<!DOCTYPE html>
<!-- BaNnErBlUrFlE-BoDy-start -->
<!-- Preheader Text : BEGIN -->
<div style="display:none !important;display:none;visibility:hidden;mso-hide:all;font-size:1px;color:#ffffff;line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden;">
Hello, I'm new to the list and have a limited knowledge of PETSc so far, but I'm trying to use a software (underworld3) that relies on petsc4py. I have built PETSc with the following configure options: --with-fortran-bindings=0 --with-mpi-dir=/usr
</div>
<!-- Preheader Text : END -->
<!-- Email Banner : BEGIN -->
<div style="display:none !important;display:none;visibility:hidden;mso-hide:all;font-size:1px;color:#ffffff;line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden;">ZjQcmQRYFpfptBannerStart</div>
<!--[if ((ie)|(mso))]>
<table border="0" cellspacing="0" cellpadding="0" width="100%" style="padding: 16px 0px 16px 0px; direction: ltr" ><tr><td>
<table border="0" cellspacing="0" cellpadding="0" style="padding: 0px 10px 5px 6px; width: 100%; border-radius:4px; border-top:4px solid #90a4ae;background-color:#D0D8DC;"><tr><td valign="top">
<table align="left" border="0" cellspacing="0" cellpadding="0" style="padding: 4px 8px 4px 8px">
<tr><td style="color:#000000; font-family: 'Arial', sans-serif; font-weight:bold; font-size:14px; direction: ltr">
This Message Is From an External Sender
</td></tr>
<tr><td style="color:#000000; font-weight:normal; font-family: 'Arial', sans-serif; font-size:12px; direction: ltr">
This message came from outside your organization.
</td></tr>
</table>
</td></tr></table>
</td></tr></table>
<![endif]-->
<![if !((ie)|(mso))]>
<div dir="ltr" id="pfptBannerokl1ezm" style="all: revert !important; display:block !important; text-align: left !important; margin:16px 0px 16px 0px !important; padding:8px 16px 8px 16px !important; border-radius: 4px !important; min-width: 200px !important; background-color: #D0D8DC !important; background-color: #D0D8DC; border-top: 4px solid #90a4ae !important; border-top: 4px solid #90a4ae;">
<div id="pfptBannerokl1ezm" style="all: unset !important; float:left !important; display:block !important; margin: 0px 0px 1px 0px !important; max-width: 600px !important;">
<div id="pfptBannerokl1ezm" style="all: unset !important; display:block !important; visibility: visible !important; background-color: #D0D8DC !important; color:#000000 !important; color:#000000; font-family: 'Arial', sans-serif !important; font-family: 'Arial', sans-serif; font-weight:bold !important; font-weight:bold; font-size:14px !important; line-height:18px !important; line-height:18px">
This Message Is From an External Sender
</div>
<div id="pfptBannerokl1ezm" style="all: unset !important; display:block !important; visibility: visible !important; background-color: #D0D8DC !important; color:#000000 !important; color:#000000; font-weight:normal; font-family: 'Arial', sans-serif !important; font-family: 'Arial', sans-serif; font-size:12px !important; line-height:18px !important; line-height:18px; margin-top:2px !important;">
This message came from outside your organization.
</div>
</div>
<div style="clear: both !important; display: block !important; visibility: hidden !important; line-height: 0 !important; font-size: 0.01px !important; height: 0px"> </div>
</div>
<![endif]>
<div style="display:none !important;display:none;visibility:hidden;mso-hide:all;font-size:1px;color:#ffffff;line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden;">ZjQcmQRYFpfptBannerEnd</div>
<!-- Email Banner : END -->
<!-- BaNnErBlUrFlE-BoDy-end -->
<html>
<head><!-- BaNnErBlUrFlE-HeAdEr-start -->
<style>
#pfptBannerokl1ezm { all: revert !important; display: block !important;
visibility: visible !important; opacity: 1 !important;
background-color: #D0D8DC !important;
max-width: none !important; max-height: none !important }
.pfptPrimaryButtonokl1ezm:hover, .pfptPrimaryButtonokl1ezm:focus {
background-color: #b4c1c7 !important; }
.pfptPrimaryButtonokl1ezm:active {
background-color: #90a4ae !important; }
</style>
<!-- BaNnErBlUrFlE-HeAdEr-end -->
<meta charset="UTF-8"></head><body><pre style="font-family: sans-serif; font-size: 100%; white-space: pre-wrap; word-wrap: break-word">Hello,
I'm new to the list and have a limited knowledge of PETSc so far, but
I'm trying to use a software (underworld3) that relies on petsc4py.
I have built PETSc with the following configure options:
--with-fortran-bindings=0 --with-mpi-dir=/usr
and `make test` gives me 160 failures which all seem to be timeouts or
arising from my having insufficient "slots" (cores?). I subsequently
built underworld3 with something like
cd $PETSC_DIR
PETSC_DIR=... PETSC_ARCH=... NUMPY_INCLUDE=... pip install src/binding/petsc4py
cd /path/to/underworld3/tree
pip install h5py
pip install mpi4py
PETSC_DIR=... PETSC_ARCH=... NUMPY_INCLUDE=... pip install -e .
following their instructions. Building their python wheel/package was
successful, however when I run their tests (using pytest) I get errors
during test collection, which all come from petsc4py and have a stack
trace that ends in the snippet attached below. Am I going about this
wrong? How do I ensure that the HDF5 types are defined?
src/underworld3/discretisation.py:86: in _from_gmsh
viewer = PETSc.ViewerHDF5().create(filename + ".h5", "w", comm=PETSc.COMM_SELF)
petsc4py/PETSc/Viewer.pyx:916: in petsc4py.PETSc.ViewerHDF5.create
???
E petsc4py.PETSc.Error: error code 86
------------------------------- Captured stderr --------------------------------
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Unknown type. Check for miss-spelling or missing package: <a href="https://urldefense.us/v3/__https://petsc.org/release/install/install/*external-packages__;Iw!!G_uCfscf7eWS!duVp7PZwdvHgymCgufX290k3tptJCHEo3vrV7dNt9zumYwqzDVsb1AG1HHargxq0LL-1JO6mjgiS7Vbykb1_siyXWw$">https://urldefense.us/v3/__https://petsc.org/release/install/install/*external-packages__;Iw!!G_uCfscf7eWS!duVp7PZwdvHgymCgufX290k3tptJCHEo3vrV7dNt9zumYwqzDVsb1AG1HHargxq0LL-1JO6mjgiS7Vbykb1_siyXWw$</a>
[0]PETSC ERROR: Unknown PetscViewer type given: hdf5
[0]PETSC ERROR: See <a href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!duVp7PZwdvHgymCgufX290k3tptJCHEo3vrV7dNt9zumYwqzDVsb1AG1HHargxq0LL-1JO6mjgiS7Vbykb1LEFOicQ$">https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!duVp7PZwdvHgymCgufX290k3tptJCHEo3vrV7dNt9zumYwqzDVsb1AG1HHargxq0LL-1JO6mjgiS7Vbykb1LEFOicQ$</a> for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.20.4, unknown
[0]PETSC ERROR: /home/leon/vcs/underworld3/.venv-underworld3/bin/pytest on a arch-linux-c-debug named roci by leon Wed Mar 13 00:01:33 2024
[0]PETSC ERROR: Configure options --with-fortran-bindings=0 --with-mpi-dir=/usr
[0]PETSC ERROR: #1 PetscViewerSetType() at /home/leon/vcs/petsc/src/sys/classes/viewer/interface/viewreg.c:535
Cheers,
Leon
</pre></body></html>