Merge pull request #31 from ucns3d-team/feature/fix-docker-builder

Feature/fix docker builder

.gitignore

@@ -1,5 +1,5 @@
 # Prerequisites
-*.d
+# *.d
 
 # Compiled Object files
 *.slo
@@ -12,19 +12,18 @@
 *.pch
 
 # Compiled Dynamic libraries
-*.so
-*.dylib
-*.dll
+# *.so
+# *.dylib
+# *.dll
 
 # Fortran module files
 *.mod
 *.smod
 
 # Compiled Static libraries
-*.lai
-*.la
-*.a
-*.lib
+# *.lai
+# *.la
+# *.lib
 
 # Executables
 *.exe

Dockerfile

@@ -29,6 +29,7 @@ RUN apt-get update && \
     libcgal-dev \
     libmpc-dev \
     # ping \
+    nano \
     libstdc++5 \
     libiberty-dev \
     software-properties-common ;\
@@ -45,27 +46,31 @@ RUN apt-get update && \
 
 WORKDIR /root/
 
-#RUN mkdir -p /root/local ;\
-#   cd /root/local \
-#    cd /root/ ;\
-#  pwd ;\
-#    git clone https://github.com/KarypisLab/GKlib.git
+# Download and install GKlib, metis and parmetis dependencies
 
-#RUN make -C /root/GKlib prefix=/root/local config
-#RUN	cd /root/GKlib && make install
+RUN mkdir -p /root/local ;\
+   cd /root/ ;\
+   git clone https://github.com/KarypisLab/GKlib.git
 
-#RUN cd /root/ ;\
-#    git clone https://github.com/KarypisLab/METIS.git
-#RUN make -C /root/METIS config shared=1 cc=gcc prefix=/root/local
-#RUN	cd /root/METIS && make install
+RUN make -C /root/GKlib config cc=gcc prefix=/root/local 
+RUN	cd /root/GKlib && make install
 
+RUN cd /root/ ;\
+   git clone https://github.com/KarypisLab/METIS.git
+RUN make -C /root/METIS config cc=gcc prefix=/root/local
+RUN	cd /root/METIS && make install
 
-#RUN cd /root/ ;\
-#    git clone https://github.com/KarypisLab/ParMETIS.git
-#RUN make -C /root/ParMETIS config cc=mpicc prefix=/root/local
-#RUN	cd /root/ParMETIS && make install
+RUN cd /root/ ;\
+   git clone https://github.com/KarypisLab/ParMETIS.git
+RUN make -C /root/ParMETIS config cc=mpicc prefix=/root/local
+RUN	cd /root/ParMETIS && make install
+
+# Add src and compile
 ADD src /root/CODE
-RUN cd /root/CODE && make -f Makefile_docker clean all
+# Add tecplot dependency
+# TODO build the download and compilation of libtecio.a
+ADD bin/lib/tecplot/libtecio.a /root/CODE
+RUN cd /root/CODE && make -f Makefile_docker all
 ENV OMPI_MCA_btl_vader_single_copy_mechanism=none
 
 # Make & set a rundir & copy executable 
@@ -83,3 +88,4 @@ WORKDIR /ucns3d_run
 COPY tests/taylor_green_vortex/* /ucns3d_run/
 COPY tests/execute-tests.sh /ucns3d_run/
 RUN chmod +x execute-tests.sh
+RUN sed -i -e 's/\r$//' /ucns3d_run/execute-tests.sh

README.md

@@ -40,19 +40,19 @@ There are two main methods to locally install the solver and run the solver.
 2. In your bash terminal build the ucns3d image, you would need invoke `docker build` from the repository root directory:
 
 ```
-$ docker build . -t ucns3d -f Dockerfile
+docker build . -t ucns3d -f Dockerfile
 ```
 
 3. Once the image is build run the image, you can run the image interactively like so:
 
 ```
-$ docker run -ti ucns3d
+docker run -ti ucns3d
 ```
 
 The current [Dockerfile](Dockerfile) contains an example case under [tests](/tests/execute-tests.sh). Alternatively, you can mount a tmp directory and copy other uses cases when you run the image like so:
 
 ```
-$ docker run -v $PWD/tmp/:/tmp/ -ti ucns3d
+docker run -v $PWD/tmp/:/tmp/ -ti ucns3d
 ```
 
 ### Manual Build
@@ -86,11 +86,11 @@ compiler options.
 
 * For a clean installation 
 ```
-$ make -f Makefile clean all
+make -f Makefile clean all
 ```
 * For recompiling changed files and their dependencies
 ```
-$ make -f Makefile
+make -f Makefile
 ```
 * the name of the executable is `ucns3d_p`.
 
@@ -104,12 +104,12 @@ For running ucns3d you will need the following files in a directory of your choi
 * the executable ucns3d_p
 * For interactively running the code specify the number of threads to be used by typing in the terminal window
 ```
-$ export OMP_NUM_THREADS=N
+export OMP_NUM_THREADS=N
 ```
 N being the number of threads to be used (use 1 for MPI only mode)
 * in the same terminal window run the code by typing
 ```
-$ mpirun -np M ./ucns3d_p
+mpirun -np M ./ucns3d_p
 ```
 M being the number of MPI processes (at least 2 are required), for running at different HPC systems sample [scripts](/scripts) and [libraries](/bin/lib) are provided.
 

bin/gnu-compiler/Makefile

@@ -52,7 +52,7 @@ LIBS = -Wl,-Bstatic libparmetis.a libmetis.a libtecio.a $(BLASLIBS) -Wl,-Bdynami
 # LIBS = libparmetis.a libmetis.a libtecio.a $(BLASLIBS) -lstdc++ 
 
 
-include Makefile.common
+include Makefile_common
 
 
 

bin/lib/archer/Makefile_archer → bin/gnu-compiler/archer/Makefile_archer

@@ -50,7 +50,7 @@ LIBS = -Wl,-Bstatic libparmetis_gnu_mpi.a libmetis.a libtecio.a $(BLASLIBS) -Wl,
 #LIBS = libparmetis.a libmetis.a libtecio.a $(BLASLIBS) -lstdc++ 
 
 
-include Makefile.common
+include Makefile_common
 
 
 

bin/gnu-compiler/archer/README.md

@@ -0,0 +1,3 @@
+# Setup for archer Supercomputer
+
+ These are libraries that work with gnu and cray ftn compilers on archer.

bin/gnu-compiler/docker-ubuntu/Makefile_docker

@@ -0,0 +1,62 @@
+## Makefile to be build in Docker.
+
+##intel
+# F90=mpiifort
+#GFORTRAN
+F90=mpif90
+LD=$(F90)
+# ifdef HPCTOOLKIT
+#    $(info HPCToolkit is loaded - building version for profiling)
+#    DBGFLAGS=-g -debug inline-debug-info
+# else
+#    $(info HPCToolkit is not loaded - building release version)
+#    DBGFLAGS=
+# endif
+
+
+#intel MKL
+# BLASFLAGS=  -I${MKLROOT}/include
+# BLASLIBS=  -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_sequential.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl
+
+BLASFLAGS= -I  /usr/include/x86_64-linux-gnu/openblas-pthread     #Ensure that you include your BLAS library path here
+BLASLIBS=  /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.a     #Ensure that you include your BLAS library path here
+GKLIB= /root/local/lib/libGKlib.a
+METISLIB= /root/local/lib/libmetis.a
+PARMETISLIB= /root/local/lib/libparmetis.a
+
+
+#amdblis aocl
+#BLASFLAGS=  -I/opt/hlrs/non-spack/libraries/aocl-gcc/2.1.0/amd-blis/include/
+#BLASLIBS= /opt/hlrs/non-spack/libraries/aocl-gcc/2.1.0/amd-blis/lib/libblis.a
+
+# OFLAGS= 
+# #intel compilers
+# # debug run
+# #FFLAGS=-i4 -r8 -O0  -g  -debug all -xHost -traceback -qopenmp -qopenmp-link=static $(BLASFLAGS) -check bounds -fp-model strict -debug inline-debug-info -zero 
+# # production run
+# #FFLAGS=-i4 -r8 -ipo -march=core-avx2 -mtune=core-avx2 -O3 -fp-model precise -zero -qopenmp  -qopenmp-link=static $(BLASFLAGS)  #amd zen
+# FFLAGS=-i4 -r8 -ipo -xHost -O3 -fp-model precise -zero -qopenmp  -qopenmp-link=static $(BLASFLAGS)
+
+
+#gfortran
+#debug run
+#FFLAGS=-ffree-line-length-none -fdefault-real-8 -fopenmp -Wall  -fbounds-check -finit-local-zero  -fdump-parse-tree -fdump-core -fbacktrace -fdefault-double-8 -fbackslash  -O0 -fcray-pointer -Wno-lto-type-mismatch -fPIE $(BLASFLAGS)
+#production run
+FFLAGS=-fdefault-real-8 -fdefault-double-8 -fbackslash -fopenmp -ffree-line-length-none -finit-local-zero -fimplicit-none -flto -fcray-pointer -O3 -march=native -Wno-lto-type-mismatch -fPIE $(BLASFLAGS) 
+
+#aocl
+#FFLAGS= -O3 -Mfreeform -Mallocatable=03 -Mdaz -fdefault-real-8 -fopenmp -mavx2 -march=znver2 $(BLASFLAGS)
+#FFLAGS= -O2 -mp -fdefault-real-8 -flto -fopenmp -mavx2 -march=znver2 $(BLASFLAGS)
+
+#gnu hybrid static dynamic
+# LIBS = -Wl,-Bstatic libparmetis.a libmetis.a libtecio.a $(BLASLIBS) -Wl,-Bdynamic -lstdc++ -lpthread -lm -ldl -lc -lmpi 
+LIBS = -Wl,-V,-Bstatic libtecio.a $(BLASLIBS) $(GKLIB) $(METISLIB) $(PARMETISLIB) -Wl,-Bdynamic -lstdc++ -lpthread -lm -ldl -lc -lmpi
+
+
+#intel static linking
+# LIBS = libparmetis.a libmetis.a libtecio.a $(BLASLIBS) -lstdc++ 
+
+include Makefile_common
+
+
+

bin/intel-compiler/Makefile

@@ -50,7 +50,7 @@ FFLAGS=-i4 -r8 -ipo -xHost -O3 -fp-model precise -zero -qopenmp  -qopenmp-link=s
 LIBS = libparmetis.a libmetis.a libtecio.a $(BLASLIBS) -lstdc++ 
 
 
-include Makefile.common
+include Makefile_common
 
 
 

bin/lib/README.md

@@ -0,0 +1,3 @@
+# Static libraries required to compile and run UCNS3D
+
+Precompiled metis, parmetis and tecplot static libraries. They can be used to link during compilation.   

bin/macos/readme.txt → bin/macos/README.md

@@ -1,4 +1,6 @@
-. Use the following dynamic libraries:
+# Setup on MacOS
+
+Use the following dynamic libraries:
 libmetis.dylib  (Compiled from source)
 libparmetis.dylib (Compiled from source)
 libtecio.dylib (Copied from Tecplot executable)
@@ -7,37 +9,49 @@ The above are also provided in this folder but probably won't work, you will hav
 --------------------------------------------------
 Locate the required libraries:
 
-1)	Download and install the latest free trial of tecpot, then the dynamic library (libtecio.dylib), is available in 360’s folder, Tecplot 360 EX 2021 r1 /Contents/Frameworks/    (you can run ucns3d without tecplot, and you can use a vtk output but this is required for compiling only)
+1. Download and install the latest free trial of tecpot, then the dynamic library (libtecio.dylib), is available in 360’s folder, Tecplot 360 EX 2021 r1 /Contents/Frameworks/    (you can run ucns3d without tecplot, and you can use a vtk output but this is required for compiling only)
 
-2)	Download the latest version of parmetis and in the CMakeLists.txt of the parmetis directory, in the section starting with: if(SHARED) you should add:
+2. Download the latest version of parmetis and in the CMakeLists.txt of the parmetis directory, in the section starting with: if(SHARED) you should add:
 set(METIS_LIBRARY_TYPE SHARED) 
 
-a.	Then open a terminal window in the parmetis directory and execute the following commands
-i.	make config shared=1
-ii.	make
-b.	Then you can use the generated libmetis.dylib and libparmetis.dylib from your directory parmetis/build/Darwin…./libmetis/ and parmetis/build/Darwin…./libparmetis/ respectively
+    2.1. Then open a terminal window in the parmetis directory and execute the following commands
+
+```
+make config shared=1
+```
+```
+make
+```
+
+2.2. Then you can use the generated libmetis.dylib and libparmetis.dylib from your directory parmetis/build/Darwin…./libmetis/ and parmetis/build/Darwin…./libparmetis/ respectively
 
-3)	Install OpenBlas with Homebrew and modify the Makefile to point to the correct location of the libraries.
+3. Install OpenBlas with Homebrew and modify the Makefile to point to the correct location of the libraries.
 
---------------------------------------------------------
 
+4. Use the Makefile.common and Makefile for MacOS from this folder and copy to the src directory
 
-2. Use the Makefile.common and Makefile for MacOS from this folder and copy to the src directory
+5. Open a terminal window and compile as:
 
-3. Open a terminal window and compile as:
+```
 make -f Makefile clean all (this is for new make and clean)
-or
-make -f Makefile
+```
 
+```
+make -f Makefile
+```
 
-4. Type the following in a terminal window prior to running the application
+6. Type the following in a terminal window prior to running the application
 
+```
 install_name_tool -change @rpath/libtecio.dylib /Users/Username/code_directory/libtecio.dylib /Users/Username/executable_directory/executable_name
+```
 
 
-
-5. Type the following in a terminal window (values for A greater than or equal to 1, and B greater than 1)
+7. Type the following in a terminal window (values for A greater than or equal to 1, and B greater than 1)
+```
 export OMP_NUM_THREADS=A
+```
+```
 mpirun -np B ./ucns3d_p
+```
 
-6. Enjoy!

bin/translators/README.txt → scripts/translators/README.md

@@ -1,8 +1,10 @@
+# Scripts to translate input formats
+
 these translators can be compiled with the following command to translate meshes generated in STAR CD format or UGRID format 
 to native UCNS3D binary format
 
-compile with
-
-ifort -i4 -r8 "name of .f90 file"
+compile with and run
 
-execute
+```
+ifort -i4 -r8 ".f90"
+```

src/Makefile_docker

@@ -1,57 +1,19 @@
-## Makefile to be build in Docker.
+# Makefile to be build with Docker.
 
-##intel
-# F90=mpiifort
-#GFORTRAN
 F90=mpif90
 LD=$(F90)
-# ifdef HPCTOOLKIT
-#    $(info HPCToolkit is loaded - building version for profiling)
-#    DBGFLAGS=-g -debug inline-debug-info
-# else
-#    $(info HPCToolkit is not loaded - building release version)
-#    DBGFLAGS=
-# endif
-
-
-#intel MKL
-# BLASFLAGS=  -I${MKLROOT}/include
-# BLASLIBS=  -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_sequential.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl
 
 BLASFLAGS= -I  /usr/include/x86_64-linux-gnu/openblas-pthread     #Ensure that you include your BLAS library path here
 BLASLIBS=  /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.a     #Ensure that you include your BLAS library path here
-#PARMETISLIBS= /root/local/lib/libparmetis.a
-
-#amdblis aocl
-#BLASFLAGS=  -I/opt/hlrs/non-spack/libraries/aocl-gcc/2.1.0/amd-blis/include/
-#BLASLIBS= /opt/hlrs/non-spack/libraries/aocl-gcc/2.1.0/amd-blis/lib/libblis.a
-
-# OFLAGS= 
-# #intel compilers
-# # debug run
-# #FFLAGS=-i4 -r8 -O0  -g  -debug all -xHost -traceback -qopenmp -qopenmp-link=static $(BLASFLAGS) -check bounds -fp-model strict -debug inline-debug-info -zero 
-# # production run
-# #FFLAGS=-i4 -r8 -ipo -march=core-avx2 -mtune=core-avx2 -O3 -fp-model precise -zero -qopenmp  -qopenmp-link=static $(BLASFLAGS)  #amd zen
-# FFLAGS=-i4 -r8 -ipo -xHost -O3 -fp-model precise -zero -qopenmp  -qopenmp-link=static $(BLASFLAGS)
+GKLIB= /root/local/lib/libGKlib.a
+METISLIB= /root/local/lib/libmetis.a
+PARMETISLIB= /root/local/lib/libparmetis.a
 
-
-#gfortran
-#debug run
-#FFLAGS=-ffree-line-length-none -fdefault-real-8 -fopenmp -Wall  -fbounds-check -finit-local-zero  -fdump-parse-tree -fdump-core -fbacktrace -fdefault-double-8 -fbackslash  -O0 -fcray-pointer -Wno-lto-type-mismatch -fPIE $(BLASFLAGS)
-#production run
 FFLAGS=-fdefault-real-8 -fdefault-double-8 -fbackslash -fopenmp -ffree-line-length-none -finit-local-zero -fimplicit-none -flto -fcray-pointer -O3 -march=native -Wno-lto-type-mismatch -fPIE $(BLASFLAGS) 
 
-#aocl
-#FFLAGS= -O3 -Mfreeform -Mallocatable=03 -Mdaz -fdefault-real-8 -fopenmp -mavx2 -march=znver2 $(BLASFLAGS)
-#FFLAGS= -O2 -mp -fdefault-real-8 -flto -fopenmp -mavx2 -march=znver2 $(BLASFLAGS)
-
-#gnu hybrid static dynamic
-LIBS = -Wl,-Bstatic libparmetis.a libmetis.a libtecio.a $(BLASLIBS) -Wl,-Bdynamic -lstdc++ -lpthread -lm -ldl -lc -lmpi 
-
-#intel static linking
-# LIBS = libparmetis.a libmetis.a libtecio.a $(BLASLIBS) -lstdc++ 
+LIBS = -Wl,-V,-Bstatic libtecio.a $(BLASLIBS) $(GKLIB) $(METISLIB) $(PARMETISLIB) -Wl,-Bdynamic -lstdc++ -lpthread -lm -ldl -lc -lmpi
 
-include Makefile.common
+include Makefile_common