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
>
