tag:blogger.com,1999:blog-8160351477288734008.post8215747758042337184..comments2024-03-15T08:18:25.585+01:00Comments on Computational Biochemistry: GotoBLAS2: A faster BLAS libraryAnonymoushttp://www.blogger.com/profile/18123073028209991396noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-8160351477288734008.post-27438687910701874202010-11-13T21:43:33.763+01:002010-11-13T21:43:33.763+01:00Thank you for correcting me on the two-electron in...Thank you for correcting me on the two-electron integrals!<br /><br />In principle GAMESS should be able to use BLAS routines from GotoBLAS2, since all BLAS libraries contain the same standard set of functions, only coded and optimized in different ways.<br /><br />I just tried and recompile the current GAMESS on my desktop at home, and it seems like you can only specify the BLAS libraries from MKL, ATLAS and ACML (or a crude, generic set of functions) because you have to go through the ./config script before compiling.<br />I will ask Casper for a definite answer and let you know! I'm fairly certain that it is possible to circumvent the standard installation procedure and introduce a non-standard BLAS library somewhere else. Casper may have done this when we tested the AMD Magny Cours machines.<br /><br />GotoBLAS2 is fully parallelized, so even if your main program is not parallelized, you can call the linear algebra routines and run those in parallel without your main program ever knowing it. The number of CPUS can be set either fixed when you compile GotoBLAS2 or later on via an environment variable.Anonymoushttps://www.blogger.com/profile/18123073028209991396noreply@blogger.comtag:blogger.com,1999:blog-8160351477288734008.post-52190171414494946172010-11-13T19:11:17.099+01:002010-11-13T19:11:17.099+01:00Interesting! Can GotoBLAS2 be used with GAMESS? ...Interesting! Can GotoBLAS2 be used with GAMESS? And is it parallelized? <br /><br /><br />"computational time, which is mainly spent doing standard linear algebra"<br /><br />That's not quite accurate. The most time-consuming part are usually the 2-electron integrals. But it is true that if the 2-electron integrals have been effectively parallelized and/or approxmiated, the linear algebra can become the bottleneck for large systems.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.com