TOUGH3 installation issue
I realized many people have difficulty in compilation of TOUGH3. After polishing the installation cmake scripts and reorganizing the installation package, compilation of TOUGH3 should be more easy, stable and fast. Attached are the introduction, updated cmake scripts, additional required files.
45 replies
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Hi, I was trying to install tough3 ECO2N during which I encountered the error as shown in the image. What is the way to rectify it? I have also replaced and copied the additional files. Kindly help me in this regard.
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Thank you for the files. I tried with the attached files and encountered an error as attached. When I went through the above CMakeLists file in esd-tough3, the nesting seemed to be fine. Can you check it once? Thanks in advance.
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I made the changes based on Cmaketough3.txt you provided. It seems Cmaketough3.txt is not from v1.1. ( difference in this section). make it same as the one in v1.1 for this section or copy my changes in Cmaketough3.txt to replace the corresponding section in v1.1
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Thanks for pointing out. I copied the changes made by you in the cmake file of V1.1 but still the error (screenshot is persisting). I have attached the cmake file also for your reference. Your help will be much appreciated. Thank you in advance.
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Neglect the earlier message. I was able to successfully solve the error. However, moving forward, I got stuck in another error which I have attached. How to overcome this error? Thanks in advance.
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The missing functions are all from BLAS and APACK. You do not have BLAS and LAPACK installed on your computer. You may install them by adding --download-fblaslapack during configure of PETSC (you need reinstall PETSC. PETSC also needs these functions
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I tried to reinstall the petsc with blas and lapack. But, now I am facing the error as attached. How it can be rectified? Thanks in advance.
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You did not follow the introduction by installing petsc separately.
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If that doesn't work, then try just using Intel OneAPI Fortran to compile everything (petsc, TOUGH3, etc.) Recent updates to gfortran make it very difficult to use with Petsc and the TOUGH-based codes.
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I want to know how you solve the problem in the picture
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This problem has been raised many times. It has been solved in TOUGH3 V1.11. The problem is caused by the compactivity of different compiler versions. You may try:
(1) downgrade your Gfortran version from V10 or higher to V9x, or
(2) upgrade you TOUGH3 to V1.11.
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I want to debug this code. When configuring tough3-eco2n, the command used is"/configure.sh --build-type=DEBUG --eos=eco2n --no-x11 --petsc-dir=/home/zhigao/petsc-3.17.0 --petsc-arch=test", And the executable file can run. But when I use gdb to debug it, the breakpoint is located to other locations. What is the reason and what is the solution.Thanks in advance.
And when I did breakpoint debugging in vscode, he did not stop at the breakpoint and ran directly. How to solve it? Thanks in advance.
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I was able to successfully solve the error.How to overcome this error? Thanks in advance.
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It seems that the PETSC library does not work properly. I would suggest you delete the original PETSC installation, reinstall a newer version and try again.
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I tried to reinstall the petsc.When configuring petsc, the command used is"./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-fblaslapack --with-debugging=0 --with-shared-libraries=0",But, now I am facing the error. How to overcome this error? Thanks in advance.
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Seems something wrong with MPI. Make sure that you are using the same version of MPI for both PETSC and TOUGH3 compilation. Please try following for PETSC setup (suppose MPI has already installed in your computer):
./configure --with-cc=mpigcc --with-cxx=mpigxx --with-fc=mpif90 --download-fblaslapack --with-debugging=0
By the way, you need to delete the ./build folder in your working directory.
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c and c++ wrap compiler may have different names for different MPI installations. If mpigcc and mpigxx do not work, you may try mpicc and mpicxx
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My petsc configuration is like this：
Petsc and TOUGH used the same MPI, but a new error occurred.How to overcome this error? Thanks in advance.
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delete the folder "/esd-tough3/tough3-install" and "/esd-tough3/build", and try again. If it still does not, please post details of the command you used and all output information.
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Has it been noted that when installing TOUGH3 with a Fortran compiler version 9 or higher, certain restrictions apply to the version of PETSc that can be used?
In particular, the CMake configuration for TOUGH3 (`/esd-tough3/CMakeLists.txt`) includes the following compiler flag settings:
if(CMAKE_Fortran_COMPILER_ID STREQUAL "Intel") set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS} -fpp -r8 -i4 -debug all -check all -check noarg_temp_created -zero") set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS} -fpp -r8 -i4 -O3 -free -CB -vec_report0 -diag-disable 8291 -zero") else () set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -cpp -fdefault-real-8 -fdefault-double-8 -fno-align-commons -Wuninitialized -ftrapv -fcheck=bounds -fcheck=do -fcheck=mem -fcheck=pointer -fcheck=recursion -fstack-check -fbacktrace -finit-local-zero") set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS} -cpp -O2 -fdefault-real-8 -fdefault-double-8 -fno-align-commons -finit-local-zero") endif() if(CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL "10") set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -fallow-argument-mismatch") set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -fallow-argument-mismatch") endif()With these flags, I have encountered limitations when installing PETSc, specifically when using the following configuration:
PETSc_tag="v3.18.0" # Last known working PETSc version with TOUGH3 cd <installation_directory>/ && git clone --branch $PETSc_tag --depth 1 https://gitlab.com/petsc/petsc.git cd petsc ./configure \ --with-debugging=0 \ --with-blaslapack-lib="$BLAS_LIB" make all make PETSC_DIR=<installation_directory>/petsc PETSC_ARCH=arch-linux-c-opt checkHas anyone else experienced similar issues when installing TOUGH3 with newer Fortran compilers? While I am aware that upgrading to TOUGH3 v1.1 may address some of these concerns, I am currently in the middle of a project and would prefer to resolve this issue without a major update.
Any insights or suggestions would be greatly appreciated.
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Several critical bugs have been fixed in the TOUGH3 compilation cmake scripts. I do not think it is worth to spend much time on the compilation issue of older version. I would suggest you install the most updated version (v1.11). The new version should not interfere your existing simulations.
