[gmx-users] gromacs.org_gmx-users at maillist.sys.kth.se

Morten Slyngborg morten at slyngborg.com
Mon Jul 11 17:07:38 CEST 2016



> Den 11/07/2016 kl. 16.52 skrev gromacs.org_gmx-users-request at maillist.sys.kth.se:
> 
> Send gromacs.org_gmx-users mailing list submissions to
>    gromacs.org_gmx-users at maillist.sys.kth.se
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>    https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
>    gromacs.org_gmx-users-request at maillist.sys.kth.se
> 
> You can reach the person managing the list at
>    gromacs.org_gmx-users-owner at maillist.sys.kth.se
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: strange GPU performance (Mark Abraham)
>   2. Using ATB to generate valid topologies (ALEXANDER DHALIWAL)
>   3. Re: strange GPU performance (Albert)
>   4. GROMACS 2016 release candidate available! (Mark Abraham)
>   5. command line issue (Albert)
>   6. Re: command line issue (Mark Abraham)
>   7. Re: command line issue (Albert)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 11 Jul 2016 13:41:07 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] strange GPU performance
> Message-ID:
>    <CAMNuMASJxMSd-z5kpJusQ5iq3CzPLcNM_6UCKaQjKDpF6p6YMA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Hi,
> 
> Why did you specify using 2 MPI ranks with 8 OpenMP threads per rank on a
> node with 10 cores and 2 GPUs? You want something that fills all the cores
> (and hyperthreads) e.g.
> 
> mpirun -np 2 gmx_mpi mdrun
> 
> or
> 
> mpirun -np 4 gmx_mpi mdrun
> 
> There are likely further improvements available along the lines Szilard
> suggests.
> 
> Mark
> 
>> On Mon, Jul 11, 2016 at 10:24 AM Albert <mailmd2011 at gmail.com> wrote:
>> 
>> Hello:
>> 
>> I submitted Gromacs GPU job with the following command line:
>> 
>> mpirun -np 2 gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc
>> -gpu_id 01 -ntomp 8 >& 7.info
>> 
>> I obtained the following log file:
>> 
>> 
>> Number of logical cores detected (20) does not match the number reported
>> by OpenMP (2).
>> Consider setting the launch configuration manually!
>> 
>> Running on 1 node with total 10 cores, 20 logical cores, 2 compatible GPUs
>> Hardware detected on host cudaA.europe.actelion.com (the node of MPI
>> rank 0):
>>   CPU info:
>>     Vendor: GenuineIntel
>>     Brand:  Intel(R) Xeon(R) CPU E5-2690 v2 @ 3.00GHz
>>     SIMD instructions most likely to fit this hardware: AVX_256
>>     SIMD instructions selected at GROMACS compile time: AVX_256
>>   GPU info:
>>     Number of GPUs detected: 2
>>     #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
>> 
>> Reading file 7.tpr, VERSION 5.1.2 (single precision)
>> Changing nstlist from 20 to 40, rlist from 1.009 to 1.064
>> 
>> Using 2 MPI processes
>> Using 8 OpenMP threads per MPI process
>> 
>> 
>> In principle, there should be 2x8=16 CPU occupied. However, I noticed
>> that there is only 4 CPU was using but it generated 16 Gromacs process.
>> The speed of GPU is very slow.... I am just wondering how to solve this
>> problem?
>> 
>> Thanks 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-request at gromacs.org.
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 11 Jul 2016 09:52:21 -0400
> From: ALEXANDER DHALIWAL <dhaliak2 at mcmaster.ca>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Using ATB to generate valid topologies
> Message-ID:
>    <CADCUEYv8OwbMjo4mropG4v4cTsYRZjxpTZzmQoQ+6aRuc1cuJw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Dear GROMACS users,
> 
> I am pioneering the use of GROMACS in my lab to supplement some of our
> experimental research. I have generated some topologies from the Automated
> Topology Builder (ATB), but I am unsure whether or not to trust the files
> provided by this service. I am only an undergrad, so I would not feel
> comfortable asking my supervisor to invest thousands of dollars into a
> program such as Gaussian09 to validate these topologies. Does this
> community trust the outputs of ATB and, if not, could you provide me with
> suggestions as to how I may validate my topologies given my restraints? Any
> advice would be much appreciated.
> 
> Sincerely,
> Alex
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Mon, 11 Jul 2016 16:02:18 +0200
> From: Albert <mailmd2011 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] strange GPU performance
> Message-ID: <5783A6EA.2030901 at gmail.com>
> Content-Type: text/plain; charset=windows-1252; format=flowed
> 
> yes.
> 
> But the job failed from to time:
> 
> vol 0.87! imb F 34% step 33600, will finish Sat Jul 23 17:26:12 2016
> 
> -------------------------------------------------------
> Program gmx mdrun, VERSION 5.1.2
> Source code file: 
> /home/albert/Downloads/gromacs/gromacs-5.1.2/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu, 
> line: 688
> 
> Fatal error:
> cudaStreamSynchronize failed in cu_blockwait_nb: unknown error
> 
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
> Halting parallel program gmx mdrun on rank 0 out of 4
> 
> -------------------------------------------------------
> Program gmx mdrun, VERSION 5.1.2
> Source code file: 
> /home/albert/Downloads/gromacs/gromacs-5.1.2/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu, 
> line: 688
> 
> Fatal error:
> cudaStreamSynchronize failed in cu_blockwait_nb: unknown error
> 
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
> Halting parallel program gmx mdrun on rank 1 out of 4
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> with errorcode 1.
> 
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> 
> 
> 
> 
>> On 07/11/2016 03:41 PM, Mark Abraham wrote:
>> Hi,
>> 
>> Why did you specify using 2 MPI ranks with 8 OpenMP threads per rank on a
>> node with 10 cores and 2 GPUs? You want something that fills all the cores
>> (and hyperthreads) e.g.
>> 
>> mpirun -np 2 gmx_mpi mdrun
>> 
>> or
>> 
>> mpirun -np 4 gmx_mpi mdrun
>> 
>> There are likely further improvements available along the lines Szilard
>> suggests.
> 
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Mon, 11 Jul 2016 14:22:44 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>,
>    "gmx-announce at gromacs.org" <gmx-announce at gromacs.org>
> Subject: [gmx-users] GROMACS 2016 release candidate available!
> Message-ID:
>    <CAMNuMAS+zm9DFXdy8KUoV3nJ=ByUdWWnULM1-ePYfodQvz4GHQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Hi GROMACS users,
> 
> The release candidate of GROMACS 2016 is available! This is pretty much the
> final form of this year's GROMACS release, but needs some final stress
> testing. Please do build it and try it out on your important workload - if
> it's broken when doing essential dynamics with velocity-verlet, on an AMD
> GPU running OpenCL, with LJ-PME, you might be the only person who can help
> us learn that!
> 
> Please do not use this version for doing science you plan to publish - it
> needs a bit more testing before it?s reliable enough for that. Similarly,
> please don?t use this version as a base for a project that bundles or forks
> GROMACS.
> 
> What new things can you expect? Please see the release notes highlights at
> http://manual.gromacs.org/documentation/2016-rc1/ReleaseNotes/index.html#highlights
> .
> 
> We've fixed lots of old and some newly found issues during the beta phase,
> but we'd really value your feedback on whether these fixes are working for
> you. We hope you will consider making that contribution, so that we can
> continue to deliver high-quality free simulation software that will be
> useful to you on day 1.
> 
> You can find the code, manual, release notes, installation instructions and
> testsuite at the links below.
> 
> Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2016-rc1.tar.gz
> Documentation: http://manual.gromacs.org/documentation/2016-rc1/index.html
> (includes install guide, user guide, reference manual)
> Release Notes:
> http://manual.gromacs.org/documentation/2016-rc1/ReleaseNotes/index.html
> Test Suite:
> http://gerrit.gromacs.org/download/regressiontests-2016-rc1.tar.gz
> 
> Happy testing!
> 
> Mark Abraham
> GROMACS Development Manager
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Mon, 11 Jul 2016 16:44:59 +0200
> From: Albert <mailmd2011 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] command line issue
> Message-ID: <5783B0EB.90007 at gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
> 
> Hello:
> 
> I noticed that each time when I type:
> 
> gmx_mpi grom
> 
> then press "tab" in the key board, the above command line sometimes can 
> fill in "grompp" automatically, sometimes nothing happens. I am just 
> wondering how can we enable this automatic filling command line function 
> correctly?
> 
> thx a lot
> 
> Albert
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Mon, 11 Jul 2016 14:48:26 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] command line issue
> Message-ID:
>    <CAMNuMARei1-S-xeA6-wC8z06qc3QjiOQ-t3h37Rt86AvdJ7aGg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Hi,
> 
> If you have used "source GMXRC" from a supported shell (bash and zsh, I
> think) then this will work. It also knows about command-line options and
> file extensions.
> 
> Mark
> 
>> On Mon, Jul 11, 2016 at 4:45 PM Albert <mailmd2011 at gmail.com> wrote:
>> 
>> Hello:
>> 
>> I noticed that each time when I type:
>> 
>> gmx_mpi grom
>> 
>> then press "tab" in the key board, the above command line sometimes can
>> fill in "grompp" automatically, sometimes nothing happens. I am just
>> wondering how can we enable this automatic filling command line function
>> correctly?
>> 
>> 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-request at gromacs.org.
> 
> 
> ------------------------------
> 
> Message: 7
> Date: Mon, 11 Jul 2016 16:51:56 +0200
> From: Albert <mailmd2011 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] command line issue
> Message-ID: <5783B28C.8090203 at gmail.com>
> Content-Type: text/plain; charset=windows-1252; format=flowed
> 
> Hi:
> 
> I do add this in my .cshrc:
> 
> source /home/albert/install/gromacs/5.1.2/bin/GMXRC
> 
> however, it doesn't work in my tcsh. It seems to work only in Bash.....
> 
> regards
> 
> 
> 
>> On 07/11/2016 04:48 PM, Mark Abraham wrote:
>> Hi,
>> 
>> If you have used "source GMXRC" from a supported shell (bash and zsh, I
>> think) then this will work. It also knows about command-line options and
>> file extensions.
>> 
>> Mark
> 
> 
> 
> ------------------------------
> 
> -- 
> 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-request at gromacs.org.
> 
> End of gromacs.org_gmx-users Digest, Vol 147, Issue 57
> ******************************************************


More information about the gromacs.org_gmx-users mailing list