[gmx-users] Gromacs 3.3.3 segmentation fault on SLES10.2 x86_64 Xeon architecture - Intel Compilers & Intel MKL

[Juan Alejandro Palomino Benito]

Hi guys.

I have installed Gromacs 3.3.3 from source code on a machine with
SLES10.2 x86_64 Xeon architecture - Intel Compilers & Intel MKL. It
was configured like this:

export CC=mpiicc
export  CXX=mpiicpc
export F77=mpiifort
export FC=mpiifort
export MPICC=mpiicc

export CFLAGS="-m64 -O2 -I$MKLROOT/include"
export LDFLAGS="-L$MKLROOT/lib/em64t"
export  LIBS="-lm -lmkl_lapack -lmkl_intel_lp64 -lmkl_sequential
-lmkl_core -lpthread"

export  CPPFLAGS="-m64  -O2"
export  FFLAGS="-m64  -O2"
export  CXXFLAGS="-m64  -O2"

./configure  \
              --prefix=/app/gromacs/x86_64/3.3.3_s/  \
              --with-fft=mkl \
              --disable-software-sqrt \
              --enable-prefetch-forces  \
              --enable-mpi  \
              --with-external-lapack \
              --with-external-blas

and properly modified configure file in order to fix the MKL problem.

The problem is that I receive a segmentation fault after starting mdrun.
I attach a backtrace calls for debuging. It seems there is a problem
with Intel MKL, but I had not this problem with latest Gromacs
versions (4.0.5 and 4.0.7, single and double precision):


Back Off! I just backed up
/scratch/jpalomino/gromacs/benzocaina/345K/bzca_2_dpps_24_dppc_48_na_24_345K_0001.pdo
to /scratch/jpalomino/gromacs/benzocaina/345K/#bzca_2_dpps_24_dppc_48_na_24_345K_0001.pdo.21#
starting mdrun '2 BZCA + 54 DPPS +12 DPPS + 12 Na + 2477 H2O'
10000000 steps,  40000.0 ps.


Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 47952891846560 (LWP 23723)]
0x00002b9ce79201e6 in LIncAny_Loop4gas_1 () from
/opt/intel/mkl/10.2.2.025/lib/em64t/libmkl_mc.so
(gdb) bt
#0  0x00002b9ce79201e6 in LIncAny_Loop4gas_1 () from
/opt/intel/mkl/10.2.2.025/lib/em64t/libmkl_mc.so
#1  0x00002b9ce51c08cc in _2__STRING.0.0 () from
/opt/intel/mkl/10.2.2.025/lib/em64t/libmkl_lapack.so
#2  0x00007fffc66a7ac8 in ?? ()
#3  0x000000000093f2a0 in ?? ()
#4  0x00002ba0e891f020 in ?? ()
#5  0x00007fffc66a7ac8 in ?? ()
#6  0x00002b9ce47ff183 in mkl_blas_xscopy () from
/opt/intel/mkl/10.2.2.025/lib/em64t/libmkl_lapack.so
#7  0x00002b9ce8425cd0 in mkl_dft_xsforward_out () from
/opt/intel/mkl/10.2.2.025/lib/em64t/libmkl_mc.so
#8  0x00002b9ce59c88f4 in mkl_dft_xsforward_out () from
/opt/intel/mkl/10.2.2.025/lib/em64t/libmkl_sequential.so
#9  0x00002b9ce832514f in mkl_dft_compute_fwd_s_r2c_1d_o ()
   from /opt/intel/mkl/10.2.2.025/lib/em64t/libmkl_mc.so
#10 0x00002b9ce558260f in DftiComputeForward_1 () from
/opt/intel/mkl/10.2.2.025/lib/em64t/libmkl_intel_lp64.so
#11 0x000000000047f356 in gmx_fft_3d_real ()
#12 0x0000000000456bd7 in gmxfft3D ()
#13 0x0000000000450c7a in do_pme ()
#14 0x000000000042f000 in force ()
#15 0x0000000000461f46 in do_force ()
#16 0x00000000004153a7 in do_md ()
#17 0x0000000000413875 in mdrunner ()
#18 0x0000000000416d31 in main ()


Than you in advance.

-- 
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Juan Alejandro Palomino Benito
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