Error While running VASP with Intel ifort, mkl and mpif90 (openmpi)

Prasanna_Kumar_N_ · ‎10-01-2015

I did installed VASP executable successfully, only I changed FC=mpif90 (openmpi compiled using Intel compiler) whatever you mentioned in the following link

https://software.intel.com/en-us/articles/building-vasp-with-intel-mkl-and-intel-compilers?page=1#comment-1842228

But I got the following error while running,

mpirun -np 4 /opt/VASP/vasp.5.3/vasp

this gives the error as follows,

WARNING: for PREC=h ENMAX is automatically increase by 25 %
this was not the case for versions prior to vasp.4.4
WARNING: for PREC=h ENMAX is automatically increase by 25 %
this was not the case for versions prior to vasp.4.4
WARNING: for PREC=h ENMAX is automatically increase by 25 %
this was not the case for versions prior to vasp.4.4
LDA part: xc-table for Ceperly-Alder, standard interpolation
POSCAR, INCAR and KPOINTS ok, starting setup
FFT: planning ...
WAVECAR not read
entering main loop
N E dE d eps ncg rms rms(c)

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libmpi.so.1 00002B3133018DE9 Unknown Unknown Unknown
libmkl_blacs_inte 00002B3130D8B273 Unknown Unknown Unknown
libmkl_blacs_inte 00002B3130D7D9FB Unknown Unknown Unknown
libmkl_blacs_inte 00002B3130D7D409 Unknown Unknown Unknown
vasp 00000000004D7BCD Unknown Unknown Unknown
vasp 00000000004CA239 Unknown Unknown Unknown
vasp 0000000000E23D62 Unknown Unknown Unknown
vasp 0000000000E447AD Unknown Unknown Unknown
vasp 0000000000472BC5 Unknown Unknown Unknown
vasp 000000000044D25C Unknown Unknown Unknown
libc.so.6 00002B31340C1C36 Unknown Unknown Unknown
vasp 000000000044D159 Unknown Unknown Unknown

--------------------------------------------------------------------------
mpirun has exited due to process rank 6 with PID 12042 on
node node01 exiting improperly. There are two reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------

Here all the libs associated with vasp executable,

ldd vasp

linux-vdso.so.1 => (0x00007fffcd1d5000)
libmkl_intel_lp64.so => /opt/intel/mkl/lib/intel64/libmkl_intel_lp64.so (0x00002b7018572000)
libmkl_cdft_core.so => /opt/intel/mkl/lib/intel64/libmkl_cdft_core.so (0x00002b7018c84000)
libmkl_scalapack_lp64.so => /opt/intel/mkl/lib/intel64/libmkl_scalapack_lp64.so (0x00002b7018ea0000)
libmkl_blacs_intelmpi_lp64.so => /opt/intel/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so (0x00002b701968b000)
libmkl_sequential.so => /opt/intel/mkl/lib/intel64/libmkl_sequential.so (0x00002b70198c8000)
libmkl_core.so => /opt/intel/mkl/lib/intel64/libmkl_core.so (0x00002b7019f66000)
libiomp5.so => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libiomp5.so (0x00002b701b174000)
libmpi_f90.so.3 => /opt/intel/openmpi-icc/lib/libmpi_f90.so.3 (0x00002b701b477000)
libmpi_f77.so.1 => /opt/intel/openmpi-icc/lib/libmpi_f77.so.1 (0x00002b701b67b000)
libmpi.so.1 => /opt/intel/openmpi-icc/lib/libmpi.so.1 (0x00002b701b8b8000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002b701bd03000)
libm.so.6 => /lib64/libm.so.6 (0x00002b701bf07000)
librt.so.1 => /lib64/librt.so.1 (0x00002b701c180000)
libnsl.so.1 => /lib64/libnsl.so.1 (0x00002b701c38a000)
libutil.so.1 => /lib64/libutil.so.1 (0x00002b701c5a2000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b701c7a5000)
libc.so.6 => /lib64/libc.so.6 (0x00002b701c9c3000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b701cd37000)
libifport.so.5 => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libifport.so.5 (0x00002b701cf4d000)
libifcore.so.5 => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libifcore.so.5 (0x00002b701d17d000)
libimf.so => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libimf.so (0x00002b701d4b3000)
libintlc.so.5 => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libintlc.so.5 (0x00002b701d96f000)
libsvml.so => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libsvml.so (0x00002b701dbbe000)
libifcoremt.so.5 => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libifcoremt.so.5 (0x00002b701e48c000)
libirng.so => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libirng.so (0x00002b701e7f1000)
/lib64/ld-linux-x86-64.so.2 (0x00002b7018351000)

Please take a look into this and help me in running the same.

TimP · ‎10-01-2015

You would need to build your MPI and application with -traceback or -debug inline-debug-info to get more useful results for the traceback. The useful advice about segfaults in https://software.intel.com/en-us/articles/determining-root-cause-of-sigsegv-or-sigbus-errors may not be enough if you need to deal with the combination of gdb-ia and MPI. Any hints from the OpenMPI site about use of gdb ought to work with gdb-ia.

If you haven't ruled out problems with your stack limit setting, and, if using OpenMP, OMP_STACKSIZE, you might start there.