Dear Developers,
I am running a simple water box molecular dynamics calculation containing 12467 water molecules and a 54 atoms peptide inside the box.
system ecceSession_ecceMdDynamics
shake
data 500000
equil 0
step 0.002
update center 1
update motion 10
isotherm 0.0 298.15 anneal 0 100
isobar
record rest 1000
record coord 1000
record prop 1000
The calculation seems to be very slow on my system, which is Cray XE6m with 64 cores Abu Dhabi ~614.4 GFLOPS. The 1ns calculation took 7 hours to complete. Could someone point out how can I improve the efficiency?
The ldd returns
/packages/nwchem-6.1.1/bin/LINUX64/nwchem: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by /packages/nwchem-6.1.1/bin/LINUX64/nwchem)
/packages/nwchem-6.1.1/bin/LINUX64/nwchem: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by /opt/cray/lib64/libga_gnu_47.so.0)
linux-vdso.so.1 => (0x00007fffeb650000)
libsci_gnu.so.2 => /opt/cray/lib64/libsci_gnu.so.2 (0x00007f0a5b93e000)
libonesided.so.1 => /opt/cray/lib64/libonesided.so.1 (0x00007f0a5b732000)
libnumatoolkit.so.1 => /opt/cray/lib64/libnumatoolkit.so.1 (0x00007f0a5b52c000)
libga_gnu_47.so.0 => /opt/cray/lib64/libga_gnu_47.so.0 (0x00007f0a5b054000)
libarmci_gnu_47.so.0 => /opt/cray/lib64/libarmci_gnu_47.so.0 (0x00007f0a5ae1a000)
libdmapp.so.1 => /opt/cray/dmapp/default/lib64/libdmapp.so.1 (0x00007f0a5abe0000)
libmpich.so.1 => /opt/cray/lib64/libmpich.so.1 (0x00007f0a5a745000)
libgfortran.so.3 => /usr/lib64/libgfortran.so.3 (0x00007f0a5a46b000)
libm.so.6 => /lib64/libm.so.6 (0x00007f0a5a1f1000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f0a59fda000)
libquadmath.so.0 => /opt/cray/lib64/cce/libquadmath.so.0 (0x00007f0a59da4000)
libc.so.6 => /lib64/libc.so.6 (0x00007f0a59a2f000)
libmpich_gnu_47.so.1 => /opt/cray/lib64/libmpich_gnu_47.so.1 (0x00007f0a59594000)
libfftw3.so.3 => /opt/cray/lib64/libfftw3.so.3 (0x00007f0a59199000)
libfftw3f.so.3 => /opt/cray/lib64/libfftw3f.so.3 (0x00007f0a58d8d000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f0a58b70000)
libhugetlbfs.so => /usr/lib64/libhugetlbfs.so (0x00007f0a58951000)
librca.so.0 => /opt/cray/rca/default/lib64/librca.so.0 (0x00007f0a5874d000)
libAtpSigHandler.so.0 => /opt/cray/lib64/libAtpSigHandler.so.0 (0x00007f0a58547000)
libsci_gnu_mp.so.2 => /opt/cray/lib64/libsci_gnu_mp.so.2 (0x00007f0a5703f000)
libgomp.so.1 => /opt/gcc/default/snos/lib64/libgomp.so.1 (0x00007f0a56e30000)
libugni.so.0 => /opt/cray/ugni/default/lib64/libugni.so.0 (0x00007f0a56c03000)
libpmi.so.0 => /opt/cray/pmi/default/lib64/libpmi.so.0 (0x00007f0a569e2000)
libudreg.so.0 => /opt/cray/udreg/default/lib64/libudreg.so.0 (0x00007f0a567da000)
/lib64/ld-linux-x86-64.so.2 (0x00007f0a5ccc6000)
libmpl.so.0 => /opt/cray/lib64/libmpl.so.0 (0x00007f0a565d4000)
libopa.so.1 => /opt/cray/lib64/libopa.so.1 (0x00007f0a563d2000)
libxpmem.so.0 => /opt/cray/xpmem/default/lib64/libxpmem.so.0 (0x00007f0a561d0000)
librt.so.1 => /lib64/librt.so.1 (0x00007f0a55fc6000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f0a55dc2000)
Many thanks.
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