Thread: [Apbs-users] parameter nlev / VMGNLEV
Biomolecular electrostatics software
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From: Gernot K. <ger...@we...> - 2004-12-10 15:26:52
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Hi! I'd like to adjust my grid geometry to save memory and cpu power. I've found out that the APBS-distribution I'm using (APBS-0.3.2) doesn't accept the nlev-parameter to be smaller than 4 (otherwise apbs would reset my grid to values consistent with nlev=4). It turned out that the VMGNLEV constant governing the minimum nlev value was set to 4. I wonder if there is deep reasoning behind this decision or if I just could recompile apbs with VMGNLEV set to 2 without any problems. With nlev=2 I could reshape my grid in a more flexible way. We compiled APBS for a 64-bit environment (AMD Opteron). TIA for suggestions! Greetings, Gernot |
From: Gernot K. <ge...@ch...> - 2004-12-10 15:29:23
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Hi! I'd like to adjust my grid geometry to save memory and cpu power. I've found out that the APBS-distribution I'm using (APBS-0.3.2) doesn't accept the nlev-parameter to be smaller than 4 (otherwise apbs would reset my grid to values consistent with nlev=4). It turned out that the VMGNLEV constant governing the minimum nlev value was set to 4. I wonder if there is a deep reasoning behind this decision or if I just could recompile apbs with VMGNLEV set to 2 without any problems. With nlev=2 I could reshape my grid in a more flexible way. We compiled APBS for a 64-bit environment (AMD Opteron). TIA for suggestions! Greetings, Gernot |
From: Nathan B. <ba...@bi...> - 2004-12-10 15:42:39
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Hello -- You could simply reset VMGNLEV to 2 but it is likely you will see some loss of performance in the code. This might not matter much for smaller systems but will get worse as the system size increases. Good luck, Nathan -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker > -----Original Message----- > From: apb...@ch... > [mailto:apb...@ch...] On Behalf Of > Gernot Kieseritzky > Sent: Friday, December 10, 2004 7:30 AM > To: apb...@ch... > Subject: [Apbs-users] parameter nlev / VMGNLEV > > Hi! > I'd like to adjust my grid geometry to save memory and cpu > power. I've found out that the APBS-distribution I'm using > (APBS-0.3.2) doesn't accept the nlev-parameter to be smaller > than 4 (otherwise apbs would reset my grid to values > consistent with nlev=4). > > It turned out that the VMGNLEV constant governing the minimum > nlev value was set to 4. I wonder if there is deep reasoning > behind this decision or if I just could recompile apbs with > VMGNLEV set to 2 without any problems. With > nlev=2 I could reshape my grid in a more flexible way. We > compiled APBS for a 64-bit environment (AMD Opteron). TIA for > suggestions! > > Greetings, > Gernot > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > |
From: Gernot K. <ge...@ch...> - 2004-12-10 18:34:23
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Hi! Am Freitag, 10. Dezember 2004 14:42 schrieb Nathan Baker: > Hello -- > > You could simply reset VMGNLEV to 2 but it is likely you will see some loss > of performance in the code. This might not matter much for smaller systems > but will get worse as the system size increases. Ok, thx. With VMGNLEV reset would I experience a general performance loss or only when I'm actually using NLEV=2? What do you mean by "smaller systems"? My molecule is about the size of 130x80x80 A. Nevertheless, I'll try it to save memory at least. Greetings, Gernot |
From: Nathan B. <ba...@bi...> - 2004-12-11 00:02:13
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You'd only see the performance problems when encountering NLEV=2 situations. Thanks, Nathan -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker > -----Original Message----- > From: apb...@ch... > [mailto:apb...@ch...] On Behalf Of > Gernot Kieseritzky > Sent: Friday, December 10, 2004 10:38 AM > To: apb...@ch... > Subject: Re: [Apbs-users] parameter nlev / VMGNLEV > > Hi! > > Am Freitag, 10. Dezember 2004 14:42 schrieb Nathan Baker: > > Hello -- > > > > You could simply reset VMGNLEV to 2 but it is likely you > will see some > > loss of performance in the code. This might not matter much for > > smaller systems but will get worse as the system size increases. > > Ok, thx. With VMGNLEV reset would I experience a general > performance loss or only when I'm actually using NLEV=2? What > do you mean by "smaller systems"? > My molecule is about the size of 130x80x80 A. Nevertheless, > I'll try it to save memory at least. > > Greetings, > Gernot > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > |