Error at codebase compilation

Question

Hello,

I'm in the process of compiling the codebase for a fresh install in Ubuntu.

At 74% I get these errors. I'm not sure where to find these files. Any help is appreciated.

Thanks!

Karl

Answer 1

Hello Karl,

did you install all the dependencies?

On Ubuntu, it would look like

sudo apt install gcc g++ libfftw3-dev gengetopt gfortran git make cmake pkg-config python3 python3-dev python3-pip zlib1g-dev

and also PETSc, that you have to install manually.

Comments

Hi Marie,

Thank you for your response. I've made sure to have the dependencies installed, shown below.

===

karl@karl-Ubuntu:~$ sudo apt install gcc g++ libfftw3-dev gengetopt gfortran git make cmake pkg-config python3 python3-dev python3-pip zlib1g-dev
[sudo] password for karl:
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
cmake is already the newest version (3.22.1-1ubuntu1).
g++ is already the newest version (4:11.2.0-1ubuntu1).
gcc is already the newest version (4:11.2.0-1ubuntu1).
gfortran is already the newest version (4:11.2.0-1ubuntu1).
libfftw3-dev is already the newest version (3.3.8-2ubuntu8).
make is already the newest version (4.3-4.1build1).
pkg-config is already the newest version (0.29.2-1ubuntu3).
python3 is already the newest version (3.10.4-0ubuntu2).
python3-dev is already the newest version (3.10.4-0ubuntu2).
zlib1g-dev is already the newest version (1:1.2.11.dfsg-2ubuntu9).
gengetopt is already the newest version (2.23+dfsg1-1).
python3-pip is already the newest version (22.0.2+dfsg-1).
git is already the newest version (1:2.34.1-1ubuntu1.2).
0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
karl@karl-Ubuntu:~$

===

With regards to installing PETSc, after purging ubuntu of a previous install, I followed the Quick Start Tutorial:
https://petsc.org/release/install/install_tutorial/#qqtw-quickest-quick-start-in-the-west

When I execute the lines below within my petsc folder, as per the instructions on the web,

./configure \
    --prefix=/home/karl/projects/petsc \
    --download-mpich \
    --download-fblaslapack \
    --download-metis \
    --download-parmetis \
    --download-hypre \
    --with-debugging=0 \
    COPTFLAGS='-O2' \
    CXXOPTFLAGS='-O2' \
    FOPTFLAGS='-O2'
make all
make install

I encounter this error during the HYPRE install

=============================================================================================                                         Running make install on HYPRE; this may take several minutes                                                              =============================================================================================                                   TESTING: alternateConfigureLibrary from config.packages.AMReX(config/BuildSystem/config/packages/AMReX.py:151)                  *******************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
-------------------------------------------------------------------------------
Incorrect option --prefix=/home/karl/projects/petsc specified. It cannot be same as PETSC_DIR!
*******************************************************************************

What I do not understand is that if my prefix cannot be the same as my PETSC_DIR then why does the environmental variable PETSC_DIR required to be export PETSC_DIR=/absolute/path/to/petsc which I've written as PETSC_DIR=/home/karl/projects/petsc

(re: https://petsc.org/release/install/multibuild/#environmental-variables-petsc-dir-and-petsc-arch)

Any tips here?

---

Hi, the prefix (the location where PETSc will be installed) must not be the same directory as the directory containing PETSc source files.
You can set the PETSC_DIR to the prefix after the installation has ended.

I think the easiest way is to export PETSC_DIR after PETSc has been compiled and installed.

---

I think I was finally successful in installing PETSc as I was able to fully build openCARP.

I followed a video tutorial on PETSc installation instead (https://bit.ly/3N92d8d) incorporating openCARP specific instructions during the install. I'm now in the process of modifying settings.yaml to begin my simulations.

Thank you again for your responses Marie, I really appreciate it.

---

I got the same error when REbuilding PETSC after a fresh pull. It turned out I had to unset the PETSC_DIR environment variable to make it work.