Merge pull request ECCO-GROUP#186 from ECCO-GROUP/Docker

Moved Docker instructions for V4r4 in to ecco-v4-configurations
crios-ut · Sep 24, 2023 · 2adf0a9 · 2adf0a9
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diff --git a/ECCOv4 Release 4/Docker/Dockerfile b/ECCOv4 Release 4/Docker/Dockerfile
@@ -0,0 +1,55 @@
+FROM debian:latest
+
+RUN ["/bin/bash", "-c", "echo I am using bash"]
+SHELL ["/bin/bash", "-c"]
+
+ARG CHIP_ARCT=x86_64
+
+USER root
+
+ENV mainpath ./
+RUN echo ${mainpath}
+
+RUN mkdir -p ${mainpath}
+
+
+# install libraries as root user
+USER root
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends build-essential && \
+    apt-get install -y --no-install-recommends vim && \
+    apt-get install -y --no-install-recommends less && \
+    apt-get install -y --no-install-recommends git && \
+    apt-get install -y --no-install-recommends wget && \
+    apt-get install -y --no-install-recommends unzip && \
+    apt-get install -y --no-install-recommends ca-certificates && \
+    apt-get install -y --no-install-recommends gfortran && \
+    apt-get install -y --no-install-recommends gnuplot && \
+    apt-get install -y --no-install-recommends openmpi-bin && \
+    apt-get install -y --no-install-recommends openmpi-doc && \
+    apt-get install -y --no-install-recommends libopenmpi-dev && \
+    apt-get install -y --no-install-recommends mpich && \
+    apt-get install -y --no-install-recommends libnetcdf-dev && \
+    apt-get install -y --no-install-recommends libnetcdff-dev && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+RUN apt-get update
+RUN update-ca-certificates
+
+# add a user called 'ecco'
+RUN useradd -ms /bin/bash ecco
+USER ecco 
+ENV USER_HOME_DIR /home/ecco
+WORKDIR /home/ecco
+
+# copy local directory 'src' to the docker image /home/ecco/docker_src
+COPY --chown=ecco:users ./src ${USER_HOME_DIR}/docker_src
+
+# set environment variables for compiling MITgcm
+ENV MPI_INC_DIR /usr/lib/${CHIP_ARCT}-linux-gnu/openmpi/include
+ENV ROOTDIR /home/ecco/MITgcm
+
+# download the mitgcm and ecco configuration files
+RUN cd ${USER_HOME_DIR}
+RUN ${USER_HOME_DIR}/docker_src/get_MITgcm_ECCO.sh
diff --git a/ECCOv4 Release 4/Docker/LICENSE b/ECCOv4 Release 4/Docker/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 gaelforget <[email protected]> and contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/ECCOv4 Release 4/Docker/README.md b/ECCOv4 Release 4/Docker/README.md
@@ -0,0 +1,53 @@
+
+This [Docker image configuration](https://www.docker.com) makes it easy to reproduce the [ECCO v4r4](https://ecco-group.org) state estimate.
+
+It includes :
+
+- gfortran, MPI, and NetCDF libraries needed to compile and run the MITgcm
+- bash script to download the 
+  1. [MITgcm](https://github.com/MITgcm/MITgcm) [checkpoint 66g](https://github.com/MITgcm/MITgcm/releases/tag/checkpoint66g)
+  2. [ECCOv4-py Configuration files](https://github.com/ECCO-GROUP/ECCO-v4-Configurations)
+
+Future versions will include Jupyter hub and the [ECCOv4-py Python Library](https://github.com/ECCO-GROUP/ECCOv4-py).
+
+
+## Directions
+
+To use on your local computer
+
+You will need [Docker Desktop](https://docs.docker.com/desktop/) installed. 
+
+To build your own image, go into the directory ECCO-Docker/ECCO_v4r4 and run
+
+```
+docker build -t ecco_v4r4_docker_image .
+```
+
+If your computer is a Mac that uses ARM-based chips (such as M1), use the following command to build the image:
+
+```
+docker build -t ecco_v4r4_docker_image . --build-arg="CHIP_ARCT=aarch64"
+```
+
+To run the image do
+
+```
+docker run -t -i --rm ecco_v4r4_docker_image bash
+```
+
+After running you will be in an interactive bash shell.  
+
+To compile the MITgcm code first need to define SIZE.h a model configuration file in the ```ECCOV4/release4/code``` directory that specifies the number of cpus on your machine. We included a few SIZE.h_NN files for different number of cpus (NN). 
+
+After you have a SIZE.h file then go to the ```/home/ecco/ECCOV4/release4/build``` directory and build the model code: 
+
+```
+>$ROOTDIR/tools/genmake2 -mods=../code -of=~/docker_src/linux_amd64_gfortran -mpi
+>make -j depend
+>make -j
+``` 
+
+The result will be an executable ```mitgcmuv```. 
+
+To run the model you will need to link all the binary files as described in the
+Instructions for reproducing ECCO Version 4 Release 4 [[https://doi.org/10.5281/zenodo.7789915](https://doi.org/10.5281/zenodo.7789915) document.
diff --git a/ECCOv4 Release 4/Docker/src/SIZE.h_12 b/ECCOv4 Release 4/Docker/src/SIZE.h_12
@@ -0,0 +1,66 @@
+CBOP
+C    !ROUTINE: SIZE.h
+C    !INTERFACE:
+C    include SIZE.h
+C    !DESCRIPTION: \bv
+C     *==========================================================*
+C     | SIZE.h Declare size of underlying computational grid.
+C     *==========================================================*
+C     | The design here support a three-dimensional model grid
+C     | with indices I,J and K. The three-dimensional domain
+C     | is comprised of nPx*nSx blocks of size sNx along one axis
+C     | nPy*nSy blocks of size sNy along another axis and one
+C     | block of size Nz along the final axis.
+C     | Blocks have overlap regions of size OLx and OLy along the
+C     | dimensions that are subdivided.
+C     *==========================================================*
+C     \ev
+CEOP
+C     Voodoo numbers controlling data layout.
+C     sNx :: No. X points in sub-grid.
+C     sNy :: No. Y points in sub-grid.
+C     OLx :: Overlap extent in X.
+C     OLy :: Overlat extent in Y.
+C     nSx :: No. sub-grids in X.
+C     nSy :: No. sub-grids in Y.
+C     nPx :: No. of processes to use in X.
+C     nPy :: No. of processes to use in Y.
+C     Nx  :: No. points in X for the total domain.
+C     Ny  :: No. points in Y for the total domain.
+C     Nr  :: No. points in Z for full process domain.
+      INTEGER sNx
+      INTEGER sNy
+      INTEGER OLx
+      INTEGER OLy
+      INTEGER nSx
+      INTEGER nSy
+      INTEGER nPx
+      INTEGER nPy
+      INTEGER Nx
+      INTEGER Ny
+      INTEGER Nr
+      PARAMETER (
+     &           sNx =  30,
+     &           sNy =  30,
+     &           OLx =   4,
+     &           OLy =   4,
+     &           nSx =   8,
+     &           nSy =   1,
+     &           nPx =  12,
+     &           nPy =   1,
+     &           Nx  = sNx*nSx*nPx,
+     &           Ny  = sNy*nSy*nPy,
+     &           Nr  =  50 )
+
+C     MAX_OLX  - Set to the maximum overlap region size of any array
+C     MAX_OLY    that will be exchanged. Controls the sizing of exch
+C                routine buufers.
+      INTEGER MAX_OLX
+      INTEGER MAX_OLY
+      PARAMETER ( MAX_OLX = OLx,
+     &            MAX_OLY = OLy )
+
+      integer     nobcs
+      parameter ( nobcs = 4 )
+
+
diff --git a/ECCOv4 Release 4/Docker/src/SIZE.h_13 b/ECCOv4 Release 4/Docker/src/SIZE.h_13
@@ -0,0 +1,66 @@
+CBOP
+C    !ROUTINE: SIZE.h
+C    !INTERFACE:
+C    include SIZE.h
+C    !DESCRIPTION: \bv
+C     *==========================================================*
+C     | SIZE.h Declare size of underlying computational grid.
+C     *==========================================================*
+C     | The design here support a three-dimensional model grid
+C     | with indices I,J and K. The three-dimensional domain
+C     | is comprised of nPx*nSx blocks of size sNx along one axis
+C     | nPy*nSy blocks of size sNy along another axis and one
+C     | block of size Nz along the final axis.
+C     | Blocks have overlap regions of size OLx and OLy along the
+C     | dimensions that are subdivided.
+C     *==========================================================*
+C     \ev
+CEOP
+C     Voodoo numbers controlling data layout.
+C     sNx :: No. X points in sub-grid.
+C     sNy :: No. Y points in sub-grid.
+C     OLx :: Overlap extent in X.
+C     OLy :: Overlat extent in Y.
+C     nSx :: No. sub-grids in X.
+C     nSy :: No. sub-grids in Y.
+C     nPx :: No. of processes to use in X.
+C     nPy :: No. of processes to use in Y.
+C     Nx  :: No. points in X for the total domain.
+C     Ny  :: No. points in Y for the total domain.
+C     Nr  :: No. points in Z for full process domain.
+      INTEGER sNx
+      INTEGER sNy
+      INTEGER OLx
+      INTEGER OLy
+      INTEGER nSx
+      INTEGER nSy
+      INTEGER nPx
+      INTEGER nPy
+      INTEGER Nx
+      INTEGER Ny
+      INTEGER Nr
+      PARAMETER (
+     &           sNx =  90,
+     &           sNy =  90,
+     &           OLx =   4,
+     &           OLy =   4,
+     &           nSx =   1,
+     &           nSy =   1,
+     &           nPx =  13,
+     &           nPy =   1,
+     &           Nx  = sNx*nSx*nPx,
+     &           Ny  = sNy*nSy*nPy,
+     &           Nr  =  50 )
+
+C     MAX_OLX  - Set to the maximum overlap region size of any array
+C     MAX_OLY    that will be exchanged. Controls the sizing of exch
+C                routine buufers.
+      INTEGER MAX_OLX
+      INTEGER MAX_OLY
+      PARAMETER ( MAX_OLX = OLx,
+     &            MAX_OLY = OLy )
+
+      integer     nobcs
+      parameter ( nobcs = 4 )
+
+
diff --git a/ECCOv4 Release 4/Docker/src/SIZE.h_16 b/ECCOv4 Release 4/Docker/src/SIZE.h_16
@@ -0,0 +1,66 @@
+CBOP
+C    !ROUTINE: SIZE.h
+C    !INTERFACE:
+C    include SIZE.h
+C    !DESCRIPTION: \bv
+C     *==========================================================*
+C     | SIZE.h Declare size of underlying computational grid.
+C     *==========================================================*
+C     | The design here support a three-dimensional model grid
+C     | with indices I,J and K. The three-dimensional domain
+C     | is comprised of nPx*nSx blocks of size sNx along one axis
+C     | nPy*nSy blocks of size sNy along another axis and one
+C     | block of size Nz along the final axis.
+C     | Blocks have overlap regions of size OLx and OLy along the
+C     | dimensions that are subdivided.
+C     *==========================================================*
+C     \ev
+CEOP
+C     Voodoo numbers controlling data layout.
+C     sNx :: No. X points in sub-grid.
+C     sNy :: No. Y points in sub-grid.
+C     OLx :: Overlap extent in X.
+C     OLy :: Overlat extent in Y.
+C     nSx :: No. sub-grids in X.
+C     nSy :: No. sub-grids in Y.
+C     nPx :: No. of processes to use in X.
+C     nPy :: No. of processes to use in Y.
+C     Nx  :: No. points in X for the total domain.
+C     Ny  :: No. points in Y for the total domain.
+C     Nr  :: No. points in Z for full process domain.
+      INTEGER sNx
+      INTEGER sNy
+      INTEGER OLx
+      INTEGER OLy
+      INTEGER nSx
+      INTEGER nSy
+      INTEGER nPx
+      INTEGER nPy
+      INTEGER Nx
+      INTEGER Ny
+      INTEGER Nr
+      PARAMETER (
+     &           sNx =  30,
+     &           sNy =  30,
+     &           OLx =   4,
+     &           OLy =   4,
+     &           nSx =   6,
+     &           nSy =   1,
+     &           nPx =  16,
+     &           nPy =   1,
+     &           Nx  = sNx*nSx*nPx,
+     &           Ny  = sNy*nSy*nPy,
+     &           Nr  =  50 )
+
+C     MAX_OLX  - Set to the maximum overlap region size of any array
+C     MAX_OLY    that will be exchanged. Controls the sizing of exch
+C                routine buufers.
+      INTEGER MAX_OLX
+      INTEGER MAX_OLY
+      PARAMETER ( MAX_OLX = OLx,
+     &            MAX_OLY = OLy )
+
+      integer     nobcs
+      parameter ( nobcs = 4 )
+
+
diff --git a/ECCOv4 Release 4/Docker/src/SIZE.h_24 b/ECCOv4 Release 4/Docker/src/SIZE.h_24
@@ -0,0 +1,66 @@
+CBOP
+C    !ROUTINE: SIZE.h
+C    !INTERFACE:
+C    include SIZE.h
+C    !DESCRIPTION: \bv
+C     *==========================================================*
+C     | SIZE.h Declare size of underlying computational grid.
+C     *==========================================================*
+C     | The design here support a three-dimensional model grid
+C     | with indices I,J and K. The three-dimensional domain
+C     | is comprised of nPx*nSx blocks of size sNx along one axis
+C     | nPy*nSy blocks of size sNy along another axis and one
+C     | block of size Nz along the final axis.
+C     | Blocks have overlap regions of size OLx and OLy along the
+C     | dimensions that are subdivided.
+C     *==========================================================*
+C     \ev
+CEOP
+C     Voodoo numbers controlling data layout.
+C     sNx :: No. X points in sub-grid.
+C     sNy :: No. Y points in sub-grid.
+C     OLx :: Overlap extent in X.
+C     OLy :: Overlat extent in Y.
+C     nSx :: No. sub-grids in X.
+C     nSy :: No. sub-grids in Y.
+C     nPx :: No. of processes to use in X.
+C     nPy :: No. of processes to use in Y.
+C     Nx  :: No. points in X for the total domain.
+C     Ny  :: No. points in Y for the total domain.
+C     Nr  :: No. points in Z for full process domain.
+      INTEGER sNx
+      INTEGER sNy
+      INTEGER OLx
+      INTEGER OLy
+      INTEGER nSx
+      INTEGER nSy
+      INTEGER nPx
+      INTEGER nPy
+      INTEGER Nx
+      INTEGER Ny
+      INTEGER Nr
+      PARAMETER (
+     &           sNx =  30,
+     &           sNy =  30,
+     &           OLx =   4,
+     &           OLy =   4,
+     &           nSx =   4,
+     &           nSy =   1,
+     &           nPx =  24,
+     &           nPy =   1,
+     &           Nx  = sNx*nSx*nPx,
+     &           Ny  = sNy*nSy*nPy,
+     &           Nr  =  50 )
+
+C     MAX_OLX  - Set to the maximum overlap region size of any array
+C     MAX_OLY    that will be exchanged. Controls the sizing of exch
+C                routine buufers.
+      INTEGER MAX_OLX
+      INTEGER MAX_OLY
+      PARAMETER ( MAX_OLX = OLx,
+     &            MAX_OLY = OLy )
+
+      integer     nobcs
+      parameter ( nobcs = 4 )
+
+