MOOSE Test Run Failure

[Asif Tanveer]

Hello,

I am a new user of Ubuntu and MOOSE. I recently installed Ubuntu 18.04 alongside Win 10 to run MOOSE. I have gone through the instructions in the following page:

https://mooseframework.org/getting_started/index.html

However, when I performed the 'compile and test' all the 50 tests that ran failed. Attached is the output of the test run.

I made sure I am running the miniconda3 in my home/username (I had Anaconda installed in Win10 previously but that should not be conflicting with this. Anyway, I uninstalled Anaconda in Win10 but still received the same errors).

I also received the same error in  WSL I used in a separate PC. I have double-checked the folders and cloning were done properly.

Is there something I am not doing correctly? Could someone please help me with this?

Thank you!

[Asif Tanveer]

I ran 'ldd moose_test-opt'. It shows 'libquadmath.so.0 => not found' in the terminal. 
Any suggestion how I could fix this? I tried 'make clobberall' but that too does not help.

[Jason Miller]

Can you post your libmesh_diagnostic.log? It should be located at:

  moose/scripts/libmesh_diagnostic.log

Also, apologies for not asking this first thing this morning. I somehow misplaced this email among the mailing list.

Thanks!

Jason

On Tue, May 5, 2020 at 2:15 PM Asif Tanveer <asiftan...@gmail.com> wrote:

I ran 'ldd moose_test-opt'. It shows 'libquadmath.so.0 => not found' in the terminal. 
Any suggestion how I could fix this? I tried 'make clobberall' but that too does not help.

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[Jason Miller]

Oh wait... haha... old habits. There is no libmesh_diagnostic.log when using Conda over the old moose-environment package.

That being said, it sounds as if you may not have the same conda environment loaded as you did when you first built moose. You mentioned you performed an `ldd` on moose_test-opt. Can you report the entire stdout?

Also, it may help if you post the return of an `env`

Thanks!

Jason

[Asif Tanveer]

Not a problem! Thanks for the reply. When I hit ldd moose_test-opt I get the following  

        linux-vdso.so.1 (0x00007fffe25b5000)

        libmoose_test-opt.so.0 => /home/tanveer2/projects/moose/test/lib/libmoose_test-opt.so.0 (0x00007f903470a000)

        libmoose-opt.so.0 => /home/tanveer2/projects/moose/framework/libmoose-opt.so.0 (0x00007f903315c000)

        libhit-opt.so.0 => /home/tanveer2/projects/moose/framework/contrib/hit/libhit-opt.so.0 (0x00007f90330fd000)

        libmesh_opt.so.0 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/libmesh_opt.so.0 (0x00007f9031f4c000)

        libtimpi_opt.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/libtimpi_opt.so.1 (0x00007f9031f33000)

        libgfortran.so.4 => /home/tanveer2/miniconda3/envs/moose/lib/libgfortran.so.4 (0x00007f9031e05000)

        libgcc_s.so.1 => /home/tanveer2/miniconda3/envs/moose/lib/libgcc_s.so.1 (0x00007f9031df1000)

        libstdc++.so.6 => /home/tanveer2/miniconda3/envs/moose/lib/libstdc++.so.6 (0x00007f9031c7d000)

        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f90318d0000)

        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f90314d0000)

        libmpi.so.12 => /home/tanveer2/miniconda3/envs/moose/lib/libmpi.so.12 (0x00007f9031185000)

        libpcre-opt.so.0 => /home/tanveer2/projects/moose/framework/contrib/pcre/libpcre-opt.so.0 (0x00007f9031156000)

        libvtkCommonCore-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/libvtkCommonCore-6.3.so.1 (0x00007f9030cfe000)

        libvtkCommonDataModel-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/libvtkCommonDataModel-6.3.so.1 (0x00007f90309e7000)

        libvtkImagingCore-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/libvtkImagingCore-6.3.so.1 (0x00007f903078b000)

        libvtkIOImage-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/libvtkIOImage-6.3.so.1 (0x00007f9030604000)

        libvtkImagingMath-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/libvtkImagingMath-6.3.so.1 (0x00007f90305bb000)

        libpetsc.so.3.12 => /home/tanveer2/miniconda3/envs/moose/lib/libpetsc.so.3.12 (0x00007f902ece0000)

        libHYPRE-2.18.2.so => /home/tanveer2/miniconda3/envs/moose/lib/libHYPRE-2.18.2.so (0x00007f902e848000)

        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f902e620000)

        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f902e410000)

        /lib64/ld-linux-x86-64.so.2 (0x00007f9034e00000)

        libgomp.so.1 => /home/tanveer2/miniconda3/envs/moose/lib/libgomp.so.1 (0x00007f902e33d000)

        libnetcdf.so.13 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/libnetcdf.so.13 (0x00007f902e1f1000)

        libvtkIOCore-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../libmesh-vtk/lib/libvtkIOCore-6.3.so.1 (0x00007f902e179000)

        libvtkIOXML-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../libmesh-vtk/lib/libvtkIOXML-6.3.so.1 (0x00007f902e0af000)

        libvtkIOParallelXML-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../libmesh-vtk/lib/libvtkIOParallelXML-6.3.so.1 (0x00007f902e078000)

        libvtkParallelMPI-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../libmesh-vtk/lib/libvtkParallelMPI-6.3.so.1 (0x00007f902e061000)

        libvtkParallelCore-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../libmesh-vtk/lib/libvtkParallelCore-6.3.so.1 (0x00007f902e008000)

        libz.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/libz.so.1 (0x00007f902dfee000)

        libslepc.so.3.12 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/libslepc.so.3.12 (0x00007f902dc96000)

        libparmetis.so => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/libparmetis.so (0x00007f902dc3f000)

        libmetis.so => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/libmetis.so (0x00007f902dbc4000)

        libquadmath.so.0 => not found

        librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f902d9b0000)

        libvtksys-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/./libvtksys-6.3.so.1 (0x00007f902d960000)

        libvtkCommonMisc-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/./libvtkCommonMisc-6.3.so.1 (0x00007f902d949000)

        libvtkCommonSystem-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/./libvtkCommonSystem-6.3.so.1 (0x00007f902d933000)

        libvtkCommonTransforms-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/./libvtkCommonTransforms-6.3.so.1 (0x00007f902d8ff000)

        libvtkCommonMath-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/./libvtkCommonMath-6.3.so.1 (0x00007f902d8dc000)

        libvtkCommonExecutionModel-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/./libvtkCommonExecutionModel-6.3.so.1 (0x00007f902d846000)

        libvtkpng-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/./libvtkpng-6.3.so.1 (0x00007f902d80d000)

        libvtktiff-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/./libvtktiff-6.3.so.1 (0x00007f902d79e000)

        libvtkmetaio-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/./libvtkmetaio-6.3.so.1 (0x00007f902d6fb000)

        libvtkDICOMParser-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/./libvtkDICOMParser-6.3.so.1 (0x00007f902d6da000)

        libvtkzlib-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/./libvtkzlib-6.3.so.1 (0x00007f902d6c0000)

        libvtkjpeg-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh-vtk/lib/./libvtkjpeg-6.3.so.1 (0x00007f902d68a000)

        libsuperlu_dist.so.6 => /home/tanveer2/miniconda3/envs/moose/lib/./libsuperlu_dist.so.6 (0x00007f902d577000)

        libmpifort.so.12 => /home/tanveer2/miniconda3/envs/moose/lib/./libmpifort.so.12 (0x00007f902d538000)

        libmfhdf.so.0 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/./libmfhdf.so.0 (0x00007f902d50c000)

        libdf.so.0 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/./libdf.so.0 (0x00007f902d450000)

        libhdf5_hl.so.100 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/./libhdf5_hl.so.100 (0x00007f902d42a000)

        libhdf5.so.103 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/./libhdf5.so.103 (0x00007f902d089000)

        libcurl.so.4 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/./libcurl.so.4 (0x00007f902d001000)

        libvtkIOXMLParser-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../libmesh-vtk/lib/./libvtkIOXMLParser-6.3.so.1 (0x00007f902cfe8000)

        libvtkIOLegacy-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../libmesh-vtk/lib/./libvtkIOLegacy-6.3.so.1 (0x00007f902cf43000)

        libquadmath.so.0 => /home/tanveer2/miniconda3/envs/moose/lib/././libquadmath.so.0 (0x00007f902cf06000)

        libjpeg.so.9 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/././libjpeg.so.9 (0x00007f902cec8000)

        libssh2.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/././libssh2.so.1 (0x00007f902ce95000)

        libssl.so.1.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/././libssl.so.1.1 (0x00007f902ce05000)

        libcrypto.so.1.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/././libcrypto.so.1.1 (0x00007f902cb34000)

        libgssapi_krb5.so.2 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/././libgssapi_krb5.so.2 (0x00007f902cae5000)

        libkrb5.so.3 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/././libkrb5.so.3 (0x00007f902ca0c000)

        libk5crypto.so.3 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/././libk5crypto.so.3 (0x00007f902c9ed000)

        libcom_err.so.3 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/././libcom_err.so.3 (0x00007f9034cf2000)

        libvtkexpat-6.3.so.1 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../libmesh-vtk/lib/././libvtkexpat-6.3.so.1 (0x00007f902c9a9000)

        libkrb5support.so.0 => /home/tanveer2/miniconda3/envs/moose/libmesh/lib/../../lib/./././libkrb5support.so.0 (0x00007f90318c1000)

        libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007f902c780000)

Are you talking about the folders in miniconda3\envs\moose ? Here they are:

I do have another version of Anaconda installed but I when I try 'which conda' and 'which python' it attributes to this one.

bin              doc      lib      libmesh      mkspecs      plugins  resources  ssl           x86_64-conda_cos6-linux-gnu

compiler_compat  etc      lib64    libmesh-vtk  moose        qml      sbin       translations

conda-meta       include  libexec  man          phrasebooks  qsci     share      var

Thank you,

Asif

[Yuxiang Wang]

For what it's worth... We had a very similar issue but then using apt to install build essentials solved the problem. It seems like the condo workflow does not work without installing a few prerequisites?

Shawn

[Asif Tanveer]

Hi Shawn,

Thanks a lot! It worked with sudo apt-get install build-essential.

Regards,

Asif Tanveer

[Jason Miller]

Interesting resolution! I suppose build-essentials is in all respects like Command Line Tools for MacOS machines. I will have to investigate if our instructions are incomplete with some sort of vanilla install. Thank you both for posting!

Jason

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[Anders Ericsson]

Hi,

I think I have a similar issue. I haven't used Moose for a month and today I updated it and rebuild libmesh.

However, when i tried to compile moose I received:

/usr/bin/ld: warning: libtimpi_opt.so.0, needed by /home/anders/MOOSE_projects/moose/framework/contrib/hit/libhit-opt.so, not found (try using -rpath or -rpath-link)

I get a similar error when I run ./moose_test-opt.

anders@anders:~/MOOSE_projects/moose/test$ ./moose_test-opt

./moose_test-opt: error while loading shared libraries: libtimpi_opt.so.0: cannot open shared object file: No such file or directory

Which causes the tests to fail. So there seems to be a problem with the compilation of libmesh. I have build-essentials installed already so that didn't work for me and I run Ubuntu 18.04.

I'm quite novice at this, so I appreciate any of your help. Please find the diagnostic from libmesh attached.

Best regards,

Anders

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From: moose...@googlegroups.com <moose...@googlegroups.com> on behalf of Jason Miller <m.jason...@gmail.com>
Sent: Wednesday, May 6, 2020 4:58:46 PM
To: moose...@googlegroups.com
Subject: Re: MOOSE Test Run Failure

 

To view this discussion on the web visit https://groups.google.com/d/msgid/moose-users/CALK7ujxze8%3Dobwj1LF%2BhohbaBtkSv94wR8VByP%3D6Si2RThgQmA%40mail.gmail.com.

[Jason Miller]

Looks like you are using the moose-environment packages (and not Conda as this thread was initially started for).

libMesh configure looks great. And I imagine the build succeeded just fine. The error may indicate that you need to clear out a previous build before building anew. Please keep in mind, the following commands are going to delete any changes you may have made in your moose repo. So please save/commit them before continuing:

cd /home/anders/MOOSE_projects/moose

git clean -xfd

and then try to build moose/test:

cd /home/anders/MOOSE_projects/moose/test

make -j (your cpu count)

Once complete, try to run tests...

Let us know how it goes! Cheers!

Jason

To view this discussion on the web visit https://groups.google.com/d/msgid/moose-users/968bb59a81d44e66b2d241eeeec0866e%40solid.lth.se.

[Yuxiang Wang]

Happy to help! Thank you Jason for all the amazing work; once it's configured using conda indeed makes life much easier! :)

Shawn

On Wednesday, May 6, 2020 at 7:59:25 AM UTC-7, Jason Miller wrote:

Interesting resolution! I suppose build-essentials is in all respects like Command Line Tools for MacOS machines. I will have to investigate if our instructions are incomplete with some sort of vanilla install. Thank you both for posting!

Jason

On Wed, May 6, 2020 at 3:26 AM Asif Tanveer <asiftan...@gmail.com> wrote:

Hi Shawn,

Thanks a lot! It worked with sudo apt-get install build-essential.

Regards,

Asif Tanveer

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[Alexander Lindsay]

TIMPI recently underwent a version change from 0 to 1, so it sounds like you have stale MOOSE objects looking for an old version that won't exist if you've updated libMesh/TIMPI

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[Anders Ericsson]

Worked like a charm!

Thanks a lot!

//Anders

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From: moose...@googlegroups.com <moose...@googlegroups.com> on behalf of Jason Miller <m.jason...@gmail.com>

Sent: Wednesday, May 6, 2020 5:51 PM

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[Scott Muller]

I'm installing MOOSE on WSL 1 and this fixed my issue as well. It might be good to add this possible fix to the MOOSE framework troubleshooting page ( https://mooseframework.inl.gov/help/troubleshooting.html ). Thanks for the solution!

[Scott Muller]

(referring to original poster's "sudo apt-get install build-essential" solution)