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mpi4py build failure (portage)

Jul 11th, 2014
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  1.  * Package: dev-python/mpi4py-1.3.1
  2.  * Repository: gentoo
  3.  * Maintainer: python@gentoo.org
  4.  * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 python_targets_python3_3 userland_GNU
  5.  * FEATURES: preserve-libs sandbox userpriv usersandbox
  6. >>> Unpacking source...
  7. >>> Unpacking mpi4py-1.3.1.tar.gz to /var/tmp/portage/dev-python/mpi4py-1.3.1/work
  8. >>> Source unpacked in /var/tmp/portage/dev-python/mpi4py-1.3.1/work
  9. >>> Preparing source in /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1 ...
  10. * Applying mpi4py-1.3.1-py3-test-backport-1.patch ...
  11.  [ ok ]
  12. * Will copy sources from /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1
  13. * python3_3: copying to /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3
  14. * python2_7: copying to /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python2_7
  15. >>> Source prepared.
  16. >>> Configuring source in /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1 ...
  17. >>> Source configured.
  18. >>> Compiling source in /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1 ...
  19. * python3_3: running distutils-r1_run_phase distutils-r1_python_compile
  20. /usr/bin/python3.3 setup.py build
  21. running build
  22. running build_src
  23. running build_py
  24. creating /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib
  25. creating /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py
  26. copying src/__init__.py -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py
  27. copying src/rc.py -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py
  28. creating /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/include
  29. creating /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/include/mpi4py
  30. copying src/include/mpi4py/mpi4py.MPI_api.h -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/include/mpi4py
  31. copying src/include/mpi4py/mpi4py.h -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/include/mpi4py
  32. copying src/include/mpi4py/mpi4py.MPI.h -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/include/mpi4py
  33. copying src/include/mpi4py/mpi_c.pxd -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/include/mpi4py
  34. copying src/include/mpi4py/MPI.pxd -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/include/mpi4py
  35. copying src/include/mpi4py/__init__.pxd -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/include/mpi4py
  36. copying src/include/mpi4py/__init__.pyx -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/include/mpi4py
  37. copying src/include/mpi4py/mpi.pxi -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/include/mpi4py
  38. copying src/include/mpi4py/mpi4py.i -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/include/mpi4py
  39. copying src/MPI.pxd -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py
  40. copying src/mpi_c.pxd -> /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py
  41. warning: build_py: byte-compiling is disabled, skipping.
  42.  
  43. running build_clib
  44. MPI configuration: [mpi] from 'mpi.cfg'
  45. MPI C compiler: /usr/bin/mpicc
  46. MPI C++ compiler: /usr/bin/mpicxx
  47. MPI F77 compiler: /usr/bin/mpif77
  48. MPI F90 compiler: /usr/bin/mpif90
  49. checking for library 'pthread' ...
  50. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -c _configtest.c -o _configtest.o
  51. /usr/bin/mpicc -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed _configtest.o -lpthread -o _configtest
  52. success!
  53. removing: _configtest.c _configtest.o _configtest
  54. checking for library 'mpe' ...
  55. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -c _configtest.c -o _configtest.o
  56. /usr/bin/mpicc -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed _configtest.o -lmpe -lpthread -o _configtest
  57. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lmpe
  58. collect2: error: ld returned 1 exit status
  59. failure.
  60. removing: _configtest.c _configtest.o
  61. checking for library 'lmpe' ...
  62. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -c _configtest.c -o _configtest.o
  63. /usr/bin/mpicc -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed _configtest.o -llmpe -lpthread -o _configtest
  64. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -llmpe
  65. collect2: error: ld returned 1 exit status
  66. failure.
  67. removing: _configtest.c _configtest.o
  68. building 'mpe' dylib library
  69. creating /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3
  70. creating /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3/src
  71. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -c src/pmpi-mpe.c -o /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3/src/pmpi-mpe.o
  72. creating /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/lib-pmpi
  73. /usr/bin/mpicc x86_64-pc-linux-gnu-gcc -shared -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3/src/pmpi-mpe.o -o /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/lib-pmpi/libmpe.so
  74. x86_64-pc-linux-gnu-gcc: error: x86_64-pc-linux-gnu-gcc: No such file or directory
  75. warning: build_clib: building library "mpe" failed
  76.  
  77. warning: build_clib: command '/usr/bin/mpicc' failed with exit status 1
  78.  
  79. checking for library 'vt-mpi' ...
  80. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -c _configtest.c -o _configtest.o
  81. /usr/bin/mpicc -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed _configtest.o -lvt-mpi -o _configtest
  82. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lvt-mpi
  83. collect2: error: ld returned 1 exit status
  84. failure.
  85. removing: _configtest.c _configtest.o
  86. checking for library 'vt.mpi' ...
  87. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -c _configtest.c -o _configtest.o
  88. /usr/bin/mpicc -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed _configtest.o -lvt.mpi -o _configtest
  89. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lvt.mpi
  90. collect2: error: ld returned 1 exit status
  91. failure.
  92. removing: _configtest.c _configtest.o
  93. building 'vt' dylib library
  94. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -c src/pmpi-vt.c -o /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3/src/pmpi-vt.o
  95. /usr/bin/mpicc x86_64-pc-linux-gnu-gcc -shared -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3/src/pmpi-vt.o -o /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/lib-pmpi/libvt.so
  96. x86_64-pc-linux-gnu-gcc: error: x86_64-pc-linux-gnu-gcc: No such file or directory
  97. warning: build_clib: building library "vt" failed
  98.  
  99. warning: build_clib: command '/usr/bin/mpicc' failed with exit status 1
  100.  
  101. checking for library 'vt-mpi' ...
  102. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -c _configtest.c -o _configtest.o
  103. /usr/bin/mpicc -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed _configtest.o -lvt-mpi -o _configtest
  104. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lvt-mpi
  105. collect2: error: ld returned 1 exit status
  106. failure.
  107. removing: _configtest.c _configtest.o
  108. building 'vt-mpi' dylib library
  109. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -c src/pmpi-vt-mpi.c -o /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3/src/pmpi-vt-mpi.o
  110. /usr/bin/mpicc x86_64-pc-linux-gnu-gcc -shared -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3/src/pmpi-vt-mpi.o -o /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/lib-pmpi/libvt-mpi.so
  111. x86_64-pc-linux-gnu-gcc: error: x86_64-pc-linux-gnu-gcc: No such file or directory
  112. warning: build_clib: building library "vt-mpi" failed
  113.  
  114. warning: build_clib: command '/usr/bin/mpicc' failed with exit status 1
  115.  
  116. checking for library 'vt-hyb' ...
  117. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -c _configtest.c -o _configtest.o
  118. /usr/bin/mpicc -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed _configtest.o -lvt-hyb -o _configtest
  119. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lvt-hyb
  120. collect2: error: ld returned 1 exit status
  121. failure.
  122. removing: _configtest.c _configtest.o
  123. building 'vt-hyb' dylib library
  124. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -c src/pmpi-vt-hyb.c -o /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3/src/pmpi-vt-hyb.o
  125. /usr/bin/mpicc x86_64-pc-linux-gnu-gcc -shared -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3/src/pmpi-vt-hyb.o -o /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/lib-pmpi/libvt-hyb.so
  126. x86_64-pc-linux-gnu-gcc: error: x86_64-pc-linux-gnu-gcc: No such file or directory
  127. warning: build_clib: building library "vt-hyb" failed
  128.  
  129. warning: build_clib: command '/usr/bin/mpicc' failed with exit status 1
  130.  
  131. running build_ext
  132. MPI configuration: [mpi] from 'mpi.cfg'
  133. MPI C compiler: /usr/bin/mpicc
  134. MPI C++ compiler: /usr/bin/mpicxx
  135. MPI F77 compiler: /usr/bin/mpif77
  136. MPI F90 compiler: /usr/bin/mpif90
  137. checking for MPI compile and link ...
  138. checking for header 'mpi.h' ...
  139. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -I/usr/include/python3.3 -c _configtest.c -o _configtest.o
  140. success!
  141. removing: _configtest.c _configtest.o
  142. success!
  143. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -I/usr/include/python3.3 -c _configtest.c -o _configtest.o
  144. success!
  145. removing: _configtest.c _configtest.o
  146. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -I/usr/include/python3.3 -c _configtest.c -o _configtest.o
  147. /usr/bin/mpicc -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed _configtest.o -L/var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3 -o _configtest
  148. success!
  149. removing: _configtest.c _configtest.o _configtest
  150. checking for missing MPI functions/symbols ...
  151. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -I/usr/include/python3.3 -c _configtest.c -o _configtest.o
  152. success!
  153. removing: _configtest.c _configtest.o
  154. checking for function 'MPI_Type_create_f90_integer' ...
  155. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -I/usr/include/python3.3 -c _configtest.c -o _configtest.o
  156. /usr/bin/mpicc -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed _configtest.o -L/var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3 -o _configtest
  157. success!
  158. removing: _configtest.c _configtest.o _configtest
  159. checking for function 'MPI_Type_create_f90_real' ...
  160. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -I/usr/include/python3.3 -c _configtest.c -o _configtest.o
  161. /usr/bin/mpicc -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed _configtest.o -L/var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3 -o _configtest
  162. success!
  163. removing: _configtest.c _configtest.o _configtest
  164. checking for function 'MPI_Type_create_f90_complex' ...
  165. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -I/usr/include/python3.3 -c _configtest.c -o _configtest.o
  166. /usr/bin/mpicc -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed _configtest.o -L/var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3 -o _configtest
  167. success!
  168. removing: _configtest.c _configtest.o _configtest
  169. building 'mpi4py.MPI' extension
  170. /usr/bin/mpicc -fPIC -Wno-unused-result -DNDEBUG -march=native -O2 -fomit-frame-pointer -pipe -I/usr/include/python3.3 -c src/MPI.c -o /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3/src/MPI.o
  171. /usr/bin/mpicc x86_64-pc-linux-gnu-gcc -shared -march=native -O2 -fomit-frame-pointer -pipe -march=native -O2 -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3/src/MPI.o -L/var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/temp.linux-x86_64-3.3 -lpython3.3 -o /var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3/build/lib/mpi4py/MPI.cpython-33.so
  172. x86_64-pc-linux-gnu-gcc: error: x86_64-pc-linux-gnu-gcc: No such file or directory
  173. error: command '/usr/bin/mpicc' failed with exit status 1
  174. * ERROR: dev-python/mpi4py-1.3.1::gentoo failed (compile phase):
  175. * (no error message)
  176. *
  177. * Call stack:
  178. * ebuild.sh, line 93: Called src_compile
  179. * environment, line 3569: Called distutils-r1_src_compile
  180. * environment, line 1126: Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile'
  181. * environment, line 253: Called python_parallel_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile'
  182. * environment, line 3427: Called multibuild_parallel_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
  183. * environment, line 2447: Called multibuild_foreach_variant '_multibuild_parallel' '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
  184. * environment, line 2390: Called _multibuild_run '_multibuild_parallel' '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
  185. * environment, line 2388: Called _multibuild_parallel '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
  186. * environment, line 2438: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile'
  187. * environment, line 684: Called distutils-r1_run_phase 'distutils-r1_python_compile'
  188. * environment, line 1115: Called distutils-r1_python_compile
  189. * environment, line 980: Called esetup.py 'build'
  190. * environment, line 1566: Called die
  191. * The specific snippet of code:
  192. * "${@}" || die
  193. *
  194. * If you need support, post the output of `emerge --info '=dev-python/mpi4py-1.3.1::gentoo'`,
  195. * the complete build log and the output of `emerge -pqv '=dev-python/mpi4py-1.3.1::gentoo'`.
  196. * The complete build log is located at '/var/tmp/portage/dev-python/mpi4py-1.3.1/temp/build.log'.
  197. * The ebuild environment file is located at '/var/tmp/portage/dev-python/mpi4py-1.3.1/temp/environment'.
  198. * Working directory: '/var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1-python3_3'
  199. * S: '/var/tmp/portage/dev-python/mpi4py-1.3.1/work/mpi4py-1.3.1'
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