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by (570 points)

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

1 Answer

+1 vote
by (3.4k points)
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Best answer

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.

by (570 points)
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?
by (3.4k points)
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.
by (570 points)
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.
by (230 points)
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.
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