Fail to build with SCOTCH and PASTIX

[getzze]

Hello, I am using ArchLinux and trying to build dolfin from the AUR (https://aur.archlinux.org/packages/dolfin-git/). Dolfin builds correctly, except the linking to the optional packages SCOTCH and PASTIX. It fails during the tests. For SCOTCH :

 -- Found SCOTCH (version 6.0.0)
-- Performing test SCOTCH_TEST_RUNS
-- Performing test SCOTCH_TEST_RUNS - Failed
-- [ /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/cmake/modules/FindSCOTCH.cmake:268 ] SCOTCH_TEST_LIB_COMPILED = FALSE
-- [ /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/cmake/modules/FindSCOTCH.cmake:270 ] SCOTCH_TEST_LIB_COMPILE_OUTPUT = Change Dir: /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTryCompileExec1886730031/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec1886730031.dir/build.make CMakeFiles/cmTryCompileExec1886730031.dir/build
make[1]: Entering directory '/tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec1886730031.dir/scotch_test_lib.cpp.o
/usr/bin/g++    -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -std=c++11  -I/opt/petsc/arch-linux2-cxx-opt/include    -o CMakeFiles/cmTryCompileExec1886730031.dir/scotch_test_lib.cpp.o -c /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/scotch_test_lib.cpp
Linking CXX executable cmTryCompileExec1886730031
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1886730031.dir/link.txt --verbose=1
/usr/bin/g++   -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -std=c++11    -Wl,-O1,--sort-common,--as-needed,-z,relro  CMakeFiles/cmTryCompileExec1886730031.dir/scotch_test_lib.cpp.o  -o cmTryCompileExec1886730031 -rdynamic -lptscotch -lscotch -lptscotcherr /usr/lib64/openmpi/libmpi_cxx.so /usr/lib64/openmpi/libmpi.so -Wl,-rpath,/usr/lib64/openmpi 
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzReadGetUnused'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzWriteClose'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzReadOpen'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzRead'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzWriteOpen'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzWrite'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzReadClose'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTryCompileExec1886730031.dir/build.make:93: recipe for target 'cmTryCompileExec1886730031' failed
make[1]: *** [cmTryCompileExec1886730031] Error 1
make[1]: Leaving directory '/tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp'
Makefile:117: recipe for target 'cmTryCompileExec1886730031/fast' failed
make: *** [cmTryCompileExec1886730031/fast] Error 2

-- [ /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/cmake/modules/FindSCOTCH.cmake:272 ] SCOTCH_TEST_LIB_EXITCODE = 
-- [ /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/cmake/modules/FindSCOTCH.cmake:274 ] SCOTCH_TEST_LIB_OUTPUT = 
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.8") 
-- Performing test SCOTCH_ZLIB_TEST_RUNS
-- Performing test SCOTCH_ZLIB_TEST_RUNS - Failed
-- [ /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/cmake/modules/FindSCOTCH.cmake:311 ] SCOTCH_ZLIB_TEST_LIB_COMPILED = FALSE
-- [ /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/cmake/modules/FindSCOTCH.cmake:313 ] SCOTCH_ZLIB_TEST_LIB_COMPILE_OUTPUT = Change Dir: /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTryCompileExec3018861140/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec3018861140.dir/build.make CMakeFiles/cmTryCompileExec3018861140.dir/build
make[1]: Entering directory '/tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec3018861140.dir/scotch_test_lib.cpp.o
/usr/bin/g++    -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -std=c++11  -I/opt/petsc/arch-linux2-cxx-opt/include    -o CMakeFiles/cmTryCompileExec3018861140.dir/scotch_test_lib.cpp.o -c /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/scotch_test_lib.cpp
Linking CXX executable cmTryCompileExec3018861140
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec3018861140.dir/link.txt --verbose=1
/usr/bin/g++   -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -std=c++11    -Wl,-O1,--sort-common,--as-needed,-z,relro  CMakeFiles/cmTryCompileExec3018861140.dir/scotch_test_lib.cpp.o  -o cmTryCompileExec3018861140 -rdynamic -lptscotch -lscotch -lptscotcherr /usr/lib64/openmpi/libmpi_cxx.so /usr/lib64/openmpi/libmpi.so -lz -Wl,-rpath,/usr/lib64/openmpi 
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzReadGetUnused'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzWriteClose'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzReadOpen'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzRead'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzWriteOpen'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzWrite'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libscotch.so: undefined reference to `BZ2_bzReadClose'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTryCompileExec3018861140.dir/build.make:94: recipe for target 'cmTryCompileExec3018861140' failed
make[1]: *** [cmTryCompileExec3018861140] Error 1
make[1]: Leaving directory '/tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp'
Makefile:117: recipe for target 'cmTryCompileExec3018861140/fast' failed
make: *** [cmTryCompileExec3018861140/fast] Error 2

-- [ /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/cmake/modules/FindSCOTCH.cmake:315 ] SCOTCH_TEST_LIB_EXITCODE = 
-- [ /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/cmake/modules/FindSCOTCH.cmake:317 ] SCOTCH_TEST_LIB_OUTPUT = 
-- SCOTCH could not be found. Be sure to set SCOTCH_DIR. (missing:  SCOTCH_TEST_RUNS)

And for PASTIX (from CMakeError.log) :

Performing C SOURCE FILE Test PASTIX_TEST_RUNS failed with the following output:
Change Dir: /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTryCompileExec4104957961/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec4104957961.dir/build.make CMakeFiles/cmTryCompileExec4104957961.dir/build
make[1]: Entering directory '/tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec4104957961.dir/src.c.o
/usr/bin/cc   -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -DPASTIX_TEST_RUNS  -fopenmp   -o CMakeFiles/cmTryCompileExec4104957961.dir/src.c.o   -c /tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTryCompileExec4104957961
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec4104957961.dir/link.txt --verbose=1
/usr/bin/cc  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -DPASTIX_TEST_RUNS  -fopenmp   -Wl,-O1,--sort-common,--as-needed,-z,relro  CMakeFiles/cmTryCompileExec4104957961.dir/src.c.o  -o cmTryCompileExec4104957961 -rdynamic -Wl,-Bstatic -lpastix -Wl,-Bdynamic -lrt -lm -lhwloc -lblas /usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libgfortran.so /usr/lib64/openmpi/libmpi.so 
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_order_save':
(.text+0x2c48): undefined reference to `SCOTCH_graphSave'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_order_load':
(.text+0x2e00): undefined reference to `SCOTCH_graphLoad'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x36aa): undefined reference to `SCOTCH_graphInit'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x36fc): undefined reference to `SCOTCH_graphBuild'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x3733): undefined reference to `SCOTCH_graphCheck'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x3745): undefined reference to `SCOTCH_stratInit'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x3751): undefined reference to `SCOTCH_graphBase'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x37be): undefined reference to `SCOTCH_stratGraphOrder'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x380f): undefined reference to `SCOTCH_graphOrderList'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x3821): undefined reference to `SCOTCH_stratExit'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x39b8): undefined reference to `SCOTCH_graphBuild'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x3b16): undefined reference to `SCOTCH_stratExit'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x3b76): undefined reference to `SCOTCH_graphOrderList'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x3ef3): undefined reference to `SCOTCH_graphBuild'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x3f16): undefined reference to `SCOTCH_graphBase'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x3fd4): undefined reference to `SCOTCH_graphExit'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x402c): undefined reference to `SCOTCH_graphExit'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_scotch':
(.text+0x40dc): undefined reference to `SCOTCH_graphSave'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(pastix.o): In function `pastix_task_fax':
(.text+0x449e): undefined reference to `SCOTCH_graphExit'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(dof.o): In function `dofGraph':
(.text+0x9f): undefined reference to `SCOTCH_graphData'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(symbol_fax_graph.o): In function `symbolFaxGraph':
(.text+0x59): undefined reference to `SCOTCH_graphData'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(bordi.o): In function `orderSplit2':
(.text+0x45b): undefined reference to `SCOTCH_graphData'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(bordi.o): In function `orderSplit3':
(.text+0x88d): undefined reference to `SCOTCH_graphData'
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../lib/libpastix.a(bordi.o): In function `bordi':
(.text+0x1744): undefined reference to `SCOTCH_graphData'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTryCompileExec4104957961.dir/build.make:95: recipe for target 'cmTryCompileExec4104957961' failed
make[1]: *** [cmTryCompileExec4104957961] Error 1
make[1]: Leaving directory '/tmp/yaourt-tmp-blacoste088/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeTmp'
Makefile:117: recipe for target 'cmTryCompileExec4104957961/fast' failed
make: *** [cmTryCompileExec4104957961/fast] Error 2

Return value: 1
Source file was:

/* Test program pastix */

#define MPICH_IGNORE_CXX_SEEK 1
#include <stdint.h>
#include <mpi.h>
#include <pastix.h>

int main()
{
  pastix_int_t iparm[IPARM_SIZE];
  double       dparm[DPARM_SIZE];
  int i = 0;
  for (i = 0; i < IPARM_SIZE; ++i)
    iparm[i] = 0;
  for (i = 0; i < DPARM_SIZE; ++i)
    dparm[i] = 0.0;

  // Set default parameters
  pastix_initParam(iparm, dparm);

  return 0;
}

The problem seems to come from library linking. Scotch needs th bz2 lib, which is not linked in the compilation of scotch_test_lib.cpp. And for pastix, the linking to scotch library seems to be missing.

I don't have the environment variables SCOTCH_DIR and PASTIX_DIR set. Can it be the problem? I set them with export SCOTCH_DIR=/usr/include to the folder where the headers of the two libraries are (/usr/include in my case) without success.

Any idea?

Thanks

[Chris Richardson]

Please try emailing [e-mail]. ArchLinux is not explicitly supported by the project.

[getzze]

The installation on ArchLinux is not different from compiling from the source. It follows the installation procedure with these special options for cmake:

cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/g++ \
-DCMAKE_INSTALL_PREFIX="${pkg}"/usr \
    -DPYTHON_EXECUTABLE:PATH="${py2_interp}" \
    -DPYTHON_INCLUDE_DIR:PATH="${py2_inc}" \
    -DPYTHON_LIBRARY:FILEPATH="${py2_lib}" \
-DDOLFIN_ENABLE_VTK=ON \
    -DCMAKE_SKIP_BUILD_RPATH=TRUE \
-DCMAKE_SKIP_RPATH=TRUE \
-DCMAKE_BUILD_TYPE="Debug"

I really think it is a problem of missing dependency to bz2 lib. I am not an expert in cmake, so I don't know how to include the dependency.

[getzze]

Solved. They were two independent problems: - with Scotch: my version was compiled with the bzip2 library, so the flag -lbz2 has to be added anytime scotch is used. Solved by rebuilding Scotch without this dependency. But a solution would be to add the bzip2 libs in dolfin/cmake/modules/FindSCOTCH.cmake

• with Pastix: my version was built with scotch support so the scotch libraries should be added:

modified file dolfin/cmake/modules/FindPaStiX.cmake after line 55 (check for hwloc libs) add the lines:

# Check for scotch header
find_path(SCOTCH_INCLUDE_DIRS scotch.h
  HINTS ${SCOTCH_DIR} $ENV{SCOTCH_DIR} ${SCOTCH_DIR}/include $ENV{SCOTCH_DIR}/include ${SCOTCH_DIR}/include/scotch
  DOC "Directory where the scotch header is located"
 )

# Check for scotch library
find_library(SCOTCH_LIBRARY scotch
  HINTS ${SCOTCH_DIR} $ENV{SCOTCH_DIR} ${SCOTCH_DIR}/lib $ENV{SCOTCH_DIR}/lib
  DOC "The scotch library"
  )

if (SCOTCH_LIBRARY)
  set(PASTIX_LIBRARIES ${PASTIX_LIBRARIES} ${SCOTCH_LIBRARY})
endif()

However Pastix provides a tool (pastix-conf on linux) to list all the libraries on which it depends. It may be a better approach to include all dependencies.

[mylese]

Since this has been reopened, I'll just say that the AUR packages for pastix and dolfin-git handle this now. Scotch still has the bz2 dependency, and therefore so does pastix, dolfin is patched to find it.

[Jan Blechta]

Please, create a pull request if you want to get this patched. We have no chance of testing this.