Siesta

Error running SIESTA-PEXSI

Asked by Pierre Capiod

Hi,

With the help of Nick, I have been able to compile SIESTA-PEXSI but now I am facing two problems.
The first one is from the Auxiliary Supercell. PEXSI doesn't like the aux supercell and ask to not use it. The only way for me to avoid that aux supercell was to put my slab with vacuum in the x,y and z direction. Is that the correct way to do it ?

And the second problem, is an error when I try to run SIESTA-PEXSI with that trick. Here is the output file:

siesta-pexsi:23767 terminated with signal 11 at PC=2aaaab1c267e SP=7fffffff98b0. Backtrace:
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x71e)[0x2aaaab1c267e]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_malloc+0x46)[0x2aaaab1c39b6]
siesta-pexsi(gk_malloc+0x32)[0xa8a6a2]
siesta-pexsi(METIS_NodeND+0x32a)[0xa95cfa]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]

siesta-pexsi:23766 terminated with signal 11 at PC=aa248c SP=7fffffff98b0. Backtrace:
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]
siesta-pexsi(libmetis__CompressGraph+0x11c)[0xaa248c]
siesta-pexsi(METIS_NodeND+0x37b)[0xa95d4b]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]

siesta-pexsi:23765 terminated with signal 11 at PC=2aaaab1c267e SP=7fffffff98b0. Backtrace:
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x71e)[0x2aaaab1c267e]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_malloc+0x46)[0x2aaaab1c39b6]
siesta-pexsi(gk_malloc+0x32)[0xa8a6a2]
siesta-pexsi(METIS_NodeND+0x32a)[0xa95cfa]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23768 terminated with signal 11 at PC=2aaaab1c267e SP=7fffffff98b0. Backtrace:
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x71e)[0x2aaaab1c267e]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_malloc+0x46)[0x2aaaab1c39b6]
siesta-pexsi(gk_malloc+0x32)[0xa8a6a2]
siesta-pexsi(METIS_NodeND+0x32a)[0xa95cfa]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23769 terminated with signal 11 at PC=2aaaab1c267e SP=7fffffff98b0. Backtrace:
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x71e)[0x2aaaab1c267e]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_malloc+0x46)[0x2aaaab1c39b6]
siesta-pexsi(gk_malloc+0x32)[0xa8a6a2]
siesta-pexsi(METIS_NodeND+0x32a)[0xa95cfa]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23770 terminated with signal 11 at PC=aa248c SP=7fffffff98b0. Backtrace:
siesta-pexsi(libmetis__CompressGraph+0x11c)[0xaa248c]
siesta-pexsi(METIS_NodeND+0x37b)[0xa95d4b]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23771 terminated with signal 11 at PC=2aaaab1c267e SP=7fffffff98b0. Backtrace:
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x71e)[0x2aaaab1c267e]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_malloc+0x46)[0x2aaaab1c39b6]
siesta-pexsi(gk_malloc+0x32)[0xa8a6a2]
siesta-pexsi(METIS_NodeND+0x32a)[0xa95cfa]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23772 terminated with signal 11 at PC=2aaaab1c267e SP=7fffffff98b0. Backtrace:
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x71e)[0x2aaaab1c267e]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_malloc+0x46)[0x2aaaab1c39b6]
siesta-pexsi(gk_malloc+0x32)[0xa8a6a2]
siesta-pexsi(METIS_NodeND+0x32a)[0xa95cfa]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23773 terminated with signal 11 at PC=2aaaab1c267e SP=7fffffff98b0. Backtrace:
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x71e)[0x2aaaab1c267e]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_malloc+0x46)[0x2aaaab1c39b6]
siesta-pexsi(gk_malloc+0x32)[0xa8a6a2]
siesta-pexsi(METIS_NodeND+0x32a)[0xa95cfa]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23774 terminated with signal 11 at PC=aa248c SP=7fffffff98b0. Backtrace:
siesta-pexsi(libmetis__CompressGraph+0x11c)[0xaa248c]
siesta-pexsi(METIS_NodeND+0x37b)[0xa95d4b]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23775 terminated with signal 11 at PC=2aaaab1c267e SP=7fffffff98b0. Backtrace:
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x71e)[0x2aaaab1c267e]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_malloc+0x46)[0x2aaaab1c39b6]
siesta-pexsi(gk_malloc+0x32)[0xa8a6a2]
siesta-pexsi(METIS_NodeND+0x32a)[0xa95cfa]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23776 terminated with signal 11 at PC=2aaaab1c267e SP=7fffffff98b0. Backtrace:
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x71e)[0x2aaaab1c267e]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_malloc+0x46)[0x2aaaab1c39b6]
siesta-pexsi(gk_malloc+0x32)[0xa8a6a2]
siesta-pexsi(METIS_NodeND+0x32a)[0xa95cfa]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23777 terminated with signal 11 at PC=2aaaab1c267e SP=7fffffff98b0. Backtrace:
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x71e)[0x2aaaab1c267e]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_malloc+0x46)[0x2aaaab1c39b6]
siesta-pexsi(gk_malloc+0x32)[0xa8a6a2]
siesta-pexsi(METIS_NodeND+0x32a)[0xa95cfa]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23778 terminated with signal 11 at PC=aa248c SP=7fffffff98b0. Backtrace:
siesta-pexsi(libmetis__CompressGraph+0x11c)[0xaa248c]
siesta-pexsi(METIS_NodeND+0x37b)[0xa95d4b]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23779 terminated with signal 11 at PC=2aaaab1c267e SP=7fffffff98b0. Backtrace:
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x71e)[0x2aaaab1c267e]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_malloc+0x46)[0x2aaaab1c39b6]
siesta-pexsi(gk_malloc+0x32)[0xa8a6a2]
siesta-pexsi(METIS_NodeND+0x32a)[0xa95cfa]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

siesta-pexsi:23780 terminated with signal 11 at PC=2aaaab1c267e SP=7fffffff98b0. Backtrace:
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x71e)[0x2aaaab1c267e]
/cm/shared/apps/openmpi/gcc/64/1.6.3/lib/libmpi.so.1(opal_memory_ptmalloc2_malloc+0x46)[0x2aaaab1c39b6]
siesta-pexsi(gk_malloc+0x32)[0xa8a6a2]
siesta-pexsi(METIS_NodeND+0x32a)[0xa95cfa]
siesta-pexsi(get_metis+0x72)[0xad0a02]
siesta-pexsi(get_perm_c_dist+0x3c6)[0xad1756]
siesta-pexsi(pdsymbfact+0x4ab)[0xa5df6b]
siesta-pexsi(_ZN5PEXSI15RealSuperLUData17SymbolicFactorizeEv+0xc6)[0xa49f76]
siesta-pexsi(_ZN5PEXSI10PPEXSIData36SymbolicFactorizeRealSymmetricMatrixESsii+0x223)[0x9e4203]
siesta-pexsi(PPEXSISymbolicFactorizeRealSymmetricMatrix+0xa6)[0x9d1e66]
siesta-pexsi(__m_pexsi_solver_MOD_pexsi_solver+0x3f02)[0x6a3202]
siesta-pexsi(__m_compute_dm_MOD_compute_dm+0x11cc)[0x55427c]
siesta-pexsi(__m_siesta_forces_MOD_siesta_forces+0x15b)[0x573fbb]
siesta-pexsi(main+0xa4)[0x957a14]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3f0061ed1d]
siesta-pexsi[0x49588d]

The end of the output file from siesta gives me this :
siesta: ******************** Simulation parameters ****************************
siesta:
siesta: The following are some of the parameters of the simulation.
siesta: A complete list of the parameters used, including default values,
siesta: can be found in file out.fdf
siesta:
redata: Spin configuration = none
redata: Number of spin components = 1
redata: Time-Reversal Symmetry = T
redata: Spin-spiral = F
redata: Long output = F
redata: Number of Atomic Species = 1
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop. = NO
redata: Matel table size (NRTAB) = 1024
redata: Mesh Cutoff = 299.9973 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 600
redata: SCF convergence failure will abort job
redata: SCF mix quantity = Hamiltonian
redata: Mix DM or H after convergence = F
redata: Recompute H after scf cycle = F
redata: Mix DM in first SCF step = T
redata: Write Pulay info on disk = F
redata: New DM Mixing Weight = 0.0500
redata: New DM Occupancy tolerance = 0.000000000001
redata: No kicks to SCF
redata: DM Mixing Weight for Kicks = 0.5000
redata: Require Harris convergence for SCF = F
redata: Harris energy tolerance for SCF = 0.000100 eV
redata: Require DM convergence for SCF = T
redata: DM tolerance for SCF = 0.000005
redata: Require EDM convergence for SCF = F
redata: EDM tolerance for SCF = 0.001000 eV
redata: Require H convergence for SCF = T
redata: Hamiltonian tolerance for SCF = 0.001000 eV
redata: Require (free) Energy convergence for SCF = T
redata: (free) Energy tolerance for SCF = 0.000100 eV
redata: Using Saved Data (generic) = F
redata: Use continuation files for DM = T
redata: Neglect nonoverlap interactions = F
redata: Method of Calculation = PEXSI
redata: Fix the spin of the system = F
redata: Dynamics option = Single-point calculation
mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 8
mix.SCF: Linear mixing weight = 0.050000
mix.SCF: Mixing weight = 0.050000
mix.SCF: SVD condition = 0.1000E-07
redata: ***********************************************************************

%block SCF.Mixers
  Pulay
%endblock SCF.Mixers

%block SCF.Mixer.Pulay
  # Mixing method
  method pulay
  variant stable

  # Mixing options
  weight 0.0500
  weight.linear 0.0500
  history 8
%endblock SCF.Mixer.Pulay

DM_history_depth set to one: no extrapolation allowed by default for geometry relaxation
Size of DM history Fstack: 1
Total number of electrons: 1650.000000
Total ionic charge: 1650.000000

* ProcessorY, Blocksize: 4 24

* Orbital distribution balance (max,min): 216 192

k-point displ. along 1 input, could be: 0.00 0.50
k-point displ. along 2 input, could be: 0.00 0.50
 Kpoints in: 84 . Kpoints trimmed: 79

siesta: k-grid: Number of k-points = 79
siesta: k-grid: Cutoff (effective) = 10.211 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid: 12 0 0 0.000
siesta: k-grid: 0 12 0 0.000
siesta: k-grid: 0 0 1 0.000

diag: Algorithm = D&C
diag: Parallel over k = F
diag: Use parallel 2D distribution = T
diag: Parallel block-size = 24
diag: Parallel distribution = 4 x 8
diag: Used triangular part = Lower
diag: Absolute tolerance = 0.100E-15
diag: Orthogonalization factor = 0.100E-05
diag: Memory factor = 1.0000
Using LatticeConstant from fdf file for BandLinesScale: 1.889727 Bohr
Beware any cell changes by the end of the run
Using LatticeConstant from fdf file for BandLinesScale: 1.889727 Bohr
Beware any cell changes by the end of the run
Using LatticeConstant from fdf file for WaveFuncKPointsScale: 1.889727 Bohr
Beware any cell changes by the end of the run

siesta: Constraint (2): pos
  [ 1 -- 2 ]

ts: **************************************************************
ts: Save H and S matrices = F
ts: Save DM and EDM matrices = F
ts: Fix Hartree potential = F
ts: Only save the overlap matrix S = F
ts: **************************************************************

************************ Begin: TS CHECKS AND WARNINGS ************************
************************ End: TS CHECKS AND WARNINGS **************************

 &m -- Max memory after siesta_init 86.13

                     ====================================
                        Single-point calculation
                     ====================================

outcell: Unit cell vectors (Ang):
       23.459398 0.000000 0.000000
       11.729699 20.316434 0.000000
        0.000000 0.000000 20.421172

outcell: Cell vector modules (Ang) : 23.459398 23.459398 20.421172
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 60.0000
outcell: Cell volume (Ang**3) : 9732.9617
<dSpData1D:S at geom step 0
  <sparsity:sparsity for geom step 0
    nrows_g=6300 nrows=216 sparsity=.0150 nnzs=594383, refcount: 7>
  <dData1D:(new from dSpData1D) n=594383, refcount: 1>
refcount: 1>
new_DM -- step: 1
Initializing Density Matrix...

Attempting to read DM from file... Failed...
DM filled with atomic data:
<dSpData2D:DM initialized from atoms
  <sparsity:sparsity for geom step 0
    nrows_g=6300 nrows=216 sparsity=.0150 nnzs=594383, refcount: 8>
  <dData2D:DM n=594383 m=1, refcount: 1>
refcount: 1>
 &m -- Max memory after state_init 114.46
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 148 1536
New grid distribution: 1
           1 1: 108 1: 27 1: 14
           2 1: 108 1: 27 15: 28
           3 1: 108 1: 27 29: 42
           4 1: 108 1: 27 43: 56
           5 1: 108 1: 27 57: 69
           6 1: 108 1: 27 70: 82
           7 1: 108 1: 27 83: 95
           8 1: 108 1: 27 96: 108
           9 1: 108 28: 54 1: 14
          10 1: 108 28: 54 15: 28
          11 1: 108 28: 54 29: 42
          12 1: 108 28: 54 43: 56
          13 1: 108 28: 54 57: 69
          14 1: 108 28: 54 70: 82
          15 1: 108 28: 54 83: 95
          16 1: 108 28: 54 96: 108
          17 1: 108 55: 81 1: 14
          18 1: 108 55: 81 15: 28
          19 1: 108 55: 81 29: 42
          20 1: 108 55: 81 43: 56
          21 1: 108 55: 81 57: 69
          22 1: 108 55: 81 70: 82
          23 1: 108 55: 81 83: 95
          24 1: 108 55: 81 96: 108
          25 1: 108 82: 108 1: 14
          26 1: 108 82: 108 15: 28
          27 1: 108 82: 108 29: 42
          28 1: 108 82: 108 43: 56
          29 1: 108 82: 108 57: 69
          30 1: 108 82: 108 70: 82
          31 1: 108 82: 108 83: 95
          32 1: 108 82: 108 96: 108

InitMesh: MESH = 216 x 216 x 216 = 10077696
InitMesh: (bp) = 108 x 108 x 108 = 1259712
InitMesh: Mesh cutoff (required, used) = 299.997 309.206 Ry
ExtMesh (bp) on 0 = 212 x 131 x 118 = 3277096
New grid distribution: 2
           1 1: 56 1: 44 1: 41
           2 53: 108 55: 65 68: 108
           3 56: 108 42: 54 55: 68
           4 1: 56 1: 43 42: 54
           5 1: 55 1: 43 55: 68
           6 1: 55 1: 43 69: 108
           7 1: 56 45: 55 1: 41
           8 1: 52 55: 67 55: 68
           9 57: 108 1: 42 1: 41
          10 57: 108 43: 55 1: 41
          11 57: 108 43: 55 42: 54
          12 57: 108 1: 42 42: 54
          13 56: 108 1: 41 55: 68
          14 56: 108 1: 41 69: 108
          15 56: 108 42: 54 69: 108
          16 1: 56 44: 55 42: 54
          17 1: 53 69: 108 1: 40
          18 1: 53 56: 68 1: 40
          19 1: 53 56: 67 41: 54
          20 1: 53 68: 108 41: 54
          21 1: 52 68: 108 55: 68
          22 1: 52 68: 108 69: 108
          23 1: 52 55: 67 69: 108
          24 1: 55 44: 54 55: 68
          25 54: 108 67: 108 1: 40
          26 54: 108 56: 66 1: 40
          27 54: 108 56: 66 41: 54
          28 54: 108 67: 108 41: 54
          29 53: 108 66: 108 55: 67
          30 53: 108 66: 108 68: 108
          31 1: 55 44: 54 69: 108
          32 53: 108 55: 65 55: 67
New grid distribution: 3
           1 1: 59 1: 35 1: 31
           2 53: 108 56: 76 30: 54
           3 60: 108 1: 29 31: 54
           4 1: 59 1: 33 32: 54
           5 1: 50 54: 75 78: 108
           6 58: 108 30: 53 55: 78
           7 1: 57 1: 32 80: 108
           8 58: 108 1: 29 79: 108
           9 60: 108 1: 32 1: 30
          10 1: 59 36: 55 1: 31
          11 60: 108 33: 55 1: 30
          12 60: 108 30: 55 31: 54
          13 1: 57 1: 32 55: 79
          14 1: 57 33: 53 55: 79
          15 58: 108 30: 53 79: 108
          16 1: 57 33: 53 80: 108
          17 1: 52 79: 108 1: 32
          18 1: 52 56: 78 1: 32
          19 53: 108 56: 75 1: 29
          20 1: 59 34: 55 32: 54
          21 58: 108 1: 29 55: 78
          22 1: 50 54: 79 55: 77
          23 1: 50 76: 108 78: 108
          24 51: 108 54: 72 78: 108
          25 53: 108 76: 108 1: 29
          26 51: 108 54: 75 55: 77
          27 53: 108 77: 108 30: 54
          28 1: 52 81: 108 33: 54
          29 51: 108 76: 108 55: 77
          30 1: 50 80: 108 55: 77
          31 51: 108 73: 108 78: 108
          32 1: 52 56: 80 33: 54
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 160 x 148 x 145 = 3433600
PhiOnMesh: Number of (b)points on node 0 = 101024
PhiOnMesh: nlist on node 0 = 10171066
 &m -- Max memory after setup_H0 609.35
 &m -- Max memory after setup_H 684.23
Electronic temperature (K): 4.06
world_rank, rank1, rank2, ing1?, ing2? 1 1 1 T T
world_rank, rank1, rank2, ing1?, ing2? 2 2 2 T T
world_rank, rank1, rank2, ing1?, ing2? 3 3 3 T T
world_rank, rank1, rank2, ing1?, ing2? 4 4-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 5 5-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 6 6-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 7 7-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 8 8-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 9 9-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 10 10-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 11 11-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 12 12-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 13 13-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 14 14-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 15 15-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 0 0 0 T T
 About to transfer numcols...
 Transferred numcols.
world_rank, rank1, rank2, ing1?, ing2? 29 29-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 30 30-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 31 31-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 16 16-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 17 17-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 18 18-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 19 19-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 20 20-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 21 21-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 22 22-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 23 23-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 24 24-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 25 25-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 26 26-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 27 27-32766 T F
world_rank, rank1, rank2, ing1?, ing2? 28 28-32766 T F
 About to transfer cols...
 About to transfer values...
 Done transfers.
 &m -- Peak memory (Mb) after setting up H+S for PEXSI (PEXSI_workers) (max,min): 790.24 650.03
 &m -- Peak memory (Mb) after setting up H+S for PEXSI (max,min): 790.24 489.83
Current PEXSI temperature (K): 4.06

and the .fdf file :
SystemName cu111_naked_4sp2_ps_6l_MD0_dip_sel
SystemLabel cu111_naked_4sp2_ps_6l_MD0_dip_sel

NumberOfSpecies 1
NumberOfAtoms 150
%block ChemicalSpecieslabel
    1 29 Cu.gga.4sp_2.1
%endblock ChemicalSpecieslabel

%block PAO.Basis
Cu.gga.4sp_2.1 3
n=3 2 3 P 1
8.9 2.2 3.7

n=4 0 3 P 1
8.3 3.7 5.6

n=4 1 3 P 1
9.0 5.7 5.6

%endblock PAO.Basis

LatticeConstant 1.0 Ang
%block LatticeVectors
    23.459397624181893 0.000000000000000 0.000000000000000
    11.729698812090946 20.316434300021822 0.000000000000000
    0.000000000000000 0.000000000000000 20.421172358872745
%endblock LatticeVectors

AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
    10.787466938 5.736888164 5.000000000 1
    13.340122418 5.736888164 5.000000000 1
    15.892777898 5.736888164 5.000000000 1
    18.445433378 5.736888164 5.000000000 1
    20.998088858 5.736888164 5.000000000 1
    12.063794678 7.947552657 5.000000000 1
    14.616450158 7.947552657 5.000000000 1
    17.169105638 7.947552657 5.000000000 1
    19.721761118 7.947552657 5.000000000 1
    22.274416598 7.947552657 5.000000000 1
    13.340122418 10.158217150 5.000000000 1
    15.892777898 10.158217150 5.000000000 1
    18.445433378 10.158217150 5.000000000 1
    20.998088858 10.158217150 5.000000000 1
    23.550744338 10.158217150 5.000000000 1
    14.616450158 12.368881643 5.000000000 1
    17.169105638 12.368881643 5.000000000 1
    19.721761118 12.368881643 5.000000000 1
    22.274416598 12.368881643 5.000000000 1
    24.827072078 12.368881643 5.000000000 1
    15.892777898 14.579546136 5.000000000 1
    18.445433378 14.579546136 5.000000000 1
    20.998088858 14.579546136 5.000000000 1
    23.550744338 14.579546136 5.000000000 1
    26.103399818 14.579546136 5.000000000 1
     9.511139198 6.473776329 7.084234472 1
    12.063794678 6.473776329 7.084234472 1
    14.616450158 6.473776329 7.084234472 1
    17.169105638 6.473776329 7.084234472 1
    19.721761118 6.473776329 7.084234472 1
    10.787466938 8.684440821 7.084234472 1
    13.340122418 8.684440821 7.084234472 1
    15.892777898 8.684440821 7.084234472 1
    18.445433378 8.684440821 7.084234472 1
    20.998088858 8.684440821 7.084234472 1
    12.063794678 10.895105314 7.084234472 1
    14.616450158 10.895105314 7.084234472 1
    17.169105638 10.895105314 7.084234472 1
    19.721761118 10.895105314 7.084234472 1
    22.274416598 10.895105314 7.084234472 1
    13.340122418 13.105769807 7.084234472 1
    15.892777898 13.105769807 7.084234472 1
    18.445433378 13.105769807 7.084234472 1
    20.998088858 13.105769807 7.084234472 1
    23.550744338 13.105769807 7.084234472 1
    14.616450158 15.316434300 7.084234472 1
    17.169105638 15.316434300 7.084234472 1
    19.721761118 15.316434300 7.084234472 1
    22.274416598 15.316434300 7.084234472 1
    24.827072078 15.316434300 7.084234472 1
     9.511139198 5.000000000 9.168468944 1
    12.063794678 5.000000000 9.168468944 1
    14.616450158 5.000000000 9.168468944 1
    17.169105638 5.000000000 9.168468944 1
    19.721761118 5.000000000 9.168468944 1
    10.787466938 7.210664493 9.168468944 1
    13.340122418 7.210664493 9.168468944 1
    15.892777898 7.210664493 9.168468944 1
    18.445433378 7.210664493 9.168468944 1
    20.998088858 7.210664493 9.168468944 1
    12.063794678 9.421328986 9.168468944 1
    14.616450158 9.421328986 9.168468944 1
    17.169105638 9.421328986 9.168468944 1
    19.721761118 9.421328986 9.168468944 1
    22.274416598 9.421328986 9.168468944 1
    13.340122418 11.631993479 9.168468944 1
    15.892777898 11.631993479 9.168468944 1
    18.445433378 11.631993479 9.168468944 1
    20.998088858 11.631993479 9.168468944 1
    23.550744338 11.631993479 9.168468944 1
    14.616450158 13.842657971 9.168468944 1
    17.169105638 13.842657971 9.168468944 1
    19.721761118 13.842657971 9.168468944 1
    22.274416598 13.842657971 9.168468944 1
    24.827072078 13.842657971 9.168468944 1
    10.787466938 5.736888164 11.252703415 1
    13.340122418 5.736888164 11.252703415 1
    15.892777898 5.736888164 11.252703415 1
    18.445433378 5.736888164 11.252703415 1
    20.998088858 5.736888164 11.252703415 1
    12.063794678 7.947552657 11.252703415 1
    14.616450158 7.947552657 11.252703415 1
    17.169105638 7.947552657 11.252703415 1
    19.721761118 7.947552657 11.252703415 1
    22.274416598 7.947552657 11.252703415 1
    13.340122418 10.158217150 11.252703415 1
    15.892777898 10.158217150 11.252703415 1
    18.445433378 10.158217150 11.252703415 1
    20.998088858 10.158217150 11.252703415 1
    23.550744338 10.158217150 11.252703415 1
    14.616450158 12.368881643 11.252703415 1
    17.169105638 12.368881643 11.252703415 1
    19.721761118 12.368881643 11.252703415 1
    22.274416598 12.368881643 11.252703415 1
    24.827072078 12.368881643 11.252703415 1
    15.892777898 14.579546136 11.252703415 1
    18.445433378 14.579546136 11.252703415 1
    20.998088858 14.579546136 11.252703415 1
    23.550744338 14.579546136 11.252703415 1
    26.103399818 14.579546136 11.252703415 1
     9.511139198 6.473776329 13.336937887 1
    12.063794678 6.473776329 13.336937887 1
    14.616450158 6.473776329 13.336937887 1
    17.169105638 6.473776329 13.336937887 1
    19.721761118 6.473776329 13.336937887 1
    10.787466938 8.684440821 13.336937887 1
    13.340122418 8.684440821 13.336937887 1
    15.892777898 8.684440821 13.336937887 1
    18.445433378 8.684440821 13.336937887 1
    20.998088858 8.684440821 13.336937887 1
    12.063794678 10.895105314 13.336937887 1
    14.616450158 10.895105314 13.336937887 1
    17.169105638 10.895105314 13.336937887 1
    19.721761118 10.895105314 13.336937887 1
    22.274416598 10.895105314 13.336937887 1
    13.340122418 13.105769807 13.336937887 1
    15.892777898 13.105769807 13.336937887 1
    18.445433378 13.105769807 13.336937887 1
    20.998088858 13.105769807 13.336937887 1
    23.550744338 13.105769807 13.336937887 1
    14.616450158 15.316434300 13.336937887 1
    17.169105638 15.316434300 13.336937887 1
    19.721761118 15.316434300 13.336937887 1
    22.274416598 15.316434300 13.336937887 1
    24.827072078 15.316434300 13.336937887 1
     9.511139198 5.000000000 15.421172359 1
    12.063794678 5.000000000 15.421172359 1
    14.616450158 5.000000000 15.421172359 1
    17.169105638 5.000000000 15.421172359 1
    19.721761118 5.000000000 15.421172359 1
    10.787466938 7.210664493 15.421172359 1
    13.340122418 7.210664493 15.421172359 1
    15.892777898 7.210664493 15.421172359 1
    18.445433378 7.210664493 15.421172359 1
    20.998088858 7.210664493 15.421172359 1
    12.063794678 9.421328986 15.421172359 1
    14.616450158 9.421328986 15.421172359 1
    17.169105638 9.421328986 15.421172359 1
    19.721761118 9.421328986 15.421172359 1
    22.274416598 9.421328986 15.421172359 1
    13.340122418 11.631993479 15.421172359 1
    15.892777898 11.631993479 15.421172359 1
    18.445433378 11.631993479 15.421172359 1
    20.998088858 11.631993479 15.421172359 1
    23.550744338 11.631993479 15.421172359 1
    14.616450158 13.842657971 15.421172359 1
    17.169105638 13.842657971 15.421172359 1
    19.721761118 13.842657971 15.421172359 1
    22.274416598 13.842657971 15.421172359 1
    24.827072078 13.842657971 15.421172359 1
%endblock AtomicCoordinatesAndAtomicSpecies

PAO.EnergyShift 0.09999997 eV
%block PS.lmax
Cu.gga.4sp_2.1 2
%endblock PS.lmax
XC.functional GGA
XC.authors PBE
MaxSCFIterations 600
DM.MixingWeight 0.05
DM.NumberPulay 8
DM.UseSaveDM true
DM.Tolerance 5e-6 eV
DM.Require.Energy.Convergence true
MeshCutoff 4081.7079 eV
ForceAuxCell false
SolutionMethod PEXSI
WriteEigenvalues false
ElectronicTemperature 0.00035000 eV
%block BandLines
1 0.5 0.0 0.0 M
200 0.333333 0.333333 0.0 K
200 0.0 0.0 0.0 G
200 0.5 0.0 0.0 M
%endblock BandLines
WriteKbands false
WriteBands false
WFS.Write.For.Bands false
%block WaveFuncKPoints
(I removed this block for the question, way too long)
%endblock WaveFuncKPoints
WriteWaveFunctions false
COOP.Write true
WFS.Energy.Min -10 eV
WFS.Energy.Max 10 eV
SlabDipoleCorrection true
SaveRho true
SaveElectrostaticPotential true
SaveTotalPotential true
SaveTotalCharge true
SaveBaderCharge true
WriteDenchar true
MD.TypeOfRun CG
MD.MaxForceTol 0.04000000 eV/Ang
WriteMDhistory true
%block GeometryConstraints
atom from 1 to 2
%endblock GeometryConstraints

#KPoint grid
%block kgrid_Monkhorst_Pack
     12 0 0 0.0
     0 12 0 0.0
     0 0 1 0.0
%endblock kgrid_Monkhorst_Pack

If you need any info, let me know !
Best regards,
Pierre

Question information

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Revision history for this message
Nick Papior (nickpapior) said : 		#1

I am here quoting Alberto Garcia:

1. The number of atoms in your problem is very small for PEXSI to be competitive
   with diagonalization.
2. This PEXSI interface cannot use k-points
3. PEXSI does not provide wavefunctions.

I.e. your problem is that you cannot have k-points in a PEXSI calculation!

Revision history for this message
Pierre Capiod (pierre.capiod) said : 		#2

Hi,

After investigating a lot with the error, I have came to the conclusion that the compilation of SuperLU_DIST is not ok.
I am using the version 4.3 of SuperLU_DIST because the PEXSI interface for SIESTA seems to work with the 0.9.2 (manual).
The problem occurs here :
/nethome/capio001/local/SuperLU_DIST_4.3/lib/libsuperlu_dist_4.3.a(get_perm_c.o): In function `get_metis':
get_perm_c.c:(.text+0x6e): undefined reference to `METIS_NodeND'
And for Pexsi, it results in this error :
/nethome/capio001/local/pexsi_v0.9.2/src/libpexsi_linux_v0.9.2.a(get_perm_c_parmetis.o): In function `get_perm_c_parmetis':
/scratch2/nethome/capio001/local/pexsi_v0.9.2/src/get_perm_c_parmetis.c:223: undefined reference to `ParMETIS_V3_NodeND'

And this is as well visible when compiling siesta :

-mpif90 -o siesta \
         automatic_cell.o atom_options.o arw.o atomlwf.o bands.o basis_enthalpy.o bessph.o bonds.o born_charge.o cellxc_mod.o cgwf.o chkdim.o chkgmx.o chempot.o coceri.o coxmol.o cross.o compute_norm.o denmat.o denmatlomem.o detover.o dfscf.o diagon.o digcel.o fft.o dhscf.o constr.o diagk_file.o diagg.o diagk.o diagkp.o diag2g.o diag2k.o diag3g.o diag3k.o diagpol.o diagsprl.o dipole.o dismin.o dnaefs.o doping_uniform.o dot.o m_efield.o egandd.o ener3.o ener3lomem.o errorf.o extrapolon.o m_fixed.o interpolation.o gradient.o gradientlomem.o grdsam.o hsparse.o idiag.o initatom.o inver.o iodm_netcdf.o iodmhs_netcdf.o iogrid_netcdf.o iolwf.o iozm.o ipack.o iopipes.o iosockets.o iowfs_netcdf.o kgrid.o kgridinit.o kinefsm.o ksv.o ksvinit.o linpack.o local_DOS.o madelung.o mesh.o meshphi.o meshdscf.o memory.o meshsubs.o metaforce.o m_supercell.o mulliken.o minvec.o naefs.o m_new_dm.o normalize_dm.o ordern.o outcell.o outcoor.o m_fft_gpfa.o pdos.o pdosg.o pdosk.o pdoskp.o phirphi.o pixmol.o plcharge.o projected_DOS.o propor.o m_partial_charges.o randomg.o reclat.o redcel.o reinit.o reord.o reordpsi.o rhoofd.o rhoofdsp.o rhooda.o savepsi.o shaper.o timer_tree.o timer.o vmb.o vmat.o vmatsp.o volcel.o cgvc.o cgvc_zmatrix.o m_convergence.o iocg.o ioeig.o iofa.o iokp.o iomd.o kpoint_pdos.o typecell.o ofc.o poison.o readsp.o radfft.o write_md_record.o kpoint_grid.o find_kgrid.o proximity_check.o state_init.o siesta_move.o setup_hamiltonian.o compute_dm.o mixer.o scfconvergence_test.o post_scf_work.o state_analysis.o write_subs.o siesta_init.o struct_init.o siesta_options.o read_options.o siesta_geom.o siesta_analysis.o siesta_end.o siesta_forces.o io.o sparse_matrices.o coor.o atm_transfer.o broadcast_basis.o eggbox.o optical.o phirphi_opt.o reoptical.o transition_rate.o initparallel.o show_distribution.o setspatial.o setatomnodes.o uncell.o cart2frac.o obc.o precision.o sys.o m_cell.o files.o spatial.o parallel.o parallelsubs.o parsing.o chemical.o atom.o atmparams.o m_mpi_utils.o fdf_extra.o m_iorho.o atmfuncs.o listsc.o memoryinfo.o m_memory.o sorting.o atomlist.o atm_types.o old_atmfuncs.o radial.o alloc.o spher_harm.o periodic_table.o version.o timestamp.o basis_types.o xml.o pseudopotential.o basis_specs.o basis_io.o ldau.o ldau_specs.o onmod.o densematrix.o writewave.o on_subs.o fermid.o m_broyddj.o electrostatic.o mneighb.o globalise.o siesta_cmlsubs.o siesta_cml.o units.o zmatrix.o m_broyden_mixing.o forhar.o m_walltime.o m_wallclock.o m_iostruct.o nlefsm.o overfsm.o overlap.o conjgr.o conjgr_old.o m_energies.o m_steps.o m_broyddj_nocomm.o broyden_optim.o ioxv.o dynamics.o md_out.o molecularmechanics.o zm_broyden_optim.o cell_broyden_optim.o remove_intramol_pressure.o m_ntm.o m_dipol.o m_kinetic.o m_rmaxh.o m_forces.o m_stress.o m_eo.o m_spin.o m_hsx.o m_fire.o setup_H0.o get_kpoints_scale.o get_target_stress.o fire_optim.o zm_fire_optim.o cell_fire_optim.o m_fire_para.o m_fire_mixing.o write_raw_efs.o pdos2g.o pdos2k.o pdos3g.o pdos3k.o spinorbit.o moments.o fsiesta_mpi.o final_H_f_stress.o debugmpi.o qsort.o save_density_matrix.o m_dscfcomm.o schecomm.o moremeshsubs.o domain_decom.o printmatrix.o mmio.o pspltm1.o lenstr.o setup_ordern_indexes.o m_iodm.o m_iodm_old.o m_filter.o m_io.o m_io_yaml.o m_timer.o extrae_module.o extrae_eventllist.o moreParallelSubs.o read_xc_info.o siesta_master.o bsc_xcmod.o bsc_cellxc.o xc.o vacuum_level.o write_orb_indx.o die.o m_pexsi.o m_pexsi_driver.o m_pexsi_dos.o m_pexsi_local_dos.o m_redist_spmatrix.o class_Distribution.o m_dminim.o m_zminim.o m_getopts.o f2kcli.o m_svd.o m_matio.o rusage.o memory_snapshot.o compute_ebs_shift.o memory_all.o matel_registry.o register_rfs.o new_matel.o kpoint_convert.o m_target_stress.o compute_max_diff.o init_output.o diag_option.o diag.o m_mixing.o m_mixing_scf.o m_trialorbitalclass.o siesta2wannier90.o m_planewavematrixvar.o delk.o m_planewavematrix.o m_digest_nnkp.o broadcast_projections.o compute_pw_matrix.o m_writedelk.o mmn.o m_noccbands.o amn.o m_overkkneig.o write_inp_wannier.o diagonalizeHk.o m_orderbands.o m_check_walltime.o print_spin.o class_OrbitalDistribution.o class_Sparsity.o class_Data1D.o class_Data2D.o class_SpData1D.o class_SpData2D.o restructSpData2D.o extrapolateSpData2D.o class_Geometry.o class_Fstack_Data1D.o class_Pair_Data1D.o class_Fstack_Pair_Data1D.o class_Pair_Geometry_SpData2D.o class_Fstack_Pair_Geometry_SpData2D.o class_Pair_SpData1D.o class_Fstack_Pair_SpData1D.o class_TriMat.o m_trimat_invert.o m_uuid.o object_debug.o m_rhog.o rhofft.o m_diis.o compute_energies.o m_char.o m_os.o intrinsic_missing.o geom_helper.o m_sparse.o m_handle_sparse.o m_mesh_node.o create_Sparsity_SC.o create_Sparsity_Union.o m_gauss_quad.o m_gauss_fermi_inf.o m_gauss_fermi_30.o m_gauss_fermi_28.o m_gauss_fermi_26.o m_gauss_fermi_24.o m_gauss_fermi_22.o m_gauss_fermi_20.o m_gauss_fermi_19.o m_gauss_fermi_18.o m_gauss_fermi_17.o m_integrate.o m_interpolate.o m_mat_invert.o m_monitor.o m_iterator.o m_pivot_array.o dm_charge.o m_pivot.o m_pivot_methods.o atom_graph.o m_geom_aux.o m_geom_objects.o m_geom_box.o m_geom_coord.o m_geom_square.o m_geom_plane.o m_charge_add.o m_hartree_add.o m_io_s.o m_region.o m_sparsity_handling.o m_ncdf_siesta.o m_ncdf_io.o m_exp_coord.o flook_siesta.o siesta_dicts.o m_cite.o m_ts_io.o m_ts_global_vars.o m_ts_options.o m_ts_aux.o m_ts_kpoints.o m_ts_iodm.o m_ts_electrode.o m_ts_gf.o m_ts_cctype.o ts_init.o ts_show_regions.o m_ts_electype.o m_ts_method.o m_ts_elec_se.o m_ts_debug.o m_ts_tdir.o m_ts_chem_pot.o m_transiesta.o m_ts_hartree.o m_ts_voltage.o m_ts_contour_eq.o m_ts_contour_neq.o m_ts_io_ctype.o m_ts_contour.o m_ts_io_contour.o m_ts_rgn2trimat.o m_ts_dm_update.o m_ts_weight.o m_ts_sparse.o m_ts_sparse_helper.o m_ts_charge.o m_ts_pivot.o m_ts_fullg.o m_ts_fullk.o m_ts_full_scat.o m_ts_tri_init.o m_ts_tri_common.o m_ts_trimat_invert.o m_ts_tri_scat.o m_ts_trig.o m_ts_trik.o m_ts_mumps_init.o m_ts_mumpsg.o m_ts_mumpsk.o m_ts_mumps_scat.o nag.o pxf.o sockets.o fsockets.o siesta.o libfdf.a libwxml.a libxmlparser.a \
               libSiestaXC.a libmpi_f90.a /scratch2/nethome/capio001/local/parmetis-4.0.3/metis/lib/libmetis.a /scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a -L/scratch2/nethome/capio001/local/scotch_6.0.6/lib/ -lscotchmetis -lscotch -lscotcherr -L/scratch2/nethome/capio001/local/scotch_6.0.6/lib/ -lptscotchparmetis -lptscotch -lptscotcherr -lscotch /cm/shared/apps/scalapack/gcc/1.8.0/lib64/libscalapack.a -lblacsF77init -lblacs -lblacsF77init /scratch2/nethome/capio001/local/lapack/lapack-3.8.0/liblapack.a /scratch2/nethome/capio001/local/blas/libblas.a /scratch2/nethome/capio001/local/SuperLU_DIST_4.3/lib/libsuperlu_dist_4.3.a -lstdc++ -lmpi -lmpi_cxx -Wl,--allow-multiple-definition
/scratch2/nethome/capio001/local/SuperLU_DIST_4.3/lib/libsuperlu_dist_4.3.a(get_perm_c.o): In function `get_metis':
get_perm_c.c:(.text+0x6e): undefined reference to `METIS_NodeND'

So two questions arise from this.
1. I have tried to include metis.h and parmetis.h where those functions are actually defined but no help. Do you have any idea ? I have tried to contact the developer of SuperLU_dist which brings me to the second question...

2. From your experience do you know if SIESTA-PEXSI would work with a much newer version like 1.2.0 ?

I will continue to investigate the issue above.

Thank you

Revision history for this message
Pierre Capiod (pierre.capiod) said : 		#3

Hi again,

by using ptscotch/scotch to compile PEXSI 0.9.2 seems to work better than metis/parmetis but I still get an error due to the fact that SuperLU 4.3 needs Metis to work. With newer version of SuperLU, it is possbile to disable Metis/parmetis
So I would like to know if newer version of PEXSI can work with SIESTA ?

Best regards,
Pierre

Revision history for this message
Pierre Capiod (pierre.capiod) said : 		#4

Hi,

Ok after some tests, the version 0.10.2 seems to not work with 4.1-b4 due to changes in the fortran interface (as expected). So I went back to the 0.9.2 and I managed to compile it without having the previous error.
SuperLU and Pexsi 0.9.2 is compiled ok.
Siesta compiled somewhat ok but I encountered this error in the process :
mpif90 -c -g -O2 -I/nethome/capio001/local/pexsi_v0.9.2/build/include -I/scratch2/nethome/capio001/local/parmetis-4.0.3/build/Linux-x86_64/include -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DSIESTA__PEXSI /scratch2/nethome/capio001/siesta-4.1-b4-mpi/Src/f_ppexsi_interface.F90
f_interface.f90:167.11:
    Included at /scratch2/nethome/capio001/siesta-4.1-b4-mpi/Src/f_ppexsi_interface.F90:4:

      fcomm ) &
           1
Warning: Variable 'fcomm' at (1) is a parameter to the BIND(C) procedure 'f_para_read_distsparsematrix' but may not be C interoperable
f_interface.f90:180.11:
    Included at /scratch2/nethome/capio001/siesta-4.1-b4-mpi/Src/f_ppexsi_interface.F90:4:

      fcomm,&
           1
Warning: Variable 'fcomm' at (1) is a parameter to the BIND(C) procedure 'f_ppexsi_plan_initialize' but may not be C interoperable
f_interface.f90:131.11:
    Included at /scratch2/nethome/capio001/siesta-4.1-b4-mpi/Src/f_ppexsi_interface.F90:4:

      fcomm ) &
           1
Warning: Variable 'fcomm' at (1) is a parameter to the BIND(C) procedure 'f_read_distsparsematrix_formatted' but may not be C interoperable
f_interface.f90:113.11:
    Included at /scratch2/nethome/capio001/siesta-4.1-b4-mpi/Src/f_ppexsi_interface.F90:4:

      fcomm ) &
           1
Warning: Variable 'fcomm' at (1) is a parameter to the BIND(C) procedure 'f_read_distsparsematrix_formatted_head' but may not be C interoperable
f_interface.f90:148.11:
    Included at /scratch2/nethome/capio001/siesta-4.1-b4-mpi/Src/f_ppexsi_interface.F90:4:

      fcomm ) &
           1
Warning: Variable 'fcomm' at (1) is a parameter to the BIND(C) procedure 'f_read_distsparsematrix_head' but may not be C interoperable

My arch.make is the following (f_interface_f90 is copied to the /include folder of pexsi):
#
# Copyright (C) 1996-2016 The SIESTA group
# This file is distributed under the terms of the
# GNU General Public License: see COPYING in the top directory
# or http://www.gnu.org/copyleft/gpl.txt.
# See Docs/Contributors.txt for a list of contributors.
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90 .c

SIESTA_ARCH=x86_64-unknown-linux-gnu--unknown

FPP=
FPP_OUTPUT=
FC=mpif90
RANLIB=ranlib

SYS=nag

SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)

FFLAGS=-g -O2
FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
LDFLAGS=

ARFLAGS_EXTRA=

FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=

BLAS_LIBS=-lblas
LAPACK_LIBS=/cm/shared/apps/lapack/gcc/64/3.4.0/liblapack.a
BLACS_LIBS=-lblacsF77init -lblacs -lblacsF77init
SCALAPACK_LIBS=/cm/shared/apps/scalapack/gcc/1.8.0/lib64/libscalapack.a

COMP_LIBS=dc_lapack.a liblapack.a

NETCDF_LIBS=
NETCDF_INTERFACE=

LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS)

#SIESTA needs an F90 interface to MPI
#This will give you SIESTA's own implementation
#If your compiler vendor offers an alternative, you may change
#to it here.
MPI_INTERFACE=libmpi_f90.a
MPI_INCLUDE=.

#Dependency rules are created by autoconf according to whether
#discrete preprocessing is necessary or not.
.F.o:
 $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F90.o:
 $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $<
.f.o:
 $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<
.f90.o:
 $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<

In the end, I have tried none the less to compute something, and I have Bad normalization errors
...
 About to transfer cols...
 About to transfer values...
 Done transfers.
Bad DM normalization: Qtot, Tr[D*S] = 1056.00000000 1055.93638426
Stopping Program from Node: 15
Bad DM normalization: Qtot, Tr[D*S] = 1056.00000000 1055.93638426
Stopping Program from Node: 0
Bad DM normalization: Qtot, Tr[D*S] = 1056.00000000 1055.93638426
Stopping Program from Node: 6
Bad DM normalization: Qtot, Tr[D*S] = 1056.00000000 1055.93638426
Stopping Program from Node: 8
Bad DM normalization: Qtot, Tr[D*S] = 1056.00000000 1055.93638426
Stopping Program from Node: 3
Bad DM normalization: Qtot, Tr[D*S] = 1056.00000000 1055.93638426
Stopping Program from Node: 1
Bad DM normalization: Qtot, Tr[D*S] = 1056.00000000 1055.93638426
Stopping Program from Node: 10
...

Not sure if this is related.

Best regards,
Pierre

Revision history for this message
Alberto Garcia (albertog) said : 		#5

Hi, Pierre,

You might try setting:

    DM.NormalizationTolerance 1.0d-1 # (true_no_electrons/no_electrons) - 1.0

but keep in mind our first response to your questions regarding the size of your system.

Also, you might be interested in new PEXSI-related developments in Siesta: In branch 'trunk-elsi-dm' we have an interface to the
ELSI library of solvers, which include PEXSI (new version). It is in pre-beta status, but you might want to experiment with it.

See www.elsi-interchange.org

Revision history for this message
Pierre Capiod (pierre.capiod) said : 		#6

Hi Alberto,

I, indeed, play recently with this variable and I could calculate with PEXSI as a solver. Thanks !

For the size of the system, this was only for a test. Even if PEXSI could not be competitive vs diagonalization, in the end, nothing was computed.

Thank you again ! I will mark this topic as solved.
Pierre

Revision history for this message
Launchpad Janitor (janitor) said : 		#7

This question was expired because it remained in the 'Open' state without activity for the last 15 days.