compilation issues when gmpfr is installed to a non-standard directory

Issue #16 closed

Thomas Hisch created an issue 2014-11-28

I tried to compile mshr on a cluster, where I had to install gmpfr into my home directory. In order to fix the find MPFR (missing: MPFR_LIBRARIES MPFR_INCLUDE_DIR) cmake error I had to specify the MPFR_INCLUDE_DIR and MPFR_LIBRARIES cmake flags.

cmake -DMPFR_INCLUDE_DIR=$HOME/software/local/include -DMPFR_LIBRARIES=$HOME/software/local/lib/libmpfr.so -DCMAKE_INSTALL_PREFIX=$HOME/miniconda3/envs/py27 ..

The MPFR vars are not used for building the external project CGAL. Therefore I get this error

[100%] Building CXX object src/CGAL/CMakeFiles/CGAL.dir/all_files.cpp.o
In file included from ~/gitrepos/fenics/dev/mshr/3rdparty/CGAL-4.5/include/CGAL/Gmp_coercion_traits.h:30:0,
                 from ~/gitrepos/fenics/dev/mshr/3rdparty/CGAL-4.5/include/CGAL/Gmpz.h:33,
                 from ~/gitrepos/fenics/dev/mshr/3rdparty/CGAL-4.5/include/CGAL/Gmpq.h:25,
                 from ~/gitrepos/fenics/dev/mshr/3rdparty/CGAL-4.5/include/CGAL/Kinetic/basic.h:53,
                 from ~/gitrepos/fenics/dev/mshr/3rdparty/CGAL-4.5/include/CGAL/Kinetic/internal/debug_counters.h:21,
                 from ~/gitrepos/fenics/dev/mshr/3rdparty/CGAL-4.5/src/CGAL/KDS_Log.cpp:28,
                 from ~/gitrepos/fenics/dev/mshr/build_test/3rdparty/CGAL-4.5-prefix/src/CGAL-4.5-build/src/CGAL/all_files.cpp:3:
~/gitrepos/fenics/dev/mshr/3rdparty/CGAL-4.5/include/CGAL/GMP/Gmpz_type.h:31:18: fatal error: mpfr.h: No such file or directory
 #include <mpfr.h>

I was able to fix this issue by editing 3rdparty/CMakeLists.txt but I still got other errors related to my mpfr installation.

Comments (14)

Thomas Hisch reporter

[ 46%] Building CXX object CMakeFiles/mshr.dir/src/CSGCGALDomain3D.cpp.o
In file included from ~/gitrepos/fenics/dev/mshr/build_test/CGAL-4.5-installdir/include/CGAL/internal/Exact_type_selector.h:39:0,
                 from ~/gitrepos/fenics/dev/mshr/build_test/CGAL-4.5-installdir/include/CGAL/Filtered_kernel.h:35,
                 from ~/gitrepos/fenics/dev/mshr/build_test/CGAL-4.5-installdir/include/CGAL/Exact_predicates_exact_constructions_kernel.h:29,
                 from ~/gitrepos/fenics/dev/mshr/src/CSGCGALDomain3D.cpp:35:
~/gitrepos/fenics/dev/mshr/build_test/CGAL-4.5-installdir/include/CGAL/Mpzf.h: In function ‘CGAL::Mpzf CGAL::Mpzf_square(const CGAL::Mpzf&)’:
~/gitrepos/fenics/dev/mshr/build_test/CGAL-4.5-installdir/include/CGAL/Mpzf.h:718:38: error: ‘mpn_sqr’ was not declared in this scope
     mpn_sqr(res.data(),a.data(),asize);

2014-11-29T00:41:34+00:00

Benjamin Dam Kehlet
Ref issue ~~#16~~. Propagate configuration details for boost, gmp and mpfr to cgal build.

→ <<cset be53b1762926>>
- 2014-12-10T13:40:30+00:00

Thomas Hisch reporter

thx. now i get

-- Preconfiguring library: GMP ...
-- GMP has been preconfigured:
--   UseGMP-file:      
--   GMP include:      /usr/include
--   GMP libraries:    /usr/lib64/libgmp.so
--   GMP definitions:  
-- USING GMP_VERSION = '4.3.1'
-- Preconfiguring library: MPFR ...
-- Could NOT find MPFR (missing:  MPFR_INCLUDE_DIR)

2014-12-10T14:21:30+00:00

Benjamin Dam Kehlet
Ah, typo! Could you pull and try again now?

(Sorry about the late reply on this issue, btw)
- 2014-12-10T14:26:45+00:00

Thomas Hisch reporter

No problem. It was not that urgent.

Installing the 3rd party libs is fixed now - thx. However, I still get the mpn_sqr error.

[ 63%] Building CXX object CMakeFiles/mshr.dir/src/CSGPrimitives2D.cpp.o
In file included from ~/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/internal/Exact_type_selector.h:39:0,
                 from ~/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Filtered_kernel.h:35,
                 from ~/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Exact_predicates_exact_constructions_kernel.h:29,
                 from ~/mshr/src/CSGCGALDomain3D.cpp:35:
~/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Mpzf.h: In function ‘CGAL::Mpzf CGAL::Mpzf_square(const CGAL::Mpzf&)’:
~/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Mpzf.h:718:38: error: ‘mpn_sqr’ was not declared in this scope
     mpn_sqr(res.data(),a.data(),asize);

2014-12-10T15:13:00+00:00

Benjamin Dam Kehlet
Strange... I'll try to reproduce this tomorrow. What compiler (and version) are you using?
- 2014-12-10T21:04:18+00:00
Thomas Hisch reporter
g++ (GCC) 4.9.1

mpfr-3.1.2
- 2014-12-10T21:41:07+00:00
Benjamin Dam Kehlet
- changed status to resolved
Patch CGAL to work around a missing symbol in certain (old) versions of GMP. Hopefully this resolves issue ~~#16~~.

→ <<cset fd6e2c78566a>>
- 2014-12-11T09:17:22+00:00
Benjamin Dam Kehlet
Bitbucket was a little too smart, so it marked the issue as resolved based on the commit message.

I applied the fix suggested here: cgal-discuss.949826.n4.nabble.com/Error-on-installing-CGAL-on-LINUX-CentOS-td4659148.html Let me know if this works for you. If not, we'll reopen the issue.
- 2014-12-11T09:19:13+00:00

Thomas Hisch reporter

The not declared in this scope error was fixed by your recent commit(s). Thx!

I still get some other errors:

[ 46%] Building CXX object CMakeFiles/mshr.dir/src/CSGCGALDomain3D.cpp.o
In file included from ~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/internal/Exact_type_selector.h:39:0,
                 from ~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Filtered_kernel.h:35,
                 from ~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Exact_predicates_exact_constructions_kernel.h:29,
                 from ~/gitrepos/fenics/dev/mshr/src/CSGCGALDomain3D.cpp:35:
~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Mpzf.h: In function ?CGAL::Mpzf CGAL::Mpzf_square(const CGAL::Mpzf&)?:
~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Mpzf.h:726:31: error: invalid conversion from ?const mp_limb_t* {aka const long unsigned int*}? to ?mp_size_t {aka long int}? [-fpermissive]
     mpn_sqr(res.data(),a.data(),asize);
                               ^
~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Mpzf.h:62:42: note: in definition of macro ?mpn_sqr?
 #define mpn_sqr(dest,a,n) mpn_mul(dest,a,a,n)
                                          ^
~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Mpzf.h:62:45: error: invalid conversion from ?int? to ?mp_srcptr {aka const long unsigned int*}? [-fpermissive]
 #define mpn_sqr(dest,a,n) mpn_mul(dest,a,a,n)
                                             ^
~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Mpzf.h:726:5: note: in expansion of macro ?mpn_sqr?
     mpn_sqr(res.data(),a.data(),asize);
     ^
~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Mpzf.h:62:45: error: too few arguments to function ?mp_limb_t __gmpn_mul(mp_ptr, mp_srcptr, mp_size_t, mp_srcptr, mp_size_t)?
 #define mpn_sqr(dest,a,n) mpn_mul(dest,a,a,n)
                                             ^
~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Mpzf.h:726:5: note: in expansion of macro ?mpn_sqr?
     mpn_sqr(res.data(),a.data(),asize);
     ^
In file included from /usr/include/gmp.h:53:0,
                 from ~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/gmp.h:30,
                 from ~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/GMP/Gmpz_type.h:30,
                 from ~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Gmp_coercion_traits.h:30,
                 from ~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Gmpz.h:33,
                 from ~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/internal/Exact_type_selector.h:36,
                 from ~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Filtered_kernel.h:35,
                 from ~/gitrepos/fenics/dev/mshr/build_openmpi_py27/CGAL-4.5-installdir/include/CGAL/Exact_predicates_exact_constructions_kernel.h:29,
                 from ~/gitrepos/fenics/dev/mshr/src/CSGCGALDomain3D.cpp:35:
/usr/include/gmp-x86_64.h:1545:26: note: declared here
 __GMP_DECLSPEC mp_limb_t mpn_mul __GMP_PROTO ((mp_ptr, mp_srcptr, mp_size_t, mp_srcptr, mp_size_t));
                          ^
make[2]: *** [CMakeFiles/mshr.dir/src/CSGCGALDomain3D.cpp.o] Error 1

2014-12-11T09:59:40+00:00

Benjamin Dam Kehlet
Fix typo. Hopefully this actually resolves issue ~~#16~~!

→ <<cset 0fe80ccaa9e0>>
- 2014-12-11T10:29:13+00:00
Benjamin Dam Kehlet
I was too quick. There are several versions of the mpn_mul function in gmp. Please try again now.
- 2014-12-11T10:30:01+00:00
Thomas Hisch reporter
Finally it compiles :). Many Thanks!
- 2014-12-11T11:30:01+00:00
Thomas Hisch reporter
- changed status to closed
fixed
- 2014-12-11T11:30:26+00:00
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Type: bug

Priority: major

Status: closed

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