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2024-05-18
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2024-05-17
Editing Qs tests on MBG cluster
The version of Qs used is dated September, 10th, 2004. The parallel version was compiled with <code> mpicc -DMPI -static -I/usr/local/include -O3 -unroll -tpp6 -xK -wp_ipo Qs_working.c -lsrfftw_intel -lsfftw_intel -limf -lm </code> where <b>mpicc</b> resolves to <code> icc -O2 -tpp6 -DUSE_STDARG -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDARG_H=1 -DUSE_STDARG=1 -DMALLOC_RET_VOID=1 -L/usr/local/mpich-ssh/lib -lmpich </code> Before measuring (using wall-clock time) the performance of the program, a comparison was made between running Qs with a simple 'mpirun' command, and running it via SGE. The setting for this test was * 4156 unique reflections * Space group <i>P422</i> * 100000 steps per minimisation * 1 minimisation * 4 processors (server + 3 celerons) The results were || *Method* || *Wall-clock time* || || mpirun || 919 seconds || || Grid Engine || 894 seconds || = The tests : Celerons & server = The parameters tested are # Number of unique reflections # Number of crystallographic symmetry operators (space group) # Number of processors In all cases only one minimisation was performed lasting 100,000 steps. The results are : == 8 symmetry operators == || /Reflections/ || /Space group/ ||/Processors/ || /Wall-clock time in seconds/ || /Scale-up/ || || 4156 || P422 || 1 (celeron) || 2032 || 1.000 || || 4156 || P422 || 1 (Pentium IV) || 1690 || 1.202 || || 4156 || P422 || 2 (mixed) || 1241|| 1.637 || || 4156 || P422 || 4 || 894 || 2.272 || || 4156 || P422 || 6 || 802 || 2.533 || || 4156 || P422 || 8 || 753 || 2.698 || || /Reflections/ || /Space group/ ||/Processors/ || /Wall-clock time in seconds/ || /Scale-up/ || || 2049 || P422 || 1 (celeron) || 1058 || 1.000 || || 2049 || P422 || 1 (Pentium IV) || 818 || 1.293 || || 2049 || P422 || 2 || 664 || 1.593 || || 2049 || P422 || 4 || 500 || 2.116 || || 2049 || P422 || 6 || 487 || 2.172 || || 2049 || P422 || 8 || 449 || 2.356 || || /Reflections/ || /Space group/ ||/Processors/ || /Wall-clock time in seconds/ || /Scale-up/ || || 8224 || P422 || 1 (celeron) || 4148 || 1.000 || || 8224 || P422 || 1 (Pentium IV) || 3449 || 1.202 || || 8224 || P422 || 2 || 2377 || 1.745 || || 8224 || P422 || 4 || 1685 || 2.501 || || 8224 || P422 || 6 || 1564 || 2.652 || || 8224 || P422 || 8 || 1329 || 3.121 || == 4 symmetry operators == || /Reflections/ || /Space group/ ||/Processors/ || /Wall-clock time in seconds/ || /Scale-up/ || || 4156 || P222 || 1 (celeron) || 1056 || 1.000 || || 4156 || P222 || 1 (Pentium IV) || 870 || 1.213 || || 4156 || P222 || 2 (mixed) || 752 || 1.404 || || 4156 || P222 || 4 || 659 || 1.602 || || 4156 || P222 || 6 || 661 || 1.597 || || 4156 || P222 || 8 || 650 || 1.624 || || /Reflections/ || /Space group/ ||/Processors/ || /Wall-clock time in seconds/ || /Scale-up/ || || 2049 || P222 || 1 (celeron) || 568 || 1.000 || || 2049 || P222 || 1 (Pentium IV) || 428 || 1.327 || || 2049 || P222 || 2 || 409 || 1.388 || || 2049 || P222 || 4 || 374 || 1.518 || || 2049 || P222 || 6 || 401 || 1.416 || || 2049 || P222 || 8 || 408 || 1.392 || || /Reflections/ || /Space group/ ||/Processors/ || /Wall-clock time in seconds/ || /Scale-up/ || || 8224 || P222 || 1 (celeron) || 2180 || 1.000 || || 8224 || P222 || 1 (Pentium IV) || 1796 || 1.213 || || 8224 || P222 || 2 || 1466 || 1.487 || || 8224 || P222 || 4 || 1211 || 1.800 || || 8224 || P222 || 6 || 1158 || 1.882 || || 8224 || P222 || 8 || 1114 || 1.956 || == 2 symmetry operators == || /Reflections/ || /Space group/ ||/Processors/ || /Wall-clock time in seconds/ || /Scale-up/ || || 10044 || P2 || 1 (celeron) || 1464 || 1.000 || || 10044 || P2 || 1 (Pentium IV) || 1208 || 1.211 || || 10044 || P2 || 2 (mixed) || 1215 || 1.204 || || 10044 || P2 || 4 || 1163 || 1.258 || || 10044 || P2 || 6 || 1216 || 1.203 || || /Reflections/ || /Space group/ ||/Processors/ || /Wall-clock time in seconds/ || /Scale-up/ || || 19879 || P2 || 1 (celeron) || 2718 || 1.000 || || 19879 || P2 || 1 (Pentium IV) || 2271 || 1.196 || || 19879 || P2 || 2 (mixed) || 2321 || 1.171 || || 19879 || P2 || 4 || 2169 || 1.253 || || 19879 || P2 || 6 || 2158 || 1.259 || = Conclusions = === On the newer nodes : === For high symmetry space groups it is probably worth using the parallel version. For orthorhombic space groups you will have to measure scale-up. For the low symmetry cases (monoclinic, triclinic), forget it. Just spawn 5 jobs (each with a different seed for the random number generator) and forget them.
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