Installation of Pentagrow does not work

[olealbe]

Hi I am trying to install CEASIOMpy on Ubuntu to create meshes with boundary layers, but the installation does not work properly.

When using the GUI I get the ERROR: FileNotFoundError: [Errno 2] No such file or directory: 'pentagrow'

Checking the installation I found that the URL in Line 20 of "/installation/Ubuntu/install_sumo.py" does not exist. Trying to find an updated one, I found a newer one which led to an AppImage. Using this didn't work.

How can I fix the installation to get pentragrow?

Thanks in advance
Ole

[GBenedett]

Hi @olealbe, yes sumo is migrating to another site, we need to update the installation process. Regarding pentagrow, we'll fix it in the following week (I hope next one). I will let you know.

Best
Giacomo

[GBenedett]

Hi @olealbe,

I have created a new branch called "new_installation" which is still a work in progress and currently only partially functional.

To download the Pentagrow executable, follow these steps

Switch to the "new_installation" branch.

Navigate to CEASIOMpy/installation/Pentagrow.

Download the Pentagrow executable.

Add the executable file to your shell path manually by adding the following line to your shell configuration file (e.g. ~/.bashrc, ~/.bash_profile, or ~/.zshrc):

export PATH="$PATH:/path/to/pentagrow"

Once I integrate this into the main branch, the process will be automated. For now, please use the manual steps above.

Best,
Giacomo

[olealbe]

Thank you @GBenedett, that worked!
Unfortunately it only worked once. Now I somehow get an Error when I try to execute pentagrow.
"pentagrow: error while loading shared libraries: libsuitesparseconfig.so.4: cannot open shared object file: No such file or directory"

Do you have an idea how to solve that problem?

Best Ole

[GBenedett]

I'm sorry to hear that, you can try to check if you have the library by doing

ldconfig -p | grep libsuitesparseconfig

You should see something like

libsuitesparseconfig.so.4 (libc6,x86-64) => /lib64/libsuitesparseconfig.so.4

If you don't see this, you can try to install the library manually by running

sudo apt-get install libsuitesparse-dev (if you use Ubuntu)

Best, Giacomo

[olealbe]

Thanks for the fast response!
Apparently I have Version 5 so: libsuitesparseconfig.so.5 (libc6,x86-64) => /lib/x86_64-linux-gnu/libsuitesparseconfig.so.5
and a Version without a number: libsuitesparseconfig.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libsuitesparseconfig.so

Since I can't do sudo on this machine I'll try sudo apt-get install libsuitesparse-dev later and will see if it solves my problem.

Best, Ole

[olealbe]

sudo apt-get install libsuitesparse-dev didn't work either.

Do you have any other ideas I could try to troubleshoot that problem?

[GBenedett]

Hi again,

There seems to be a problem with the library configuration. Could you please check if the LD_LIBRARY_PATH environment variable is set correctly in your shell?

You can check and set the LD_LIBRARY_PATH variable by running the following command in your terminal:
export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH

Check if the library position is correct.
Then you can try to run agin the command

[olealbe]

Hi, thank you for all your help!

I checked that and there I only have libsuitesparseconfig.so.5.
When executing sudo apt-get install libsuitesparse-dev the newest version 5 is installed.
I am using Ubuntu 20.04 and also tried downloading libsuitesparseconfig.so.4 via conda install suitesparse=4 and I can find libsuitesparseconfig.so.4 in ~/.conda/envs/ceasiompy/lib/.
Also tried setting the LD_LIBRARY_PATH to ~/.conda/envs/ceasiompy/lib/ but that didn't help either.

We are currently out of ideas. Maybe the pentagrow executable and the libsuitesparseconfig.so.4 I have could be binary incompatible?

Best, Ole

[GBenedett]

It shouldn't be.

You can check where libsuitesparseconfig4 is by running dpkg -L libsuitesparseconfig4.

Have you tried to manually install all the libraries that should be installed by "installation_sumo.sh"?

These are the libraries pentagrow needs:

linux-vdso.so.1
libspqr.so.2
libumfpack.so.5
libcholmod.so.3
libsuitesparseconfig.so.4
libccolamd.so.2
libcolamd.so.2
libcamd.so.2
libamd.so.2
libmetis.so.0
libtbb.so.2
libopenblas.so.0
librt.so.1
libdl.so.2
libz.so.1
libpthread.so.0
libstdc++.so.6
libm.so.6
libgomp.so.1
libgcc_s.so.1
libc.so.6
libgfortran.so.3
libquadmath.so.0

Anyway, soon I will try to move forward with developing a better installation process.

[GBenedett]

Hi @olealbe,

Yesterday I tried to use pentagrow on my WLS and at the beginning I had your problem, but I managed to solve it. I attach the log, let me know if it works also for you

(ceasiompy) giacomo@PC-Giacomo:~/CEASIOMpy/installation/Pentagrow$ sudo apt-get install libmetis-devsudo ln -s /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so.5 /usr/lib/x86_64-linux-gnu/l^C
(ceasiompy) giacomo@PC-Giacomo:~/CEASIOMpy/installation/Pentagrow$ sudo ln -s /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so.5 /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so.4
(ceasiompy) giacomo@PC-Giacomo:~/CEASIOMpy/installation/Pentagrow$ sudo ln -s /usr/lib/x86_64-linux-gnu/libmetis.so.5 /usr/lib/x86_64-linux-gnu/libmetis.so.0
(ceasiompy) giacomo@PC-Giacomo:~/CEASIOMpy/installation/Pentagrow$ sudo apt-get install libtbb-dev
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
libtbb-dev is already the newest version (2017~U7-8).
The following packages were automatically installed and are no longer required:
  libamd2 libblas-dev libblas3 libbtf1 libcamd2 libccolamd2 libcholmod3 libcxsparse3 libgraphblas1 libklu1
  liblapack-dev liblapack3 libldl2 libllvm13 librbio2 libspqr2 libumfpack5 libvulkan1 libwayland-client0
  mesa-vulkan-drivers
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 79 not upgraded.
(ceasiompy) giacomo@PC-Giacomo:~/CEASIOMpy/installation/Pentagrow$ sudo ldconfig
/sbin/ldconfig.real: /usr/lib/wsl/lib/libcuda.so.1 is not a symbolic link

(ceasiompy) giacomo@PC-Giacomo:~/CEASIOMpy/installation/Pentagrow$ sudo apt-get install libtbb-dev
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
libtbb-dev is already the newest version (2017~U7-8).
The following packages were automatically installed and are no longer required:
  libamd2 libblas-dev libblas3 libbtf1 libcamd2 libccolamd2 libcholmod3 libcxsparse3 libgraphblas1 libklu1
  liblapack-dev liblapack3 libldl2 libllvm13 librbio2 libspqr2 libumfpack5 libvulkan1 libwayland-client0
  mesa-vulkan-drivers
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 79 not upgraded.
(ceasiompy) giacomo@PC-Giacomo:~/CEASIOMpy/installation/Pentagrow$ sudo ldconfig
/sbin/ldconfig.real: /usr/lib/wsl/lib/libcuda.so.1 is not a symbolic link

(ceasiompy) giacomo@PC-Giacomo:~/CEASIOMpy/installation/Pentagrow$ ls -l /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so.4
lrwxrwxrwx 1 root root 51 Jun 12 22:44 /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so.4 -> /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so.5
(ceasiompy) giacomo@PC-Giacomo:~/CEASIOMpy/installation/Pentagrow$ ls -l /usr/lib/x86_64-linux-gnu/libmetis.so.0
lrwxrwxrwx 1 root root 39 Jun 12 22:44 /usr/lib/x86_64-linux-gnu/libmetis.so.0 -> /usr/lib/x86_64-linux-gnu/libmetis.so.5
(ceasiompy) giacomo@PC-Giacomo:~/CEASIOMpy/installation/Pentagrow$ sudo ldconfig
/sbin/ldconfig.real: /usr/lib/wsl/lib/libcuda.so.1 is not a symbolic link

(ceasiompy) giacomo@PC-Giacomo:~/CEASIOMpy/installation/Pentagrow$ sudo ldconfig
/sbin/ldconfig.real: /usr/lib/wsl/lib/libcuda.so.1 is not a symbolic link

(ceasiompy) giacomo@PC-Giacomo:~/CEASIOMpy/installation/Pentagrow$ ldd pentagrow
        linux-vdso.so.1 (0x00007ffc18f65000)
        libspqr.so.2 => /usr/lib/x86_64-linux-gnu/libspqr.so.2 (0x00007f5965c00000)
        libumfpack.so.5 => /usr/lib/x86_64-linux-gnu/libumfpack.so.5 (0x00007f5965800000)
        libcholmod.so.3 => /usr/lib/x86_64-linux-gnu/libcholmod.so.3 (0x00007f5965400000)
        libsuitesparseconfig.so.4 => /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so.4 (0x00007f5965e64000)
        libccolamd.so.2 => /usr/lib/x86_64-linux-gnu/libccolamd.so.2 (0x00007f5965000000)
        libcolamd.so.2 => /usr/lib/x86_64-linux-gnu/libcolamd.so.2 (0x00007f5964c00000)
        libcamd.so.2 => /usr/lib/x86_64-linux-gnu/libcamd.so.2 (0x00007f5964800000)
        libamd.so.2 => /usr/lib/x86_64-linux-gnu/libamd.so.2 (0x00007f5964400000)
        libmetis.so.0 => /usr/lib/x86_64-linux-gnu/libmetis.so.0 (0x00007f5964000000)
        libtbb.so.2 => /usr/lib/x86_64-linux-gnu/libtbb.so.2 (0x00007f5963c00000)
        libopenblas.so.0 => /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (0x00007f5961800000)
        librt.so.1 => /usr/lib/x86_64-linux-gnu/librt.so.1 (0x00007f5965e5b000)
        libdl.so.2 => /usr/lib/x86_64-linux-gnu/libdl.so.2 (0x00007f5965e56000)
        libz.so.1 => /usr/lib/x86_64-linux-gnu/libz.so.1 (0x00007f5965e3a000)
        libpthread.so.0 => /usr/lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f5965e35000)
        libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f59615d4000)
        libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007f5965b19000)
        libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f5965acf000)
        libgcc_s.so.1 => /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f5965aaf000)
        libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007f59613ab000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f5965e6b000)
        liblapack.so.3 => /usr/lib/x86_64-linux-gnu/liblapack.so.3 (0x00007f5960a00000)
        libblas.so.3 => /usr/lib/x86_64-linux-gnu/libblas.so.3 (0x00007f5960600000)
        libgfortran.so.4 => /usr/lib/x86_64-linux-gnu/libgfortran.so.4 (0x00007f5960200000)
        libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f59657b8000)

[olealbe]

Great! Thank you, that worked and now I don't get the error anymore!

But we just discovered that I also don't have Tetgen. I think that is related to the migration of sumo you mentioned before.
When I execute the install_sumo.sh the INSTALLDIR stays empty an the URL https://www.larosterna.com/packages/sumo-standalone-Qt4-2.7.9.tgz which is in the script doesn't work.

Is there a way I still can get Sumo and/or Tetgen?

[GBenedett]

try to do in the same place, using the command line pentagrow mesh_2d.stl config.cfg

[olealbe]

I get a "Segmentation fault". These are the last lines of the output:

Memory usage statistics:

Maximum number of tetrahedra: 2597221
Maximum number of tet blocks (blocksize = 8188): 318
Approximate memory for tetrahedral mesh (bytes): 482,503,400
Approximate memory for extra pointers (bytes): 62,311,776
Approximate memory for algorithms (bytes): 88,000
Approximate memory for working arrays (bytes): 100,625,408
Approximate total used memory (bytes): 645,528,584

done. 115.425s
Reading tet mesh and adapting wall...
Segmentation fault

[GBenedett]

It seems there might be an issue related to the surface mesh. Which CPACS file did you use? Could you please show the surface mesh? It might be too refined.

For troubleshooting, please try to use the labARscaled.xml file to see if it meshes correctly. If you select this CPACS file from the test files (here: CEASIOMpy/test_files/CPACSfile) and leave the default settings, you should be able to get a mesh within a few seconds.

[olealbe]

I used the simpletest. But I tried the labARscaled.xml and it didn't work either.

The only option I changed was "RANS mesh".

[GBenedett]

It's weird, can you please attach an image of the mesh? And maybe also attach the surface mesh file so we can see if it's your pentagrow.

write me an email: giacomo.benedetti@cfse.ch