On 5/28/10 11:08 AM, Juan Alejandro Palomino Benito wrote:
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.
If you really need gromacs 3.3.3 then the simple workaround is to use
FFTW3. MKL is only a few % faster since FFT is not the bottleneck in
gromacs.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[email protected] [email protected] http://folding.bmc.uu.se
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
