Pkg.build errors

[yuzhangbit]

OS: ubuntu 16.04
Julia version: 0.5.1

When I run

Pkg.add("Cbc")
Pkg.build("Cbc")

I get the error output below:

make[4]: Entering directory '/home/robot/.julia/v0.5/Cbc/deps/src/Cbc-2.9.8/Osi'
PKG_CONFIG_PATH=/home/robot/.julia/v0.5/Cbc/deps/usr/lib64/pkgconfig:/home/robot/.julia/v0.5/Cbc/deps/usr/lib/pkgconfig:/home/robot/.julia/v0.5/Cbc/deps/usr/share/pkgconfig:/home/robot/catkin_ws/devel/lib/pkgconfig:/opt/ros/kinetic/lib/pkgconfig:/opt/ros/kinetic/lib/x86_64-linux-gnu/pkgconfig:/home/robot/.julia/v0.5/Cbc/deps/usr/lib/pkgconfig \
pkg-config --libs osi > /home/robot/.julia/v0.5/Cbc/deps/usr/share/coin/doc/Osi/osi_addlibs.txt
make[4]: Leaving directory '/home/robot/.julia/v0.5/Cbc/deps/src/Cbc-2.9.8/Osi'
make[3]: Leaving directory '/home/robot/.julia/v0.5/Cbc/deps/src/Cbc-2.9.8/Osi'
make[2]: Leaving directory '/home/robot/.julia/v0.5/Cbc/deps/src/Cbc-2.9.8/Osi'
make[1]: Leaving directory '/home/robot/.julia/v0.5/Cbc/deps/src/Cbc-2.9.8/Osi'
Making install in Clp
make[1]: Entering directory '/home/robot/.julia/v0.5/Cbc/deps/src/Cbc-2.9.8/Clp'
Making install in src
make[2]: Entering directory '/home/robot/.julia/v0.5/Cbc/deps/src/Cbc-2.9.8/Clp/src'
if /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I`echo .`  -I/usr/local/include/coin/ThirdParty -DCOIN_USE_MUMPS_MPI_H -I/usr/local/include/coin/ThirdParty -I/home/robot/.julia/v0.5/Cbc/deps/src/Cbc-2.9.8/CoinUtils/src  -DCOIN_HAS_CLP     -O3 -pipe -DNDEBUG -pedantic-errors -Wparentheses -Wreturn-type -Wcast-qual -Wall -Wpointer-arith -Wwrite-strings -Wconversion -Wno-unknown-pragmas -Wno-long-long   -DCLP_BUILD -MT ClpCholeskyMumps.lo -MD -MP -MF ".deps/ClpCholeskyMumps.Tpo" -c -o ClpCholeskyMumps.lo ClpCholeskyMumps.cpp; \
then mv -f ".deps/ClpCholeskyMumps.Tpo" ".deps/ClpCholeskyMumps.Plo"; else rm -f ".deps/ClpCholeskyMumps.Tpo"; exit 1; fi
 g++ -DHAVE_CONFIG_H -I. -I. -I/usr/local/include/coin/ThirdParty -DCOIN_USE_MUMPS_MPI_H -I/usr/local/include/coin/ThirdParty -I/home/robot/.julia/v0.5/Cbc/deps/src/Cbc-2.9.8/CoinUtils/src -DCOIN_HAS_CLP -O3 -pipe -DNDEBUG -pedantic-errors -Wparentheses -Wreturn-type -Wcast-qual -Wall -Wpointer-arith -Wwrite-strings -Wconversion -Wno-unknown-pragmas -Wno-long-long -DCLP_BUILD -MT ClpCholeskyMumps.lo -MD -MP -MF .deps/ClpCholeskyMumps.Tpo -c ClpCholeskyMumps.cpp  -fPIC -DPIC -o .libs/ClpCholeskyMumps.o
ClpCholeskyMumps.cpp:17:17: fatal error: mpi.h: No such file or directory
compilation terminated.
Makefile:931: recipe for target 'ClpCholeskyMumps.lo' failed
make[2]: *** [ClpCholeskyMumps.lo] Error 1
make[2]: Leaving directory '/home/robot/.julia/v0.5/Cbc/deps/src/Cbc-2.9.8/Clp/src'
Makefile:519: recipe for target 'install-recursive' failed
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory '/home/robot/.julia/v0.5/Cbc/deps/src/Cbc-2.9.8/Clp'
Makefile:323: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1
===========================================[ ERROR: Cbc ]===========================================

LoadError: failed process: Process(`make install`, ProcessExited(2)) [2]
while loading /home/robot/.julia/v0.5/Cbc/deps/build.jl, in expression starting on line 62

====================================================================================================

[blegat]

It seems you are missing MPI headers, could you try doing

$ sudo apt-get install mpi-default-dev
$ julia -e 'Pkg.build("Cbc")'

and tell us if it worked ?

[yuzhangbit]

@blegat Thanks for your quick reply. I tried your method. The same error still happens.

[blegat]

Did the installation work ? It should have also installed libopenmpi-dev as a dependency which has installed a file mpi.h at /usr/lib/openmpi/include/mpi.h.
Can you check that it is indeed there with e.g. $ ls /usr/lib/openmpi/include/mpi.h ?

[mlubin]

It's probably finding a version of Mumps that requires MPI. If you don't need this, reinstall a version of Mumps that doesn't link against MPI.

[yuzhangbit]

@blegat The installation worked. But I still get the same error when installing Cbc in Julia.
If I run ls /usr/lib/openmpi/include/mpi.h, the output is

/usr/lib/openmpi/include/mpi.h

@mlubin I do need Mumps for other optimization solvers. If I install Cbc from source in C++, the installation(C++ version) works fine. So I assume something is wrong with the julia Cbc deps build script.

[mlubin]

@yuzhangbit, the entire build script is here.

[yuzhangbit]

@mlubin Thanks for your information.

[blegat]

It seems that the issue is that mpi.h is not in /usr/lib/openmpi/include is scanned for by g++ when looking for the header. You can see where it looks for by running

$ cpp -v /dev/null -o /dev/null

If you add -I /usr/lib/openmpi/include to the g++ line that is failing, it should find mpi.h.
However, it is weird that you should do that since normally when you install a -dev package with apt-get, you should have to use -I... Have you tried to close your terminal and start a new one ?

[yuzhangbit]

Still can't resolve it.

[blegat]

You can try

$ ln -s /usr/lib/openmpi/include/mpi.h /usr/include

even if it's just a hack

[mlubin]

If I install Cbc from source in C++, the installation(C++ version) works fine. So I assume something is wrong with the julia Cbc deps build script.

@yuzhangbit, can you reproduce the issue by building from source and using the Cbc.jl script that I pointed to?

[yuzhangbit]

@mlubin Yes. By building Julia 0.5.1 from source and using the Cbc.jl, I can recreate the issue.

[mlubin]

@yuzhangbit, I meant building Cbc from source independent of Julia, as you said you had done before.

[yuzhangbit]

@blegat Thanks for your information. I tried. It's not just 'mpi.h' file. If I hacked it in this way, the compiling asks for other mpi header files as well. It's the whole mpi include directory that is not passed to the build script.

[blegat]

Then do

$ ln -s /usr/lib/openmpi/include /usr/include/openmpi

[mlubin]

The ubuntu cbc package coinor-libcbc-dev might also work. Just install it then run Pkg.build("Cbc").

[yuzhangbit]

@mlubin Cool! Thanks a lot. The coinor-libcbc-dev solves the problem.

[blegat]

@yuzhangbit glad to hear this. If you have the time, it would help us to know what is in the build script that makes Cbc not compile while when you compile it by hands it works.

[yuzhangbit]

@blegat Sure thing. It's the Clp/src build script under the Cbc-2.9.8 folder that can not find the include directory for the mpi. I also notice that the Cbc build script doesn't follow exactly the instruction from the Cbc website. The

BuildTools/get.dependencies fetch

part is missing.