Dear Mark, many thanks for your suggestions. At present, the problem I reported here seems to be solved using the gcc442 compilers, we are doing a lot of checks on the machine and we will take into account all your observations. Many thanks also for the correction on the web site.
Anna ------------------------------ Message: 4 Date: Thu, 27 May 2010 17:28:48 +1000 From: Mark Abraham <[email protected]> Subject: Re: [gmx-users] Re: stepsize too small: help to solve problem in GROMACS installation To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; CHARSET=US-ASCII ----- Original Message ----- From: Anna Marabotti <[email protected]> Date: Thursday, May 27, 2010 16:55 Subject: [gmx-users] Re: stepsize too small: help to solve problem in GROMACS installation To: [email protected] > Dear Justin, dear all, > sorry for not having seen the warning before asking the question about > compilers (just a little justification, however: the warning > appears only on > the Download page, not on the Installation page; I went directly > to the > installation page and I did not notice it). Fixed. > The only other possibility we have is to try compiling GROMACS > with gcc-442 > compiler. This time I checked more carefully (at least, I hope > so!) on the > site and it seems to me that no problems are reported. For your > experience,is it a good choice or we can expect other problems? > In this last case, what > do you suggest as the best compiler for Gromacs? GROMACS performance is pretty insensitive to compiler version so long as you are using assembly-language inner loops (e.g. always true by default on x86). Most of the compute time is spent there, so most of the rest is irrelevant. The main side issue is the FFT performance for PME. Make sure you're using either vendor FFT libraries, or suitably well-compiled FFTW. Even there, FFTW with gcc -O5 (making sure the SSE(n) optimization is used) was only a hair behind icc+mkl in some tests I did a year ago. Mark -- 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
