Dear all, we installed GROMACS v. 3.3.2 on a cluster formed by 20 biprocessor nodes with Centos 4 x86_64, following instructions on the GROMACS web site. We compiled it in single precision, parallel version using the --enable-mpi option (LAM MPI was already present on the cluster). After the final installation, I made calculations and found that the parallel scalability of the software is very bad: in fact, when I use 3 or more processors, the performance is the same (or even worse) than using a single processor. As benchmarks, I used two systems: the spider toxin peptide (GROMACS tutorial) in a cubic box of 0.7 nm filled with 2948 water molecules (model: spc216) (Total: ~3200 atoms), and a dimeric protein of 718 aa in a cubic box (box edge 0.7 nm) filled with 18425 water molecules (model: spc216) and 6 Na+ ions (Total: ~62700 atoms). In both cases I set the Gromos 96 FF (G43a1). I used the following commands:
grompp_mpi -np "nofprocessors" -f pr.mdp -c systemmini.gro -o systempr.tpr -p system.top mpirun -np "nofprocessors" mdrun_mpi -s systempr.tpr -o systempr.trr -c systempr.gro -e systempr.edr -g systempr.log I paste here the results of the performances of position-restrained MD: spider toxin peptide: np time Mnbf/s GFlops ns/day hours/ns 1 1m 51s 237 10.797 2.425 7.806 3.074 2 0m 59s 614 19.561 4.402 14.664 1.694 3 2m 11s 622 9.261 2.082 6.698 3.583 4 1m 58s 722 10.283 2.315 7.448 3.222 5 1m 40s 580 11.813 2.659 8.554 2.806 6 1m 50s 830 10.859 2.442 7.855 3.056 7 1m 49s 232 10.878 2.442 7.855 3.056 8 2m 2s 292 6.190 1.392 4.477 5.361 9 2m 5s 778 9.533 2.150 6.912 3.472 10 2m 22s 540 8.349 1.879 6.042 3.972 dimeric protein: np time Mnbf/s GFlops ns/day hours/ns 1 13m 51s 391 14.041 2.179 1.043 23.016 2 7m 45s 321 25.011 3.883 1.858 12.917 3 15m 26s 621 12.586 1.954 0.935 25.667 4 15m 15s 3 12.749 1.978 0.946 25.361 5 12m 35s 274 15.481 2.401 1.149 20.889 6 13m 23s 750 14.517 2.255 1.079 22.250 7 12m 25s 659 15.669 2.435 1.164 20.611 8 13m 0s 434 14.977 2.325 1.112 21.583 9 12m 12s 601 15.949 2.475 1.184 20.278 10 13m 1s 724 14.962 2.322 1.111 21.611 I saw in the GROMACS mailing list that it could be due to a problem of communication between nodes, but it seems to me that nobody obtained so bad results before. Has anybody some suggestions - apart waiting for GROMACS 4.0 version ;-) - about some further checks to do on the system or different compilation/installation to try? Many thanks in advance and regards Anna ______________________________________________ Anna Marabotti, Ph.D. Laboratorio di Bioinformatica e Biologia Computazionale Istituto di Scienze dell'Alimentazione, CNR Via Roma 52 A/C 83100 Avellino (Italy) Tel: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: [EMAIL PROTECTED] Web page: http://bioinformatica.isa.cnr.it/anna.htm ____________________________________________________ "If you think you are too small to make a difference, try sleeping with a mosquito" _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
