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Hi again,
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<div class="">It looks from </div>
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<div class=""><a href="https://gitlab.dune-project.org/dune-fem/dune-fem/blob/master/dune/fem/misc/mpimanager.hh#L122" class="">https://gitlab.dune-project.org/dune-fem/dune-fem/blob/master/dune/fem/misc/mpimanager.hh#L122</a></div>
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<div class="">That you can get the communicator using something like Dune::Fem::MPIManager::comm() (not tested yet though)</div>
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<div class="">Best wishes,</div>
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Dr. Roland Guichard </div>
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Research Software Engineer</div>
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UCL-RITS</div>
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Internal Extension: 86947</div>
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<div class="">On 5 Jul 2019, at 13:28, Guichard, Roland <<a href="mailto:r.guichard@ucl.ac.uk" class="">r.guichard@ucl.ac.uk</a>> wrote:</div>
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Hi,
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<div class="">I see thanks.</div>
<div class="">A quick question though, does it mean that there are several MPI initializations possible within Dune and the communicator that needs to be passed to the GridPtr (from dune-fem) is responsible for handling the mesh in parallel ?</div>
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<div class="">Best wishes,</div>
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Dr. Roland Guichard </div>
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Research Software Engineer</div>
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UCL-RITS</div>
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Internal Extension: 86947</div>
External Number: 02031086947
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<div class="">On 5 Jul 2019, at 12:51, Markus Blatt <<a href="mailto:markus@dr-blatt.de" class="">markus@dr-blatt.de</a>> wrote:</div>
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<div class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Hi,</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">please
always reply to the list (using e.g. reply to all). I took the liberty</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">to
bounce your mail to list.</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">You
definitely need to pass the communicator to the constructor of the GridPtr.</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Not
sure whether this is the complete fix.</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Without
dune-fem one would do</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Dune::MPIHelper&
helper = Dune::MPIHelper::instance(argc, argv);</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">//
Dune::GridPtr< HGridType > gridPtr( meshName.str() );</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Dune::GridPtr<GridType>
gridPtr(meshName.str(),helper.getCommunicator());</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">gridPtr.loadBalance();</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">How
to get the communicator using dune-fem somebody else needs to tell you.</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Markus</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">On
Fri, Jul 05, 2019 at 11:28:36AM +0000, Guichard, Roland wrote:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
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Dear Markus,<br class="">
<br class="">
Thank you for your prompt response.<br class="">
<br class="">
Sure, you can find attached a stripped out version of the main. I only have inherited that code, not developed it myself.<br class="">
<br class="">
You’ll see that the same path to the dgf file is passed to all MPI ranks but I don’t understand why initialising the DGFGridFactory is rank dependent.<br class="">
<br class="">
Besides, any comments/suggestions on the code are very welcome. Part of my job is also to refactor it for a better use. The main issue is that there is such a gap between Dune2.3 and Dune2.6 which makes it uneasy to track (owing that I have never used Dune
before :)<br class="">
<br class="">
Thank you again for your time<br class="">
<br class="">
Kind regards,<br class="">
<br class="">
Dr. Roland Guichard<br class="">
Research Software Engineer<br class="">
UCL-RITS<br class="">
Internal Extension: 86947<br class="">
External Number: 02031086947<br class="">
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On 5 Jul 2019, at 12:00, Markus Blatt <<a href="mailto:markus@dr-blatt.de" class="">markus@dr-blatt.de</a><<a href="mailto:markus@dr-blatt.de" class="">mailto:markus@dr-blatt.de</a>>> wrote:<br class="">
<br class="">
Hi,<br class="">
<br class="">
would you mind to share your setup code for the grid?<br class="">
<br class="">
Markus<br class="">
<br class="">
On Fri, Jul 05, 2019 at 09:24:33AM +0000, Guichard, Roland wrote:<br class="">
Dear Dune people,<br class="">
<br class="">
I am currently working on a project to update a home made Dune module (peits) to the newest Dune modules. Peits was previously running fine with Dune modules (common, fem, grid, alugrid, geometry) v2.3.<br class="">
<br class="">
Now I am trying to update to the same Dune modules v2.6. I have managed to compile (under GNU compiler) and run serially Peits with Dune2.6 but the issue appears when I run in parallel using MPI. This occurs when the gridPtr is called,<br class="">
<br class="">
And trying to create the grid from a dgf file, especially the assertion:<br class="">
<br class="">
<a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgitlab.dune-project.org%2Fcore%2Fdune-grid%2Fblob%2Fmaster%2Fdune%2Fgrid%2Fio%2Ffile%2Fdgfparser%2Fgridptr.hh%23L281&data=02%7C01%7C%7C6894be42ceb84941f59108d701445643%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636979265323126881&sdata=Ldn%2BCq1cmUz6EyZAid2a8%2BGSCz0OiUb1SP3zGoeVbJ8%3D&reserved=0" originalsrc="https://gitlab.dune-project.org/core/dune-grid/blob/master/dune/grid/io/file/dgfparser/gridptr.hh#L281" shash="zR/pNV9BQno1q0AOv92puPpqpB6/EFCNwlu3f/d5F5FpriQqiihqdkrG2BOLCIS/oG78pO5ip/pGOM97930yZNejO2b5Sa15po/lp9QYIrJVz/9r4pzyPwVC+hQgBlxBPhe2+2Wvecd+whq9z3zdR5MpeHplUUJmJsBHOPUkrpg=" class="">https://gitlab.dune-project.org/core/dune-grid/blob/master/dune/grid/io/file/dgfparser/gridptr.hh#L281</a><br class="">
<br class="">
Basically, what I have narrowed down is:<br class="">
<br class="">
<br class="">
* The MPI rank 0 runs fine. It fetches all parameters from files, calls the DGFGridFactory, initializes it etc.<br class="">
* The MPI rank 1 comes to the same point but I have checked that the initialisation of the DGFGridFactory is not setting the necessary parameters the same way, I.e. the elParam_ size is set to 0 (whereas ~57000 in MPI rank 0) causing the above assertion to
fail.<br class="">
<br class="">
I wanted to know if there is a dedicated procedure to create a grid in parallel which I am missing at this point. Could you advise on this issue ?<br class="">
<br class="">
That would be really helpful.<br class="">
<br class="">
Kind regards,<br class="">
<br class="">
Dr. Roland Guichard<br class="">
Research Software Engineer<br class="">
UCL-RITS<br class="">
Internal Extension: 86947<br class="">
External Number: 02031086947<br class="">
<br class="">
<br class="">
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Dr. Markus Blatt - HPC-Simulation-Software & Services<span class="Apple-converted-space"> </span><a href="https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.dr-blatt.de%2F&data=02%7C01%7C%7C6894be42ceb84941f59108d701445643%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636979265323136877&sdata=l7JjPJkzv%2B0cOH63F1lrkjbOB4xwV7mkyMsQeGi%2Fj%2Bk%3D&reserved=0" originalsrc="http://www.dr-blatt.de/" shash="HDwETR8A5LfBTVG3WH9xrdbiamNQxYg3BqvekWF+7Jx04WrxKsMvfjtUXn49lPKHSuzJ/9L/0j0AnkCrTKHY5bYk8aUnbZIiFFpoGp7e8+q2rC/7xVvJ5snEPS6oZFkQcNu0vhBzBoM01jeSfECrCE8NDAxkC4cLGBgsVkhds0Q=" class="">http://www.dr-blatt.de</a><br class="">
Pedettistr. 38, 85072 Eichstätt, Germany<br class="">
Tel.: +49 (0) 160 97590858<br class="">
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<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">--<span class="Apple-converted-space"> </span></span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Dr.
Markus Blatt - HPC-Simulation-Software & Services<span class="Apple-converted-space"> </span></span><a href="https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.dr-blatt.de%2F&data=02%7C01%7C%7C6894be42ceb84941f59108d701445643%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636979265323146869&sdata=olkW1mL2yOxxGRdAaF1lFdm%2BPGm6%2Br%2BidMK2wutYJSE%3D&reserved=0" originalsrc="http://www.dr-blatt.de/" shash="iX7zkjVBBoaQB3jjYtHbVcHNa12XVVymPMl3jLIb9MqW3Zksxb/uRdh62LldOTbvUs32LdTKVuq2TDaEM2EZf2l8Xwz75ETzCdqeSqW2QPQHo27EATyABKjyK+aFhgMRHOoHjYNb10VZVEabhbO6P8z1vIs7NeiqEH9OJCClq4U=" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://www.dr-blatt.de</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Pedettistr.
38, 85072 Eichstätt, Germany, USt-Id: DE279960836</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Tel.:
+49 (0) 160 97590858</span></div>
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