Installation problems probably related to libmesh

[aceb...@berkeley.edu]

First time user interested in doing some Joule heating simulations. I have a virtual machine running ubuntu 14.04 LTS and I've been following the instructions. The libmesh compilation took a long time upwards of an hour for me. I don't know if that's normal. When I type:

make -j8

I get the following:

/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/libtool: not found
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
Traceback (most recent call last):
  File "/home/nmag/projects/moose/framework/scripts/get_repo_revision.py", line 114, in <module>
    revision = repoVersionString( repo_location )
  File "/home/nmag/projects/moose/framework/scripts/get_repo_revision.py", line 71, in repoVersionString
    version = gitVersionString( cwd )
  File "/home/nmag/projects/moose/framework/scripts/get_repo_revision.py", line 41, in gitVersionString
    return tag + "git commit " + SHA1 + " on " + date
TypeError: Can't convert 'bytes' object to str implicitly
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
MOOSE Compiling C++ (in opt mode) /home/nmag/projects/moose/framework/src/utils/RandomData.C...
/bin/sh: 1: /home/nmag/projects/moose/libmesh/installed/contrib/bin/libmesh-config: not found
make: /home/nmag/projects/moose/libmesh/installed/libtool: Command not found
make: *** [/home/nmag/projects/moose/framework/src/utils/RandomData..opt.lo] Error 127
make: *** Waiting for unfinished jobs....
MOOSE Compiling C++ (in opt mode) /home/nmag/projects/moose/framework/src/utils/MooseEnum.C...
make: /home/nmag/projects/moose/libmesh/installed/libtool: Command not found
make: *** [/home/nmag/projects/moose/framework/src/utils/MooseEnum..opt.lo] Error 127

I went to look in my computer for those files and the contrib folder does not exist under the installed folder but rather under the libmesh folder.

What I mean is that projects/moose/libmesh/installed/contrib/bin/libmesh-config is not the right path but rather: projects/moose/libmesh/contrib/bin/libmesh-config is the right one.

Can I just copy paste the contrib folder to the place where it is looking for them or is there another fix for this?

[Andrew....@csiro.au]

I can’t help with your problem, but 1 hour compilation time for libmesh is a little slow but certainly not unbelievable.

 

a

 

 

Ph: +61 7 3327 4497.  Fax: +61 7 3327 4666
Queensland Centre for Advanced Technologies
PO Box 883, Kenmore, Qld, 4069 
 

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[Andrs, David]

How did you build libmesh? The exact command line, please.

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David

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[Alejandro Ceballos]

Once in the /projects/moose folder, I typed in the terminal:

scripts/update_and_rebuild_libmesh.sh

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[Andrs, David]

Ok. So what you see is a result of `make install` not being ran (for some reason). If you still have your console open with all the build output, scroll up and try to find a place that printed out some error. Then copy and paste that error here.

One possible reason when make install did not happen is that you ran out of disk space. Check that you have enough disk space by: df -H

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[Alejandro Ceballos]

I don't have the output from installing libmesh on my terminal anymore. Should I run the

scripts/update_and_rebuild_libmesh.sh command again to look for the error?

The VM still has plenty of allocated space (60 GB).

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[Andrs, David]

First, try this:

$ cd <where/ever/my/moose/is>/libmesh/build

$ make

Does it finish with no errors?

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[Derek Gaston]

The problem is that you haven't allocated enough RAM to your virtual machine.  Linking the libMesh library requires several GB of RAM.  Allocate as much as you can spare and it will work.

Derek

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[Derek Gaston]

To be clear: change how much RAM you have allocated to your VM and then rerun the script... it will work this time.

Also: if you want it to compile faster allocate more processors to your VM.  Our scripts automatically sense how many processors are available and use them for compiling.

Derek

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[Alejandro Ceballos]

I attached the output after typing make. I have 4 GB of RAM allocated.

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[Derek Gaston]

It looks like you haven't set up your environment quite right (you're not referencing the correct MPI)

At this point I would recommend using our prebuilt VM package where everything is ready to go: http://mooseframework.org/getting-started/virtual-machine/

If you don't want to do that then we're going to need to dig into your environment.

Did you install our prebuilt package for Ubuntu 14.04?  ( http://mooseframework.org/getting-started/ubuntu-1404/ )

Did you modify your .bashrc file and restart all of your Terminals?

Can you do this:

env > env.txt

And email us the env.txt file it generates?

Derek

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[Alejandro Ceballos]

Ok I started everything again but using the VM you guys provide. I got up to step 4 and I got that 858 tests were run of which 857 passed, 17 skipped and 1 failed.

This is the one that failed:

misc/selective_reinit.test.................................................................. FAILED (TIMEOUT)

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[Derek Gaston]

That's perfectly fine - that test will fail if your computer isn't very fast (it's testing that the code can do something complicated in a set amount of time).

Glad you got it all working!! Let us know if we can help with your application!

Derek

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