Changes between Version 20 and Version 21 of docker

Timestamp:

11/17/20 15:49:54 (5 years ago)

Author:

downs

Comment:

--

docker

@@ -22 +22 @@
 [[Image(shot2.png,800px)]] 
 
-Click continue and you will receive a file installation key and license file. Place the license file in issm_matlab.
-
+Click continue and you will receive a file installation key and license file. Place the license file in issm_matlab.Then, create a text file called installer_input.txt with the following contents
 {{{
 #!sh
-cp license.lic issm_matlab
-}}}
-
-Creat a text file called installer_input.txt with the following contents
-{{{
-#!sh
-
 fileInstallationKey=<key>
-
 agreeToLicense=yes
-
 outputFile=log.txt
-
 licensePath=../license.lic
-
 
 }}}
 replacing <key> with the file installation key you received.
 
-Next, we need all Matlab install files. Download the Matlab installer from the license center and run it. Login with your Mathworks account, accept the license agreement, then under advanced options, select "I want to download without installing." Download the files to docker_issm/matlab
+Next, we need all Matlab install files. Download the Matlab installer from the license center and run it. Login with your Mathworks account, accept the license agreement, then under advanced options, select "I want to download without installing." Download the files to docker_matlab/matlab
 
-The issm_matlab directory should now have a license file license.lic, the installer_input.txt file, and a directory called matlab with the install files. Create a dockerfile called DOCKERFILE in issm_matlab with the following contents
+The issm_matlab directory should now have a license file license.lic, the installer_input.txt file, and a directory called matlab with the install files. Create a dockerfile called DOCKERFILE in issm_matlab with the following contents:
 
 {{{
 #!sh
-# Use the official image as a parent image.
+# Ubuntu parent image
 FROM ubuntu:20.04
 
@@ -74 +62 @@
 RUN echo 'alias matlab="/usr/local/MATLAB/R2020a/bin/matlab -nojvm -nodesktop"' >> ~/.bashrc
 }}}
+
+Note: You can probably remove the line to install Emacs somehow. I did this because it's my preferred editor, and incidentally it installed some other dependencies that made the Matlab install actually work. 
 
 From the docker_matlab direcotry build the Docker image.
@@ -103 +93 @@
 }}}
 
-= Installing Matlab on Docker =
+= Installing ISSM on Docker =
+
+
+To install ISSM from source, create a new directory called docker_issm. We'll build off the Matlab image built previously. Copy the ISSM trunk into docker_issm. Create a new Docker file in the directory called DOCKERFILE. 
+
+{{
+#!sh
+# Build on the matlab image
+FROM ubuntu/matlab
+
+# Dependencies
+RUN apt-get install -y libtool cmake autotools-dev curl python python-numpy g++ gfortran unzip patch git
+
+# Add ISSM source
+WORKDIR /home/issm/
+ADD trunk-jpl ./trunk-jpl
+
+# Set environment var
+ENV ISSM_DIR=/home/issm/trunk-jpl/
+RUN ["/bin/bash", "-c", "source $ISSM_DIR/etc/environment.sh"]
+
+# Install external packages
+WORKDIR $ISSM_DIR/externalpackages/petsc
+RUN ./install-3.12-linux.sh
+WORKDIR $ISSM_DIR/externalpackages/triangle
+RUN ./install-linux.sh
+WORKDIR $ISSM_DIR/externalpackages/chaco
+RUN ./install.sh
+WORKDIR $ISSM_DIR/externalpackages/m1qn3
+RUN ./install.sh
+WORKDIR $ISSM_DIR/externalpackages/semic
+RUN ./install.sh
+
+# Configure and run
+WORKDIR $ISSM_DIR
+RUN autoreconf -ivf 
+RUN ./configure \
+        --prefix=$ISSM_DIR \
+        --with-matlab-dir="/usr/local/MATLAB/R2020a/" \
+        --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu/ -lgfortran" \
+        --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
+        --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include"  \
+        --with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/lib/ -lmpi -lmpicxx -lmpifort" \
+        --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
+        --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
+        --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
+        --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \
+        --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \
+        --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
+        --with-numthreads=2
+
+RUN make
+RUN make install
+
+# A fix to get stuff to run in matlab
+WORKDIR /usr/local/MATLAB/R2020a/sys/os/glnxa64/
+RUN mkdir OLD
+RUN mv libstdc++.so* OLD/
+RUN mv libgcc_s.so* OLD/
+RUN ln -s /usr/lib/libstd* .
+RUN ln -s /lib/libgcc_s.so* .
+
+WORKDIR /home/issm/
+}}}