+# BLAS_<lang>_LIBRARIES
+# BLAS_<lang>_COMPILER_WRAPPER
+
+
+if(CMAKE_C_COMPILER_LOADED)
+	#check_function_exists(cblas_sgemm SGEMM_C_FOUND) # this is also found if it is in the standard library paths, so we can not be sure we already have it in the wrapper
+
+	include(CheckCSourceCompiles)
+	set(CMAKE_REQUIRED_FLAGS -c)
+	check_c_source_compiles([[
+	#include <cblas.h>
+	typedef void (*foo)(const enum CBLAS_ORDER, const enum CBLAS_TRANSPOSE,
+		const enum CBLAS_TRANSPOSE, const int, const int,
+		const int, const float, const float *,
+		const int, const float *, const int,
+		const float, float *, const int);
+	foo func = &cblas_sgemm;
+]] BLAS_C_COMPILER_WRAPPER)
+
+	if(NOT BLAS_C_COMPILER_WRAPPER)
+		# try to locate BLAS via the find module shipped with cmake
+		# the module does not search for C based blas if the Fortran language is enabled
+		include(${CMAKE_ROOT}/Modules/FindBLAS.cmake)
+		set(BLAS_C_LIBRARIES ${BLAS_LIBRARIES})
+		# unset the results from the original FindBlas.cmake
+		unset(BLAS_FOUND)
+		unset(BLAS_LIBRARIES)
+	else()
+		set(BLAS_C_LIBRARIES "") # we do not want to explicitly add libraries as the wrapper will do it
+		set(BLAS_C_FOUND TRUE)
+	endif()
+
+	if(BLAS_C_LIBRARIES)
+		set(BLAS_C_FOUND TRUE)
+	endif()
+endif()
+
+
+# include(${CMAKE_ROOT}/Modules/FindBLAS.cmake)
+# This module sets the following variables:
+#
+# ::
+#
+#   BLAS_FOUND - set to true if a library implementing the BLAS interface
+#     is found
+#   BLAS_LINKER_FLAGS - uncached list of required linker flags (excluding -l
+#     and -L).
+#   BLAS_LIBRARIES - uncached list of libraries (using full path name) to
+#     link against to use BLAS
+#   BLAS95_LIBRARIES - uncached list of libraries (using full path name)
+#     to link against to use BLAS95 interface
+#   BLAS95_FOUND - set to true if a library implementing the BLAS f95 interface
+#     is found
+#   BLA_STATIC  if set on this determines what kind of linkage we do (static)
+#   BLA_VENDOR  if set checks only the specified vendor, if not set checks
+#      all the possibilities
+#   BLA_F95     if set on tries to find the f95 interfaces for BLAS/LAPACK

fesom2_ci/oasis/cmake/FindHDF5.cmake

@@ -0,0 +1,15 @@
+# HDF5_C_INCLUDE_DIRECTORIES
+# HDF5_C_LIBRARIES
+
+
+if(CMAKE_C_COMPILER_LOADED OR CMAKE_CXX_COMPILER_LOADED)
+   include(CheckFunctionExists)
+   check_function_exists(H5get_libversion HAVE_C_HDF5)
+   if(HAVE_C_HDF5)
+      set(HDF5_C_INCLUDE_DIRECTORIES "")
+      set(HDF5_C_LIBRARIES "")
+   else()
+      find_path(HDF5_C_INCLUDE_DIRECTORIES hdf5.h HINTS $ENV{HDF5_DIR}/include ENV HDF5_C_INCLUDE_DIRECTORIES)
+      find_library(HDF5_C_LIBRARIES hdf5 HINTS ${HDF5_C_INCLUDE_DIRECTORIES}/../lib)
+   endif()
+endif()