Re: [gmx-users] GROMACS 2019: CorrelationsTest and TrajectoryAnalysisUnitTests segfaults on CentOS 7.6
The build where we have seen it is with intel 2018.3.222 using GCC 7.3.0 as base compiler and binutils 2.30. The same combo on Ubuntu 16.04 does not have a problem. Just wanted to know if it is a known problem or not. On 1/17/19 6:54 PM, Mark Abraham wrote: > Hi, > > Sounds novel. Fedora CI testing hasn't found that, but probably not done > with icc. Which icc version was that? The 1x.0.0 versions have tended to > have some codegen issues found by our tests... But of course we can't rule > out that our code can be improved! > > Mark > > On Thu., 17 Jan. 2019, 16:36 Åke Sandgren, > wrote: > >> Hi! >> >> We're seeing segfaults on the CorrelationsTest and >> TrajectoryAnalysisUnitTests on CentOS 7.5 and 7.6 systems. >> >> It only happens when building with Intel not with GCC. >> >> Has anyone else seen this happen? >> >> -- >> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden >> Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 >> Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] use of DPOSRES without pdb2gmx
Justin, Thanks, Bartimaeus -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: Thursday, January 17, 2019 2:44 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] use of DPOSRES without pdb2gmx On 1/17/19 3:33 PM, pbusc...@q.com wrote: > Dear Users, > > Suppose you do not use pdb2gmx and therefore do not use the -I > option for all constraints. Suppose further you do not generate a > restraint file for the non-protein molecules in the model. > > Then what effect, if any, does setting constraints = all-bonds or > h-bonds have ? Constraints and restraints are totally different. If you tell mdrun to constrain bonds, it will do precisely what you tell it. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] About GMX_PRINT_DEBUG_LINES
On 1/17/19 9:39 AM, Mahmood Naderan wrote: Hi, I set GMX_PRINT_DEBUG_LINE before the mdrun command, however, I don't see any debug message $ GMX_PRINT_DEBUG_LINES=1 $ gmx mdrun -nb gpu -ntmpi 8 -ntomp 1 -v -deffnm nvt ...NOTE: DLB can now turn on, when beneficialstep 1100, will finish Fri Jan 18 19:24:07 2019imb F 8% step 1200 Turning on dynamic load balancing, because the performance loss due to load imbalance is 5.0 %. step 7900, will finish Fri Jan 18 17:42:40 2019vol 0.74! imb F 4% Without setting that variable, those messages are still printed! Any thought? That's not a valid environment variable; it doesn't appear anywhere in the code. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] use of DPOSRES without pdb2gmx
On 1/17/19 3:33 PM, pbusc...@q.com wrote: Dear Users, Suppose you do not use pdb2gmx and therefore do not use the -I option for all constraints. Suppose further you do not generate a restraint file for the non-protein molecules in the model. Then what effect, if any, does setting constraints = all-bonds or h-bonds have ? Constraints and restraints are totally different. If you tell mdrun to constrain bonds, it will do precisely what you tell it. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] use of DPOSRES without pdb2gmx
Dear Users, Suppose you do not use pdb2gmx and therefore do not use the -I option for all constraints. Suppose further you do not generate a restraint file for the non-protein molecules in the model. Then what effect, if any, does setting constraints = all-bonds or h-bonds have ? Thanks Paul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
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Re: [gmx-users] core dumped
Thank you very much Justin. Sent from my iPhone > On Jan 17, 2019, at 1:38 AM, Justin Lemkul wrote: > > > >> On 1/15/19 12:58 PM, rabee khorram wrote: >> Hello; >> >> Thank you Justin for your answer. >> >> I have mailed fe2o3.pdb file in this gmail for you. > > The mailing list does not accept attachments, nor would a PDB file be useful > here. > >> in atomname2type.n2t, for Fe-O bonds, I have used Fe type From the >> atomtype.atp of charmm36 force field, >> >> : (FE 55.84700 ; heme iron 56) >> >> is it correct? > > The CHARMM Fe atom type has only been parametrized for heme. I have no idea > if it will be suitable for any other system. Likely not. Charge assignment is > also non-trivial for a system like this. > > -Justin > >> >> >> >>> On Tue, Jan 15, 2019 at 5:30 PM Justin Lemkul wrote: >>> >>> On 1/15/19 6:47 AM, rabee khorram wrote: Segmentation fault (core dumped)? *Hello everyone, I am runnig nano Fe2O3 structure with PEN drug with gromacs5.* >>> How did you parametrize and validate these species? >>> *but in step :* * gmx mdrun -v -deffnm nvt * * I am getting an error : step 2600, remaining wall clock time: 60 s Segmentation fault (core dumped)* *and don't create nvt.gro.!* *can you explain to me what is my problem?* *thank you very much.* >>> http://manual.gromacs.org/current/user-guide/terminology.html#blowing-up >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Office: 301 Fralin Hall >>> Lab: 303 Engel Hall >>> >>> Virginia Tech Department of Biochemistry >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.thelemkullab.com >>> >>> == >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GROMACS 2019: CorrelationsTest and TrajectoryAnalysisUnitTests segfaults on CentOS 7.6
Hi, Sounds novel. Fedora CI testing hasn't found that, but probably not done with icc. Which icc version was that? The 1x.0.0 versions have tended to have some codegen issues found by our tests... But of course we can't rule out that our code can be improved! Mark On Thu., 17 Jan. 2019, 16:36 Åke Sandgren, wrote: > Hi! > > We're seeing segfaults on the CorrelationsTest and > TrajectoryAnalysisUnitTests on CentOS 7.5 and 7.6 systems. > > It only happens when building with Intel not with GCC. > > Has anyone else seen this happen? > > -- > Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden > Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 > Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] combine -rerun and -multi features of mdrun
Hi, On Thu., 17 Jan. 2019, 13:42 Andreas Mecklenfeld, < a.mecklenf...@tu-braunschweig.de> wrote: > Dear Gromacs users, > > I would like to combine the -rerun with the -multi feature of the mdrun > command. > I don't know if the multisim feature works with rerun, but I would strongly suggest using -multidir (which is anyway the only one remaining in GROMACS 2019). For the -multi feature, I understand that I have to rename my input > files to e.g. system0.tpr, system1.tpr, ... - correct? > You would, but it is much easier to leave the names alone and put them in directories that can be passed to -multidir with a wildcard. Be aware that shell wildcards will not order multiple digits numerically. I would like to interpret energies for these systems, based on the same > trajectory file. Is it possible to refer to the trajetory file as e.g. > system*.trr, so that I don't have to duplicate and rename the files to > system0.trr, system1.trr etc.? > You'd have to provide copies. But the workload for a rerun is so light that I suggest you not bother with combining multisim! Mark > Thanks and regards, > Andreas > > -- > M. Sc. Andreas Mecklenfeld > Technische Universität Braunschweig > Institut für Thermodynamik > Hans-Sommer-Straße 5 > 38106 Braunschweig > Deutschland / Germany > > Tel: +49 (0)531 391-2634 > +49 (0)531 391-65685 > Fax: +49 (0)531 391-7814 > > http://www.ift-bs.de > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GROMACS 2019: CorrelationsTest and TrajectoryAnalysisUnitTests segfaults on CentOS 7.6
Hi! We're seeing segfaults on the CorrelationsTest and TrajectoryAnalysisUnitTests on CentOS 7.5 and 7.6 systems. It only happens when building with Intel not with GCC. Has anyone else seen this happen? -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] About GMX_PRINT_DEBUG_LINES
Hi, I set GMX_PRINT_DEBUG_LINE before the mdrun command, however, I don't see any debug message $ GMX_PRINT_DEBUG_LINES=1 $ gmx mdrun -nb gpu -ntmpi 8 -ntomp 1 -v -deffnm nvt ...NOTE: DLB can now turn on, when beneficialstep 1100, will finish Fri Jan 18 19:24:07 2019imb F 8% step 1200 Turning on dynamic load balancing, because the performance loss due to load imbalance is 5.0 %. step 7900, will finish Fri Jan 18 17:42:40 2019vol 0.74! imb F 4% Without setting that variable, those messages are still printed! Any thought? Regards,Mahmood -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] combine -rerun and -multi features of mdrun
Dear Gromacs users, I would like to combine the -rerun with the -multi feature of the mdrun command. For the -multi feature, I understand that I have to rename my input files to e.g. system0.tpr, system1.tpr, ... - correct? I would like to interpret energies for these systems, based on the same trajectory file. Is it possible to refer to the trajetory file as e.g. system*.trr, so that I don't have to duplicate and rename the files to system0.trr, system1.trr etc.? Thanks and regards, Andreas -- M. Sc. Andreas Mecklenfeld Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 +49 (0)531 391-65685 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] [MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany
Dear list subscribers, we are very delighted to announce this year’s “33rd Molecular Modelling Workshop (MMWS)” (http://mmws2019.mgms-ds.de) that takes place on April, Monday 8th to Wednesday 10th, 2019, at the Friedrich-Alexander-University in Erlangen, Germany. The MMWS has a long history of giving young scientists (especially graduate students) the opportunity to present their work and dive into discussions with each other and the "older experts" of the field to gain valuable feedback from academic as well as industrial colleagues. Oral and poster contributions are welcome from all areas of molecular modelling – from the life sciences, computational biology and chemistry, cheminformatics, to materials sciences. Starting with the scientific program on Monday after lunch should allow to avoid travelling on weekend keeping the expenses at a minimum. A hearty workshop dinner and a traditional joint evening in Erlangen’s Steinbach-Bräu brewery complement the scientific program. The workshop is organised by the German Section of the Molecular Graphics and Modelling Society (MGMS-DS e.V.). ### Satellite symposium in honour of Tim Clark's 70th birthday ### Directly after the MMWS, there will be a one-day symposium on Thursday April 11th, 2019 to celebrate the occasion of Tim Clark's 70th birthday. You are invited to attend this meeting and extend your stay in Erlangen by an extra day. There will be invited lectures only and no contributed talks. There is no registration, conference desk, or extra fee. Nevertheless, we expect that you indicate your interest in attending on Thursday by checking the corresponding field during registration for the MMWS. For further information about our Birthday Symposium, please refer to "Tim-Clark-Day" via https://mmws2019.mgms-ds.de/index.php?m=113 ### Pre-conference workshop ### For the second time at our Molecular Modeling Workshop, Schrödinger is offering a pre-conference workshop entiteled "Structure-based Drug Design using the Schrödinger Suite". If you are interested in participating at the software session, please checkmark the corresponding field upon filling the registration form. ### Plenary Speakers ### We are very happy to announce that four outstanding researchers accepted our invitation to present a plenary lecture at the Modeling workshop: Matthias Bremer (Merck KGaA, Darmstadt) "The Role of Quantum Chemistry in the Development of Liquid Crystals for Display Applications" Ruth Brenk (University of Bergen) "Structure-based design of riboswitch ligands and selective NMT inhibitors" Bernd Meyer (University of Erlangen) "Chemistry at the solid-liquid interface" Rochus Schmid (Ruhr-University Bochum) "Force fields for porous coordination polymers - a tricky business" ### Poster and Lecture Awards ### As in the past years, there will be two poster awards of EUR 100 each and three lecture awards for the best contributed oral presentations: 1st winner: Travel bursary to attend the Young Modeller's Forum in London, UK, plus a speaker slot option at YMF (travel expenses are reimbursed up to EUR 500) 2nd winner: EUR 200 travel expenses reimbursement 3rd winner: EUR 100 travel expenses reimbursement Only undergraduate and graduate research students qualify for the poster and lecture awards. ### Registration and poster/talk submission ### Submit talks and/or poster titles via the registration form accessible on the workshop website https://mmws2019.mgms-ds.de/index.php?m=register The deadline for all submissions is February 22nd, 2019. ### General information ### Website http://mmws2019.mgms-ds.de will provide all necessary information about the meeting. We are looking forward to meeting you in Erlangen! - Paul Czodrowski, Scientific Committee Workshop Organisation 2019 - Harald Lanig, Chairman of the MGMS-DS e.V. (http://www.mgms-ds.de) -- PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Zentralinstitut fuer Scientific Computing (ZISC) Geschaeftsfuehrer Martensstrasse 5a, 91058 Erlangen Fon +49 9131-85 20781 harald.la...@fau.de Fax +49 9131-85 20785 http://www.zisc.uni-erlangen.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
