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#21 |
New Member
Dean
Join Date: Jun 2021
Posts: 4
Rep Power: 5 ![]() |
Hi Arun,
Success!!!!, now working after a few changes. Here's what I did - 1. Upgraded my Windows WSL to WSL2 - don't know why this worked, but my failed attempts were on WSL1. Set the default WSL to WSL2 2. Fresh install of Ubuntu 20.04 LTS and Windows Terminal 3. Set up all the Prerequisites, then sudo update and upgrade 4. Realised I'd been using Eigen 3.4-rc1 on the failed attempts, used Eigen 3.3.9 and the M10 error went away Here's my full build steps, maybe others who suffer a similar issue can try what worked for me. Thanks for you help, much appreciated. 'Upgrade the windows linux sub system to ver2' 'Goto Windows Powershell as Admin' dism.exe /online /enable-feature /featurename:Microsoft-Windows-Subsystem-Linux /all /norestart dism.exe /online /enable-feature /featurename:VirtualMachinePlatform /all /norestart 'download the latest WSL2 kernel and install' https://wslstorestorage.blob.core.wi...update_x64.msi wsl --set-default-version 2 'Install Ubuntu 20.04 LTS' https://www.microsoft.com/store/apps/9n6svws3rx71 'Install Windows terminal' https://docs.microsoft.com/en-us/win...al/get-started 'Get Prerequisites installed and set up' sudo apt-get update sudo apt install build-essential sudo apt install bison sudo apt install flex sudo apt install unzip sudo apt install mpi sudo apt install mpich sudo apt install openmpi-bin sudo apt install openmpi-doc sudo apt-get update sudo apt-get upgrade 'for REEF3D and DiveMESH' mkdir libraries cd libraries/ cp /mnt/c/Users/User/hypre-master.tar ./ tar -xvf hypre-master.tar cd hypre-master/ cd src/ ./configure --prefix=/usr/local/hypre make all sudo make install cd echo 'export PATH=/usr/local/hypre/lib:/usr/local/hypre/include:$PATH' >> ~/.bashrc source .bashrc cp /mnt/c/Users/User/eigen-3.3.9.tar.gz libraries/ cd libraries tar -xvf eigen-3.3.9.tar.gz rm -f eigen-3.3.9.tar.gz hypre-master.tar cd cp /mnt/c/Users/User/REEF3D-master.zip ./ cp /mnt/c/Users/User/DIVEMesh-master.zip ./ unzip DIVEMesh-master.zip unzip REEF3D-master.zip cd DIVEMesh-master/ 'make for all the processors you have on your pc, mine has 12' make -j 12 cd .. cd REEF3D-master/ make -j 12 cd 'Test It' mkdir test1 cp REEF3D-master/bin/reef3d test1/ cp DIVEMesh-master/bin/DiveMESH test1/ cd test1/ 'copy the ctrl and control files from Tutorials, check the M 10 n line entry for the processors number. Make sure they're the same and within the available processors on your pc. The 2D Dam Break M 10 number is 4, so we'll use 4. Generates ~ 330MB of simulation results for 25000 steps' ./DiveMESH mpirun -n 4 reef3d |
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#22 |
Senior Member
Arun Kamath
Join Date: Nov 2014
Location: Trondheim, Norway
Posts: 265
Rep Power: 13 ![]() |
That is great to know Dean!
Good luck ahead!
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Arun X years with REEF3D |
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#23 | |
New Member
Joao Brazao
Join Date: Aug 2021
Posts: 7
Rep Power: 5 ![]() |
Quote:
Any idea what the origin of this may be? I even did a "brew reinstall mpfr" without errors. The only error I could not address but also not find again, was the "configure: error: Could not determine if REAL*16 bit-matches (...)". See attached. I have been running the 2017 version to go around this issue, but some properties of the 2021 look very interesting and I would really like to upgrade. Thank you. |
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#24 |
Senior Member
Arun Kamath
Join Date: Nov 2014
Location: Trondheim, Norway
Posts: 265
Rep Power: 13 ![]() |
I am not entirely sure from your post which platform you are on. I will assume it is a mac as you use brew.
Then the question is when do you get that error that you state? Possibly when you compile reef3d? You could add - no-multibyte-chars to the CXXFLAGS if REEF3D is not compiled. But that does not explain the issue you have with DiveMESH. I would recommend though that you operate with the latest version.
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#25 |
New Member
Joao Brazao
Join Date: Aug 2021
Posts: 7
Rep Power: 5 ![]() |
Hi Arun,
Sorry, should've reported my system: Model Name: MacBook Pro Model Identifier: MacBookPro15,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 Memory: 16 GB The error I previously showed has occurred during the installation of openMPI with Brew, which all-in-all, should end with a perfect installation of Reef3D/DiveMESH... but it doesn't, because I went back using the method described on the manual, and found the source of the error during compiling, after providing the compilers (& their locations or lack thereof): FCLD libmpi_usempif08.la ld: library not found for -lhwloc collect2: error: ld returned 1 exit status make[2]: *** [libmpi_usempif08.la] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive] Error 1 Seems it's a common issue with more recent Macs, as described by the FAQ 92 of openMPI: https://www.open-mpi.org/faq/?catego...inking-fortran (Likely to become a common issue, as more users adopt Reef3D in more recent Macs) It is described that different sources of installation or suites, can cause the failure when looking for libraries, so I've used the same code as in the manual, but specifying the source installation to be used: ./configure --with-hwloc-libdir=/usr/local/lib CC=gcc CXX=g++ F77=gfortran FC=gfortran --prefix=/usr/local/openmpi This method hasn't worked, the DiveMESH still generates only 1 grd.. gonna try the other methods now, but if you have any advise, it would be welcome. ![]() Thank you. |
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#26 |
Senior Member
Arun Kamath
Join Date: Nov 2014
Location: Trondheim, Norway
Posts: 265
Rep Power: 13 ![]() |
I have recently installed REEF3D on a MacbookPro 16.1 so this problem should not be connected.
Good news: I can reproduce your problem with the file you have uploaded. Bad news: I am not entirely sure why. Solution: Firstly (unrelated) remove the capital letters SC at the top. DiveMESH looks for commands when it encounters capital letters and will not execute in their presence. Finally, somehow removing all the comments associated with the domain, starting with // domain.. // no of processors resulted in the a 3 2 1 decomposition for 6 processors. Why? Good question! Could have something to do with whitespace characters?
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Arun X years with REEF3D Last edited by kamath; August 3, 2021 at 03:36. Reason: missed completing a point |
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#27 |
New Member
Joao Brazao
Join Date: Aug 2021
Posts: 7
Rep Power: 5 ![]() |
Thank you! Indeed, I ran some tests on a previously compiled DiveMESH and removing the comments did solve the 6 grids.
I also replaced the spacing with TAB for a space - also solved. Then replaced again the space for 1 TAB, then several TABS and hasn't failed since then. There must be a an issue around the spacing characters, but not clear if it's the TAB format.. Lesson learned for now is to remove comments before running. Would you like me to test a bit further? (this also means I had an issue with the hwloc libraries, but running the previous code fixed that) |
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#28 |
Senior Member
Arun Kamath
Join Date: Nov 2014
Location: Trondheim, Norway
Posts: 265
Rep Power: 13 ![]() |
Good to know about the hwloc. I have been including it in the Linux compilations and WSL compilations, but had not thought about it for Mac. Probably was available as native previously? I am unsure.
With respect to the spacing and comments: I would recommend not commenting, though it would be a little annoying/difficult when you start off. There seems to be some issue with white space characters but testing each one of them would be quite arduous. I generally use a single space between letter and number and the following number and a return after a command. If you really need to make a small note, just use simple text with small letters, no need to to use //
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Arun X years with REEF3D |
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#29 |
New Member
Taufik
Join Date: Aug 2021
Posts: 6
Rep Power: 5 ![]() |
Hi Team,
i have problem to run DiveMESH, with notes: taufik@TaufikS:~/test1$ ls DiveMESH control.txt ctrl.txt reef3d taufik@TaufikS:~/test1$ DiveMESH DiveMESH: command not found please advise Thank You |
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#30 |
Senior Member
Arun Kamath
Join Date: Nov 2014
Location: Trondheim, Norway
Posts: 265
Rep Power: 13 ![]() |
Please use
./ before DiveMESH The program does not exist in your path. Therefore you have to navigate to the folder where the program exists (which you have done) and then instruct to run the program from the current location (./)
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#31 | |
New Member
Taufik
Join Date: Aug 2021
Posts: 6
Rep Power: 5 ![]() |
Quote:
Thank you for your response, it is works. |
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#32 | |
New Member
Joao Brazao
Join Date: Aug 2021
Posts: 7
Rep Power: 5 ![]() |
Quote:
For OpenMPI:Deleting the folders created by previous attempts to install OpenMPI and Hypre was also important (in /usr/local/...). It seems some files are not overwritten, just by reinstalling. |
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