[gmx-users] trjconv - two chains are separated
Hi Gromacs Users, I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my trajectories. My protein has two chains (A and B) and they closely bind to each other. after running trjconv with "-pbc nojump", two chains are greatly separated by a certain distance. It is mostly likely that the pbc is not successfully removed and the program takes a chain from one unit cell and another from another unit cell. Does anybody have any idea to solve the problem? Best Yunlong -- 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] Iodide ion LJ parameters
Hi, I am trying to simulate a protein with an iodide ion ligand. However, I can't find the non-bonded force field parameters for iodide ion. Does anybody have any suggestions or have the source of those parameters? Thank you. Best Yunlong -- 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] iodine non-bonded parameters for charmm36 force field
Hi Justin, I am sorry to miss your email and send to the mail list another one. I understand that there are no official parameters but is there any other source that I can look up? Thank you. Yunlong On 5/27/15 4:37 PM, Justin Lemkul wrote: On 5/27/15 4:32 PM, Yunlong Liu wrote: Hi all, I am trying to build up a model with iodide ion but I don't know where I can obtain those non-bonded parameters for this ion. I am using CHARMM36 force field. Is there any suggestions for that. Thank you. There aren't any official CHARMM parameters for iodide. -Justin -- 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] iodine non-bonded parameters for charmm36 force field
Hi all, I am trying to build up a model with iodide ion but I don't know where I can obtain those non-bonded parameters for this ion. I am using CHARMM36 force field. Is there any suggestions for that. Thank you. Best Yunlong -- 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] Is it possible to generate lipid.itp with Charmm36 ff?
Hi Justin, I mean I would like to set it up with Charmm36. The provided one is under OPLS and gromos ff. Yunlong On Apr 7, 2015, at 4:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/7/15 4:18 PM, Yunlong Liu wrote: Hi, I am doing membrane-protein simulation with Charmm36 forcefield. I would like to know whether I can generate the lipid force field with Charmm36 by some available tools? No need to generate anything. We provide the whole force field here: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Is it possible to generate lipid.itp with Charmm36 ff?
Hi, I am doing membrane-protein simulation with Charmm36 forcefield. I would like to know whether I can generate the lipid force field with Charmm36 by some available tools? Yunlong -- 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] Is it possible to generate lipid.itp with Charmm36 ff?
Oh I see. I saw the website this afternoon. Do you refer to the package charmm36-nov2014? I checked the file inside but see no dppc or popc entry inside. I just want to make sure whether it can work for popc membrane? I ask this since I don't quite understand how the lipid membrane force field top files should be correctly represented in GROMACS. I read your tutorial and see you are talking about lipid.itp. Thank you. Yunlong On Apr 7, 2015, at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/7/15 4:27 PM, Yunlong Liu wrote: Hi Justin, I mean I would like to set it up with Charmm36. The provided one is under OPLS and gromos ff. Visit the link I posted. Our force field files have nothing to do with OPLS or GROMOS. There is no such thing as lipid.itp for CHARMM36; that commonly refers to the Berger parameters, as distributed by Peter Tieleman's group. -Justin Yunlong On Apr 7, 2015, at 4:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/7/15 4:18 PM, Yunlong Liu wrote: Hi, I am doing membrane-protein simulation with Charmm36 forcefield. I would like to know whether I can generate the lipid force field with Charmm36 by some available tools? No need to generate anything. We provide the whole force field here: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Performance drops when simulating protein with small ligands
Hi, I am running my protein with two ligands. Both ligands are small molecules like ATP. However, my simulation performance drops a lot by adding this two ligands with the same set of other parameters. Previously with ligands, I have 30 ns/day with 64-cpus and 4gpus. But now I can only gain 17 ns/day with the same setting. I want to know whether this is a common phenomenon or I do something stupid. Yunlong -- 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] Performance drops when simulating protein with small ligands
Hi Justin, I am running this simulation on Stampede/TACC. I don't think there are other processes running on the nodes assigned to me. This is a little weird. Yunlong On Mar 20, 2015, at 2:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/20/15 1:13 PM, Yunlong Liu wrote: Hi, I am running my protein with two ligands. Both ligands are small molecules like ATP. However, my simulation performance drops a lot by adding this two ligands with the same set of other parameters. Previously with ligands, I have 30 ns/day with 64-cpus and 4gpus. But now I can only gain 17 ns/day with the same setting. I want to know whether this is a common phenomenon or I do something stupid. Probably some other process is using resources and degrading your performance, or you're using different run settings (the .log file is definitive here). The mere addition of ligands does not degrade performance. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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 API AnalysisData Class
Hi, I am developing some personal trajectory analysis code with Gromacs API. I have a question on using the AnalysisData class. I would like to have access to the data stored in the AnalysisData object after running a single pass over all the frames in the trajectory. I don't know how to do it and where to find the stored data. For example, I extract a position vector from each frame and use setPoint to set it into AnalysisDataHandle in the function analysisFrame. After my program run through all the frames, how can I access those position vectors stored in my AnalysisData object. Thank you. Yunlong -- 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] 答复: membrane protein simulation - errors
Hi Justin, I built Gromacs 5.0.1 but it doesn't work even with pdb2gmx. Since my protein is patched with -NH3+ and -COO- at the N-terminus and C-terminus. I used -ter flag. But the program cannot recognize the terminus and returns error. I switched back to the Gromacs 5.0-rc1. It works fine with pdb2gmx and it fixed the error but got the previous Non default U-B types errors. I don't know what is the U-B types and how it is define in the gromacs. Yunlong 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Justin Lemkul jalem...@vt.edu 发送时间: 2014年9月18日 20:30 收件人: gmx-us...@gromacs.org 主题: Re: [gmx-users] membrane protein simulation - errors On 9/17/14 6:54 PM, Yunlong Liu wrote: Hi, I am trying to use Gromacs 5.0 to run membrane protein simulation. I built my membrane protein system with POPC membrane and TIP3P water in VMD. Then I used gmx pdb2gmx to build gromacs topology files. My force field is charmm22* and it contains a lipids.rtp entry. It can successfully recognize the POPC molecules in my pdb and the water. But it keeps complaining something like this : Processing chain 7 'L' (5360 atoms, 40 residues) Warning: Starting residue POPC1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPC2 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPC3 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPC7 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPC8 in chain not identified as Protein/RNA/DNA. More than 5 unidentified residues at start of chain - disabling further warnings. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. Then I modified the residuestypes.dat to add POPC and TIP3 into the file but it still keeps complaining. I tried to ignore this and run grompp -f minim.mdp -c my.gro .. to generate the tpr file but I got an error like this: --- Program gmx, VERSION 5.0-rc1 Source code file: /home/yunlong/Downloads/gromacs-5.0-rc1/src/gromacs/gmxpreprocess/toppush.c, line: 2393 Fatal error: Invalid Atomnr j: 5, b2-nr: 3 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ---? I am wondering whether I can do membrane protein simulation in Gromacs without building the system in Gromacs. It's certainly possible, but I'd start with using an actual release version of Gromacs, rather than 5.0-rc1. Try again with 5.0.1. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] membrane protein simulation - errors
Hi, I am trying to use Gromacs 5.0 to run membrane protein simulation. I built my membrane protein system with POPC membrane and TIP3P water in VMD. Then I used gmx pdb2gmx to build gromacs topology files. My force field is charmm22* and it contains a lipids.rtp entry. It can successfully recognize the POPC molecules in my pdb and the water. But it keeps complaining something like this : Processing chain 7 'L' (5360 atoms, 40 residues) Warning: Starting residue POPC1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPC2 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPC3 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPC7 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPC8 in chain not identified as Protein/RNA/DNA. More than 5 unidentified residues at start of chain - disabling further warnings. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. Then I modified the residuestypes.dat to add POPC and TIP3 into the file but it still keeps complaining. I tried to ignore this and run grompp -f minim.mdp -c my.gro .. to generate the tpr file but I got an error like this: --- Program gmx, VERSION 5.0-rc1 Source code file: /home/yunlong/Downloads/gromacs-5.0-rc1/src/gromacs/gmxpreprocess/toppush.c, line: 2393 Fatal error: Invalid Atomnr j: 5, b2-nr: 3 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ---? I am wondering whether I can do membrane protein simulation in Gromacs without building the system in Gromacs. Thanks. Yunlong Davis Yunlong Liu BCMB - First Year PhD Candidate School of Medicine The Johns Hopkins University E-mail: yliu...@jhmi.edumailto:yliu...@jhmi.edu -- 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] GPU job failed
Same idea with Szilard. How many nodes are you using? On one nodes, how many MPI ranks do you have? The error is complaining about you assigned two GPUs to only one MPI process on one node. If you spread your two MPI ranks on two nodes, that means you only have one at each. Then you can't assign two GPU for only one MPI rank. How many GPU do you have on one node? If there are two, you can either launch two PPMPI processes on one node and assign two GPU for them. If you only want to launch one MPI rank on each node, you can assign only one GPU for each node ( by -gpu_id 0 ) Yunlong Try to run Sent from my iPhone On Sep 8, 2014, at 5:35 PM, Szilárd Páll pall.szil...@gmail.com wrote: Hi, It looks like you're starting two ranks and passing two GPU IDs so it should work. The only think I can think of is that you are either getting the two MPI ranks placed on different nodes or that for some reason mpirun -np 2 is only starting one rank (MPI installation broken?). Does the same setup work with thread-MPI? Cheers, -- Szilárd On Mon, Sep 8, 2014 at 2:50 PM, Albert mailmd2...@gmail.com wrote: Hello: I am trying to use the following command in Gromacs-5.0.1: mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g npt2.log -gpu_id 01 -ntomp 10 but it always failed with messages: 2 GPUs detected on host cudaB: #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible 2 GPUs user-selected for this run. Mapping of GPUs to the 1 PP rank in this node: #0, #1 --- Program mdrun_mpi, VERSION 5.0.1 Source code file: /soft2/plumed-2.2/gromacs-5.0.1/src/gromacs/gmxlib/gmx_detect_hardware.c, line: 359 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 1 PP MPI process per node, but you provided 2 GPUs. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors However, this command works fine in Gromacs-4.6.5, and I don't know why it failed in 5.0.1. Does anybody have any idea? thx a lot Albert -- 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. -- 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] [gmx-developers] About dynamics loading balance
Hi Szilard, I would like to send you the log file and i really need your help. Please trust me that i have tested many times when i turned on the dlb, the gpu nodes reported cannot allocate memory error and shut all MPI processes down. I have to tolerate the large loading imbalance (50%) to run my simulations. I wish i can figure out some way that makes my simulation run on GPU and have better performance. Where can i post the log file? If i paste it here, it will be really long. Yunlong On Aug 24, 2014, at 2:20 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Thu, Aug 21, 2014 at 8:25 PM, Yunlong Liu yliu...@jh.edu wrote: Hi Roland, I just compiled the latest gromacs-5.0 version released on Jun 29th. I will recompile it as you suggested by using those Flags. It seems like the high loading imbalance doesn't affect the performance as well, which is weird. How did you draw that conclusion? Please show us log files of the respective runs, that will help to assess what is gong on. -- Szilárd Thank you. Yunlong On 8/21/14, 2:13 PM, Roland Schulz wrote: Hi, On Thu, Aug 21, 2014 at 1:56 PM, Yunlong Liu yliu...@jh.edu mailto:yliu...@jh.edu wrote: Hi Roland, The problem I am posting is caused by trivial errors (like not enough memory) and I think it should be a real bug inside the gromacs-GPU support code. It is unlikely a trivial error because otherwise someone else would have noticed. You could try the release-5-0 branch from git, but I'm not aware of any bugfixes related to memory allocation. The memory allocation which causes the error isn't the problem. The printed size is reasonable. You could recompile with PRINT_ALLOC_KB (add -DPRINT_ALLOC_KB to CMAKE_C_FLAGS) and rerun the simulation. It might tell you where the usual large memory allocation happens. PS: Please don't reply to an individual Gromacs developer. Keep all conversation on the gmx-users list. Roland That is the reason why I post this problem to the developer mailing-list. My system contains ~240,000 atoms. It is a rather big protein. The memory information of the node is : top - 12:46:59 up 15 days, 22:18, 1 user, load average: 1.13, 6.27, 11.28 Tasks: 510 total, 2 running, 508 sleeping, 0 stopped, 0 zombie Cpu(s): 6.3%us, 0.0%sy, 0.0%ni, 93.7%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 32815324k total, 4983916k used, 27831408k free, 7984k buffers Swap: 4194296k total,0k used, 4194296k free, 700588k cached I am running the simulation on 2 nodes, 4 MPI ranks and each rank with 8 OPENMP-threads. I list the information of their CPU and GPU here: c442-702.stampede(1)$ nvidia-smi Thu Aug 21 12:46:17 2014 +--+ | NVIDIA-SMI 331.67 Driver Version: 331.67 | |---+--+--+ | GPU NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 Tesla K20m Off | :03:00.0 Off |0 | | N/A 22CP046W / 225W |172MiB / 4799MiB | 0% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| |0113588 /work/03002/yliu120/gromacs-5/bin/mdrun_mpi 77MiB | |0113589 /work/03002/yliu120/gromacs-5/bin/mdrun_mpi 77MiB | +-+ c442-702.stampede(4)$ lscpu Architecture: x86_64 CPU op-mode(s):32-bit, 64-bit Byte Order:Little Endian CPU(s):16 On-line CPU(s) list: 0-15 Thread(s) per core:1 Core(s) per socket:8 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family:6 Model: 45 Stepping: 7 CPU MHz: 2701.000 BogoMIPS: 5399.22 Virtualization:VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 20480K NUMA node0 CPU(s): 0-7 NUMA node1 CPU(s): 8-15 I hope this information will help. Thank you. Yunlong On 8/21/14, 1:38 PM, Roland Schulz wrote: Hi, please don't use gmx-developers for user questions. Feel free to use it if you want to fix the problem, and have
[gmx-users] Too much PME mesh wall time.
Hi gromacs users, I met a problem with too much PME Mesh time in my simulation. The following is my time accounting. I am running my simulation on 2 nodes. Each of them has 16 CPUs and 1 Tesla K20m Nvidia GPU. And my mdrun command is ibrun /work/03002/yliu120/gromacs-5/bin/mdrun_mpi -pin on -ntomp 8 -dlb no -deffnm pi3k-wt-charm-4 -gpu_id 00. I manually turned off dlb since when it is turned on, the simulation will crash. I have reported it to both mailing lists and talked to Roland. R E A L C Y C L E A N D T I M E A C C O U N T I N G On 4 MPI ranks, each using 8 OpenMP threads Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Domain decomp. 48 151592.099 137554.334 2.2 DD comm. load 48751 0.057 4.947 0.0 Neighbor search48 150001 665.072 57460.919 0.9 Launch GPU ops.48 1502 967.023 83548.916 1.3 Comm. coord. 487352488.263 214981.185 3.5 Force 487517037.401 608018.042 9.8 Wait + Comm. F 487513931.222 339650.132 5.5 * PME mesh 48 751 40799.9373525036.971 56.7* Wait GPU nonlocal 487511985.151 171513.300 2.8 Wait GPU local 48751 68.365 5906.612 0.1 NB X/F buffer ops. 48 29721229.406 106218.328 1.7 Write traj.48830 28.245 2440.304 0.0 Update 487512479.611 214233.669 3.4 Constraints487517041.030 608331.635 9.8 Comm. energies 48 150001 14.250 1231.154 0.0 Rest1601.588 138374.139 2.2 - Total 71928.719 6214504.588 100.0 - Breakdown of PME mesh computation - PME redist. X/F48 15028362.454 722500.151 11.6 PME spread/gather 48 1502 14836.350 1281832.463 20.6 PME 3D-FFT 48 15028985.776 776353.949 12.5 PME 3D-FFT Comm. 48 15027547.935 652127.220 10.5 PME solve Elec 487511025.249 88579.550 1.4 - First, I would like to know whether this is a big problem and second, I want to know how to improve my performance? Does it mean that my GPU is running too fast and CPU is waiting. BTW, what does the wait GPU nonlocal refer to? Thank you. Yunlong -- Yunlong Liu, PhD Candidate Computational Biology and Biophysics Department of Biophysics and Biophysical Chemistry School of Medicine, The Johns Hopkins University Email: yliu...@jhmi.edu Address: 725 N Wolfe St, WBSB RM 601, 21205 -- 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] Recommendations on how to increase performance
Hi Gromacs Users, I got an time accounting table from a single run. Can anyone give me any advice on how to further increase performance? R E A L C Y C L E A N D T I M E A C C O U N T I N G On 16 MPI ranks, each using 8 OpenMP threads Computing: Num Num CallWall time Giga-Cycles Nodes Threads Count (s) total sum% - Domain decomp.168 10001 42.603 14723.278 3.3 DD comm. load 168 2001 0.034 11.807 0.0 Neighbor search 168 10001 50.194 17346.533 3.9 Comm. coord. 168 19 33.143 11454.105 2.6 Force 168 21 530.787 183435.628 41.7 Wait + Comm. F168 21 30.357 10491.253 2.4 PME mesh 168 21 491.803 169963.077 38.7 NB X/F buffer ops.168 580001 12.216 4221.874 1.0 Write traj. 168 4 0.081 28.145 0.0 Update168 21 5.612 1939.518 0.4 Constraints 168 21 67.633 23373.282 5.3 Comm. energies168 20001 2.636910.895 0.2 Rest 4.649 1606.573 0.4 - Total 1271.748 439505.968 100.0 - Breakdown of PME mesh computation - PME redist. X/F 168 42 135.738 46909.937 10.7 PME spread/gather 168 42 119.991 41467.827 9.4 PME 3D-FFT168 42 59.470 20552.340 4.7 PME 3D-FFT Comm. 168 84 170.363 58876.121 13.4 PME solve Elec168 21 5.465 1888.524 0.4 - Thank you. Yunlong Davis Yunlong Liu BCMB - First Year PhD Candidate School of Medicine The Johns Hopkins University E-mail: yliu...@jhmi.edumailto:yliu...@jhmi.edu -- 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] 答复: Questions on reducing large loading imbalance
Thank you, Szilard. I will try -dlb yes to see whether the situation gets better. Yunlong 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Szilárd Páll pall.szil...@gmail.com 发送时间: 2014年8月19日 2:10 收件人: Discussion list for GROMACS users 主题: Re: [gmx-users] Questions on reducing large loading imbalance 13% is not that large and as far as I can tell the dynamic load balancing has not even kicked in (the above message would show the min/average cell volume due to the domain rescaling). You can try manually turning on load balancing with -dlb yes. -- Szilárd On Mon, Aug 18, 2014 at 7:14 PM, Yunlong Liu yliu...@jhmi.edu wrote: Hi Gromacs Users, I have experienced a problem of large loading imbalance for a long time. I usually got a log file like this: DD step 9 load imb.: force 13.2% Step Time Lambda 10 200.00.0 Energies (kJ/mol) U-BProper Dih. Improper Dih. CMAP Dih. LJ-14 5.17644e+041.49735e+043.26712e+03 -1.31906e+032.01143e+04 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 2.55757e+054.04666e+05 -3.15240e+04 -3.74303e+062.30293e+04 Position Rest. PotentialKinetic En. Total Energy Conserved En. 7.72298e+03 -2.99458e+066.15259e+05 -2.37932e+06 -3.10501e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.09333e+02 -2.16110e+02 -2.79932e+013.19468e-05 I don't know how to reduce the large loading imbalance. Can anyone please give me any advices on that? Thank you. Yunlong -- 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. -- 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] 答复: Can't allocate memory problem
Hi, Thank you for your reply. I am actually not doing anything unusual, just common MD simulation of a protein. My system contains ~25 atoms, more or less depend on how many water molecules I put in it. The way I called mdrun is ibrun mdrun_mpi_gpu -pin on -ntomp 8 -deffnm pi3k-wt-1 -gpu_id 00 I pinned 8 threads on 1 MPI task (this is the optimal way to run simulation on Stampede). It has been problem with other systems like lysosome. But my system is a little unusual and I don't really understand where is unusual. The systems are doing fine if I use CPU to run the simulation but as soon as I turned on the GPU, the simulation sucks frequently. One of the guesses is that GPU is more sensitvie in dealing with the non-bonded interactions. Thank you. Yunlong 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Mark Abraham mark.j.abra...@gmail.com 发送时间: 2014年7月18日 23:52 收件人: Discussion list for GROMACS users 主题: Re: [gmx-users] Can't allocate memory problem Hi, That's highly unusual, and suggests you are doing something highly unusual, like trying to run on huge numbers of threads, or very large numbers of bonded interactions. How are you setting up to call mdrun, and what is in your tpr? Mark On Jul 17, 2014 10:13 PM, Yunlong Liu yliu...@jhmi.edu wrote: Hi, I am currently experiencing a Can't allocate memory problem on Gromacs 4.6.5 with GPU acceleration. Actually, I am running my simulations on Stampede/TACC supercomputers with their GPU queue. My first experience is when the simulation length longer than 10 ns, the system starts to throw out the Can't allocate memory problem as follows: Fatal error: Not enough memory. Failed to realloc 1403808 bytes for f_t-f, f_t-f=0xa912a010 (called from file /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c, line 3840) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- These Gromacs Guys Really Rock (P.J. Meulenhoff) : Cannot allocate memory Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi_gpu on CPU 0 out of 4 --- Program mdrun_mpi_gpu, VERSION 4.6.5 Source code file: /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/smalloc.c, line: 241 Fatal error: Not enough memory. Failed to realloc 1403808 bytes for f_t-f, f_t-f=0xaa516e90 (called from file /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c, line 3840) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Recently, this error occurs even I run a short NVT equilibrium. This problem also exists when I use Gromacs 5.0 with GPU acceleration. I looked up the Gromacs errors website to check the reasons for this. But it seems that none of those reasons will fit in this situation. I use a very good computer, the Stampede and I run short simulations. And I know gromacs use nanometers as unit. I tried all the solutions that I can figure out but the problem becomes more severe. Is there anybody that has an idea on solving this issue? Thank you. Yunlong Davis Yunlong Liu BCMB - Second Year PhD Candidate School of Medicine The Johns Hopkins University E-mail: yliu...@jhmi.edumailto:yliu...@jhmi.edu -- 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. -- 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] 答复: Can't allocate memory problem
) -3.01747e+066.08815e+05 -2.40865e+063.09700e+02 -2.17744e+02 Pressure (bar) Constr. rmsd -1.15302e+013.22109e-05 DD step 18 load imb.: force 13.4% Step Time Lambda 19 380.00.0 Energies (kJ/mol) U-BProper Dih. Improper Dih. CMAP Dih. LJ-14 5.07811e+042.99541e+042.98628e+03 -7.39091e+031.97456e+04 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 2.01761e+054.03922e+05 -3.13225e+04 -3.71005e+062.19542e+04 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) -3.01766e+066.10133e+05 -2.40753e+063.10370e+02 -2.18064e+02 Pressure (bar) Constr. rmsd -2.96181e+013.28160e-05 If you want to see the full log file, please give me an email address that I could send it to. Thank you. Yunlong 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Mark Abraham mark.j.abra...@gmail.com 发送时间: 2014年7月18日 23:52 收件人: Discussion list for GROMACS users 主题: Re: [gmx-users] Can't allocate memory problem Hi, That's highly unusual, and suggests you are doing something highly unusual, like trying to run on huge numbers of threads, or very large numbers of bonded interactions. How are you setting up to call mdrun, and what is in your tpr? Mark On Jul 17, 2014 10:13 PM, Yunlong Liu yliu...@jhmi.edu wrote: Hi, I am currently experiencing a Can't allocate memory problem on Gromacs 4.6.5 with GPU acceleration. Actually, I am running my simulations on Stampede/TACC supercomputers with their GPU queue. My first experience is when the simulation length longer than 10 ns, the system starts to throw out the Can't allocate memory problem as follows: Fatal error: Not enough memory. Failed to realloc 1403808 bytes for f_t-f, f_t-f=0xa912a010 (called from file /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c, line 3840) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- These Gromacs Guys Really Rock (P.J. Meulenhoff) : Cannot allocate memory Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi_gpu on CPU 0 out of 4 --- Program mdrun_mpi_gpu, VERSION 4.6.5 Source code file: /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/smalloc.c, line: 241 Fatal error: Not enough memory. Failed to realloc 1403808 bytes for f_t-f, f_t-f=0xaa516e90 (called from file /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c, line 3840) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Recently, this error occurs even I run a short NVT equilibrium. This problem also exists when I use Gromacs 5.0 with GPU acceleration. I looked up the Gromacs errors website to check the reasons for this. But it seems that none of those reasons will fit in this situation. I use a very good computer, the Stampede and I run short simulations. And I know gromacs use nanometers as unit. I tried all the solutions that I can figure out but the problem becomes more severe. Is there anybody that has an idea on solving this issue? Thank you. Yunlong Davis Yunlong Liu BCMB - Second Year PhD Candidate School of Medicine The Johns Hopkins University E-mail: yliu...@jhmi.edumailto:yliu...@jhmi.edu -- 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. -- 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] 答复: 答复: Can't allocate memory problem
Hi Szilard, Thank you for your comments. I really learn a lot from that. Can you please explain more on the -nb gpu_cpu tag? And what I know is the Stampede node contains 16 Intel Xeon cores with only one Tesla K20m GPU. But you mention there are two CPU XEON cores. I am a little confused on this. Yunlong 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Szilárd Páll pall.szil...@gmail.com 发送时间: 2014年7月19日 2:41 收件人: Discussion list for GROMACS users 主题: Re: [gmx-users] 答复: Can't allocate memory problem On Fri, Jul 18, 2014 at 7:31 PM, Yunlong Liu yliu...@jhmi.edu wrote: Hi, Thank you for your reply. I am actually not doing anything unusual, just common MD simulation of a protein. My system contains ~25 atoms, more or less depend on how many water molecules I put in it. The way I called mdrun is ibrun mdrun_mpi_gpu -pin on -ntomp 8 -deffnm pi3k-wt-1 -gpu_id 00 I pinned 8 threads on 1 MPI task (this is the optimal way to run simulation on Stampede). FYI: That can't be universally true. The best run configuration will always depend on at least the machine characteristics parallelization capabilities and behavior of the software/algorithms used as well as often the setting/size of input too (especially as different type of runs may use different algorithms). More concretely, GROMACS will not always perform best with 8 threads/rank - even though that's the number of cores/socket on Stampede. My guess is that you'll be better off with 2-4 threads per rank. One thing you may have noticed is that a single K20 that Stampede's visualization nodes seem to have (based on http://goo.gl/9fG7Vd), will probably not be enough to keep up with two Xeon E5 2680-s and a considerable amount of runtime will be lost as the CPU will be idling while waiting for the GPU to complete the non-bonded calculation. You may want to give a try to the -nb gpu_cpu option. Cheers, -- Szilárd It has been problem with other systems like lysosome. But my system is a little unusual and I don't really understand where is unusual. The systems are doing fine if I use CPU to run the simulation but as soon as I turned on the GPU, the simulation sucks frequently. One of the guesses is that GPU is more sensitvie in dealing with the non-bonded interactions. Thank you. Yunlong 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Mark Abraham mark.j.abra...@gmail.com 发送时间: 2014年7月18日 23:52 收件人: Discussion list for GROMACS users 主题: Re: [gmx-users] Can't allocate memory problem Hi, That's highly unusual, and suggests you are doing something highly unusual, like trying to run on huge numbers of threads, or very large numbers of bonded interactions. How are you setting up to call mdrun, and what is in your tpr? Mark On Jul 17, 2014 10:13 PM, Yunlong Liu yliu...@jhmi.edu wrote: Hi, I am currently experiencing a Can't allocate memory problem on Gromacs 4.6.5 with GPU acceleration. Actually, I am running my simulations on Stampede/TACC supercomputers with their GPU queue. My first experience is when the simulation length longer than 10 ns, the system starts to throw out the Can't allocate memory problem as follows: Fatal error: Not enough memory. Failed to realloc 1403808 bytes for f_t-f, f_t-f=0xa912a010 (called from file /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c, line 3840) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- These Gromacs Guys Really Rock (P.J. Meulenhoff) : Cannot allocate memory Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi_gpu on CPU 0 out of 4 --- Program mdrun_mpi_gpu, VERSION 4.6.5 Source code file: /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/smalloc.c, line: 241 Fatal error: Not enough memory. Failed to realloc 1403808 bytes for f_t-f, f_t-f=0xaa516e90 (called from file /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c, line 3840) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Recently, this error occurs even I run a short NVT equilibrium. This problem also exists when I use Gromacs 5.0 with GPU acceleration. I looked up the Gromacs errors website to check the reasons for this. But it seems that none of those reasons will fit in this situation. I use a very good computer, the Stampede and I run short simulations. And I know gromacs use nanometers as unit. I tried all the solutions that I can
[gmx-users] Can't allocate memory problem
Hi, I am currently experiencing a Can't allocate memory problem on Gromacs 4.6.5 with GPU acceleration. Actually, I am running my simulations on Stampede/TACC supercomputers with their GPU queue. My first experience is when the simulation length longer than 10 ns, the system starts to throw out the Can't allocate memory problem as follows: Fatal error: Not enough memory. Failed to realloc 1403808 bytes for f_t-f, f_t-f=0xa912a010 (called from file /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c, line 3840) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- These Gromacs Guys Really Rock (P.J. Meulenhoff) : Cannot allocate memory Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi_gpu on CPU 0 out of 4 --- Program mdrun_mpi_gpu, VERSION 4.6.5 Source code file: /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/smalloc.c, line: 241 Fatal error: Not enough memory. Failed to realloc 1403808 bytes for f_t-f, f_t-f=0xaa516e90 (called from file /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c, line 3840) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Recently, this error occurs even I run a short NVT equilibrium. This problem also exists when I use Gromacs 5.0 with GPU acceleration. I looked up the Gromacs errors website to check the reasons for this. But it seems that none of those reasons will fit in this situation. I use a very good computer, the Stampede and I run short simulations. And I know gromacs use nanometers as unit. I tried all the solutions that I can figure out but the problem becomes more severe. Is there anybody that has an idea on solving this issue? Thank you. Yunlong Davis Yunlong Liu BCMB - Second Year PhD Candidate School of Medicine The Johns Hopkins University E-mail: yliu...@jhmi.edumailto:yliu...@jhmi.edu -- 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.
