First, did you try my suggestion? It is not clear at all whether you did and you still have the problem?
Secondly, those libraries are dependencies normal to the intel compiler. Intel isn't a completely separate compiler, it still relies on system libraries. Lastly, the pthread dependency is probably due to mkl=parallel (which you do not need, so try and remove it). 2017-04-05 21:53 GMT+02:00 I. Camps <[email protected]>: > Running the command "ldd siesta" and "ldd -v siesta" returns that all > libraries are on my system. > > Some dubs: > - why using libpthread from system instead from Intel? > - why using libgcc_s? > > It is not a memory problem (16GB) and a system size (1 atom). > > ldd siesta > linux-vdso.so.1 (0x00007ffc57f9b000) > libm.so.6 => /lib64/libm.so.6 (0x00002b38a65da000) > libdl.so.2 => /lib64/libdl.so.2 (0x00002b38a68d7000) > libmpifort.so.12 => /mnt/SoftIns/intel_MPI/ > compilers_and_libraries_2017.1.132/linux/mpi/intel64/lib/libmpifort.so.12 > (0x00002b38a6adc000) > libmpi.so.12 => /mnt/SoftIns/intel_MPI/ > compilers_and_libraries_2017.1.132/linux/mpi/intel64/lib/libmpi.so.12 > (0x00002b38a6e85000) > librt.so.1 => /lib64/librt.so.1 (0x00002b38a7b9c000) > libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b38a7da5000) > libc.so.6 => /lib64/libc.so.6 (0x00002b38a7fc2000) > /lib64/ld-linux-x86-64.so.2 (0x0000561c6c580000) > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b38a8365000) > > ldd -v siesta > linux-vdso.so.1 (0x00007ffe01da7000) > libm.so.6 => /lib64/libm.so.6 (0x00002ab261e3f000) > libdl.so.2 => /lib64/libdl.so.2 (0x00002ab26213c000) > libmpifort.so.12 => /mnt/SoftIns/intel_MPI/ > compilers_and_libraries_2017.1.132/linux/mpi/intel64/lib/libmpifort.so.12 > (0x00002ab262341000) > libmpi.so.12 => /mnt/SoftIns/intel_MPI/ > compilers_and_libraries_2017.1.132/linux/mpi/intel64/lib/libmpi.so.12 > (0x00002ab2626ea000) > librt.so.1 => /lib64/librt.so.1 (0x00002ab263401000) > libpthread.so.0 => /lib64/libpthread.so.0 (0x00002ab26360a000) > libc.so.6 => /lib64/libc.so.6 (0x00002ab263827000) > /lib64/ld-linux-x86-64.so.2 (0x000055f13aa31000) > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002ab263bca000) > > Version information: > ./siesta: > ld-linux-x86-64.so.2 (GLIBC_2.3) => > /lib64/ld-linux-x86-64.so.2 > libdl.so.2 (GLIBC_2.2.5) => /lib64/libdl.so.2 > libpthread.so.0 (GLIBC_2.2.5) => /lib64/libpthread.so.0 > libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6 > libgcc_s.so.1 (GCC_3.0) => /lib64/libgcc_s.so.1 > libgcc_s.so.1 (GCC_3.3) => /lib64/libgcc_s.so.1 > libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.3) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6 > /lib64/libm.so.6: > libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6 > /lib64/libdl.so.2: > ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => > /lib64/ld-linux-x86-64.so.2 > libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6 > /mnt/SoftIns/intel_MPI/compilers_and_libraries_2017. > 1.132/linux/mpi/intel64/lib/libmpifort.so.12: > libdl.so.2 (GLIBC_2.2.5) => /lib64/libdl.so.2 > libgcc_s.so.1 (GCC_3.3) => /lib64/libgcc_s.so.1 > libgcc_s.so.1 (GCC_3.0) => /lib64/libgcc_s.so.1 > libc.so.6 (GLIBC_2.4) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.3) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.3.4) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6 > /mnt/SoftIns/intel_MPI/compilers_and_libraries_2017. > 1.132/linux/mpi/intel64/lib/libmpi.so.12: > libdl.so.2 (GLIBC_2.2.5) => /lib64/libdl.so.2 > librt.so.1 (GLIBC_2.2.5) => /lib64/librt.so.1 > libgcc_s.so.1 (GCC_3.3) => /lib64/libgcc_s.so.1 > libgcc_s.so.1 (GCC_3.0) => /lib64/libgcc_s.so.1 > libc.so.6 (GLIBC_2.5) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.3.4) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.6) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.3) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.7) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.3.2) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6 > /lib64/librt.so.1: > libpthread.so.0 (GLIBC_2.3.2) => /lib64/libpthread.so.0 > libpthread.so.0 (GLIBC_PRIVATE) => /lib64/libpthread.so.0 > libpthread.so.0 (GLIBC_2.2.5) => /lib64/libpthread.so.0 > libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.3.2) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6 > libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6 > /lib64/libpthread.so.0: > ld-linux-x86-64.so.2 (GLIBC_2.2.5) => > /lib64/ld-linux-x86-64.so.2 > ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => > /lib64/ld-linux-x86-64.so.2 > libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.3.2) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6 > libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6 > /lib64/libc.so.6: > ld-linux-x86-64.so.2 (GLIBC_2.3) => > /lib64/ld-linux-x86-64.so.2 > ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => > /lib64/ld-linux-x86-64.so.2 > /lib64/libgcc_s.so.1: > libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6 > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6 > > > > []'s, > > Camps > > On Tue, Apr 4, 2017 at 4:36 PM, I. Camps <[email protected]> wrote: > >> Hello, >> >> I successfully compile SIESTa with the set Intel Fortran Compiler/Intel >> MPI/Intel MKL >> ifort: Intel(R) Fortran Intel(R) 64 Compiler XE for applications running >> on Intel(R) 64, Version 15.0.1.133 Build 20141023 >> MPI: Intel(R) MPI Library for Linux* OS, Version 2017 Update 1 Build >> 20161016 (id: 16418) >> MKL: 11.2.1 >> >> My arch.make file is attached. >> >> When running SIESTA with the silicon FDF (attached) I got the message: >> >> ################ >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> Image PC Routine Line Source >> siesta 0000000001A94261 Unknown Unknown >> Unknown >> siesta 0000000001A929B7 Unknown Unknown >> Unknown >> siesta 0000000001A43464 Unknown Unknown >> Unknown >> siesta 0000000001A43276 Unknown Unknown >> Unknown >> siesta 00000000019F339F Unknown Unknown >> Unknown >> siesta 00000000019F993D Unknown Unknown >> Unknown >> libpthread.so.0 00002B9436D60B00 Unknown Unknown >> Unknown >> siesta 0000000001F25615 Unknown Unknown >> Unknown >> >> Stack trace terminated abnormally. >> ################ >> >> This is driving me crazy...so, any help will be very appreciated. >> >> []'s, >> >> Camps >> > > -- Kind regards Nick
