CallumG-Ed commented 4 years ago

Hi, I'm having an issue getting the OpenFAST solvers in SOWFA to compile. I'm running ubuntu 18.04 and OpenFOAM-2.4.0.

The error I'm getting on the OpenFAST solvers is:

In file included from /home/callum/OpenFAST/openfast/install/include/OpenFAST.H:20:0, from /home/callum/OpenFOAM/callum-2.4.0/SOWFA/src/turbineModels/turbineModelsOpenFAST/lnInclude/horizontalAxisWindTurbinesALMOpenFAST.H:68, from pisoFoamTurbine.C:38: /home/callum/OpenFAST/openfast/install/include/SC.h:5:10: fatal error: hdf5.h: No such file or directory

include "hdf5.h"

      ^~~~~~~~

compilation terminated. pisoFoamTurbine.dep:759: recipe for target 'Make/linux64GccDPOpt/pisoFoamTurbine.o' failed make: *** [Make/linux64GccDPOpt/pisoFoamTurbine.o] Error 1

I have tryed:

setting the variable $HDF5_DIR to /usr/include/hdf5/serial and also added the same location to the variable $LD_LIBRARY_PATH
linked folder hdf5 to my OpenFAST location ~/OpenFAST/openfast/install/include (resetting the above variables to match)

I'd appreciate any help.

Cheers Callum

pablo-benito commented 4 years ago

Open the file pisoFoamTurbine.ALMAdvancedOpenFAST/Make/options and in the EXE_INC variable, at the end, add the include path to the HDF5 headers, like this:

EXE_INC = \
    -I$(LIB_SRC)/turbulenceModels/incompressible/turbulenceModel \
    -I$(LIB_SRC)/transportModels \
    -I$(LIB_SRC)/transportModels/incompressible/singlePhaseTransportModel \
    -I$(LIB_SRC)/finiteVolume/lnInclude \
    -I$(LIB_SRC)/meshTools/lnInclude \
    -I$(LIB_SRC)/fvOptions/lnInclude \
    -I$(LIB_SRC)/sampling/lnInclude \
    -I$(SOWFA_DIR)/src/turbineModels/turbineModelsOpenFAST/lnInclude \
    $(PFLAGS) \
    $(PINC) \
    -I$(OPENFAST_DIR)/include \
    -I$(HDF5_DIR)/include

Of course, the HDF5_DIR environment variable must point to /usr/include/hdf5/serial (the default installation path for Ubuntu HDF5 serial library)

CallumG-Ed commented 4 years ago

Hi thanks for the reply.

I have added: -I$(HDF5_DIR) to both

/home/callum/OpenFOAM/callum-2.4.0/SOWFA/applications/solvers/incompressible/windEnergy

pisoFoamTurbine.ALMAdvancedOpenFAST/Make/options

and

windPlantSolver.ALMAdvancedOpenFAST/Make/options

(because the header files are in /usr/include/hdf5/serial not /usr/include/hdf5/serial/include)

I updated the variable $HDF5 to equal /usr/include/hdf5/serial

and unfortunately I am still getting the error.

pablo-benito commented 4 years ago

Ops, my mistake.. The path that I told you was for Ubuntu 16.. You're right, on Ubuntu 18, the header files are inside /usr/include/hdf5/serial

It's weird.. What happens if you directly plug the full hdf5 path in the options file?, like this:

EXE_INC = \
    -I$(LIB_SRC)/turbulenceModels/incompressible/turbulenceModel \
    -I$(LIB_SRC)/transportModels \
    -I$(LIB_SRC)/transportModels/incompressible/singlePhaseTransportModel \
    -I$(LIB_SRC)/finiteVolume/lnInclude \
    -I$(LIB_SRC)/meshTools/lnInclude \
    -I$(LIB_SRC)/fvOptions/lnInclude \
    -I$(LIB_SRC)/sampling/lnInclude \
    -I$(SOWFA_DIR)/src/turbineModels/turbineModelsOpenFAST/lnInclude \
    $(PFLAGS) \
    $(PINC) \
    -I$(OPENFAST_DIR)/include \
   -I/usr/include/hdf5/serial/

If the hdf5.h file is on that path, this should work. Maybe the environment variable HDF5_DIR was not properly set, or you forgot to export it.

CallumG-Ed commented 4 years ago

Hi Pablo,

So I have reassigned the $HDF5_DIR variable to /usr/lib/x86_64-linux-gnu/hdf5/serial so that it is inline with I$(HDF5_DIR)/include. I then source the bash_profile here:

bash_profile.txt

And run the function SOWFA-2.4.0 within it.

I have added I$(HDF5_DIR)/include to EXE_INC in 3 files:

1) SOWFA/src/turbineModelsOpenFAST/Make/options

2) SOWFA/applications/solvers/incompressible/windEnergy/pisoFoamTurbine.ALMAdvancedOpenFAST/Make/options

3) SOWFA/applications/solvers/incompressible/windEnergy/windPlantSolver.ALMAdvancedOpenFAST/Make/options

After running the ./Allwclean and then ./Allwmake command now I get:

OPENFAST_DIR is set to '/home/callum/OpenFAST/openfast/install'. Attempting to compile OpenFAST pisoFoam solver. Making dependency list for source file pisoFoamTurbine.C could not open file horizontalAxisWindTurbinesALMOpenFAST.H for source file pisoFoamTurbine.C due to No such file or directory SOURCE=pisoFoamTurbine.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-100 -I/home/callum/OpenFOAM/OpenFOAM-2.4.0/src/turbulenceModels/incompressible/turbulenceModel -I/home/callum/OpenFOAM/OpenFOAM-2.4.0/src/transportModels -I/home/callum/OpenFOAM/OpenFOAM-2.4.0/src/transportModels/incompressible/singlePhaseTransportModel -I/home/callum/OpenFOAM/OpenFOAM-2.4.0/src/finiteVolume/lnInclude -I/home/callum/OpenFOAM/OpenFOAM-2.4.0/src/meshTools/lnInclude -I/home/callum/OpenFOAM/OpenFOAM-2.4.0/src/fvOptions/lnInclude -I/home/callum/OpenFOAM/OpenFOAM-2.4.0/src/sampling/lnInclude -I/home/callum/OpenFOAM/callum-2.4.0/SOWFA/src/turbineModels/turbineModelsOpenFAST/lnInclude -DOMPI_SKIP_MPICXX -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -pthread -I/home/callum/OpenFAST/openfast/install/include -I/usr/lib/x86_64-linux-gnu/hdf5/serial/include -IlnInclude -I. -I/home/callum/OpenFOAM/OpenFOAM-2.4.0/src/OpenFOAM/lnInclude -I/home/callum/OpenFOAM/OpenFOAM-2.4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/pisoFoamTurbine.o pisoFoamTurbine.C:38:10: fatal error: horizontalAxisWindTurbinesALMOpenFAST.H: No such file or directory

include "horizontalAxisWindTurbinesALMOpenFAST.H"

      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

compilation terminated. pisoFoamTurbine.dep:687: recipe for target 'Make/linux64GccDPOpt/pisoFoamTurbine.o' failed make: *** [Make/linux64GccDPOpt/pisoFoamTurbine.o] Error 1

pablo-benito commented 4 years ago

ok, from what I see in the SOWFA_compile_log.txt, now you have a link error. (The compiler cannot find the libhdf5.so and libhdf5_hl files)

The things is, that in Ubuntu 18, the HDF5 heades (the .h files) are located inside /usr/include/hdf5/serial, but the libraries (the libhdf5.so and libhdf5_hl.so) are inside /usr/lib/x86_64-linux-gnu/hdf5/serial/. So, it is impossible to define a single base directory for the headers and the libraries. And in the options file, at the end, in the EXE_LIBS variable, it defines the location of the HDF5 libraries with the line

-L$(HDF5_DIR)/lib/ \

which, in your case, it will point to an incorrect path (/usr/include/hdf5/serial/lib).. I recommend you to replace that line with the full path to the proper location:

-L/usr/lib/x86_64-linux-gnu/hdf5/serial/ \

CallumG-Ed commented 4 years ago

Apologies Pablo,

I think I recognised the same as you replied so I editted my comment above. I have done as you said and the error remains as in my previous comment.

pablo-benito commented 4 years ago

Sorry, I just saw the first comment..

Again, in the options file of pisoFoamTurbine.ALMAdvancedOpenFAST, the location of that header, horizontalAxisWindTurbinesALMOpenFAST.H, is selected with the line:

-I$(SOWFA_DIR)/src/turbineModels/turbineModelsOpenFAST/lnInclude \

and, looking at your logs, this gets resolved to

-I/home/callum/OpenFOAM/callum-2.4.0/SOWFA/src/turbineModels/turbineModelsOpenFAST/lnInclude

Can you check if this path is correct? The horizontalAxisWindTurbinesALMOpenFAST.H must be inside that path

CallumG-Ed commented 4 years ago

Yes you are quite correct the line in the pisoFoamTurbine.ALMAdvancedOpenFAST options file is:

-I$(SOWFA_DIR)/src/turbineModels/turbineModelsOpenFAST/lnInclude \

which resolves as you say to:

-I/home/callum/OpenFOAM/callum-2.4.0/SOWFA/src/turbineModels/turbineModelsOpenFAST/lnInclude

So I've made a directory lnInclude in:

$SOWFA_DIR/src/turbineModels/turbineModelsOpenFAST

and symlinked into

$SOWFA_DIR/src/turbineModels/turbineModelsOpenFAST/horizontalAxisWindTurbinesALMOpenFAST

that has done the trick!

Thanks very much for the support Pablo, it's much appreciated! Great work!

Cheers Callum

pablo-benito commented 4 years ago

You're welcome. It's always a pleasure to help

Cheers!

CallumG-Ed commented 4 years ago

Just when I thought everything was compiled, I realised the FAST coupled solvers still haven't worked! I have attached log here:

log.Allwmake_SOWFA.txt

Any help on this would be much appreciated

pablo-benito commented 4 years ago

You linker is failing to locate the Lapack routines. I think that you compiled OpenFAST without turning on the BUILD_SHARED_LIBS flag..

In that case, the shared version of OpenFAST libraries have implicit the dependency to the blas/lapack library, and you don't have to declare them again when compiling Sowfa. When you only have static libraries (libnwtclibs.a, libopenfastlib.a, etc.), that information is lost. You have to add it explicitly when you link to those libraries. As pisoFoamTurbine.ALMAdvancedOpenFAST do not declare this dependency (to liblapack.so/.a) in the options file, the compilation fails..

You can try to add the dependency to lapack (-llapack) in the EXE_LIBS variable of the options file, and see if that works. Or, recompile OpenFAST with that flag turned on, and then recompile the SOWFA binaries..

Also, I will suggest you to take a look at the document I uploaded some time ago to my github, on how to compile this thing:

https://github.com/pablo-benito/SOWFA-installation

P.S. I have to update the document with the modifications about the location of the HDF5 headers/library on Ubuntu 18.04, that we talked the other day..

CallumG-Ed commented 4 years ago

Hi Pablo thanks again for the info! I hadn't realised you'd put together a nice install guide.

I'm trying to re-compile OpenFAST with the added flag -BUILD_SHARED_LIBS:BOOL=ON, however now cmake warning:

CMake Warning:
  Manually-specified variables were not used by the project:

     BUILD_FAST_CPP_API

which I know is required for coulping SOWFA. I know it's probably something silly but I can't seem to get it to take the flag.

The steps I've taken to get OpenFAST are:

sudo apt install gcc gfortran cmake libblas-dev liblapack-dev libxml2-dev libhdf5-serial-dev libyaml-cpp-dev python3-pip libopenblas-dev libyaml-cpp-dev

pip3 install numpy matplotlib

mkdir OpenFAST && cd OpenFAST

git clone --recursive https://github.com/OpenFAST/openfast.git

cd openfast/

after that I've made a little bash script with all the options etc:

#!/bin/bash

#build openfast script

git checkout dev

git submodule update

if [ -d "build" ]; then
    rm -r build
    echo "build exists - deleting"
fi

if [ -d "install" ]; then
    rm -r install
    echo "install exists - deleting"
fi

echo "creating new directories"
mkdir build install && cd build

cmake \
    -DCMAKE_INSTALL_PREFIX=~/OpenFAST/openfast/install/ \
    -DFPE_TRAP_ENABLED=ON \
    -DBUILD_FAST_CPP_API:BOOL=ON \
    -DBUILD_SHARED_LIBS:BOOL=ON \
    ../

make install

Any help would be apppreciated as always.

Thanks again for your time Pablo!

pablo-benito commented 4 years ago

uops, my document is a little outdated... The flag name changed from BUILD_FAST_CPP_API to BUILD_OPENFAST_CPP_API

CallumG-Ed commented 4 years ago

Cheers Pablo you're awesome! Recompiling now hopefully thats got it, I will let you know when I recompile SOWFA.

CallumG-Ed commented 4 years ago

Thats got it Pablo all the FAST solvers have now compiled with SOWFA! Again thanks very much, I appreciate all you efforts!

gaoshijingand commented 1 year ago

Hi, I'm having an issue getting the OpenFAST solvers in SOWFA to compile. I'm running ubuntu 18.04 and OpenFOAM-2.4.0.

The error I'm getting on the SOWFA compile solvers is:

OPENFAST_DIR is set to '/home/gx/OpenFAST'. Attempting to compile OpenFAST windPlant solver. SOURCE=windPlantSolver.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-100 -I/home/gx/OpenFOAM/OpenFOAM-2.4.x/src/turbulenceModels/incompressible/turbulenceModel -I/home/gx/OpenFOAM/OpenFOAM-2.4.x/src/transportModels -I/home/gx/OpenFOAM/OpenFOAM-2.4.x/src/transportModels/incompressible/singlePhaseTransportModel -I/home/gx/OpenFOAM/OpenFOAM-2.4.x/src/finiteVolume/lnInclude -I/home/gx/OpenFOAM/OpenFOAM-2.4.x/src/meshTools/lnInclude -I/home/gx/OpenFOAM/OpenFOAM-2.4.x/src/fvOptions/lnInclude -I/home/gx/OpenFOAM/OpenFOAM-2.4.x/src/sampling/lnInclude -I/home/gx/SOWFA/src/turbineModels/turbineModelsOpenFAST/lnInclude -DOMPI_SKIP_MPICXX -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -pthread -I/home/gx/OpenFAST/include -I./interpolate2D -I/usr/lib/x86_64-linux-gnu/hdf5/serial/include/ -IlnInclude -I. -I/home/gx/OpenFOAM/OpenFOAM-2.4.x/src/OpenFOAM/lnInclude -I/home/gx/OpenFOAM/OpenFOAM-2.4.x/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/windPlantSolver.o In file included from windPlantSolver.C:63:0: /home/gx/SOWFA/src/turbineModels/turbineModelsOpenFAST/lnInclude/horizontalAxisWindTurbinesALMOpenFAST.H:68:10: fatal error: OpenFAST.H: No such file or directory

include "OpenFAST.H"

      ^~~~~~~~~~~~

compilation terminated. windPlantSolver.dep:724: recipe for target 'Make/linux64GccDPOpt/windPlantSolver.o' failed make: *** [Make/linux64GccDPOpt/windPlantSolver.o] Error 1

So I would like to ask, how to solve this problem

NREL / SOWFA

Another Issue coupleing SOWFA with OpenFAST #64

include "hdf5.h"

include "horizontalAxisWindTurbinesALMOpenFAST.H"

include "OpenFAST.H"