Yep. There are lots of known bugs in old compilers. It's not an accident that the GROMACS installation instructions tell you to get up to date compilers - both for correctness and performance of the resulting code. 4.4.7 might be correct (if you can run the 4.6.3 regression tests on it, it might pass), but I would bet 4.7 or 4.8 will be faster.
Mark On Wed, Sep 11, 2013 at 3:28 PM, Xu, Jianqing <x...@medimmune.com> wrote: > Thanks again for the message! > > I am using the Gromacs 4.6.3. > > Hmm, indeed a lot of information from "mdrun -version"..... > > Both servers used gcc, and they are in different versions. > Server 1 (AMD) has gcc 4.1.2 > Server 2 (Intel) has gcc 4.4.7 > > I know the compilers are a bit old, but can this cause big difference in > results? > > Thanks a lot, > > Jianqing > > > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Mark Abraham [mark.j.abra...@gmail.com] > Sent: 11 September 2013 14:13 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Gromacs on Intel Xeon and AMD Opteron > > Hmm, that looks like a problem. Which GROMACS version, and which > compiler version? (See mdrun -version) > > On Wed, Sep 11, 2013 at 3:06 PM, Xu, Jianqing <x...@medimmune.com> wrote: >> >> Thanks for the comments, Mark. >> >> Sorry that I did not explain my question clear enough. >> >> I am actually talking about post-equilibration time average. I understand >> that some instantaneous deviations are expected, but the simulations should >> be correct as long as the ensemble averages are the same (or close enough), >> but the differences that I observed seemed beyond that. >> >> I firstly realized the total energy reported from two servers are obviously >> different (again, two simulations started from the same *.tpr file, and the >> executable on each server were compiled independently using the same >> arguments). I then checked the potential energy and kinetic energy as shown >> the below link: >> >> https://docs.google.com/file/d/0B7MGQ6N_2Ln7emRySENsZU40d2s/edit?usp=sharing >> >> >> Looks like the differences are from the potential energy. I then took a >> quick look at the LJ (SR) and Coulomb (SR) components, and it looks like the >> Coulomb (SR) component has big deviation which beyond the numerical errors. >> There are other differences, but looks like the Coulomb (SR) is the most >> obvious one. I was not able to understand how this can happen. >> >> https://docs.google.com/file/d/0B7MGQ6N_2Ln7bzB4YVhvMjdsNkE/edit?usp=sharing >> >> I hope the figures can clarify my situation better, and I will appreciate if >> you or anyone else on the list could provide more suggestions. >> >> Thanks a lot! >> >> Regards, >> >> Jianqing >> >> >> >> ________________________________________ >> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on >> behalf of Mark Abraham [mark.j.abra...@gmail.com] >> Sent: 11 September 2013 10:56 >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] Gromacs on Intel Xeon and AMD Opteron >> >> It's not clear whether you are reporting single points or >> post-equilibration time averages, but either way you must expect >> differences. MD simulations are chaotic. However, the long-time >> ensemble averages should agree well - that's the point of the >> simulation. >> >> Mark >> >> On Wed, Sep 11, 2013 at 10:35 AM, Xu, Jianqing <x...@medimmune.com> wrote: >>> Dear all, >>> >>> This is my first time here. I apologize if I am not aware any rules for >>> posting a new message. >>> >>> I was testing Gromacs on two servers, one server has AMD Opteron processor >>> (Server 1), and the other has Intel Xeon processor (Server 2). The >>> simulation system that I tried is the lysozyme system from the online >>> tutorial >>> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/). >>> Briefly, it has a lysozyme in 10824 water, and 8 Cl-. Box size is around >>> 6.99 nm. >>> >>> I finished all the preparation steps advised by the tutorials, and tested >>> the final NPT production runs on two servers, using the same final input >>> file "md_0_1.tpr". It is strange that the results from Server 1 (AMD) has >>> higher potential energy than the results from Server2 (Intel), >>> specifically, results from Server1 (AMD) has higher "Coulomb-(SR)" than >>> Server2 (Intel) ( ~ -5.5*10^5 .vs. ~ -5.7*10^5 kj/mol ). >>> >>> I was wondering if anyone could give me any suggestions about what could be >>> the reasons causing this discrepancy. >>> >>> Some additional information: >>> 1). Jobs run on my local computer, which also has Intel CPUs (Intel(R) >>> Xeon(R) CPU E5620 @ 2.40GHz), reported the same results as the Server2 >>> (Intel(R) Xeon(R) CPU X7550 @ 2.00GHz). >>> 2). All installations (Gromacs and OpenMPI) on Server 1 and 2 were compiled >>> independently, but with the same arguments. >>> >>> >>> I understand that the information I provided may not be sufficient. If I >>> should provide more specific information, please let me know. >>> >>> Any help will be highly appreciated! >>> >>> Thanks, >>> >>> Jianqing >>> To the extent this electronic communication or any of its attachments >>> contain information that is not in the public domain, such information is >>> considered by MedImmune to be confidential and proprietary. This >>> communication is expected to be read and/or used only by the individual(s) >>> for whom it is intended. If you have received this electronic communication >>> in error, please reply to the sender advising of the error in transmission >>> and delete the original message and any accompanying documents from your >>> system immediately, without copying, reviewing or otherwise using them for >>> any purpose. Thank you for your cooperation. >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> To the extent this electronic communication or any of its attachments >> contain information that is not in the public domain, such information is >> considered by MedImmune to be confidential and proprietary. This >> communication is expected to be read and/or used only by the individual(s) >> for whom it is intended. If you have received this electronic communication >> in error, please reply to the sender advising of the error in transmission >> and delete the original message and any accompanying documents from your >> system immediately, without copying, reviewing or otherwise using them for >> any purpose. Thank you for your cooperation. >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > To the extent this electronic communication or any of its attachments contain > information that is not in the public domain, such information is considered > by MedImmune to be confidential and proprietary. This communication is > expected to be read and/or used only by the individual(s) for whom it is > intended. If you have received this electronic communication in error, please > reply to the sender advising of the error in transmission and delete the > original message and any accompanying documents from your system immediately, > without copying, reviewing or otherwise using them for any purpose. Thank you > for your cooperation. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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