Update PETSc to v3.12

.travis.yml

@@ -12,12 +12,12 @@ jobs:
   allow_failures:
     # Currently unstable tests that do not affect the build status
     # To add a test here, list its exact name
+    - name: "[18.04] deal.ii adapter [Job failure permitted]"
     - name: "[18.04] FEniCS adapter [Job failure permitted]"
     - name: "Ubuntu 18.04.sudo.mpich [Job failure permitted]"
-    - name: "Ubuntu 16.04 home PETSc [Job failure permitted]"
-    - name: "[16.04] deal.ii <-> OpenFOAM [Job failure permitted]"
-    - name: "[16.04 PETSc] OpenFOAM <-> CalculiX [FSI] [Job failure permitted]"
-    - name: "[16.04] SU2 <-> Calculix [unstable][Job failure permitted]"
+    - name: "[18.04] deal.ii <-> OpenFOAM [Job failure permitted]"
+    - name: "[18.04] SU2 <-> Calculix [unstable][Job failure permitted]"
+    - name: "[18.04 PETSc] OpenFOAM <-> CalculiX [FSI][Job failure permitted]"
 
   include:
     - stage: Building preCICE
@@ -151,7 +151,7 @@ jobs:
       if: fork = false
       script:
         - python build_adapter.py --dockerfile adapters/Dockerfile.su2-adapter --operating-system ubuntu1604 --precice-installation home --docker-username $DOCKER_USERNAME
-        - python push.py --adapter adapters/Dockerfile.su2-adapter
+        - python push.py --adapter adapters/Dockerfile.su2-adapter --base Ubuntu1604.home
       deploy:
         skip_cleanup: true
         provider: script
@@ -161,11 +161,26 @@ jobs:
           echo $DOCKER_PASSWORD | docker login -u $DOCKER_USERNAME --password-stdin &&
           python push_adapter.py --dockerfile adapters/Dockerfile.su2-adapter --operating-system ubuntu1604 --precice-installation home --docker-username $DOCKER_USERNAME
 
+    - name: "[18.04] SU2 adapter"
+      if: fork = false
+      script:
+        - python build_adapter.py --dockerfile adapters/Dockerfile.su2-adapter --operating-system ubuntu1804 --precice-installation home --docker-username $DOCKER_USERNAME
+        - python push.py --adapter adapters/Dockerfile.su2-adapter
+      deploy:
+        skip_cleanup: true
+        provider: script
+        on:
+          all_branches: true
+        script: >-
+          echo $DOCKER_PASSWORD | docker login -u $DOCKER_USERNAME --password-stdin &&
+          python push_adapter.py --dockerfile adapters/Dockerfile.su2-adapter --operating-system ubuntu1804 --precice-installation home --docker-username $DOCKER_USERNAME
+
+
     - name: "[16.04] CalculiX adapter"
       if: fork = false
       script:
-        - python build_adapter.py --dockerfile adapters/Dockerfile.calculix-adapter --operating-system ubuntu1604 --precice-installation home --docker-username $DOCKER_USERNAME
-        - python push.py --adapter adapters/Dockerfile.calculix-adapter
+        - python build_adapter.py --dockerfile adapters/Dockerfile.calculix-adapter --operating-system ubuntu1604 --precice-installation home --docker-username $DOCKER_USERNAME -ab makefile-dep-apt
+        - python push.py --adapter adapters/Dockerfile.calculix-adapter --base Ubuntu1604.home
       deploy:
         skip_cleanup: true
         provider: script
@@ -175,11 +190,26 @@ jobs:
           echo $DOCKER_PASSWORD | docker login -u $DOCKER_USERNAME --password-stdin &&
           python push_adapter.py --dockerfile adapters/Dockerfile.calculix-adapter --operating-system ubuntu1604 --precice-installation home --docker-username $DOCKER_USERNAME
 
+    - name: "[18.04] CalculiX adapter"
+      if: fork = false
+      script:
+        - python build_adapter.py --dockerfile adapters/Dockerfile.calculix-adapter --operating-system ubuntu1804 --precice-installation home --docker-username $DOCKER_USERNAME -ab makefile-dep-apt
+        - python push.py --adapter adapters/Dockerfile.calculix-adapter
+      deploy:
+        skip_cleanup: true
+        provider: script
+        on:
+          all_branches: true
+        script: >-
+          echo $DOCKER_PASSWORD | docker login -u $DOCKER_USERNAME --password-stdin &&
+          python push_adapter.py --dockerfile adapters/Dockerfile.calculix-adapter --operating-system ubuntu1804 --precice-installation home --docker-username $DOCKER_USERNAME
+
+
     - name: "[16.04] deal.ii adapter"
       if: fork = false
       script:
         - python build_adapter.py --dockerfile adapters/Dockerfile.dealii-adapter --operating-system ubuntu1604 --precice-installation home --docker-username $DOCKER_USERNAME
-        - python push.py --adapter adapters/Dockerfile.dealii-adapter
+        - python push.py --adapter adapters/Dockerfile.dealii-adapter --base Ubuntu1604.home
       deploy:
         skip_cleanup: true
         provider: script
@@ -189,6 +219,21 @@ jobs:
           echo $DOCKER_PASSWORD | docker login -u $DOCKER_USERNAME --password-stdin &&
           python push_adapter.py --dockerfile adapters/Dockerfile.dealii-adapter --operating-system ubuntu1604 --precice-installation home --docker-username $DOCKER_USERNAME
 
+    - name: "[18.04] deal.ii adapter [Job failure permitted]"
+      if: fork = false
+      script:
+        - python build_adapter.py --dockerfile adapters/Dockerfile.dealii-adapter --operating-system ubuntu1804 --precice-installation home --docker-username $DOCKER_USERNAME
+        - python push.py --adapter adapters/Dockerfile.dealii-adapter
+      deploy:
+        skip_cleanup: true
+        provider: script
+        on:
+          all_branches: true
+        script: >-
+          echo $DOCKER_PASSWORD | docker login -u $DOCKER_USERNAME --password-stdin &&
+          python push_adapter.py --dockerfile adapters/Dockerfile.dealii-adapter --operating-system ubuntu1804 --precice-installation home --docker-username $DOCKER_USERNAME
+
+
     - name: "[16.04] OpenFOAM adapter"
       if: fork = false
       script:
@@ -206,16 +251,16 @@ jobs:
     - name: "[18.04] OpenFOAM adapter"
       if: fork = false
       script:
-        - python build_adapter.py --dockerfile adapters/Dockerfile.openfoam-adapter.Ubuntu1804 --operating-system ubuntu1804 --precice-installation home --docker-username $DOCKER_USERNAME
-        - python push.py --adapter adapters/Dockerfile.openfoam-adapter.Ubuntu1804
+        - python build_adapter.py --dockerfile adapters/Dockerfile.openfoam-adapter --operating-system ubuntu1804 --precice-installation home --docker-username $DOCKER_USERNAME
+        - python push.py --adapter adapters/Dockerfile.openfoam-adapter
       deploy:
         skip_cleanup: true
         provider: script
         on:
           all_branches: true
         script: >-
           echo $DOCKER_PASSWORD | docker login -u $DOCKER_USERNAME --password-stdin &&
-          python push_adapter.py --dockerfile adapters/Dockerfile.openfoam-adapter.Ubuntu1804 --operating-system ubuntu1804 --precice-installation home --docker-username $DOCKER_USERNAME
+          python push_adapter.py --dockerfile adapters/Dockerfile.openfoam-adapter --operating-system ubuntu1804 --precice-installation home --docker-username $DOCKER_USERNAME
 
     - name: "[18.04] FEniCS adapter [Job failure permitted]"
       if: fork = false
@@ -244,10 +289,10 @@ jobs:
           echo $DOCKER_PASSWORD | docker login -u $DOCKER_USERNAME --password-stdin &&
           python push_adapter.py --dockerfile adapters/Dockerfile.codeaster-adapter --operating-system ubuntu1804 --precice-installation home --docker-username $DOCKER_USERNAME
 
-    - name: "[16.04] OpenFOAM adapter [PETSc]"
+    - name: "[18.04] OpenFOAM adapter [PETSc]"
       if: fork = false
       script:
-        - python build_adapter.py --dockerfile adapters/Dockerfile.openfoam-adapter --operating-system ubuntu1604 --precice-installation home --petsc yes --docker-username $DOCKER_USERNAME
+        - python build_adapter.py --dockerfile adapters/Dockerfile.openfoam-adapter --operating-system ubuntu1804 --precice-installation home --petsc yes --docker-username $DOCKER_USERNAME
         - python push.py --adapter adapters/Dockerfile.openfoam-adapter
       deploy:
         skip_cleanup: true
@@ -256,12 +301,12 @@ jobs:
           all_branches: true
         script: >-
           echo $DOCKER_PASSWORD | docker login -u $DOCKER_USERNAME --password-stdin &&
-          python push_adapter.py --dockerfile adapters/Dockerfile.openfoam-adapter --operating-system ubuntu1604 --precice-installation home --petsc yes --docker-username $DOCKER_USERNAME
+          python push_adapter.py --dockerfile adapters/Dockerfile.openfoam-adapter --operating-system ubuntu1804 --precice-installation home --petsc yes --docker-username $DOCKER_USERNAME
 
-    - name: "[16.04] CalculiX adapter [PETSc]"
+    - name: "[18.04] CalculiX adapter [PETSc]"
       if: fork = false
       script:
-        - python build_adapter.py --dockerfile adapters/Dockerfile.calculix-adapter --operating-system ubuntu1604 --precice-installation home --petsc yes --docker-username $DOCKER_USERNAME
+        - python build_adapter.py --dockerfile adapters/Dockerfile.calculix-adapter --operating-system ubuntu1804 --precice-installation home --petsc yes --docker-username $DOCKER_USERNAME -ab makefile-dep-apt
         - python push.py --adapter adapters/Dockerfile.calculix-adapter
       deploy:
         skip_cleanup: true
@@ -270,7 +315,7 @@ jobs:
           all_branches: true
         script: >-
           echo $DOCKER_PASSWORD | docker login -u $DOCKER_USERNAME --password-stdin &&
-          python push_adapter.py --dockerfile adapters/Dockerfile.calculix-adapter --operating-system ubuntu1604 --precice-installation home --petsc yes --docker-username $DOCKER_USERNAME
+          python push_adapter.py --dockerfile adapters/Dockerfile.calculix-adapter --operating-system ubuntu1804 --precice-installation home --petsc yes --docker-username $DOCKER_USERNAME
 
 
     - name: "[Build adapters on fork] Using cached version"
@@ -280,67 +325,67 @@ jobs:
 
 
     - stage: Tests
-      name: "[16.04] SU2 <-> Calculix [unstable][Job failure permitted]"
+      name: "[18.04] SU2 <-> Calculix [unstable][Job failure permitted]"
       script:
         - python system_testing.py -s su2-ccx -v
         - python push.py --test su2-ccx
 
-    - name: "[16.04] OpenFOAM <-> OpenFOAM"
+    - name: "[18.04] OpenFOAM <-> OpenFOAM"
       script:
         - python system_testing.py -s of-of -v
         - python push.py --test of-of
 
-    - name: "[16.04] Calculix <-> OpenFOAM"
+    - name: "[18.04] Calculix <-> OpenFOAM"
       script:
         - python system_testing.py -s of-ccx -v
-        - python push.py --test of-ccx -o
+        - python push.py --test of-ccx
 
     - name: "[18.04] FEniCS <-> FEniCS"
       script:
-        - python system_testing.py -s fe-fe --base Ubuntu1804.home -v
-        - python push.py --test fe-fe --base Ubuntu1804.home
+        - python system_testing.py -s fe-fe -v
+        - python push.py --test fe-fe
 
     - name: "[16.04] Bindings/Solverdummies"
       script:
-        - python system_testing.py -s bindings -v
-        - python push.py --test bindings
+        - python system_testing.py -s bindings --base Ubuntu1604.home -v
+        - python push.py --test bindings  --base Ubuntu1604.home
 
     - name: "[18.04] Bindings/Solverdummies"
       script:
-        - python system_testing.py -s bindings --base Ubuntu1804.home -v
-        - python push.py --test bindings --base Ubuntu1804.home
+        - python system_testing.py -s bindings -v
+        - python push.py --test bindings
 
-    - name: "[16.04] deal.ii <-> OpenFOAM [Job failure permitted]"
+    - name: "[18.04] deal.ii <-> OpenFOAM [Job failure permitted]"
       script:
-        - python system_testing.py -s dealii-of -v
-        - python push.py --test dealii-of
+        - python system_testing.py -s dealiif -v
+        - python push.py --test dealiif
 
     - name: "[18.04] nutils <-> OpenFOAM"
       script:
-        - python system_testing.py -s nutils-of --base Ubuntu1804.home -v
-        - python push.py --test nutils-of --base Ubuntu1804.home
+        - python system_testing.py -s nutils-of -v
+        - python push.py --test nutils-of
 
-    - name: "[16.04] OpenFOAM <-> OpenFOAM [nearest projection]"
+    - name: "[18.04] OpenFOAM <-> OpenFOAM [nearest projection]"
       script:
         - python system_testing.py -s of-of_np -v
         - python push.py --test of-of_np
 
     - name: "[18.04] OpenFOAM <-> Code_Aster"
       script:
-        - python system_testing.py -s of-ca --base Ubuntu1804.home -v
+        - python system_testing.py -s of-ca -v
         - python push.py --test of-ca
 
-    - name: "[16.04] Elastictube1D - Python"
+    - name: "[18.04] Elastictube1D - Python"
       script:
         - python system_testing.py -s 1dtube_py -v
         - python push.py --test 1dtube_py
 
-    - name: "[16.04] Elastictube1D - C++"
+    - name: "[18.04] Elastictube1D - C++"
       script:
         - python system_testing.py -s 1dtube_cxx -v
         - python push.py --test 1dtube_cxx
 
-    - name: "[16.04 PETSc] OpenFOAM <-> CalculiX [FSI] [Job failure permitted]"
+    - name: "[18.04 PETSc] OpenFOAM <-> CalculiX [FSI][Job failure permitted]"
       script:
-        - python system_testing.py -s of-ccx_fsi --base Ubuntu1604.home.PETSc -v
-        - python push.py --test of-ccx_fsi --petsc
+        - python system_testing.py -s of-ccx_fsi --base Ubuntu1804.home.PETSc -v
+        - python push.py --test of-ccx_fsi --base Ubuntu1804.home.PETSc

adapters/Dockerfile.calculix-adapter

@@ -1,9 +1,9 @@
-ARG from=precice/precice-ubuntu1604.home-develop
-ARG base_solver=precice/calculix:2.16
-FROM ${base_solver} as calculix
+ARG branch=develop
+ARG from=precice/precice-ubuntu1804.home-${branch}
 FROM $from
 
 USER root
+
 # ( since we are importing form the precice image )
 RUN apt-get -qq update && apt-get -qq install \
     build-essential \
@@ -14,30 +14,22 @@ RUN apt-get -qq update && apt-get -qq install \
     autoconf \
     autotools-dev \
     bzip2 \
+    libarpack2-dev \
+    libspooles2.2 \
     libyaml-cpp-dev && \
     rm -rf /var/lib/apt/lists/*
 
 ARG CACHEBUST
-# copy arpack and spooles
-COPY --from=calculix  /usr/local/ARPACK /usr/local/ARPACK
-COPY --from=calculix  /spooles.2.2 /spooles.2.2
 
 USER precice
 # get calculix source
 WORKDIR /home/precice
 RUN curl -s http://www.dhondt.de/ccx_2.16.src.tar.bz2 | tar -xj
-ARG branch=develop
-RUN git clone --branch $branch https://github.com/precice/calculix-adapter.git
-WORKDIR calculix-adapter/
-# specify proper locations of libraries
-RUN sed -i  -e 's|CCX\s\+=.*|CCX	= /home/precice/CalculiX/ccx_2.16/src|g'\
-            -e 's|SPOOLES\s\+=.*|SPOOLES	 = /spooles.2.2|g'\
-            -e 's|ARPACK\s\+=.*|ARPACK  = /usr/local/ARPACK|g'\
-            -e 's|-L$(YAML)/build||g' \
-            -e 's|-I$(YAML)/include||g' \
-            -e 's|CC\s\+=.*|CC=cc|g' Makefile
+ARG adapter_branch=develop
+RUN git clone --branch $adapter_branch https://github.com/precice/calculix-adapter.git
 
-# build and clean-up
+# build adapter
+WORKDIR calculix-adapter/
 RUN make -j $(nproc)
 
 # create directory for input/out/exchange

adapters/Dockerfile.codeaster-adapter

@@ -1,4 +1,5 @@
-ARG from=precice/precice-ubuntu1804.home-develop
+ARG branch=develop
+ARG from=precice/precice-ubuntu1804.home-${branch}
 ARG base_solver=precice/codeaster
 FROM ${base_solver}
 FROM $from
@@ -25,7 +26,8 @@ WORKDIR /home/precice
 
 COPY --from=precice/codeaster /home/precice/Code_Aster /home/precice/Code_Aster
 
-RUN git clone https://github.com/precice/code_aster-adapter.git
+ARG adapter_branch=develop
+RUN git clone --branch $adapter_branch https://github.com/precice/code_aster-adapter.git
 
 RUN \
     sed -i "s|.rmed|.resu|g" code_aster-adapter/cht/adapter.comm && \

adapters/Dockerfile.dealii-adapter

@@ -1,4 +1,5 @@
-ARG from=precice/precice-ubuntu1604.home-develop
+ARG branch=develop
+ARG from=precice/precice-ubuntu1604.home-${branch}
 ARG base_solver=precice/deal.ii
 FROM ${base_solver} as deal.ii
 FROM $from
@@ -10,8 +11,10 @@ COPY --from=deal.ii /root/dealii/ /home/precice/dealii/
 USER precice
 WORKDIR /home/precice
 RUN mkdir -p Logs Data/Input Data/Output Data/Exchange
-ARG branch=develop
-RUN git clone --branch $branch https://github.com/precice/dealii-adapter.git
+
+ARG adapter_branch=develop
+RUN git clone --branch $adapter_branch https://github.com/precice/dealii-adapter.git
+
 RUN cd dealii-adapter/linear_elasticity/ && \
     cmake -DDEAL_II_DIR=$HOME/dealii -DDIM=3 -DCMAKE_BUILD_TYPE=Release . && \
     make -j $(nproc)

adapters/Dockerfile.fenics-adapter

@@ -1,7 +1,8 @@
 # System testing preCICE with fenics-adapter
 
 # Building on top of the latest preCICE-build
-ARG from=precice/precice-ubuntu1804.home-develop
+ARG branch=develop
+ARG from=precice/precice-ubuntu1804.home-${branch}
 FROM $from
 
 USER root

adapters/Dockerfile.openfoam-adapter

@@ -1,4 +1,5 @@
-ARG from=precice/precice-ubuntu1604.home-develop
+ARG branch=develop
+ARG from=precice/precice-ubuntu1804.home-${branch}
 ARG base_solver=precice/openfoam
 FROM ${base_solver} as openfoam
 FROM $from
@@ -12,17 +13,27 @@ RUN apt-get -qq update && apt-get -qq install \
     wget apt-transport-https && \
     rm -rf /var/lib/apt/lists/*
 
+
 ARG CACHEBUST
 
+# # Installing OpenFOAM5 manually
+# RUN sh -c "wget -O - http://dl.openfoam.org/gpg.key | apt-key add -" && \
+# add-apt-repository http://dl.openfoam.org/ubuntu && \
+# apt-get update && \
+# apt-get -y install openfoam5
+
+# Get OpenFOAM5 install via folder copy
 COPY --from=openfoam /opt/openfoam5 /opt/openfoam5/
 
+
 # Building openfoam-adapter
 USER precice
-SHELL ["/bin/bash", "-c"]
+SHELL ["/bin/bash", "-c"]  # without this command /opt/openfoam5/etc/bashrc cannot be sourced
 WORKDIR /home/precice
 RUN mkdir -p Logs Data/Input Data/Output Data/Exchange
-ARG branch=develop
-RUN git clone  --branch $branch https://github.com/precice/openfoam-adapter.git
+ARG adapter_branch=develop
+RUN git clone  --branch $adapter_branch https://github.com/precice/openfoam-adapter.git
 WORKDIR /home/precice/openfoam-adapter
-RUN . /opt/openfoam5/etc/bashrc && ./Allwmake
-RUN cp wmake.log Allwmake.log ldd.log $HOME/Logs
+RUN . /opt/openfoam5/etc/bashrc && ./Allwmake && cp wmake.log Allwmake.log ldd.log $HOME/Logs
+
+ENV LD_LIBRARY_PATH="/usr/lib:${LD_LIBRARY_PATH}"