Dear Nick, I just finished to successful compile and run SIESTA-4.1-b2 (I just run with the previous silicon example). Everything was fine.
One thing that is strange, to me, is that I just previously compile SIESTA with the same Intel set (compiler, MKL, MPI) in a different Linux flavor without any problem. My server was with OpenSUSE Tumbleweed (compile without any issue) and now is with OpenSUSE Leap. Thank you very much for your support. []'s, Camps On Thu, Apr 6, 2017 at 2:56 AM, Nick Papior <[email protected]> wrote: > 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/compile >> rs_and_libraries_2017.1.132/linux/mpi/intel64/lib/libmpifort.so.12 >> (0x00002b38a6adc000) >> libmpi.so.12 => /mnt/SoftIns/intel_MPI/compile >> rs_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/compile >> rs_and_libraries_2017.1.132/linux/mpi/intel64/lib/libmpifort.so.12 >> (0x00002ab262341000) >> libmpi.so.12 => /mnt/SoftIns/intel_MPI/compile >> rs_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 >
