Re: [gmx-users] old patch for slow networks
Jones de Andrade wrote: Hi all. I'm writing this message to ask a simple and direct question: the available patch of gmx3 for slow networks, that includes the ordered-all-to-all procedures, seems fo be indicated for version 3.1. Hi Jones, this is actually a patch for gromacs 3.3.1. It's still necessary for slow networks using gmx3.3? Whether it is necessary depends on your setup. In the patched version the all-to-all communication happens in an orderly fashion such that TCP packet drops are avoided. So the patch will speed up your parallel performance if you have packet drops in the first place. An indication for such drops is when you make speedup measurements on 1, 2, 3, ... nodes (each node may have multiple CPUs) and your performance curve is not smooth but abruptly drops down when you go to more than two nodes. With the patch comes a test program for all-to-all problems. Hope that helps, Carsten Thanks a lot in advance... Sincerally yours, Jones ___ gmx-users mailing listgmx-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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department Am Fassberg 11 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/research/dep/grubmueller/ http://www.gwdg.de/~ckutzne ___ gmx-users mailing listgmx-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
RE: [gmx-users] Blue Gene/P
Hi, Gromacs 4 has blue gene optimized inner loops, which give a factor of 2 performance improvement. On a BG/L it runs at 20-25% of the speed of x86 cores, but it scales quite well. Berk. Date: Mon, 31 Mar 2008 17:29:57 -0700 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] Blue Gene/P Thanks. I've seen the BG/L argument, but BG/P processors are faster. I have no idea how much though, and am looking for actual numbers or if those are not available a guess based on actual BG/L numbers and some argument about scaling to a BG/P. Cheers, Peter Mark Abraham wrote: Peter Tieleman wrote: Hi, Has anyone run benchmarks on a BlueGene/P ? The word from IBM in December was that since GROMACS 3.x would lack both assembly inner-loops and threading on BlueGene/L, that it wasn't worthwhile running GROMACS on onw. I figure that goes for BlueGene/P too. Mark ___ gmx-users mailing listgmx-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 ___ gmx-users mailing listgmx-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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-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
[gmx-users] how to simulate 2 structures together
Hii I want to simmulate and minimize two protein structures together in water, can you tell me any tutorial online or send me any information. Radhika On 4/1/08, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. RE: Blue Gene/P (Berk Hess) 2. Re: Blue Gene/P (Hannes Loeffler) -- Message: 1 Date: Tue, 1 Apr 2008 09:34:54 +0200 From: Berk Hess [EMAIL PROTECTED] Subject: RE: [gmx-users] Blue Gene/P To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi, Gromacs 4 has blue gene optimized inner loops, which give a factor of 2 performance improvement. On a BG/L it runs at 20-25% of the speed of x86 cores, but it scales quite well. Berk. Date: Mon, 31 Mar 2008 17:29:57 -0700 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] Blue Gene/P Thanks. I've seen the BG/L argument, but BG/P processors are faster. I have no idea how much though, and am looking for actual numbers or if those are not available a guess based on actual BG/L numbers and some argument about scaling to a BG/P. Cheers, Peter Mark Abraham wrote: Peter Tieleman wrote: Hi, Has anyone run benchmarks on a BlueGene/P ? The word from IBM in December was that since GROMACS 3.x would lack both assembly inner-loops and threading on BlueGene/L, that it wasn't worthwhile running GROMACS on onw. I figure that goes for BlueGene/P too. Mark ___ gmx-users mailing listgmx-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 ___ gmx-users mailing listgmx-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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080401/8d0d044f/attachment-0001.html -- Message: 2 Date: Tue, 01 Apr 2008 09:10:09 +0100 From: Hannes Loeffler [EMAIL PROTECTED] Subject: Re: [gmx-users] Blue Gene/P To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain Ok, here just a few numbers. System: 52.000 atoms, coarse-grained, 500.000 steps BlueGene/P: 16(procs) x 4(threads) = 64 tasks (or whatever they are called) 8x4 7.25 h 16x4 11h 32x4 12 h (queue only allows = 12 h) BlueGene/L: 16x2 10 h 64x2 12 h Note: the procs x threads figures above are the numbers I asked for. It may be possible that the scheduler distributes in a different manner. I don't now. That's all I have for the moment. On Mon, 2008-03-31 at 17:29 -0700, Peter Tieleman wrote: Thanks. I've seen the BG/L argument, but BG/P processors are faster. I have no idea how much though, and am looking for actual numbers or if those are not available a guess based on actual BG/L numbers and some argument about scaling to a BG/P. Cheers, Peter Mark Abraham wrote: Peter Tieleman wrote: Hi, Has anyone run benchmarks on a BlueGene/P ? The word from IBM in December was that since GROMACS 3.x would lack both assembly inner-loops and threading on BlueGene/L, that it wasn't worthwhile running GROMACS on onw. I figure that goes for BlueGene/P too. Mark ___ gmx-users mailing listgmx-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
Re: [gmx-users] Blue Gene/P
Ok, here just a few numbers. System: 52.000 atoms, coarse-grained, 500.000 steps BlueGene/P: 16(procs) x 4(threads) = 64 tasks (or whatever they are called) 8x4 7.25 h 16x4 11h 32x4 12 h (queue only allows = 12 h) BlueGene/L: 16x2 10 h 64x2 12 h Note: the procs x threads figures above are the numbers I asked for. It may be possible that the scheduler distributes in a different manner. I don't now. That's all I have for the moment. On Mon, 2008-03-31 at 17:29 -0700, Peter Tieleman wrote: Thanks. I've seen the BG/L argument, but BG/P processors are faster. I have no idea how much though, and am looking for actual numbers or if those are not available a guess based on actual BG/L numbers and some argument about scaling to a BG/P. Cheers, Peter Mark Abraham wrote: Peter Tieleman wrote: Hi, Has anyone run benchmarks on a BlueGene/P ? The word from IBM in December was that since GROMACS 3.x would lack both assembly inner-loops and threading on BlueGene/L, that it wasn't worthwhile running GROMACS on onw. I figure that goes for BlueGene/P too. Mark ___ gmx-users mailing listgmx-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 ___ gmx-users mailing listgmx-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 ___ gmx-users mailing listgmx-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
Re: [gmx-users] how to simulate 2 structures together
Quoting Radhika Jaswal [EMAIL PROTECTED]: Hii I want to simmulate and minimize two protein structures together in water, can you tell me any tutorial online or send me any information. I would suggest starting with basic tutorial material regarding simple protein-in-water systems. That way, you can gain appreciation for how to set up a generic system within Gromacs, as well as understanding the topology format. Once you feel comfortable using the basic tools to set up a basic system, then move on to a two-component system. There are relevant discussions in the list archive on how to deal with peptides with two chains, multiple proteins, and so forth. Do a thorough search of the archive, and post specific questions when they arise. -Justin Radhika On 4/1/08, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. RE: Blue Gene/P (Berk Hess) 2. Re: Blue Gene/P (Hannes Loeffler) -- Message: 1 Date: Tue, 1 Apr 2008 09:34:54 +0200 From: Berk Hess [EMAIL PROTECTED] Subject: RE: [gmx-users] Blue Gene/P To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi, Gromacs 4 has blue gene optimized inner loops, which give a factor of 2 performance improvement. On a BG/L it runs at 20-25% of the speed of x86 cores, but it scales quite well. Berk. Date: Mon, 31 Mar 2008 17:29:57 -0700 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] Blue Gene/P Thanks. I've seen the BG/L argument, but BG/P processors are faster. I have no idea how much though, and am looking for actual numbers or if those are not available a guess based on actual BG/L numbers and some argument about scaling to a BG/P. Cheers, Peter Mark Abraham wrote: Peter Tieleman wrote: Hi, Has anyone run benchmarks on a BlueGene/P ? The word from IBM in December was that since GROMACS 3.x would lack both assembly inner-loops and threading on BlueGene/L, that it wasn't worthwhile running GROMACS on onw. I figure that goes for BlueGene/P too. Mark ___ gmx-users mailing listgmx-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 ___ gmx-users mailing listgmx-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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080401/8d0d044f/attachment-0001.html -- Message: 2 Date: Tue, 01 Apr 2008 09:10:09 +0100 From: Hannes Loeffler [EMAIL PROTECTED] Subject: Re: [gmx-users] Blue Gene/P To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain Ok, here just a few numbers. System: 52.000 atoms, coarse-grained, 500.000 steps BlueGene/P: 16(procs) x 4(threads) = 64 tasks (or whatever they are called) 8x4 7.25 h 16x4 11h 32x4 12 h (queue only allows = 12 h) BlueGene/L: 16x2 10 h 64x2 12 h Note: the procs x threads figures above are the numbers I asked for. It may be possible that the scheduler distributes in a different manner. I don't now. That's all I have for the moment. On Mon, 2008-03-31 at 17:29 -0700, Peter Tieleman wrote: Thanks. I've seen the BG/L argument, but BG/P processors are faster. I have no idea how much though, and am looking for actual numbers
[gmx-users] Problem with lipid simulations
Dear All, I have been trying to simulate a small peptide in a DMPC lipid bylayer. Same setup is working fine in one computer (cluster) but I am getting the following error message in another cluster. grompp_mpi -f test.mdp -c lipid_protein.gro -p topology.top -o test.tpr checking input for internal consistency... calling /lib/cpp... processing topology... WARNING 1 [file lipid.itp, line 14]: Overriding atomtype LO WARNING 2 [file lipid.itp, line 15]: Overriding atomtype LOM WARNING 3 [file lipid.itp, line 16]: Overriding atomtype LNL WARNING 4 [file lipid.itp, line 17]: Overriding atomtype LC WARNING 5 [file lipid.itp, line 18]: Overriding atomtype LH1 WARNING 6 [file lipid.itp, line 19]: Overriding atomtype LH2 WARNING 7 [file lipid.itp, line 20]: Overriding atomtype LP WARNING 8 [file lipid.itp, line 21]: Overriding atomtype LOS WARNING 9 [file lipid.itp, line 22]: Overriding atomtype LP2 WARNING 10 [file lipid.itp, line 23]: Overriding atomtype LP3 Cleaning up temporary file grompp16bicP --- Program grompp_mpi, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp_mpi terminated --- Please let me know how to get rid of this problem. Thanks in advance Regards Chandu ___ gmx-users mailing listgmx-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
[gmx-users] Problem with lipid simulations
Where is lipid.itp and your other forcefield files. Check that they are identical between your two clusters. This appears to be a problem with files and not with the installation. If you can't figure it out, you will need to post your topology at the very least and also post 'grep LO ffoplsaa*.itp' or xxx in place of oplsaa for whatever ff you are using. That said, the error messages are pretty explicit. I assume that you checked to see that you are including atomtype LO, etc. more than once? You can probably figure out exactly where the problem is occurring by yourself and you are more likely to get some good advice ifyou do that. Chris. -- original message -- Dear All, I have been trying to simulate a small peptide in a DMPC lipid bylayer. Same setup is working fine in one computer (cluster) but I am getting the following error message in another cluster. grompp_mpi -f test.mdp -c lipid_protein.gro -p topology.top -o test.tpr checking input for internal consistency... calling /lib/cpp... processing topology... WARNING 1 [file lipid.itp, line 14]: Overriding atomtype LO WARNING 2 [file lipid.itp, line 15]: Overriding atomtype LOM WARNING 3 [file lipid.itp, line 16]: Overriding atomtype LNL WARNING 4 [file lipid.itp, line 17]: Overriding atomtype LC WARNING 5 [file lipid.itp, line 18]: Overriding atomtype LH1 WARNING 6 [file lipid.itp, line 19]: Overriding atomtype LH2 WARNING 7 [file lipid.itp, line 20]: Overriding atomtype LP WARNING 8 [file lipid.itp, line 21]: Overriding atomtype LOS WARNING 9 [file lipid.itp, line 22]: Overriding atomtype LP2 WARNING 10 [file lipid.itp, line 23]: Overriding atomtype LP3 Cleaning up temporary file grompp16bicP --- Program grompp_mpi, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp_mpi terminated --- Please let me know how to get rid of this problem. Thanks in advance Regards Chandu ___ gmx-users mailing listgmx-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
Re: [gmx-users] Problem with lipid simulations
Hi Chandu, this looks like you have two statements #include lipid.itp, so check all your *.top and *.itp files. Ciao, Patrick [EMAIL PROTECTED] a écrit : Dear All, I have been trying to simulate a small peptide in a DMPC lipid bylayer. Same setup is working fine in one computer (cluster) but I am getting the following error message in another cluster. grompp_mpi -f test.mdp -c lipid_protein.gro -p topology.top -o test.tpr checking input for internal consistency... calling /lib/cpp... processing topology... WARNING 1 [file lipid.itp, line 14]: Overriding atomtype LO WARNING 2 [file lipid.itp, line 15]: Overriding atomtype LOM WARNING 3 [file lipid.itp, line 16]: Overriding atomtype LNL WARNING 4 [file lipid.itp, line 17]: Overriding atomtype LC WARNING 5 [file lipid.itp, line 18]: Overriding atomtype LH1 WARNING 6 [file lipid.itp, line 19]: Overriding atomtype LH2 WARNING 7 [file lipid.itp, line 20]: Overriding atomtype LP WARNING 8 [file lipid.itp, line 21]: Overriding atomtype LOS WARNING 9 [file lipid.itp, line 22]: Overriding atomtype LP2 WARNING 10 [file lipid.itp, line 23]: Overriding atomtype LP3 Cleaning up temporary file grompp16bicP --- Program grompp_mpi, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp_mpi terminated --- Please let me know how to get rid of this problem. Thanks in advance Regards Chandu ___ gmx-users mailing listgmx-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 -- _ new E-mail address: [EMAIL PROTECTED] Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing listgmx-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
