Problems testing MOOSE

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Thomas Wood

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Nov 3, 2016, 11:16:18 AM11/3/16
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I've installed PETSc from source before running 

PETSC_DIR=/path/to/petsc ./update_and_rebuild_libmesh.sh 

and when I run make followed by ./run_tests -j8 in the tests directory I get 1315 errors that look like the following:

Running command: /path/to/moose/test/moose_test-opt -i time_derivative.i --error --no-gdb-backtrace
auxkernels/time_derivative.implicit_euler: /path/to/moose/test/moose_test-opt: symbol lookup error: /path/to/petsc/arch-linux2-c-debug/lib/libmpifort.so.12: undefined symbol: MPIR_F_TRUE

but objdump -tT /path/to/petsc/PETSC_ARCH/lib/libmpifort.so.12 | grep MPIR_F_TRUE yields

0000000000000000       O *UND* 0000000000000000              MPIR_F_TRUE
0000000000000000      DO *UND* 0000000000000000              MPIR_F_TRUE

so I'm not sure what the problem is. Any help would be greatly appreciated.

Peterson, JW

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Nov 3, 2016, 11:23:01 AM11/3/16
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On Thu, Nov 3, 2016 at 9:16 AM, Thomas Wood <odell...@gmail.com> wrote:
I've installed PETSc from source before running 

PETSC_DIR=/path/to/petsc ./update_and_rebuild_libmesh.sh 

and when I run make followed by ./run_tests -j8 in the tests directory I get 1315 errors that look like the following:

This sets PETSC_DIR just for the one command... this might work, but it's not really tested by us, I'd recommend just setting it in the environment.

 

Running command: /path/to/moose/test/moose_test-opt -i time_derivative.i --error --no-gdb-backtrace
auxkernels/time_derivative.implicit_euler: /path/to/moose/test/moose_test-opt: symbol lookup error: /path/to/petsc/arch-linux2-c-debug/lib/libmpifort.so.12: undefined symbol: MPIR_F_TRUE

but objdump -tT /path/to/petsc/PETSC_ARCH/lib/libmpifort.so.12 | grep MPIR_F_TRUE yields

0000000000000000       O *UND* 0000000000000000              MPIR_F_TRUE
0000000000000000      DO *UND* 0000000000000000              MPIR_F_TRUE

so I'm not sure what the problem is. Any help would be greatly appreciated.

According to "man objdump"

Next is the section with which the symbol is associated or *ABS* if the section is absolute (ie not connected with any section), or *UND* if the section is referenced
           in the file being dumped, but not defined there.


So I'd say that you aren't linking against all the MPI libraries that are required on this system.  Are you using the "mpicxx" compiler scripts on the system for compiling?  You might need to send us the $MOOSE_DIR/libmesh/build/config.log file so we have more information...

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Kong, Fande

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Nov 3, 2016, 11:25:31 AM11/3/16
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On Thu, Nov 3, 2016 at 9:16 AM, Thomas Wood <odell...@gmail.com> wrote:
I've installed PETSc from source before running 

PETSC_DIR=/path/to/petsc ./update_and_rebuild_libmesh.sh 

export PETSC_DIR=/path/to/petsc

and

 ./update_and_rebuild_libmesh.sh

 

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Thomas Wood

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Nov 3, 2016, 12:12:59 PM11/3/16
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Thanks for the prompt reply John.

My config.log can be found here. 

Thomas Wood

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Nov 3, 2016, 12:13:29 PM11/3/16
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Thank you for the suggestion Fande. I'm trying it out right now and will get back with you ASAP.


On Thursday, November 3, 2016 at 8:25:31 AM UTC-7, fande.kong wrote:
On Thu, Nov 3, 2016 at 9:16 AM, Thomas Wood <odell...@gmail.com> wrote:
I've installed PETSc from source before running 

PETSC_DIR=/path/to/petsc ./update_and_rebuild_libmesh.sh 

export PETSC_DIR=/path/to/petsc

and

 ./update_and_rebuild_libmesh.sh

 

and when I run make followed by ./run_tests -j8 in the tests directory I get 1315 errors that look like the following:

Running command: /path/to/moose/test/moose_test-opt -i time_derivative.i --error --no-gdb-backtrace
auxkernels/time_derivative.implicit_euler: /path/to/moose/test/moose_test-opt: symbol lookup error: /path/to/petsc/arch-linux2-c-debug/lib/libmpifort.so.12: undefined symbol: MPIR_F_TRUE

but objdump -tT /path/to/petsc/PETSC_ARCH/lib/libmpifort.so.12 | grep MPIR_F_TRUE yields

0000000000000000       O *UND* 0000000000000000              MPIR_F_TRUE
0000000000000000      DO *UND* 0000000000000000              MPIR_F_TRUE

so I'm not sure what the problem is. Any help would be greatly appreciated.

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Peterson, JW

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Nov 3, 2016, 12:18:45 PM11/3/16
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On Thu, Nov 3, 2016 at 10:12 AM, Thomas Wood <odell...@gmail.com> wrote:
Thanks for the prompt reply John.

My config.log can be found here. 


Unfortunately, pastebin links are blocked by INL...

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Thomas Wood

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Nov 3, 2016, 12:30:08 PM11/3/16
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Sincerely,

Thomas O. Wood

Peterson, JW

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Nov 3, 2016, 1:10:50 PM11/3/16
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On Thu, Nov 3, 2016 at 10:30 AM, Thomas Wood <odell...@gmail.com> wrote:

It appears that you are using a PETSc that you built in /home/thomas/code/petsc/arch-linux2-c-debug/lib along with the Ubuntu MPI from /usr/lib/openmpi?

So I'd like to make sure that your PETSc install is working first.  Can you successfully execute the "make test" command that it suggests to run at the end of the PETSc installation process?

Is there, by any chance, more than one MPI installed on your system?

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John

Thomas Wood

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Nov 3, 2016, 2:18:58 PM11/3/16
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PETSc tests run without errors when I tell it to download mpich. When I give it all the flags needed to use /usr/lib/openmpi and /usr/lib/lapack / /usr/lib/blas it won't properly configure mpi. Either it uses mpicc/cxx/fort, all of which throw a -lmpi on the end that invokes the non-openmpi I have installed (can't get rid of it, needed for ROS). Anyway, when I tell configure not to use mpi* compilers, PETSC_DIR/config/MPI.py fails when seeing if the g++ can link to /usr/lib/openmpi/include/mpi.h


$ ./configure --with-mpi-dir=/usr/lib/openmpi --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --with-blas-dir=/usr/lib/blas --with-lapack-dir=/usr/lib/lapack --with-mpi-compilers=0 --with-batch=8
===============================================================================
             Configuring PETSc to compile on your system                       
===============================================================================
TESTING: CxxMPICheck from config.packages.MPI(config/BuildSystem/config/packages
*******************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
-------------------------------------------------------------------------------
C++ error! mpi.h could not be located at: ['/usr/lib/openmpi/include']
*******************************************************************************

even though it is soooo there.

Thank you for your help. I'm raising an issue with PETSc.

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Kong, Fande

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Nov 3, 2016, 2:28:31 PM11/3/16
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On Thu, Nov 3, 2016 at 12:18 PM, Thomas Wood <odell...@gmail.com> wrote:
PETSc tests run without errors when I tell it to download mpich. When I give it all the flags needed to use /usr/lib/openmpi and /usr/lib/lapack / /usr/lib/blas it won't properly configure mpi. Either it uses mpicc/cxx/fort, all of which throw a -lmpi on the end that invokes the non-openmpi I have installed (can't get rid of it, needed for ROS). Anyway, when I tell configure not to use mpi* compilers, PETSC_DIR/config/MPI.py fails when seeing if the g++ can link to /usr/lib/openmpi/include/mpi.h


$ ./configure --with-mpi-dir=/usr/lib/openmpi --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --with-blas-dir=/usr/lib/blas --with-lapack-dir=/usr/lib/lapack --with-mpi-compilers=0 --with-batch=8

Delete --with-cc=gcc --with-fc=gfortran --with-cxx=g++ and --with-mpi-compilers=0.

Cody Permann

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Nov 3, 2016, 2:53:54 PM11/3/16
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If he's trying to get MOOSE running, telling him to build without MPI compilers is not going to be useful to him. Even though PETSc and libMesh can be built without MPI support, we don't support that workflow with MOOSE. You need to get your environment set up so that all of these libraries are available with the proper variables exported.

Instead of trying to change the configure lines, try making sure that PETSC_DIR is set, and your compilers are properly set. These instructions are detailed if you look at the "manual" build processes on our getting started pages. Alternatively, you could always start with one of our redistributable packages which comes with everything that you need with the instructions for getting your environment to a sane state.

Cody 

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Peterson, JW

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Nov 3, 2016, 2:53:58 PM11/3/16
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On Thu, Nov 3, 2016 at 12:18 PM, Thomas Wood <odell...@gmail.com> wrote:
PETSc tests run without errors when I tell it to download mpich. When I give it all the flags needed to use /usr/lib/openmpi and /usr/lib/lapack / /usr/lib/blas it won't properly configure mpi. Either it uses mpicc/cxx/fort, all of which throw a -lmpi on the end that invokes the non-openmpi I have installed (can't get rid of it, needed for ROS). Anyway, when I tell configure not to use mpi* compilers, PETSC_DIR/config/MPI.py fails when seeing if the g++ can link to /usr/lib/openmpi/include/mpi.h


$ ./configure --with-mpi-dir=/usr/lib/openmpi --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --with-blas-dir=/usr/lib/blas --with-lapack-dir=/usr/lib/lapack --with-mpi-compilers=0 --with-batch=8
===============================================================================
             Configuring PETSc to compile on your system                       
===============================================================================
TESTING: CxxMPICheck from config.packages.MPI(config/BuildSystem/config/packages
*******************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
-------------------------------------------------------------------------------
C++ error! mpi.h could not be located at: ['/usr/lib/openmpi/include']
*******************************************************************************

even though it is soooo there.

Thank you for your help. I'm raising an issue with PETSc.

OK, once you get PETSc installed with the MPI you want, let us know if you still have issues with building libmesh and MOOSE.

Theoretically, you can of course have multiple MPIs installed on your machine at the same time, and MOOSE should handle this fine.  You just have to be a little careful, as you can potentially get into a situation where libmesh is configured and compiled against one MPI, but then attempts to link against a *different* MPI at linktime.  This can happen if e.g. there is an ordering issue with the "-L" flags in the link line used by libmesh.  Based on the value of libmesh_optional_LIBS in the file you sent us, I think you should be fine, but this is another place to troubleshoot if things go wrong again...

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John

Thomas Wood

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Nov 3, 2016, 3:03:42 PM11/3/16
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I tried that and it's still not working. With 
./configure --with-mpi-dir=/usr/lib/openmpi --with-blas=/usr/lib/blas --with-lapack=/usr/lib/lapack

I get errors telling me I'm compiling with a non-openmpi version of mpi, probably due to the -lmpi in mpicc --show-me when trying to build. I can't get rid of my mpich install because ROS requires it.

I'm rebuilding libMesh now with --download-openmpi instead of --download-mpich version of PETSc. I'll give a status update on that approach in a minute.

Thomas Wood

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Nov 3, 2016, 3:08:22 PM11/3/16
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Thanks for helping me out with my issue John. I definitely realize how this is a PETSc problem. I've had issues with PETSc keeping my mpi libraries straight when I was using it with proteus in the past.

I would just download the binary but I lend to loathe binaries. They usually only work 1/2 the time, so if a project I want to know more about is open source... I build.

Cody Permann

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Nov 3, 2016, 3:10:57 PM11/3/16
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You may loathe it, but you'd be up and running by now. If you really do insist on building from source, follow the instructions on our website:



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Thomas Wood

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Nov 3, 2016, 3:51:59 PM11/3/16
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Thank you Cody. I've been using the instructions at http://mooseframework.org/getting-started/, but I'll use those from now on.

Derek Gaston

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Nov 4, 2016, 12:34:30 AM11/4/16
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On Thu, Nov 3, 2016 at 3:15 PM Thomas Wood <odell...@gmail.com> wrote:
I can't get rid of my mpich install because ROS requires it.

Two things:

1.  You really should try our binary redistributable.  We take great care and spend large amounts of time to make it correct.  In addition to it quickly getting you up and running with MOOSE it will also give you a "module" environment that you can use to load/unload the MOOSE environment so that you can continue to work with other codes as you were before.

Note that the "binary" is not for MOOSE itself... only for the dependencies of MOOSE.  You will still be compiling MOOSE (and libMesh actually)... so you'll still be building from source.  It just removes all of this trouble of trying to get the dependencies in place.

2.  Is there a reason why you don't want to use your mpich install with MOOSE/PETSc?  If it's working for your other application (and you need to keep it anyway) it should work with MOOSE.

Keep us informed on your progress!

Derek

Thomas Wood

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Nov 4, 2016, 5:57:05 PM11/4/16
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Hi Derek,

    I see what you mean about the binaries, but all the same I'm still determined to build it myself. I wrote a python script to perform the actions found at the URL Cody directed me to:

and uploaded it to:


However, this method required me to add i386 to my list of architectures, which broke my CUDA, so I don't recommend it to anyone.

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Miller, Jason M

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Nov 4, 2016, 6:18:08 PM11/4/16
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Well if you're after running a script which runs more scripts which builds the entire compiler suite.... you can always use what we're using to actually build that redistributable!


As Derek said, we do invest quite a chunk of time into making that redistributable functional.

Thanks!
Jason

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Daniel Schwen

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Nov 4, 2016, 6:19:52 PM11/4/16
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myself. I wrote a python script to perform the actions found at the URL Cody directed me to:

and uploaded it to:


I don't like using black box scripts. I'd rather write my own installation script :-D 

Thomas Wood

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Nov 4, 2016, 7:19:36 PM11/4/16
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Thank you Jason! I will be sure to use those scripts instead.


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Thomas Wood

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Nov 5, 2016, 5:40:00 PM11/5/16
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I used make_all.py from the package_builder to build all of the dependencies, sourced $PACKAGE_DIR/moose_profile and then ran scripts/update_and_rebuild_libmesh.sh before testing moose.

I got the following warning/errors:

/usr/bin/ld: warning: libopen-pal.so.13, needed by //usr/lib/libmpi_mpifh.so.12, may conflict with libopen-pal.so.6
/home/thomas/code/moose/framework/contrib/ice_updater/libice_updater-opt.so: undefined reference to `std::thread::_State::~_State()@GLIBCXX_3.4.22'
/home/thomas/code/moose/framework/contrib/ice_updater/libice_updater-opt.so: undefined reference to `std::thread::_M_start_thread(std::unique_ptr<std::thread::_State, std::default_delete<std::thread::_State> >, void (*)())@GLIBCXX_3.4.22'
/home/thomas/code/petsc/arch-linux2-c-debug/lib/libmpifort.so: undefined reference to `MPID_Wtick'
/home/thomas/code/moose/framework/contrib/ice_updater/libice_updater-opt.so: undefined reference to `typeinfo for std::thread::_State@GLIBCXX_3.4.22'
/home/thomas/code/petsc/arch-linux2-c-debug/lib/libmpifort.so: undefined reference to `MPID_Wtime_todouble'
/home/thomas/code/petsc/arch-linux2-c-debug/lib/libmpifort.so: undefined reference to `MPID_Wtime'
collect2: error: ld returned 1 exit status
/home/thomas/code/moose/framework/app.mk:160: recipe for target '/home/thomas/code/moose/test/moose_test-opt' failed
make: *** [/home/thomas/code/moose/test/moose_test-opt] Error 1

Thomas Wood

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Nov 6, 2016, 6:37:58 AM11/6/16
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I meant to say $PACKAGE_DIR/environment/moose_profile, ie the right one.

Miller, Jason M

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Nov 7, 2016, 9:14:21 AM11/7/16
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Looks like your system implementation of MPI is getting in our way. And reading the earlier threads in this post, it also looks like your system implementation of MPI is failing to build PETSc from source (odd, as I have never ran into this):

$ ./configure --with-mpi-dir=/usr/lib/openmpi --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --with-blas-dir=/usr/lib/blas --with-lapack-dir=/usr/lib/lapack --with-mpi-compilers=0 --with-batch=8
===============================================================================
             Configuring PETSc to compile on your system                       
===============================================================================
TESTING: CxxMPICheck from config.packages.MPI(config/BuildSystem/config/packages
*******************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
-------------------------------------------------------------------------------
C++ error! mpi.h could not be located at: ['/usr/lib/openmpi/include']
*******************************************************************************


What I would suggest is removing this implementation of MPI if at all possible. Or perhaps re-install it / try again.

You say you like to build from source? Well, you did by running that make_all scripts =D...  MPI and all. <-- thats me trying to nudge you into removing your system supplied MPI and using the compiler suite you just built...  _if_ you do decide to remove your system MPI, you should also rebuild libMesh and MOOSE.


Jason



Thomas Wood

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Nov 7, 2016, 9:26:39 AM11/7/16
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Thanks Jason. I sort of figured that was the problem all along. Unfortunately, I rely on my system's mpich for ROS, so I'm going to have to give this another go once I have another dedicated box to install PETSc on.

This was my last experience with PETSc, which expects to be your #1 priority and doesn't play well with others at all. And since I only have a single machine PETSc is also pretty pointless. Normal threading or cuBLAS would be better for my situation.  Thanks for all your help!


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Derek Gaston

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Nov 7, 2016, 9:52:56 AM11/7/16
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This is actually not a PETSc thing at all... it's a Linux/MPI thing.

We've found that if you install MPI into your system directories that it is essentially impossible to keep from linking those MPI libraries when trying to use a different MPI. My advice: don't install MPI into the system. Keep MPI installations in separate directories and switch between them by changing your PATH. Our redistributable package does exactly that: using a "module" system to keep your operating system clean.

So: you could remove the mpich installed in your system directories... and recompile it and install it somewhere safe (like /opt/ros_mpi or whatever) and then point your PATH, etc. to it when you are working with ROS. Then do a similar thing for MOOSE. If you grab our redistributable then it will make it easy to switch in and out of the MOOSE environment (you could even add your own local modules for switching to/from the environment you need for ROS).

That said...

I asked earlier: but I'm not sure I got a response... why can't you just use the mpich you've installed on the system for ROS for compiling PETSc / MOOSE? It should work fine.

Finally, if you're just trying to get started with MOOSE... just download our VMWare image and use it. It will give you a nice clean Linux image that you can instantly use without messing with your current system...

Derek


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Sincerely,

Thomas O. Wood



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Thomas Wood

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Nov 7, 2016, 9:57:35 AM11/7/16
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I did hand my system's mpich to PETSc and I was actually able to compile the MOOSE code and run some test, but the coverage was something like 300/1315 passed with the rest failing, so I kept looking for other options.

I'll look into massaging my mpich installation/configuration into a format that's acceptable for PETSc. 

Thanks again Derek!

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Miller, Jason M

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Nov 7, 2016, 10:00:17 AM11/7/16
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Well I am curious! And I have at my disposal a virtual machine that a can fool around with.

What version of Ubuntu are you running?
and, in a nut shell, what system packages are required to get ROS running?

I'd like to apt-get install those things, and then try to build PETSc against that... see if it works.  As Derek just posted, I to also want to state, PETSc/MOOSE should work with your currently implementation of MPI. I'd like to find out why not.

Also I forgot to mention: Thanks for trying that package_builder repo. Warms my heart someone finally used it besides myself haha

Thanks!
Jason


Derek Gaston

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Nov 7, 2016, 10:03:24 AM11/7/16
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The first email I see from you seems to suggest that you used "--download-mpich" with PETSc... that wouldn't use your system installed mpich.

Can you describe again the actual steps you took, and what the outcome was, when you tried to let PETSc just use the system installed MPI (i.e. Don't tell PETSc to download/install one).

If you have mpich installed and working... we should be able to use it.

Derek
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Thomas Wood

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Nov 7, 2016, 10:17:12 AM11/7/16
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Hi Jason,

    The package_builder script worked great. Fantastic job.

    I'm using Ubuntu 16.04 and ROS Kinetic. To install ROS (Robot Operating System) you can follow the short directions (add ROS to software sources, apt update, apt install) at http://wiki.ros.org/kinetic/Installation/Ubuntu.

    Thinking I might try to use Bocker (Docker in < 100 lines of bash) or something like that to encapsulate MOOSE from the rest of my system, but it's a little ways down my TODO list.


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Thomas Wood

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Nov 7, 2016, 10:20:56 AM11/7/16
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HI Derek,

    I've tried a few dozen different things at this point. I used the --with-mpi-dir=/usr/lib/mpich flag when configuring PETSc to hand it my system version of mpich when I was still using the instructions at moose-framework.org/getting-started once I realized that the downloaded mpich PETSc was using was messing things up.

    The most recent and relevant steps I took were:
        1. package_builder/build_from_source/make_all.py
        2. source $PACKAGE_DIR/environment/moose_profile
        3. /path/to/moose/scripts/update_and_rebuild_libmesh.sh
        4. cd tests && make -j8
        5. There is no step 5. Failed at step 4.

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Miller, Jason M

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Nov 7, 2016, 10:36:42 AM11/7/16
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I'll get started on that VM, and see what happens. The fact that one needs to add additional repositories to apt-get from, does shed some light on the issue. This 'ros-kinetic-desktop-full' package no doubt will include MPI of some kind, as its the only package the ROS instructions call for the user installing.

I do not know the ins and outs of MPI, but I do know not installing the 'devel' branch of several packages we require (apt-get install tkl as apposed to tkl-dev) yields errors later on when attempting to build stuff.

At any rate, thanks! I'll look into it.

Jason

Miller, Jason M

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Nov 7, 2016, 11:14:35 AM11/7/16
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Well... I can sorta see why things are colliding... okay I can't... not yet. But I am pretty sure something in here is at fault. Here is the details of an apt-get install ros-kinetic-desktop-full, on an Ubuntu 16.04 VM I just finished installing:

moose@ros-test:~$ sudo apt-get install ros-kinetic-desktop-full
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  autotools-dev binfmt-support binutils blt build-essential bzip2-doc cmake cmake-data comerr-dev cpp cpp-5 debhelper dh-strip-nondeterminism docutils-common docutils-doc dpkg-dev fakeroot fltk1.3-doc fluid fontconfig fontconfig-config
  fonts-dejavu-core fonts-lato fonts-liberation fonts-lyx freeglut3 freeglut3-dev g++ g++-5 gazebo7 gazebo7-common gazebo7-plugin-base gcc gcc-4.8-base gcc-5 gettext gfortran gfortran-5 gir1.2-atk-1.0 gir1.2-freedesktop gir1.2-gdkpixbuf-2.0
  gir1.2-gtk-2.0 gir1.2-pango-1.0 graphviz gstreamer1.0-plugins-base hddtemp hdf5-helpers hicolor-icon-theme i965-va-driver icu-devtools intltool-debian javascript-common krb5-multidev libaacs0 libaec-dev libaec0 libalgorithm-diff-perl
  libalgorithm-diff-xs-perl libalgorithm-merge-perl libapr1 libapr1-dev libaprutil1 libaprutil1-dev libarchive-zip-perl libarchive13 libarmadillo6 libarpack2 libasan0 libasan2 libasound2 libasound2-data libasprintf-dev libassimp-dev libassimp3v5
  libasyncns0 libatk1.0-0 libatk1.0-data libatk1.0-dev libatomic1 libaudio2 libavahi-client3 libavahi-common-data libavahi-common3 libavcodec-dev libavcodec-ffmpeg56 libavformat-dev libavformat-ffmpeg56 libavutil-dev libavutil-ffmpeg54 libbdplus0
  libblas-common libblas-dev libblas3 libbluray1 libboost-all-dev libboost-atomic-dev libboost-atomic1.58-dev libboost-atomic1.58.0 libboost-chrono-dev libboost-chrono1.58-dev libboost-chrono1.58.0 libboost-context-dev libboost-context1.58-dev
  libboost-context1.58.0 libboost-coroutine-dev libboost-coroutine1.58-dev libboost-coroutine1.58.0 libboost-date-time-dev libboost-date-time1.58-dev libboost-date-time1.58.0 libboost-dev libboost-exception-dev libboost-exception1.58-dev
  libboost-filesystem-dev libboost-filesystem1.58-dev libboost-filesystem1.58.0 libboost-graph-dev libboost-graph-parallel-dev libboost-graph-parallel1.58-dev libboost-graph-parallel1.58.0 libboost-graph1.58-dev libboost-graph1.58.0
  libboost-iostreams-dev libboost-iostreams1.58-dev libboost-iostreams1.58.0 libboost-locale-dev libboost-locale1.58-dev libboost-locale1.58.0 libboost-log-dev libboost-log1.58-dev libboost-log1.58.0 libboost-math-dev libboost-math1.58-dev
  libboost-math1.58.0 libboost-mpi-dev libboost-mpi-python-dev libboost-mpi-python1.58-dev libboost-mpi-python1.58.0 libboost-mpi1.58-dev libboost-mpi1.58.0 libboost-program-options-dev libboost-program-options1.58-dev
  libboost-program-options1.58.0 libboost-python-dev libboost-python1.58-dev libboost-python1.58.0 libboost-random-dev libboost-random1.58-dev libboost-random1.58.0 libboost-regex-dev libboost-regex1.58-dev libboost-regex1.58.0
  libboost-serialization-dev libboost-serialization1.58-dev libboost-serialization1.58.0 libboost-signals-dev libboost-signals1.58-dev libboost-signals1.58.0 libboost-system-dev libboost-system1.58-dev libboost-system1.58.0 libboost-test-dev
  libboost-test1.58-dev libboost-test1.58.0 libboost-thread-dev libboost-thread1.58-dev libboost-thread1.58.0 libboost-timer-dev libboost-timer1.58-dev libboost-timer1.58.0 libboost-tools-dev libboost-wave-dev libboost-wave1.58-dev
  libboost-wave1.58.0 libboost1.58-dev libboost1.58-tools-dev libbulletcollision2.83.6 libbulletdynamics2.83.6 libbz2-dev libc-dev-bin libc6-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcc1-0 libcdparanoia0 libcdt5
  libcgraph6 libcilkrts5 libcollada-dom2.4-dp-dev libcollada-dom2.4-dp0 libconsole-bridge-dev libconsole-bridge0.2v5 libcroco3 libcrystalhd3 libcups2 libcurl3 libcurl4-openssl-dev libdap-dev libdap17v5 libdapclient6v5 libdapserver7v5 libdatrie1
  libdc1394-22 libdouble-conversion1v5 libdpkg-perl libdrm-amdgpu1 libdrm-dev libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libegl1-mesa libegl1-mesa-dev libeigen3-dev libepsilon1 libevdev2 libexpat1-dev libfakeroot libfile-fcntllock-perl
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  libfreetype6-dev libfreexl1 libgazebo7 libgazebo7-dev libgbm1 libgcc-4.8-dev libgcc-5-dev libgd3 libgdal-dev libgdal1i libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgdk-pixbuf2.0-dev libgeos-3.5.0 libgeos-c1v5 libgeos-dev libgettextpo-dev
  libgettextpo0 libgfortran-5-dev libgfortran3 libgif-dev libgif7 libgl1-mesa-dev libgl1-mesa-dri libgl1-mesa-glx libgl2ps-dev libgl2ps0 libglade2-0 libglapi-mesa libgles2-mesa libgles2-mesa-dev libglib2.0-bin libglib2.0-dev libglu1-mesa
  libglu1-mesa-dev libgme0 libgomp1 libgraphite2-3 libgsm1 libgssrpc4 libgstreamer-plugins-base1.0-0 libgstreamer1.0-0 libgtest-dev libgtk2.0-0 libgtk2.0-bin libgtk2.0-common libgtk2.0-dev libgtkglext1 libgts-0.7-5 libgts-bin libgts-dev
  libgudev-1.0-0 libgvc6 libgvpr2 libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libhdf4-0-alt libhdf4-alt-dev libhdf5-10 libhdf5-cpp-11 libhdf5-dev libhdf5-mpi-dev libhdf5-openmpi-10 libhdf5-openmpi-dev libhwloc-dev
  libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libice-dev libice6 libicu-dev libignition-math2 libignition-math2-dev libilmbase12 libinput-dev libinput10 libisl15 libitm1 libjasper-dev libjasper1 libjbig-dev libjbig0 libjpeg-dev
  libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjsoncpp-dev libjsoncpp1 libjxr0 libkadm5clnt-mit9 libkadm5srv-mit9 libkdb5-8 libkmlbase1 libkmldom1 libkmlengine1
  liblapack-dev liblapack3 liblcms2-2 libldap2-dev liblinearmath2.83.6 libllvm3.8 liblog4cxx-dev liblog4cxx10-dev liblog4cxx10v5 liblsan0 libltdl-dev libltdl7 liblz4-dev liblzma-dev libmail-sendmail-perl libminizip1 libmirclient-dev libmirclient9
  libmircommon-dev libmircommon5 libmircookie-dev libmircookie2 libmirprotobuf3 libmng2 libmodplug1 libmp3lame0 libmpc3 libmpx0 libmtdev1 libmysqlclient-dev libmysqlclient20 libnetcdf-c++4 libnetcdf-cxx-legacy-dev libnetcdf-dev libnetcdf11
  libnuma-dev libodbc1 libogdi3.2 libogg-dev libogg0 libogre-1.9-dev libogre-1.9.0v5 libopencv-calib3d2.4v5 libopencv-contrib2.4v5 libopencv-core2.4v5 libopencv-features2d2.4v5 libopencv-flann2.4v5 libopencv-highgui2.4v5 libopencv-imgproc2.4v5
  libopencv-legacy2.4v5 libopencv-ml2.4v5 libopencv-objdetect2.4v5 libopencv-photo2.4v5 libopencv-video2.4v5 libopenexr22 libopenjp2-7 libopenjpeg5 libopenmpi-dev libopenmpi1.10 libopenni-dev libopenni-sensor-pointclouds0 libopenni0 libopus0
  liborc-0.4-0 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0 libpangoft2-1.0-0 libpangox-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpathplan4 libpciaccess0 libpcl-apps1.7 libpcl-common1.7 libpcl-dev libpcl-features1.7
  libpcl-filters1.7 libpcl-io1.7 libpcl-kdtree1.7 libpcl-keypoints1.7 libpcl-octree1.7 libpcl-outofcore1.7 libpcl-people1.7 libpcl-recognition1.7 libpcl-registration1.7 libpcl-sample-consensus1.7 libpcl-search1.7 libpcl-segmentation1.7
  libpcl-surface1.7 libpcl-tracking1.7 libpcl-visualization1.7 libpcl1.7 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpixman-1-0 libpixman-1-dev libpng12-dev libpoco-dev libpococrypto9v5 libpocodata9v5 libpocofoundation9v5 libpocomysql9v5
  libpoconet9v5 libpoconetssl9v5 libpocoodbc9v5 libpocosqlite9v5 libpocoutil9v5 libpocoxml9v5 libpocozip9v5 libpoppler58 libpq-dev libpq5 libproj-dev libproj9 libprotobuf-dev libprotobuf-lite9v5 libprotobuf9v5 libprotoc-dev libprotoc9v5
  libproxy1v5 libpthread-stubs0-dev libpulse0 libpyside-py3-2.0 libpyside2-dev libpyside2.0 libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3.5 libqgsttools-p1 libqhull-dev libqhull7
  libqt4-dbus libqt4-declarative libqt4-designer libqt4-dev libqt4-dev-bin libqt4-help libqt4-network libqt4-opengl libqt4-opengl-dev libqt4-qt3support libqt4-script libqt4-scripttools libqt4-sql libqt4-sql-mysql libqt4-svg libqt4-test libqt4-xml
  libqt4-xmlpatterns libqt5clucene5 libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5designer5 libqt5designercomponents5 libqt5gui5 libqt5help5 libqt5multimedia5 libqt5multimediaquick-p5 libqt5multimediawidgets5 libqt5network5 libqt5opengl5
  libqt5opengl5-dev libqt5printsupport5 libqt5qml5 libqt5quick5 libqt5quickparticles5 libqt5quicktest5 libqt5quickwidgets5 libqt5script5 libqt5scripttools5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5svg5-dev libqt5test5 libqt5webkit5
  libqt5webkit5-dev libqt5widgets5 libqt5x11extras5 libqt5x11extras5-dev libqt5xml5 libqt5xmlpatterns5 libqt5xmlpatterns5-dev libqt5xmlpatterns5-private-dev libqtcore4 libqtdbus4 libqtgui4 libqtwebkit-dev libqtwebkit4 libquadmath0 libraw1394-11
  libraw15 libruby2.3 libschroedinger-1.0-0 libsctp-dev libsctp1 libsdformat4 libsdformat4-dev libshiboken-py3-2.0 libshiboken2-dev libshiboken2.0 libshine3 libsimbody-dev libsimbody3.5v5 libsm-dev libsm6 libsnappy1v5 libsndfile1 libsoxr0
  libspatialite-dev libspatialite7 libspeex1 libspnav0 libsqlite3-dev libssh-gcrypt-4 libssl-dev libssl-doc libstdc++-4.8-dev libstdc++-5-dev libsuperlu4 libswresample-dev libswresample-ffmpeg1 libswscale-dev libswscale-ffmpeg3
  libsys-hostname-long-perl libsz2 libtar-dev libtar0 libtbb-dev libtbb2 libtcl8.6 libthai-data libthai0 libtheora-dev libtheora0 libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtinyxml-dev libtinyxml2-2v5 libtinyxml2.6.2v5 libtk8.6 libtool
  libtsan0 libtwolame0 libtxc-dxtn-s2tc0 libubsan0 libunistring0 liburdfdom-dev liburdfdom-headers-dev liburdfdom-model-state0.4 liburdfdom-model0.4 liburdfdom-sensor0.4 liburdfdom-tools liburdfdom-world0.4 liburiparser1 libusb-1.0-0-dev
  libusb-1.0-doc libv4l-0 libv4lconvert0 libva1 libvdpau1 libvisual-0.4-0 libvorbis0a libvorbisenc2 libvpx3 libvtk-java libvtk5.10 libvtk6-dev libvtk6-java libvtk6-qt-dev libvtk6.2 libvtk6.2-qt libwacom-bin libwacom-common libwacom2 libwavpack1
  libwayland-client0 libwayland-cursor0 libwayland-dev libwayland-egl1-mesa libwayland-server0 libwebp-dev libwebp5 libwebpdemux1 libwebpmux1 libx11-dev libx11-doc libx11-xcb-dev libx11-xcb1 libx264-148 libx265-79 libxau-dev libxaw7 libxcb-dri2-0
  libxcb-dri2-0-dev libxcb-dri3-0 libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present-dev libxcb-present0 libxcb-randr0 libxcb-randr0-dev libxcb-render-util0 libxcb-render0 libxcb-render0-dev
  libxcb-shape0 libxcb-shape0-dev libxcb-shm0 libxcb-shm0-dev libxcb-sync-dev libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb-xkb1 libxcb1-dev libxcomposite-dev libxcomposite1 libxcursor-dev libxcursor1 libxdamage-dev
  libxdamage1 libxdmcp-dev libxerces-c-dev libxerces-c3.1 libxext-dev libxfixes-dev libxfixes3 libxft-dev libxft2 libxi-dev libxi6 libxinerama-dev libxinerama1 libxkbcommon-dev libxkbcommon-x11-0 libxkbcommon0 libxml2-dev libxml2-utils libxmu-dev
  libxmu-headers libxmu6 libxpm4 libxrandr-dev libxrandr2 libxrender-dev libxrender1 libxshmfence-dev libxshmfence1 libxslt1.1 libxss-dev libxss1 libxt-dev libxt6 libxtst6 libxv1 libxvidcore4 libxxf86dga1 libxxf86vm-dev libxxf86vm1 libyaml-0-2
  libyaml-cpp-dev libyaml-cpp0.5v5 libzvbi-common libzvbi0 libzzip-0-13 linux-libc-dev make manpages-dev mesa-common-dev mesa-vdpau-drivers mpi-default-bin mpi-default-dev mysql-common ocl-icd-libopencl1 odbcinst odbcinst1debian2 openmpi-bin
  openmpi-common openni-utils pkg-config po-debconf proj-bin proj-data pyqt5-dev python python-attr python-autobahn python-cairo python-catkin-pkg python-cffi-backend python-chardet python-concurrent.futures python-crypto python-cryptography
  python-cycler python-dateutil python-defusedxml python-dev python-docutils python-ecdsa python-empy python-enum34 python-funcsigs python-glade2 python-gobject-2 python-gtk2 python-idna python-imaging python-ipaddress python-lz4 python-matplotlib
  python-matplotlib-data python-minimal python-mock python-mpi4py python-msgpack python-netifaces python-nose python-numpy python-opencv python-opengl python-openssl python-pam python-paramiko python-pbr python-pil python-pkg-resources
  python-psutil python-pyasn1 python-pyasn1-modules python-pycurl python-pydot python-pygments python-pyparsing python-pyqt5 python-pyqt5.qtopengl python-pyqt5.qtsvg python-pyside2 python-pyside2.qtconcurrent python-pyside2.qtcore
  python-pyside2.qtgui python-pyside2.qthelp python-pyside2.qtnetwork python-pyside2.qtprintsupport python-pyside2.qtqml python-pyside2.qtquick python-pyside2.qtquickwidgets python-pyside2.qtscript python-pyside2.qtsql python-pyside2.qtsvg
  python-pyside2.qttest python-pyside2.qtuitools python-pyside2.qtwebkit python-pyside2.qtwebkitwidgets python-pyside2.qtwidgets python-pyside2.qtx11extras python-pyside2.qtxml python-roman python-rosdep python-rosdistro python-rospkg
  python-serial python-service-identity python-setuptools python-sip python-sip-dev python-six python-snappy python-tk python-trollius python-twisted python-twisted-bin python-twisted-core python-txaio python-tz python-urlgrabber python-vtk6
  python-yaml python-zope.interface python2.7 python2.7-dev python2.7-minimal qdbus qt-at-spi qt4-linguist-tools qt4-qmake qt5-qmake qtbase5-dev qtbase5-dev-tools qtbase5-private-dev qtchooser qtcore4-l10n qtdeclarative5-dev
  qtdeclarative5-private-dev qtmultimedia5-dev qtscript5-dev qtscript5-private-dev qttools5-dev qttools5-dev-tools qttools5-private-dev qttranslations5-l10n rake ros-kinetic-actionlib ros-kinetic-actionlib-msgs ros-kinetic-actionlib-tutorials
  ros-kinetic-angles ros-kinetic-bond ros-kinetic-bond-core ros-kinetic-bondcpp ros-kinetic-bondpy ros-kinetic-camera-calibration ros-kinetic-camera-calibration-parsers ros-kinetic-camera-info-manager ros-kinetic-catkin ros-kinetic-class-loader
  ros-kinetic-cmake-modules ros-kinetic-collada-parser ros-kinetic-collada-urdf ros-kinetic-common-msgs ros-kinetic-common-tutorials ros-kinetic-compressed-depth-image-transport ros-kinetic-compressed-image-transport ros-kinetic-control-msgs
  ros-kinetic-cpp-common ros-kinetic-cv-bridge ros-kinetic-depth-image-proc ros-kinetic-desktop ros-kinetic-diagnostic-aggregator ros-kinetic-diagnostic-analysis ros-kinetic-diagnostic-common-diagnostics ros-kinetic-diagnostic-msgs
  ros-kinetic-diagnostic-updater ros-kinetic-diagnostics ros-kinetic-dynamic-reconfigure ros-kinetic-eigen-conversions ros-kinetic-eigen-stl-containers ros-kinetic-executive-smach ros-kinetic-filters ros-kinetic-gazebo-msgs
  ros-kinetic-gazebo-plugins ros-kinetic-gazebo-ros ros-kinetic-gazebo-ros-pkgs ros-kinetic-gencpp ros-kinetic-geneus ros-kinetic-genlisp ros-kinetic-genmsg ros-kinetic-gennodejs ros-kinetic-genpy ros-kinetic-geometric-shapes ros-kinetic-geometry
  ros-kinetic-geometry-msgs ros-kinetic-geometry-tutorials ros-kinetic-gl-dependency ros-kinetic-image-common ros-kinetic-image-geometry ros-kinetic-image-pipeline ros-kinetic-image-proc ros-kinetic-image-rotate ros-kinetic-image-transport
  ros-kinetic-image-transport-plugins ros-kinetic-image-view ros-kinetic-interactive-marker-tutorials ros-kinetic-interactive-markers ros-kinetic-joint-state-publisher ros-kinetic-kdl-conversions ros-kinetic-kdl-parser ros-kinetic-laser-assembler
  ros-kinetic-laser-filters ros-kinetic-laser-geometry ros-kinetic-laser-pipeline ros-kinetic-librviz-tutorial ros-kinetic-map-msgs ros-kinetic-media-export ros-kinetic-message-filters ros-kinetic-message-generation ros-kinetic-message-runtime
  ros-kinetic-mk ros-kinetic-nav-msgs ros-kinetic-nodelet ros-kinetic-nodelet-core ros-kinetic-nodelet-topic-tools ros-kinetic-nodelet-tutorial-math ros-kinetic-octomap ros-kinetic-opencv3 ros-kinetic-orocos-kdl ros-kinetic-pcl-conversions
  ros-kinetic-pcl-msgs ros-kinetic-pcl-ros ros-kinetic-perception ros-kinetic-perception-pcl ros-kinetic-pluginlib ros-kinetic-pluginlib-tutorials ros-kinetic-polled-camera ros-kinetic-pr2-description ros-kinetic-python-orocos-kdl
  ros-kinetic-python-qt-binding ros-kinetic-qt-dotgraph ros-kinetic-qt-gui ros-kinetic-qt-gui-cpp ros-kinetic-qt-gui-py-common ros-kinetic-qwt-dependency ros-kinetic-random-numbers ros-kinetic-resource-retriever ros-kinetic-robot
  ros-kinetic-robot-model ros-kinetic-robot-state-publisher ros-kinetic-ros ros-kinetic-ros-base ros-kinetic-ros-comm ros-kinetic-ros-core ros-kinetic-ros-tutorials ros-kinetic-rosbag ros-kinetic-rosbag-migration-rule ros-kinetic-rosbag-storage
  ros-kinetic-rosbash ros-kinetic-rosboost-cfg ros-kinetic-rosbuild ros-kinetic-rosclean ros-kinetic-rosconsole ros-kinetic-rosconsole-bridge ros-kinetic-roscpp ros-kinetic-roscpp-core ros-kinetic-roscpp-serialization ros-kinetic-roscpp-traits
  ros-kinetic-roscpp-tutorials ros-kinetic-roscreate ros-kinetic-rosgraph ros-kinetic-rosgraph-msgs ros-kinetic-roslang ros-kinetic-roslaunch ros-kinetic-roslib ros-kinetic-roslint ros-kinetic-roslisp ros-kinetic-roslz4 ros-kinetic-rosmake
  ros-kinetic-rosmaster ros-kinetic-rosmsg ros-kinetic-rosnode ros-kinetic-rosout ros-kinetic-rospack ros-kinetic-rosparam ros-kinetic-rospy ros-kinetic-rospy-tutorials ros-kinetic-rosservice ros-kinetic-rostest ros-kinetic-rostime
  ros-kinetic-rostopic ros-kinetic-rosunit ros-kinetic-roswtf ros-kinetic-rqt-action ros-kinetic-rqt-bag ros-kinetic-rqt-bag-plugins ros-kinetic-rqt-common-plugins ros-kinetic-rqt-console ros-kinetic-rqt-dep ros-kinetic-rqt-graph
  ros-kinetic-rqt-gui ros-kinetic-rqt-gui-cpp ros-kinetic-rqt-gui-py ros-kinetic-rqt-image-view ros-kinetic-rqt-launch ros-kinetic-rqt-logger-level ros-kinetic-rqt-moveit ros-kinetic-rqt-msg ros-kinetic-rqt-nav-view ros-kinetic-rqt-plot
  ros-kinetic-rqt-pose-view ros-kinetic-rqt-publisher ros-kinetic-rqt-py-common ros-kinetic-rqt-py-console ros-kinetic-rqt-reconfigure ros-kinetic-rqt-robot-dashboard ros-kinetic-rqt-robot-monitor ros-kinetic-rqt-robot-plugins
  ros-kinetic-rqt-robot-steering ros-kinetic-rqt-runtime-monitor ros-kinetic-rqt-rviz ros-kinetic-rqt-service-caller ros-kinetic-rqt-shell ros-kinetic-rqt-srv ros-kinetic-rqt-tf-tree ros-kinetic-rqt-top ros-kinetic-rqt-topic ros-kinetic-rqt-web
  ros-kinetic-rviz ros-kinetic-rviz-plugin-tutorials ros-kinetic-rviz-python-tutorial ros-kinetic-self-test ros-kinetic-sensor-msgs ros-kinetic-shape-msgs ros-kinetic-simulators ros-kinetic-smach ros-kinetic-smach-msgs ros-kinetic-smach-ros
  ros-kinetic-smclib ros-kinetic-stage ros-kinetic-stage-ros ros-kinetic-std-msgs ros-kinetic-std-srvs ros-kinetic-stereo-image-proc ros-kinetic-stereo-msgs ros-kinetic-tf ros-kinetic-tf-conversions ros-kinetic-tf2 ros-kinetic-tf2-eigen
  ros-kinetic-tf2-geometry-msgs ros-kinetic-tf2-kdl ros-kinetic-tf2-msgs ros-kinetic-tf2-py ros-kinetic-tf2-ros ros-kinetic-theora-image-transport ros-kinetic-topic-tools ros-kinetic-trajectory-msgs ros-kinetic-turtle-actionlib
  ros-kinetic-turtle-tf ros-kinetic-turtle-tf2 ros-kinetic-turtlesim ros-kinetic-urdf ros-kinetic-urdf-parser-plugin ros-kinetic-urdf-tutorial ros-kinetic-vision-opencv ros-kinetic-visualization-marker-tutorials ros-kinetic-visualization-msgs
  ros-kinetic-visualization-tutorials ros-kinetic-viz ros-kinetic-xacro ros-kinetic-xmlrpcpp ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration sbcl sdformat-sdf shiboken2 sip-dev
  tango-icon-theme tcl tcl-dev tcl-vtk6 tcl8.6 tcl8.6-dev tk tk-dev tk8.6 tk8.6-blt2.5 tk8.6-dev ttf-bitstream-vera ttf-dejavu-core ttf-liberation unixodbc unixodbc-dev unzip uuid-dev va-driver-all vdpau-driver-all vdpau-va-driver vtk6 x11-common
  x11-utils x11proto-composite-dev x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-input-dev x11proto-kb-dev x11proto-randr-dev x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev
  x11proto-xf86vidmode-dev x11proto-xinerama-dev xbitmaps xorg-sgml-doctools xterm xtrans-dev zip zlib1g-dev
Suggested packages:
  binutils-doc blt-demo codeblocks eclipse ninja-build doc-base cpp-doc gcc-5-locales dh-make debian-keyring g++-multilib g++-5-multilib gcc-5-doc libstdc++6-5-dbg gazebo7-doc gcc-multilib autoconf automake flex bison gdb gcc-doc gcc-5-multilib
  libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan2-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx0-dbg libquadmath0-dbg gettext-doc autopoint gfortran-multilib gfortran-doc gfortran-5-multilib gfortran-5-doc
  libgfortran3-dbg gsfonts graphviz-doc gvfs ksensors apache2 | lighttpd | httpd krb5-doc lrzip libasound2-plugins alsa-utils nas liblapack-doc-man liblapack-doc libbluray-bdj libboost-doc libboost1.58-doc gccxml libmpfrc++-dev libntl-dev xsltproc
  doxygen docbook-xml docbook-xsl default-jdk fop glibc-doc libcairo2-doc libbullet2-dev libbullet2 firmware-crystalhd cups-common libcurl4-doc libcurl3-dbg libidn11-dev libkrb5-dev librtmp-dev libeigen3-doc libmrpt-dev libgd-tools libgdal-doc
  libglib2.0-doc krb5-user libvisual-0.4-plugins gstreamer1.0-tools librsvg2-common libgtk2.0-doc libgts-doc libhdf4-doc hdf4-tools libnetcdf4 libhdf5-doc libhwloc-contrib-plugins libice-doc icu-doc libjasper-runtime libjs-jquery-ui-docs
  liblcms2-utils liblog4cxx-doc libtool-doc liblzma-doc netcdf-bin netcdf-doc libmyodbc odbc-postgresql tdsodbc unixodbc-bin ogdi-bin ogre-1.9-doc libogre-1.9.0v5-dbg opennmpi-doc openni-doc opus-tools imagemagick libpango1.0-doc libpcl-doc
  libpoco-doc libpococrypto9v5-dbg libpocodata9v5-dbg libpocofoundation9v5-dbg libpocomysql9v5-dbg libpoconet9v5-dbg libpoconetssl9v5-dbg libpocoodbc9v5-dbg libpocosqlite9v5-dbg libpocoutil9v5-dbg libpocoxml9v5-dbg libpocozip9v5-dbg poppler-data
  postgresql-doc-9.5 pulseaudio libqt4-declarative-folderlistmodel libqt4-declarative-gestures libqt4-declarative-particles libqt4-declarative-shaders qt4-qmlviewer firebird-dev libsqlite0-dev qt4-dev-tools qt4-doc libqt5libqgtk2
  qt5-image-formats-plugins qtwayland5 qt4-qtconfig libraw1394-doc lksctp-tools libsm-doc speex spacenavd sqlite3-doc libstdc++-4.8-doc libstdc++-5-doc tbb-examples libtbb-doc libtinyxml-doc automaken gcj-jdk java-virtual-machine libvtk5-dev
  vtk-doc vtk-examples vtk6-doc vtk6-examples libxcb-doc libxerces-c-doc libxext-doc libxt-doc make-doc opencl-icd openmpi-checkpoint libmail-box-perl python-doc python-crypto-dbg python-crypto-doc python-cryptography-doc
  python-cryptography-vectors texlive-latex-recommended texlive-latex-base texlive-lang-french fonts-linuxlibertine | ttf-linux-libertine python-enum34-doc python-funcsigs-doc python-gtk2-doc python-gobject-2-dbg dvipng ffmpeg gir1.2-gtk-3.0
  ghostscript inkscape ipython python-cairocffi python-configobj python-excelerator python-gobject python-matplotlib-doc python-qt4 python-scipy python-tornado python-traits python-wxgtk3.0 texlive-extra-utils texlive-latex-extra ttf-staypuft
  python-mock-doc python-coverage python-nose-doc python-numpy-dbg python-numpy-doc libgle3 python-openssl-doc python-openssl-dbg python-pam-dbg python-pil-doc python-pil-dbg python-psutil-doc libcurl4-gnutls-dev python-pycurl-dbg
  python-pycurl-doc python-pyqt5-dbg python-wxgtk3.0 | python-wxgtk python-setuptools-doc python-sip-doc tix python-tk-dbg python-twisted-bin-dbg python-qt3 python-txaio-doc mayavi2 python2.7-doc ri ruby-dev bundler sbcl-doc sbcl-source slime
  gnome-icon-theme kdelibs-data tcl-doc tcl-tclreadline tcl8.6-doc tk-doc tk8.6-doc libfglrx-amdxvba1 libvdpau-va-gl1 nvidia-vdpau-driver nvidia-legacy-340xx-vdpau-driver mesa-utils xfonts-cyrillic
The following NEW packages will be installed:
  autotools-dev binfmt-support binutils blt build-essential bzip2-doc cmake cmake-data comerr-dev cpp cpp-5 debhelper dh-strip-nondeterminism docutils-common docutils-doc dpkg-dev fakeroot fltk1.3-doc fluid fontconfig fontconfig-config
  fonts-dejavu-core fonts-lato fonts-liberation fonts-lyx freeglut3 freeglut3-dev g++ g++-5 gazebo7 gazebo7-common gazebo7-plugin-base gcc gcc-4.8-base gcc-5 gettext gfortran gfortran-5 gir1.2-atk-1.0 gir1.2-freedesktop gir1.2-gdkpixbuf-2.0
  gir1.2-gtk-2.0 gir1.2-pango-1.0 graphviz gstreamer1.0-plugins-base hddtemp hdf5-helpers hicolor-icon-theme i965-va-driver icu-devtools intltool-debian javascript-common krb5-multidev libaacs0 libaec-dev libaec0 libalgorithm-diff-perl
  libalgorithm-diff-xs-perl libalgorithm-merge-perl libapr1 libapr1-dev libaprutil1 libaprutil1-dev libarchive-zip-perl libarchive13 libarmadillo6 libarpack2 libasan0 libasan2 libasound2 libasound2-data libasprintf-dev libassimp-dev libassimp3v5
  libasyncns0 libatk1.0-0 libatk1.0-data libatk1.0-dev libatomic1 libaudio2 libavahi-client3 libavahi-common-data libavahi-common3 libavcodec-dev libavcodec-ffmpeg56 libavformat-dev libavformat-ffmpeg56 libavutil-dev libavutil-ffmpeg54 libbdplus0
  libblas-common libblas-dev libblas3 libbluray1 libboost-all-dev libboost-atomic-dev libboost-atomic1.58-dev libboost-atomic1.58.0 libboost-chrono-dev libboost-chrono1.58-dev libboost-chrono1.58.0 libboost-context-dev libboost-context1.58-dev
  libboost-context1.58.0 libboost-coroutine-dev libboost-coroutine1.58-dev libboost-coroutine1.58.0 libboost-date-time-dev libboost-date-time1.58-dev libboost-date-time1.58.0 libboost-dev libboost-exception-dev libboost-exception1.58-dev
  libboost-filesystem-dev libboost-filesystem1.58-dev libboost-filesystem1.58.0 libboost-graph-dev libboost-graph-parallel-dev libboost-graph-parallel1.58-dev libboost-graph-parallel1.58.0 libboost-graph1.58-dev libboost-graph1.58.0
  libboost-iostreams-dev libboost-iostreams1.58-dev libboost-iostreams1.58.0 libboost-locale-dev libboost-locale1.58-dev libboost-locale1.58.0 libboost-log-dev libboost-log1.58-dev libboost-log1.58.0 libboost-math-dev libboost-math1.58-dev
  libboost-math1.58.0 libboost-mpi-dev libboost-mpi-python-dev libboost-mpi-python1.58-dev libboost-mpi-python1.58.0 libboost-mpi1.58-dev libboost-mpi1.58.0 libboost-program-options-dev libboost-program-options1.58-dev
  libboost-program-options1.58.0 libboost-python-dev libboost-python1.58-dev libboost-python1.58.0 libboost-random-dev libboost-random1.58-dev libboost-random1.58.0 libboost-regex-dev libboost-regex1.58-dev libboost-regex1.58.0
  libboost-serialization-dev libboost-serialization1.58-dev libboost-serialization1.58.0 libboost-signals-dev libboost-signals1.58-dev libboost-signals1.58.0 libboost-system-dev libboost-system1.58-dev libboost-system1.58.0 libboost-test-dev
  libboost-test1.58-dev libboost-test1.58.0 libboost-thread-dev libboost-thread1.58-dev libboost-thread1.58.0 libboost-timer-dev libboost-timer1.58-dev libboost-timer1.58.0 libboost-tools-dev libboost-wave-dev libboost-wave1.58-dev
  libboost-wave1.58.0 libboost1.58-dev libboost1.58-tools-dev libbulletcollision2.83.6 libbulletdynamics2.83.6 libbz2-dev libc-dev-bin libc6-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcc1-0 libcdparanoia0 libcdt5
  libcgraph6 libcilkrts5 libcollada-dom2.4-dp-dev libcollada-dom2.4-dp0 libconsole-bridge-dev libconsole-bridge0.2v5 libcroco3 libcrystalhd3 libcups2 libcurl3 libcurl4-openssl-dev libdap-dev libdap17v5 libdapclient6v5 libdapserver7v5 libdatrie1
  libdc1394-22 libdouble-conversion1v5 libdpkg-perl libdrm-amdgpu1 libdrm-dev libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libegl1-mesa libegl1-mesa-dev libeigen3-dev libepsilon1 libevdev2 libexpat1-dev libfakeroot libfile-fcntllock-perl
  libfile-stripnondeterminism-perl libflac8 libflann-dev libflann1.8 libfltk-cairo1.3 libfltk-forms1.3 libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1 libfontconfig1-dev libfontenc1 libfreeimage-dev libfreeimage3
  libfreetype6-dev libfreexl1 libgazebo7 libgazebo7-dev libgbm1 libgcc-4.8-dev libgcc-5-dev libgd3 libgdal-dev libgdal1i libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgdk-pixbuf2.0-dev libgeos-3.5.0 libgeos-c1v5 libgeos-dev libgettextpo-dev
  libgettextpo0 libgfortran-5-dev libgfortran3 libgif-dev libgif7 libgl1-mesa-dev libgl1-mesa-dri libgl1-mesa-glx libgl2ps-dev libgl2ps0 libglade2-0 libglapi-mesa libgles2-mesa libgles2-mesa-dev libglib2.0-bin libglib2.0-dev libglu1-mesa
  libglu1-mesa-dev libgme0 libgomp1 libgraphite2-3 libgsm1 libgssrpc4 libgstreamer-plugins-base1.0-0 libgstreamer1.0-0 libgtest-dev libgtk2.0-0 libgtk2.0-bin libgtk2.0-common libgtk2.0-dev libgtkglext1 libgts-0.7-5 libgts-bin libgts-dev
  libgudev-1.0-0 libgvc6 libgvpr2 libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libhdf4-0-alt libhdf4-alt-dev libhdf5-10 libhdf5-cpp-11 libhdf5-dev libhdf5-mpi-dev libhdf5-openmpi-10 libhdf5-openmpi-dev libhwloc-dev
  libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libice-dev libice6 libicu-dev libignition-math2 libignition-math2-dev libilmbase12 libinput-dev libinput10 libisl15 libitm1 libjasper-dev libjasper1 libjbig-dev libjbig0 libjpeg-dev
  libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjsoncpp-dev libjsoncpp1 libjxr0 libkadm5clnt-mit9 libkadm5srv-mit9 libkdb5-8 libkmlbase1 libkmldom1 libkmlengine1
  liblapack-dev liblapack3 liblcms2-2 libldap2-dev liblinearmath2.83.6 libllvm3.8 liblog4cxx-dev liblog4cxx10-dev liblog4cxx10v5 liblsan0 libltdl-dev libltdl7 liblz4-dev liblzma-dev libmail-sendmail-perl libminizip1 libmirclient-dev libmirclient9
  libmircommon-dev libmircommon5 libmircookie-dev libmircookie2 libmirprotobuf3 libmng2 libmodplug1 libmp3lame0 libmpc3 libmpx0 libmtdev1 libmysqlclient-dev libmysqlclient20 libnetcdf-c++4 libnetcdf-cxx-legacy-dev libnetcdf-dev libnetcdf11
  libnuma-dev libodbc1 libogdi3.2 libogg-dev libogg0 libogre-1.9-dev libogre-1.9.0v5 libopencv-calib3d2.4v5 libopencv-contrib2.4v5 libopencv-core2.4v5 libopencv-features2d2.4v5 libopencv-flann2.4v5 libopencv-highgui2.4v5 libopencv-imgproc2.4v5
  libopencv-legacy2.4v5 libopencv-ml2.4v5 libopencv-objdetect2.4v5 libopencv-photo2.4v5 libopencv-video2.4v5 libopenexr22 libopenjp2-7 libopenjpeg5 libopenmpi-dev libopenmpi1.10 libopenni-dev libopenni-sensor-pointclouds0 libopenni0 libopus0
  liborc-0.4-0 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0 libpangoft2-1.0-0 libpangox-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpathplan4 libpciaccess0 libpcl-apps1.7 libpcl-common1.7 libpcl-dev libpcl-features1.7
  libpcl-filters1.7 libpcl-io1.7 libpcl-kdtree1.7 libpcl-keypoints1.7 libpcl-octree1.7 libpcl-outofcore1.7 libpcl-people1.7 libpcl-recognition1.7 libpcl-registration1.7 libpcl-sample-consensus1.7 libpcl-search1.7 libpcl-segmentation1.7
  libpcl-surface1.7 libpcl-tracking1.7 libpcl-visualization1.7 libpcl1.7 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpixman-1-0 libpixman-1-dev libpng12-dev libpoco-dev libpococrypto9v5 libpocodata9v5 libpocofoundation9v5 libpocomysql9v5
  libpoconet9v5 libpoconetssl9v5 libpocoodbc9v5 libpocosqlite9v5 libpocoutil9v5 libpocoxml9v5 libpocozip9v5 libpoppler58 libpq-dev libpq5 libproj-dev libproj9 libprotobuf-dev libprotobuf-lite9v5 libprotobuf9v5 libprotoc-dev libprotoc9v5
  libproxy1v5 libpthread-stubs0-dev libpulse0 libpyside-py3-2.0 libpyside2-dev libpyside2.0 libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3.5 libqgsttools-p1 libqhull-dev libqhull7
  libqt4-dbus libqt4-declarative libqt4-designer libqt4-dev libqt4-dev-bin libqt4-help libqt4-network libqt4-opengl libqt4-opengl-dev libqt4-qt3support libqt4-script libqt4-scripttools libqt4-sql libqt4-sql-mysql libqt4-svg libqt4-test libqt4-xml
  libqt4-xmlpatterns libqt5clucene5 libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5designer5 libqt5designercomponents5 libqt5gui5 libqt5help5 libqt5multimedia5 libqt5multimediaquick-p5 libqt5multimediawidgets5 libqt5network5 libqt5opengl5
  libqt5opengl5-dev libqt5printsupport5 libqt5qml5 libqt5quick5 libqt5quickparticles5 libqt5quicktest5 libqt5quickwidgets5 libqt5script5 libqt5scripttools5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5svg5-dev libqt5test5 libqt5webkit5
  libqt5webkit5-dev libqt5widgets5 libqt5x11extras5 libqt5x11extras5-dev libqt5xml5 libqt5xmlpatterns5 libqt5xmlpatterns5-dev libqt5xmlpatterns5-private-dev libqtcore4 libqtdbus4 libqtgui4 libqtwebkit-dev libqtwebkit4 libquadmath0 libraw1394-11
  libraw15 libruby2.3 libschroedinger-1.0-0 libsctp-dev libsctp1 libsdformat4 libsdformat4-dev libshiboken-py3-2.0 libshiboken2-dev libshiboken2.0 libshine3 libsimbody-dev libsimbody3.5v5 libsm-dev libsm6 libsnappy1v5 libsndfile1 libsoxr0
  libspatialite-dev libspatialite7 libspeex1 libspnav0 libsqlite3-dev libssh-gcrypt-4 libssl-dev libssl-doc libstdc++-4.8-dev libstdc++-5-dev libsuperlu4 libswresample-dev libswresample-ffmpeg1 libswscale-dev libswscale-ffmpeg3
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Thats quite the number of changes... Most interesting, is that I am not seeing MPICH. But I am seeing OpenMPI. We might have found the culprit right there. As you mentioned ROS needs MPICH. I'll continue to install these and attempt to build PETSc. I'll report my findings shortly.



Jason

Thomas Wood

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Nov 7, 2016, 11:41:33 AM11/7/16
to moose...@googlegroups.com
Yup. That's ROS.

When I tried to remove my system's openmpi (not mpich apparently) earlier, apt-get tried to remove my all my ROS packages. I got openmpi mixed up with mpich because I just removed mpich. Sorry about that.

All the errors I've been seeing are header/library version mismatch errors between the system's libopenmpi and the mpich package_builder just made for PETSc.


For more options, visit https://groups.google.com/d/optout.

Miller, Jason M

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Nov 7, 2016, 12:03:30 PM11/7/16
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Once all those packages installed, I rebooted the VM for good measure. And then proceeded to build PETSc.

moose@ros-test:~/projects/petsc-3.6.4$ cat build.sh 
./configure \
--prefix=/home/moose/petsc_installed/petsc-3.6.4 \
--download-hypre=1 \
--with-ssl=0 \
--with-debugging=no \
--with-pic=1 \
--with-shared-libraries=1 \
--with-cc=mpicc \
--with-cxx=mpicxx \
--with-fc=mpif90 \
--download-fblaslapack=1 \
--download-metis=1 \
--download-parmetis=1 \
--download-superlu_dist=1 \
--download-mumps=1 \
--download-scalapack=1 \
-CC=mpicc -CXX=mpicxx -FC=mpif90 -F77=mpif77 -F90=mpif90 \
-CFLAGS='-fPIC -fopenmp' \
-CXXFLAGS='-fPIC -fopenmp' \
-FFLAGS='-fPIC -fopenmp' \
-FCFLAGS='-fPIC -fopenmp' \
-F90FLAGS='-fPIC -fopenmp' \
-F77FLAGS='-fPIC -fopenmp' \
PETSC_DIR=`pwd`
moose@ros-test:~/projects/petsc-3.6.4$ which mpif90
/usr/bin/mpif90
moose@ros-test:~/projects/petsc-3.6.4$ which mpicc
/usr/bin/mpicc
moose@ros-test:~/projects/petsc-3.6.4$ which mpicxx
/usr/bin/mpicxx
moose@ros-test:~/projects/petsc-3.6.4$ sh build.sh 
===============================================================================
             Configuring PETSc to compile on your system                       
===============================================================================

...
...
trimmed
...
...
                                                                                                                                  
  C Compiler:         mpicc -fPIC -fopenmp -fPIC -O 
  C++ Compiler:       mpicxx -fPIC -fopenmp -O   -fPIC  
  Fortran Compiler:   mpif90 -fPIC -fopenmp -fPIC -O  
Linkers:
  Shared linker:   mpicc  -shared -fPIC -fopenmp -fPIC -O
  Dynamic linker:   mpicc  -shared -fPIC -fopenmp -fPIC -O
make:
BLAS/LAPACK: -Wl,-rpath,/home/moose/petsc_installed/petsc-3.6.4/lib -L/home/moose/petsc_installed/petsc-3.6.4/lib -lflapack -Wl,-rpath,/home/moose/petsc_installed/petsc-3.6.4/lib -L/home/moose/petsc_installed/petsc-3.6.4/lib -lfblas
MPI:
  Includes: -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi
fblaslapack:
cmake:
X:
  Library:  -lX11
hypre:
  Includes: -I/home/moose/petsc_installed/petsc-3.6.4/include
  Library:  -Wl,-rpath,/home/moose/petsc_installed/petsc-3.6.4/lib -L/home/moose/petsc_installed/petsc-3.6.4/lib -lHYPRE -Wl,-rpath,/usr/lib/openmpi/lib -L/usr/lib/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lmpi_cxx -lstdc++
scalapack:
  Library:  -Wl,-rpath,/home/moose/petsc_installed/petsc-3.6.4/lib -L/home/moose/petsc_installed/petsc-3.6.4/lib -lscalapack
parmetis:
  Includes: -I/home/moose/petsc_installed/petsc-3.6.4/include
  Library:  -Wl,-rpath,/home/moose/petsc_installed/petsc-3.6.4/lib -L/home/moose/petsc_installed/petsc-3.6.4/lib -lparmetis
metis:
  Includes: -I/home/moose/petsc_installed/petsc-3.6.4/include
  Library:  -Wl,-rpath,/home/moose/petsc_installed/petsc-3.6.4/lib -L/home/moose/petsc_installed/petsc-3.6.4/lib -lmetis
MUMPS:
  Includes: -I/home/moose/petsc_installed/petsc-3.6.4/include
  Library:  -Wl,-rpath,/home/moose/petsc_installed/petsc-3.6.4/lib -L/home/moose/petsc_installed/petsc-3.6.4/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord
SuperLU_DIST:
  Includes: -I/home/moose/petsc_installed/petsc-3.6.4/include
  Library:  -Wl,-rpath,/home/moose/petsc_installed/petsc-3.6.4/lib -L/home/moose/petsc_installed/petsc-3.6.4/lib -lsuperlu_dist_4.1
hwloc:
  Library:  -lhwloc
  Arch:     
pthread:
PETSc:
  PETSC_ARCH: arch-linux2-c-opt
  PETSC_DIR: /home/moose/projects/petsc-3.6.4
  Clanguage: C
  Integer size: 32
  shared libraries: enabled
  Scalar type: real
  Precision: double
  Memory alignment: 16
xxx=========================================================================xxx
 Configure stage complete. Now build PETSc libraries with (gnumake build):
   make PETSC_DIR=/home/moose/projects/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-opt all
xxx=========================================================================xxx


moose@ros-test:~/projects/petsc-3.6.4$ make PETSC_DIR=/home/moose/projects/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-opt all                                                                                                                                  
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
The version of PETSc you are using is out-of-date, we recommend updating to the new release
 Available Version: 3.7.4   Installed Version: 3.6.4
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
make[1]: Entering directory '/home/moose/projects/petsc-3.6.4'
==========================================

...
...
trimmed
...
...

          CC arch-linux2-c-opt/obj/src/tao/linesearch/interface/ftn-auto/taolinesearchf.o
          CC arch-linux2-c-opt/obj/src/tao/linesearch/interface/ftn-custom/ztaolinesearchf.o
          CC arch-linux2-c-opt/obj/src/tao/leastsquares/impls/pounders/pounders.o
          CC arch-linux2-c-opt/obj/src/tao/leastsquares/impls/pounders/gqt.o
     CLINKER /home/moose/projects/petsc-3.6.4/arch-linux2-c-opt/lib/libpetsc.so.3.6.4
make[2]: Leaving directory '/home/moose/projects/petsc-3.6.4'
=========================================
make[1]: Leaving directory '/home/moose/projects/petsc-3.6.4'
Now to install the libraries do:
make PETSC_DIR=/home/moose/projects/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-opt install
=========================================
moose@ros-test:~/projects/petsc-3.6.4$ make PETSC_DIR=/home/moose/projects/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-opt install
*** Using PETSC_DIR=/home/moose/projects/petsc-3.6.4 PETSC_ARCH=arch-linux2-c-opt ***
*** Installing PETSc at prefix location: /home/moose/petsc_installed/petsc-3.6.4  ***
====================================
Install complete.
Now to check if the libraries are working do (in current directory):
make PETSC_DIR=/home/moose/petsc_installed/petsc-3.6.4 PETSC_ARCH="" test
====================================
/usr/bin/make  --no-print-directory PETSC_ARCH=arch-linux2-c-opt PETSC_DIR=/home/moose/projects/petsc-3.6.4 mpi4py-install petsc4py-install
make[1]: Nothing to be done for 'mpi4py-install'.
make[1]: Nothing to be done for 'petsc4py-install'.


So far so good... PETSc built with ROS's desired OpenMPI implementation. I'll next try to build libMesh and then MOOSE with only exporting one thing:

  export PETSC_DIR=/home/moose/petsc_installed/petsc-3.6.4

After reading your email about MPICH/OpenMPI mix up, and being that my VM has already surpassed the original issue... I might suggest removing ROS, and any MPI still lingering around on the machine (including the one you build using package_builder), and then re-installing ROS again... ? That might clean up what-ever-it-is that is getting in the way. But still, allow me to finish building libMesh/MOOSE, and if that all passes... profit?

Jason


Miller, Jason M

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Nov 7, 2016, 12:42:09 PM11/7/16
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libMesh, moose/framework, moose/test compiled fine.

run_tests however, failed all the parallel tests because the implementation of MPI is only allowing one slot when `-host localhost` arguments are used...
In short, to get around this, I instructed the TeshHarness to not use `-host localhost`:

  export MOOSE_MPI_COMMAND='mpiexec'

And then the run_tests script.

misc/serialized_solution.adapt............................................................................ OK
misc/selective_reinit.test................................................................................ OK
misc/line_source.test..................................................................................... OK
preconditioners/pbp.lots_of_variables....................................................... FAILED (TIMEOUT)
-------------------------------------------------------------------------------------------------------------
Ran 1301 tests in 354.9 seconds
1300 passed, 10 skipped, 0 pending, 1 FAILED

 All tests passed, except for one, with a timeout issue. So bottom line, interesting findings while using system supplied version of MPI. It works, with some tweaking.
Next, I will try to install our moose-environment package, and see if I can get our MPI and the system MPI not to collide. If I can, I'll post what I did.

Jason



Jed Brown

unread,
Nov 7, 2016, 12:47:42 PM11/7/16
to Thomas Wood, moose...@googlegroups.com
Thomas Wood <odell...@gmail.com> writes:

> Yup. That's ROS.
>
> When I tried to remove my system's openmpi (not mpich apparently) earlier,
> apt-get tried to remove my all my ROS packages. I got openmpi mixed up with
> mpich because I just removed mpich. Sorry about that.
>
> All the errors I've been seeing are header/library version mismatch errors
> between the system's libopenmpi and the mpich package_builder just made for
> PETSc.

Yes, this is a common problem. The ABIs are different, so it's
essential to get straight. (I blame the MPI Forum for not paying more
attention to this issue. It really inflicts an undue cost on users.)
signature.asc

Miller, Jason M

unread,
Nov 7, 2016, 1:07:11 PM11/7/16
to moose...@googlegroups.com
Well that is not going to work... The dependencies I have listed in the moose-environment package will cause ROS to be removed:


moose@ros-test:~$ sudo dpkg -i moose-environment-6_Ubuntu-16.04_x86_64.deb 
[sudo] password for moose: 
Selecting previously unselected package moose-environment.
(Reading database ... 142451 files and directories currently installed.)
Preparing to unpack moose-environment-6_Ubuntu-16.04_x86_64.deb ...
Unpacking moose-environment (1.1-6) ...
dpkg: dependency problems prevent configuration of moose-environment:
 moose-environment depends on m4; however:
  Package m4 is not installed.
 moose-environment depends on doxygen; however:
  Package doxygen is not installed.
 moose-environment depends on libcurl4-gnutls-dev; however:
  Package libcurl4-gnutls-dev is not installed.

dpkg: error processing package moose-environment (--install):
 dependency problems - leaving unconfigured
Errors were encountered while processing:
 moose-environment
moose@ros-test:~$ sudo apt-get install -f
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Correcting dependencies... Done
The following packages were automatically installed and are no longer required:
  cmake cmake-data comerr-dev docutils-common docutils-doc fltk1.3-doc fluid fonts-lato fonts-lyx freeglut3-dev gazebo7 gazebo7-common gazebo7-plugin-base gcc-4.8-base gir1.2-atk-1.0 gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 gir1.2-gtk-2.0
  gir1.2-pango-1.0 gstreamer1.0-plugins-base hddtemp hdf5-helpers hicolor-icon-theme i965-va-driver icu-devtools javascript-common krb5-multidev libaacs0 libaec-dev libaec0 libapr1 libapr1-dev libaprutil1 libaprutil1-dev libarchive13 libarmadillo6
  libarpack2 libasan0 libasound2 libasound2-data libassimp-dev libassimp3v5 libasyncns0 libatk1.0-0 libatk1.0-data libatk1.0-dev libaudio2 libavahi-client3 libavahi-common-data libavahi-common3 libavcodec-dev libavcodec-ffmpeg56 libavformat-dev
  libavformat-ffmpeg56 libavutil-dev libavutil-ffmpeg54 libbdplus0 libbluray1 libboost-all-dev libboost-atomic-dev libboost-atomic1.58-dev libboost-atomic1.58.0 libboost-chrono-dev libboost-chrono1.58-dev libboost-chrono1.58.0 libboost-context-dev
  libboost-context1.58-dev libboost-context1.58.0 libboost-coroutine-dev libboost-coroutine1.58-dev libboost-coroutine1.58.0 libboost-date-time-dev libboost-date-time1.58-dev libboost-date-time1.58.0 libboost-dev libboost-exception-dev
  libboost-exception1.58-dev libboost-filesystem-dev libboost-filesystem1.58-dev libboost-filesystem1.58.0 libboost-graph-dev libboost-graph-parallel-dev libboost-graph-parallel1.58-dev libboost-graph-parallel1.58.0 libboost-graph1.58-dev
  libboost-graph1.58.0 libboost-iostreams-dev libboost-iostreams1.58-dev libboost-iostreams1.58.0 libboost-locale-dev libboost-locale1.58-dev libboost-locale1.58.0 libboost-log-dev libboost-log1.58-dev libboost-log1.58.0 libboost-math-dev
  libboost-math1.58-dev libboost-math1.58.0 libboost-mpi-dev libboost-mpi-python-dev libboost-mpi-python1.58-dev libboost-mpi-python1.58.0 libboost-mpi1.58-dev libboost-mpi1.58.0 libboost-program-options-dev libboost-program-options1.58-dev
  libboost-program-options1.58.0 libboost-python-dev libboost-python1.58-dev libboost-python1.58.0 libboost-random-dev libboost-random1.58-dev libboost-random1.58.0 libboost-regex-dev libboost-regex1.58-dev libboost-regex1.58.0
  libboost-serialization-dev libboost-serialization1.58-dev libboost-serialization1.58.0 libboost-signals-dev libboost-signals1.58-dev libboost-signals1.58.0 libboost-system-dev libboost-system1.58-dev libboost-system1.58.0 libboost-test-dev
  libboost-test1.58-dev libboost-test1.58.0 libboost-thread-dev libboost-thread1.58-dev libboost-thread1.58.0 libboost-timer-dev libboost-timer1.58-dev libboost-timer1.58.0 libboost-tools-dev libboost-wave-dev libboost-wave1.58-dev
  libboost-wave1.58.0 libboost1.58-dev libboost1.58-tools-dev libbulletcollision2.83.6 libbulletdynamics2.83.6 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2-dev libcdparanoia0 libcollada-dom2.4-dp-dev libcollada-dom2.4-dp0
  libconsole-bridge-dev libconsole-bridge0.2v5 libcrystalhd3 libcups2 libcurl3 libdap-dev libdap17v5 libdapclient6v5 libdapserver7v5 libdc1394-22 libdouble-conversion1v5 libdrm-dev libegl1-mesa libegl1-mesa-dev libeigen3-dev libepsilon1 libevdev2
  libexpat1-dev libflac8 libflann-dev libflann1.8 libfltk-cairo1.3 libfltk-forms1.3 libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1-dev libfreeimage-dev libfreeimage3 libfreetype6-dev libfreexl1 libgazebo7 libgbm1
  libgcc-4.8-dev libgdal-dev libgdal1i libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgdk-pixbuf2.0-dev libgeos-3.5.0 libgeos-c1v5 libgeos-dev libgif-dev libgif7 libgl1-mesa-dev libgl2ps-dev libgl2ps0 libglade2-0 libgles2-mesa libgles2-mesa-dev
  libglib2.0-bin libglib2.0-dev libglu1-mesa libglu1-mesa-dev libgme0 libgsm1 libgssrpc4 libgstreamer-plugins-base1.0-0 libgstreamer1.0-0 libgtest-dev libgtk2.0-0 libgtk2.0-bin libgtk2.0-common libgtk2.0-dev libgtkglext1 libgts-0.7-5 libgts-bin
  libgts-dev libgudev-1.0-0 libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libhdf4-0-alt libhdf4-alt-dev libhdf5-10 libhdf5-cpp-11 libhdf5-dev libhdf5-mpi-dev libhdf5-openmpi-10 libhdf5-openmpi-dev libibverbs-dev libibverbs1 libice-dev
  libicu-dev libignition-math2 libignition-math2-dev libilmbase12 libinput-dev libinput10 libjasper-dev libjasper1 libjbig-dev libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjsoncpp-dev
  libjsoncpp1 libjxr0 libkadm5clnt-mit9 libkadm5srv-mit9 libkdb5-8 libkmlbase1 libkmldom1 libkmlengine1 liblcms2-2 liblinearmath2.83.6 liblog4cxx-dev liblog4cxx10-dev liblog4cxx10v5 liblz4-dev liblzma-dev libminizip1 libmirclient-dev libmirclient9
  libmircommon-dev libmircommon5 libmircookie-dev libmircookie2 libmirprotobuf3 libmng2 libmodplug1 libmp3lame0 libmtdev1 libmysqlclient-dev libmysqlclient20 libnetcdf-c++4 libnetcdf-cxx-legacy-dev libnetcdf-dev libnetcdf11 libodbc1 libogdi3.2
  libogg-dev libogg0 libogre-1.9-dev libogre-1.9.0v5 libopencv-calib3d2.4v5 libopencv-contrib2.4v5 libopencv-core2.4v5 libopencv-features2d2.4v5 libopencv-flann2.4v5 libopencv-highgui2.4v5 libopencv-imgproc2.4v5 libopencv-legacy2.4v5
  libopencv-ml2.4v5 libopencv-objdetect2.4v5 libopencv-photo2.4v5 libopencv-video2.4v5 libopenexr22 libopenjp2-7 libopenjpeg5 libopenmpi-dev libopenmpi1.10 libopenni-dev libopenni-sensor-pointclouds0 libopenni0 libopus0 liborc-0.4-0
  libpango1.0-dev libpangox-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpcl-apps1.7 libpcl-common1.7 libpcl-dev libpcl-features1.7 libpcl-filters1.7 libpcl-io1.7 libpcl-kdtree1.7 libpcl-keypoints1.7 libpcl-octree1.7 libpcl-outofcore1.7
  libpcl-people1.7 libpcl-recognition1.7 libpcl-registration1.7 libpcl-sample-consensus1.7 libpcl-search1.7 libpcl-segmentation1.7 libpcl-surface1.7 libpcl-tracking1.7 libpcl-visualization1.7 libpcl1.7 libpcre16-3 libpcre3-dev libpcre32-3
  libpcrecpp0v5 libpixman-1-dev libpng12-dev libpoco-dev libpococrypto9v5 libpocodata9v5 libpocofoundation9v5 libpocomysql9v5 libpoconet9v5 libpoconetssl9v5 libpocoodbc9v5 libpocosqlite9v5 libpocoutil9v5 libpocoxml9v5 libpocozip9v5 libpoppler58
  libpq-dev libpq5 libproj-dev libproj9 libprotobuf-dev libprotobuf-lite9v5 libprotobuf9v5 libprotoc-dev libprotoc9v5 libproxy1v5 libpulse0 libpyside-py3-2.0 libpyside2-dev libpyside2.0 libpython-dev libpython2.7 libpython2.7-dev libpython3.5
  libqgsttools-p1 libqhull-dev libqhull7 libqt4-dbus libqt4-declarative libqt4-designer libqt4-dev libqt4-dev-bin libqt4-help libqt4-network libqt4-opengl libqt4-opengl-dev libqt4-qt3support libqt4-script libqt4-scripttools libqt4-sql
  libqt4-sql-mysql libqt4-svg libqt4-test libqt4-xml libqt4-xmlpatterns libqt5clucene5 libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5designer5 libqt5designercomponents5 libqt5gui5 libqt5help5 libqt5multimedia5 libqt5multimediaquick-p5
  libqt5multimediawidgets5 libqt5network5 libqt5opengl5 libqt5opengl5-dev libqt5printsupport5 libqt5qml5 libqt5quick5 libqt5quickparticles5 libqt5quicktest5 libqt5quickwidgets5 libqt5script5 libqt5scripttools5 libqt5sql5 libqt5sql5-sqlite
  libqt5svg5 libqt5svg5-dev libqt5test5 libqt5webkit5 libqt5webkit5-dev libqt5widgets5 libqt5x11extras5 libqt5x11extras5-dev libqt5xml5 libqt5xmlpatterns5 libqt5xmlpatterns5-dev libqt5xmlpatterns5-private-dev libqtcore4 libqtdbus4 libqtgui4
  libqtwebkit-dev libqtwebkit4 libraw1394-11 libraw15 libruby2.3 libschroedinger-1.0-0 libsctp-dev libsctp1 libsdformat4 libsdformat4-dev libshiboken-py3-2.0 libshiboken2-dev libshiboken2.0 libshine3 libsimbody-dev libsimbody3.5v5 libsm-dev
  libsnappy1v5 libsndfile1 libsoxr0 libspatialite-dev libspatialite7 libspeex1 libspnav0 libsqlite3-dev libssh-gcrypt-4 libssl-dev libssl-doc libstdc++-4.8-dev libsuperlu4 libswresample-dev libswresample-ffmpeg1 libswscale-dev libswscale-ffmpeg3
  libsz2 libtar-dev libtar0 libtbb-dev libtbb2 libtheora-dev libtheora0 libtiff5-dev libtiffxx5 libtinyxml-dev libtinyxml2-2v5 libtinyxml2.6.2v5 libtwolame0 liburdfdom-dev liburdfdom-headers-dev liburdfdom-model-state0.4 liburdfdom-model0.4
  liburdfdom-sensor0.4 liburdfdom-tools liburdfdom-world0.4 liburiparser1 libusb-1.0-0-dev libusb-1.0-doc libv4l-0 libv4lconvert0 libva1 libvdpau1 libvisual-0.4-0 libvorbis0a libvorbisenc2 libvtk-java libvtk5.10 libvtk6-dev libvtk6-java
  libvtk6-qt-dev libvtk6.2 libvtk6.2-qt libwacom-bin libwacom-common libwacom2 libwavpack1 libwayland-client0 libwayland-cursor0 libwayland-dev libwayland-egl1-mesa libwayland-server0 libwebp-dev libwebp5 libwebpdemux1 libwebpmux1 libx11-xcb-dev
  libx264-148 libx265-79 libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present-dev libxcb-randr0 libxcb-randr0-dev libxcb-render-util0 libxcb-render0-dev libxcb-shape0-dev libxcb-shm0-dev
  libxcb-sync-dev libxcb-util1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb-xkb1 libxcomposite-dev libxcursor-dev libxcursor1 libxdamage-dev libxerces-c-dev libxerces-c3.1 libxext-dev libxfixes-dev libxft-dev libxi-dev libxinerama-dev libxkbcommon-dev
  libxkbcommon-x11-0 libxkbcommon0 libxml2-dev libxml2-utils libxmu-dev libxmu-headers libxrandr-dev libxrender-dev libxshmfence-dev libxslt1.1 libxss-dev libxt-dev libxvidcore4 libxxf86vm-dev libyaml-0-2 libyaml-cpp-dev libyaml-cpp0.5v5
  libzvbi-common libzvbi0 libzzip-0-13 mesa-common-dev mesa-vdpau-drivers mpi-default-bin mpi-default-dev mysql-common odbcinst odbcinst1debian2 openmpi-bin openmpi-common openni-utils proj-bin proj-data pyqt5-dev python-attr python-autobahn
  python-cairo python-catkin-pkg python-cffi-backend python-chardet python-concurrent.futures python-crypto python-cryptography python-cycler python-dateutil python-defusedxml python-dev python-docutils python-ecdsa python-empy python-enum34
  python-funcsigs python-glade2 python-gobject-2 python-gtk2 python-idna python-imaging python-ipaddress python-lz4 python-matplotlib python-matplotlib-data python-mock python-mpi4py python-msgpack python-netifaces python-nose python-numpy
  python-opencv python-opengl python-openssl python-pam python-paramiko python-pbr python-pil python-pkg-resources python-psutil python-pyasn1 python-pyasn1-modules python-pycurl python-pydot python-pygments python-pyparsing python-pyqt5
  python-pyqt5.qtopengl python-pyqt5.qtsvg python-pyside2 python-pyside2.qtconcurrent python-pyside2.qtcore python-pyside2.qtgui python-pyside2.qthelp python-pyside2.qtnetwork python-pyside2.qtprintsupport python-pyside2.qtqml
  python-pyside2.qtquick python-pyside2.qtquickwidgets python-pyside2.qtscript python-pyside2.qtsql python-pyside2.qtsvg python-pyside2.qttest python-pyside2.qtuitools python-pyside2.qtwebkit python-pyside2.qtwebkitwidgets python-pyside2.qtwidgets
  python-pyside2.qtx11extras python-pyside2.qtxml python-roman python-rosdep python-rosdistro python-rospkg python-serial python-service-identity python-setuptools python-sip python-sip-dev python-six python-snappy python-trollius python-twisted
  python-twisted-bin python-twisted-core python-txaio python-tz python-urlgrabber python-vtk6 python-yaml python-zope.interface python2.7-dev qdbus qt-at-spi qt4-linguist-tools qt4-qmake qt5-qmake qtbase5-dev qtbase5-dev-tools qtbase5-private-dev
  qtchooser qtcore4-l10n qtdeclarative5-dev qtdeclarative5-private-dev qtmultimedia5-dev qtscript5-dev qtscript5-private-dev qttools5-dev qttools5-dev-tools qttools5-private-dev qttranslations5-l10n rake ros-kinetic-actionlib
  ros-kinetic-actionlib-msgs ros-kinetic-actionlib-tutorials ros-kinetic-angles ros-kinetic-bond ros-kinetic-bond-core ros-kinetic-bondcpp ros-kinetic-bondpy ros-kinetic-camera-calibration ros-kinetic-camera-calibration-parsers
  ros-kinetic-camera-info-manager ros-kinetic-catkin ros-kinetic-class-loader ros-kinetic-cmake-modules ros-kinetic-collada-parser ros-kinetic-common-msgs ros-kinetic-common-tutorials ros-kinetic-compressed-depth-image-transport
  ros-kinetic-compressed-image-transport ros-kinetic-control-msgs ros-kinetic-cpp-common ros-kinetic-cv-bridge ros-kinetic-depth-image-proc ros-kinetic-diagnostic-aggregator ros-kinetic-diagnostic-analysis ros-kinetic-diagnostic-common-diagnostics
  ros-kinetic-diagnostic-msgs ros-kinetic-diagnostic-updater ros-kinetic-diagnostics ros-kinetic-dynamic-reconfigure ros-kinetic-eigen-conversions ros-kinetic-eigen-stl-containers ros-kinetic-executive-smach ros-kinetic-filters
  ros-kinetic-gazebo-msgs ros-kinetic-gencpp ros-kinetic-geneus ros-kinetic-genlisp ros-kinetic-genmsg ros-kinetic-gennodejs ros-kinetic-genpy ros-kinetic-geometry ros-kinetic-geometry-msgs ros-kinetic-geometry-tutorials ros-kinetic-gl-dependency
  ros-kinetic-image-common ros-kinetic-image-geometry ros-kinetic-image-pipeline ros-kinetic-image-proc ros-kinetic-image-rotate ros-kinetic-image-transport ros-kinetic-image-transport-plugins ros-kinetic-image-view
  ros-kinetic-interactive-marker-tutorials ros-kinetic-interactive-markers ros-kinetic-joint-state-publisher ros-kinetic-kdl-conversions ros-kinetic-kdl-parser ros-kinetic-laser-assembler ros-kinetic-laser-filters ros-kinetic-laser-geometry
  ros-kinetic-laser-pipeline ros-kinetic-map-msgs ros-kinetic-media-export ros-kinetic-message-filters ros-kinetic-message-generation ros-kinetic-message-runtime ros-kinetic-mk ros-kinetic-nav-msgs ros-kinetic-nodelet ros-kinetic-nodelet-core
  ros-kinetic-nodelet-topic-tools ros-kinetic-nodelet-tutorial-math ros-kinetic-octomap ros-kinetic-opencv3 ros-kinetic-orocos-kdl ros-kinetic-pcl-conversions ros-kinetic-pcl-msgs ros-kinetic-pcl-ros ros-kinetic-perception
  ros-kinetic-perception-pcl ros-kinetic-pluginlib ros-kinetic-pluginlib-tutorials ros-kinetic-polled-camera ros-kinetic-pr2-description ros-kinetic-python-orocos-kdl ros-kinetic-python-qt-binding ros-kinetic-qt-dotgraph ros-kinetic-qt-gui
  ros-kinetic-qt-gui-cpp ros-kinetic-qt-gui-py-common ros-kinetic-qwt-dependency ros-kinetic-random-numbers ros-kinetic-robot-state-publisher ros-kinetic-ros ros-kinetic-ros-base ros-kinetic-ros-comm ros-kinetic-ros-core ros-kinetic-ros-tutorials
  ros-kinetic-rosbag ros-kinetic-rosbag-migration-rule ros-kinetic-rosbag-storage ros-kinetic-rosbash ros-kinetic-rosboost-cfg ros-kinetic-rosbuild ros-kinetic-rosclean ros-kinetic-rosconsole ros-kinetic-rosconsole-bridge ros-kinetic-roscpp
  ros-kinetic-roscpp-core ros-kinetic-roscpp-serialization ros-kinetic-roscpp-traits ros-kinetic-roscpp-tutorials ros-kinetic-roscreate ros-kinetic-rosgraph ros-kinetic-rosgraph-msgs ros-kinetic-roslang ros-kinetic-roslaunch ros-kinetic-roslib
  ros-kinetic-roslint ros-kinetic-roslisp ros-kinetic-roslz4 ros-kinetic-rosmake ros-kinetic-rosmaster ros-kinetic-rosmsg ros-kinetic-rosnode ros-kinetic-rosout ros-kinetic-rospack ros-kinetic-rosparam ros-kinetic-rospy ros-kinetic-rospy-tutorials
  ros-kinetic-rosservice ros-kinetic-rostest ros-kinetic-rostime ros-kinetic-rostopic ros-kinetic-rosunit ros-kinetic-roswtf ros-kinetic-rqt-action ros-kinetic-rqt-bag ros-kinetic-rqt-bag-plugins ros-kinetic-rqt-common-plugins
  ros-kinetic-rqt-console ros-kinetic-rqt-dep ros-kinetic-rqt-graph ros-kinetic-rqt-gui ros-kinetic-rqt-gui-cpp ros-kinetic-rqt-gui-py ros-kinetic-rqt-image-view ros-kinetic-rqt-launch ros-kinetic-rqt-logger-level ros-kinetic-rqt-moveit
  ros-kinetic-rqt-msg ros-kinetic-rqt-nav-view ros-kinetic-rqt-plot ros-kinetic-rqt-pose-view ros-kinetic-rqt-publisher ros-kinetic-rqt-py-common ros-kinetic-rqt-py-console ros-kinetic-rqt-reconfigure ros-kinetic-rqt-robot-dashboard
  ros-kinetic-rqt-robot-monitor ros-kinetic-rqt-robot-steering ros-kinetic-rqt-runtime-monitor ros-kinetic-rqt-service-caller ros-kinetic-rqt-shell ros-kinetic-rqt-srv ros-kinetic-rqt-tf-tree ros-kinetic-rqt-top ros-kinetic-rqt-topic
  ros-kinetic-rqt-web ros-kinetic-self-test ros-kinetic-sensor-msgs ros-kinetic-shape-msgs ros-kinetic-smach ros-kinetic-smach-msgs ros-kinetic-smach-ros ros-kinetic-smclib ros-kinetic-stage ros-kinetic-stage-ros ros-kinetic-std-msgs
  ros-kinetic-std-srvs ros-kinetic-stereo-image-proc ros-kinetic-stereo-msgs ros-kinetic-tf ros-kinetic-tf-conversions ros-kinetic-tf2 ros-kinetic-tf2-eigen ros-kinetic-tf2-geometry-msgs ros-kinetic-tf2-kdl ros-kinetic-tf2-msgs ros-kinetic-tf2-py
  ros-kinetic-tf2-ros ros-kinetic-theora-image-transport ros-kinetic-topic-tools ros-kinetic-trajectory-msgs ros-kinetic-turtle-actionlib ros-kinetic-turtle-tf ros-kinetic-turtle-tf2 ros-kinetic-turtlesim ros-kinetic-urdf
  ros-kinetic-urdf-parser-plugin ros-kinetic-vision-opencv ros-kinetic-visualization-marker-tutorials ros-kinetic-visualization-msgs ros-kinetic-xacro ros-kinetic-xmlrpcpp ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert
  ruby-test-unit ruby2.3 rubygems-integration sbcl sdformat-sdf shiboken2 sip-dev tango-icon-theme tcl-dev tcl-vtk6 tcl8.6-dev tk tk-dev tk8.6-dev ttf-dejavu-core ttf-liberation unixodbc unixodbc-dev unzip uuid-dev va-driver-all vdpau-driver-all
  vdpau-va-driver vtk6 x11proto-composite-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-randr-dev x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev x11proto-xf86vidmode-dev x11proto-xinerama-dev
  zip
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
  doxygen libclang1-3.6 libcurl4-gnutls-dev libllvm3.6v5 libobjc-5-dev libobjc4 m4
Suggested packages:
  doxygen-latex doxygen-doc doxygen-gui libcurl4-doc libcurl3-dbg libgnutls-dev libidn11-dev libkrb5-dev librtmp-dev
The following packages will be REMOVED:
  libcurl4-openssl-dev libgazebo7-dev ros-kinetic-collada-urdf ros-kinetic-desktop ros-kinetic-desktop-full ros-kinetic-gazebo-plugins ros-kinetic-gazebo-ros ros-kinetic-gazebo-ros-pkgs ros-kinetic-geometric-shapes ros-kinetic-librviz-tutorial
  ros-kinetic-resource-retriever ros-kinetic-robot ros-kinetic-robot-model ros-kinetic-rqt-robot-plugins ros-kinetic-rqt-rviz ros-kinetic-rviz ros-kinetic-rviz-plugin-tutorials ros-kinetic-rviz-python-tutorial ros-kinetic-simulators
  ros-kinetic-urdf-tutorial ros-kinetic-visualization-tutorials ros-kinetic-viz
The following NEW packages will be installed:
  doxygen libclang1-3.6 libcurl4-gnutls-dev libllvm3.6v5 libobjc-5-dev libobjc4 m4
0 upgraded, 7 newly installed, 22 to remove and 9 not upgraded.
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This does not feel right to me at all. Lets find out which package the moose-environment depends on that is getting in our way...

Looks like the moose-environment package is set to depended on:  libcurl4-gnutls-dev. If you install ROS, and then try to install libcurl4-gnutls-dev, ROS will be removed. I am going to _remove_ that dependency requirement from the moose-environment package and try again. I'll keep you posted.


Jason



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Thomas Wood

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Nov 7, 2016, 2:15:57 PM11/7/16
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Thank you Jason!

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Miller, Jason M

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Nov 7, 2016, 4:27:04 PM11/7/16
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I took care of the dependency issue (removed libcurl as a requirement). Installed the moose-environment package with out a hitch (I have also posted this new version to mooseframework.org as Ubuntu 16.04 build 7 - cheers).

libMesh and MOOSE built successfully, as do the tests:

moose@ros-test:~/projects/moose/test$ ./run_tests -j 12
...
trimmed
...
misc/check_error.check_syntax_error....................................................................... OK
misc/serialized_solution.uniform_refine................................................................... OK
misc/serialized_solution.test............................................................................. OK
misc/serialized_solution.adapt............................................................................ OK
misc/selective_reinit.test................................................................................ OK
misc/jacobian.simple...................................................................................... OK
misc/line_source.test..................................................................................... OK
-------------------------------------------------------------------------------------------------------------
Ran 1274 tests in 54.6 seconds
1274 passed, 37 skipped, 0 pending, 0 failed
moose@ros-test:~/projects/moose/test$ module list
Currently Loaded Modulefiles:
  1) moose/.gcc-6.2.0               3) moose/.mpich_petsc-3.6.4-gcc   5) moose/.cppunit-1.12.1-gcc      7) miniconda
  2) moose/.mpich-3.2_gcc           4) moose/.tbb44_20150728          6) moose-dev-gcc                  8) moose-tools
moose@ros-test:~/projects/moose/test$ which mpicc
/opt/moose/mpich/mpich-3.2/gcc-opt/bin/mpicc
moose@ros-test:~/projects/moose/test$ module purge
moose@ros-test:~/projects/moose/test$ which mpicc
/usr/bin/mpicc
moose@ros-test:~/projects/moose/test$ module load moose-dev-gcc moose-tools
moose@ros-test:~/projects/moose/test$ which mpicc
/opt/moose/mpich/mpich-3.2/gcc-opt/bin/mpicc


Everything is looking good. There are two implementations of MPI on the machine, and I am demonstrating in bold how one could use both of them through the use of modules.

So I suppose you have one of two ways of going about a solution;

* Build PETSc using ROS's MPI (after fixing it of course)
or
* Install the package, and let them coexist through the use of `module` commands. You can always control what is available by default when you open a terminal window by modifying your ~/.bashrc file (adding a `module purge` command)... or by modifying the /opt/moose/environments/moose_profile file directly by removing all the `module load` commands.

Hope this information helps!
Jason



Jesse Carter

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Nov 9, 2016, 11:08:18 AM11/9/16
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I know I'm coming in to this late but FWIW I've had experience manually building PETSc/libmesh/MOOSE with multiple MPI versions floating around (I do most of my work on a cluster). What sometimes does the trick for me is setting the LIBRARY_PATH environment variable (not LD_LIBRARY_PATH) to contain the MPI libraries you want to compile with before you build. LIBRARY_PATH gets called when compiling while LD_LIBRARY_PATH gets called during execution. In practice I set the two equal so the same paths are searched for libraries when compiling as when running. I only did it this way though because I'm lazy and didn't want to write modules.

http://stackoverflow.com/questions/4250624/ld-library-path-vs-library-path

   - Jesse

On Thursday, November 3, 2016 at 11:16:18 AM UTC-4, Thomas Wood wrote:
I've installed PETSc from source before running 

PETSC_DIR=/path/to/petsc ./update_and_rebuild_libmesh.sh 

and when I run make followed by ./run_tests -j8 in the tests directory I get 1315 errors that look like the following:

Running command: /path/to/moose/test/moose_test-opt -i time_derivative.i --error --no-gdb-backtrace
auxkernels/time_derivative.implicit_euler: /path/to/moose/test/moose_test-opt: symbol lookup error: /path/to/petsc/arch-linux2-c-debug/lib/libmpifort.so.12: undefined symbol: MPIR_F_TRUE

but objdump -tT /path/to/petsc/PETSC_ARCH/lib/libmpifort.so.12 | grep MPIR_F_TRUE yields

0000000000000000       O *UND* 0000000000000000              MPIR_F_TRUE
0000000000000000      DO *UND* 0000000000000000              MPIR_F_TRUE

so I'm not sure what the problem is. Any help would be greatly appreciated.

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